Ordering bin-mapped ESTs of Group 3 chromosomes of wheat using scaffold sequences | Dev Kumar Arya

ORDERING BIN-MAPPED ESTs OF GROUP 3
CHROMOSOMES OF WHEAT USING SCAFFOLD
SEQUENCES
THESIS
SUBMITTED IN PARTIAL FULFILLMENT
OF THE REQUIREMENTS
FOR THE DEGREE OF MASTER OF SCIENCE
(AGRICULTURE)
IN
(GENETICS AND PLANT BREEDING)
BY
DEVKUMAR ARYA
DEPARTMENT OF GENETICS AND PLANT BREEDING
CHAUDHARY CHARAN SINGH UNIVERSITY
MEERUT - 250 004 (UP) INDIA
2018

Ch. Charan Singh University, Meerut
Department of Genetics and Plant Breeding
Dharmendra Pratap, Ph.D. Sachin Kumar, Ph.D.
Assistant Professor Assistant Professor
Certificate
This is to certify that this project report entitled “Ordering Bin-Mapped ESTs of Group 3
Chromosomes of Wheat Using Scaffold Sequences” submitted for the partial fulfillment of the
requirements for the degree of Master of Science (Agriculture) in the Department of Genetics and
Plant Breeding of Ch. Charan Singh University Meerut (U.P.) is a record of bonafide research work
carried out by Mr. Dev Kumar Arya under my supervision and that no part of this project report has
been submitted for any other degree or diploma.
The assistance and help received during the course of this investigation have been fully
acknowledged.
(Dharmendra Pratap) (Sachin Kumar)
Supervisor Co-supervisor

DEDICATED TO
MY BELOVED PARENTS
AND GRANDPARENTS

ACKNOWLEDGEMENTS
I would like to express my deepest gratitude to my supervisors, Dr. Dharmendra Pratap and Dr.
Sachin Kumar, Assistant Professors, Department of Genetics and Plant Breeding, Chaudhary
Charan Singh University, Meerut, for their supervision, continuous involvement, constructive
criticism, thesis writing and constant encouragement at every stage during the course of this study.
I am also grateful to Professor S.S. Gaurav, Head of department, Professor P.K. Sharma, (Ex-Head
and Dean Faculty of Agriculture; Professor Shailendra Sharma; Dr.Rahul Kumar; Emeritus
Professors P.K. Gupta, S.P. Singh, H.S. Balyan for their guidance and valuable help and motivation.
I am also thankful to all the lab members, my seniors, my colleagues including Mr. Vikas Kumar
Singh, Sushil Kumar, Rahul Kumar, Ms.Muskan Rastogi and technical & non-technical staff of the
Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, for their
time to time help during this study.
I also wish to express my gratitude to my parents and grandparents Mr.Veer Singh and Smt. Om vati
Devi, my brothers Mr.Dharm Singh, Prakash Chandera , Satypal Singh, Dinesh Kumar, Saini, Sanjay
Kumar Verma, Narender Kumar, Pushpender Kumar lodhi, Anuj Kumar, Naresh Kumar, Neeraj
Kumar, Satya Prakash, Yashpal Singh; my brother in low Mr.Dharmender Singh; my sisters
Mrs.Shakuntala, Ms.Chanderavati; my Nephew Aniket Singh, Jai Prakash, Sanjay Singh, Monu
Singh, Mayank Singh and Niece Kumari Seema, Poonam, Anjali, Mamta, Prinka, Priti, Sapna) for
their constant support and suggestions.
Date: 04 September 2018
Place: Meerut (Dev Kumar Arya)

CONTENTS
Chapter Page No.
1. INTRODUCTION 10-11
2. REVIEW OF LITERATURE 12-22
2.1. Taxonomic classification of wheat
2.2. Construction of expressed sequence tag ESTs
2.2.1. Isolation of messenger RNA
2.2.2. Isolation of eukaryotic mRNA via oligo (dT) - cellulose chromatography
2.2.3. Synthesis of first and second strand of cDNA
2.2.4. Integration of cDNA into a suitable vector
2.3. Applications of Expressed Sequence Tags
2.4. EST Databases.
2.5. DNA Based Molecular Marker
2.6. Expressed sequence tag-simple sequence repeats (EST-SSRs)
2.7. Uses of molecular marker
3. MATERIALS AND METHODS 23-25
3.1. Wheat ESTs Sequences
3.2. Sequence database
3.3. Criteria used for sequence alignment
3.4. Comparison of our results with the published results by Munkvoled et al (2004)
4. RESULTS AND DISCUSSION 26-34
4.1. Analysis of group 3chromosome bin-mapped EST that matched scaffold sequences in wheat
4.2. Order of bin-mapped EST
4.3. Comparison to previous deletion bin mapping of group 3 chromosomes
5. SUMMARY 35-36
6. REFERENCES 37-41
APPENDIX I. Details of bin-mapped wheat ESTs of chromosome 3A and their matching to 3A
scaffolds with sequence coordinates. Duplicate loci of ESTs are also presented. 42-52
APPENDIX II. Details of bin-mapped wheat ESTs of chromosome 3B and their matching to 3B

APPENDIX III. Details of bin-mapped wheat ESTs of chromosome 3D and their matching to 3D
LIST OF TABLES
Table 2.1. A summary of the number of ESTs belonging to genomes of some important plant species
available in NCBI database (updated on June 12, 2018)
Table 3.1. Distribution of ESTs among the homeologous group of wheat
Table 4.1. Summary of BLAST results of bin mapped wheat EST with scaffold sequences
Table 4.2. Differences in mapping results between present study and earlier study by Munkvold et al.
(2004) using 1,268 ESTs of group 3 chromosomes
Table 4.3. Number of ESTs mapped earlier in the deletion bins of group 3 chromosome now matched
to other groups of wheat chromosomes

LIST OF FIGURES
Figure 2.1. Synthesis of first and second strand of cDNA.
Figure 2.2. Modification of cDNA termini using linkers.
Figure 3.1. ESTs showing top single hit from the alignments were allocated to specific bins of wheat
chromosomes 3A, 3B and 3D.
Figure. 3.2. A query sequence subject to BLAST (for instance, EST ID No: BF145392) against the
wheat genomic sequence in ensemble Gramene, it splits into 4 different segments (1, 2, 3 and 4) as
per matching found in wheat genomic sequence and considered as HSPs. These HSPs covers the
query sequence as following, 1' HSP cover 53bases, 2' cover 185bases, 3' HSP cover 161bases and 4'
HSP cover 29bases. There are three gaps, one bet segments 1' and 2', second between 2' and 3' and
third one between 3' and 4' which is due to the presence of introns between the exons. The query
segments (1, 2, 3 and 4) of wheat EST sequence matching with segments (1' 2' 3' and 4') of wheat
genome sequence make longest consecutive HSP in correct order.
Figure 4.1. Distribution pattern of EST loci on deletion-bins of group 3 chromosome. The bin
fraction is indicated to the right of each chromosome. Numbers (red font) indicate EST loci; numbers
(green font) inside parenthesis are number of scaffolds matched. This figure is based on only those
ESTs having bin-mapped position and matched to scaffold sequences of group 3 chromosomes.
Figure 4.2. Diagrammatic representation of alignment of bin-mapped wheat ESTs with scaffold
sequence of chromosome 3A. The bin fraction is indicated to the left of chromosome 3A (green).
Scaffold (Scaffold_3 A_194186_96323-117325) is shown as vertical bar (blue) and aligned ESTs
(BE494219, BE406587, BE489130) are shown in red colour boxes. Name and size of aligned ESTs
and their sequence coordinates (start-end) are given to the right of scaffold.
sequence of chromosome 3B. The bin fraction is indicated to the left of chromosome 3B (green).
Scaffold (Scaffold_3B_220619_140901-365343) is shown as vertical bar (blue) and aligned ESTs
(BE443132, BE497749, BF429274, BM138221) are shown in red colour boxes. Name and size of
aligned ESTs and their sequence coordinates (start-end) are given to the right of scaffold.
sequence of chromosome 3D. The bin fraction is indicated to the left of chromosome 3D (green).
Scaffold (Scaffold_3D_249102_8066-30149) is shown as vertical bar (blue) and aligned ESTs

Figure 4.5: Diagram represented assignment for 68 EST to chromosome arms 3AS (21) and 3AL
(47). These EST were only assigned to chromosome 3A previously by Munkvold et al. (2004).
Figure 4.6. Diagram showed assignment for 33 EST to chromosome arms 3DS (9) and 3DL (24).
These EST were only assigned to chromosome 3D previously by Munkvold et al. (2004).
Figure 4.7. Diagram represented assignment for 179 ESTs to chromosome arms 3AS (69) and 3AL
(110). These ESTs were failed to hybridize with chromosome 3A in previous study by Munkvold et
al. (2004).
Figure 4.8. Diagram represented assignment for 149 ESTs to chromosome 3B. These ESTs were
failed to hybridize with chromosome 3B in previous study by Munkvold et al. (2004).
Figure 4.9. Diagram represented assignment for 165 ESTs to chromosome arms 3DS (56) and 3DL
(109). These ESTs were failed to hybridize with chromosome 3D in previous study by Munkvold et
al. (2004).

1. INTRODUCTION
Common or bread wheat (Triticum aestivum L.) is the most important staple food crop of the world
and is grown on about 230 million hectares land which is more than any other crop grown at
commercial level. After China, India occupies second rank in terms of wheat production in the world.
Being an important source of dietary fibers, wheat alone provides 20% of the calories and proteins in
our daily intake (Gupta et al. 2008).
Bread wheat is a hexaploid species possess three sets of seven homoeologous chromosomes
thus giving a total of 42 chromosomes. This hexaploid genome (2n=6x=42; AABBDD) of wheat
shaped from two separate spontaneous hybridization events where each hybridization event was
followed by chromosomes doubling (whole-genome duplication) and thus normal bivalent formation
at meiosis produced today’s wheat.
Wheat genome sequencing was initially considered challenging due to large size genome (~17
Gbp), high content of repetitive sequences (80%) and evolution. However, useful genomic resources
(DNA sequences) were developed and molecular maps (cytogenetic, genetic and physical) were
prepared by several labs utilizing a variety of molecular markers. In the beginning, molecular linkage
maps based on restriction fragment length polymorphism (RFLP) analyses were developed for all the
21 wheat chromosomes (Devos and Gale 1993; Xie et al. 1993; Nelson et al. 1995). To expedite the
whole-genome sequencing of wheat, many researchers were turned to produce transcript sequences of
cDNA library generated from mRNA. Single-end (either 5’ or 3’) sequences of cDNAs are
recognized as expressed sequence tags (ESTs), which proved a powerful recourse for discovery of
genes in wheat genome. As a result, a major research project funded by National Science Foundation,
USA generated and deposited 1,17,000 wheat EST sequences in the NCBI EST database (db). At the
end of this project, ~16,000 EST loci from 7,104 EST representing wheat unigenes were physically
mapped to individual chromosome using 42 nullisomic-tetrasomic lines, 42 ditelosomic lines and 436
deletion lines of Chinese Spring (Sears 1954; Endo and Gill 1996; Qi et al. 2004). Integrated physical
maps based on SSR markers have also been prepared and a comparison of these maps with the
available genetic maps has been carried out (Balyan et al. 2008; Gupta et al. 2008c). On the

availability of EST sequences in databases, these were searched for identification of simple sequence
repeats (SSRs) or microsatellites. Primers flanking SSRs were synthesized and extensively used for
preparation of wheat genetic maps (Somars et al. 2004; Torada et al. 2006). The SSRs belonging to
both the expressed sequence tags (ESTs) and genomic survey sequences (GSSs) have later been used
for construction of SSR-based physical maps of wheat genome (Sourdille et al. 2004; Goyal et al.
2005; Song et al. 2005; Mohan et al. 2007). Integrated physical maps based on SSR markers were
prepared and comparison of these maps with the available genetic maps was carried out (Balyan et al.
2008).
In the absence of availability of the whole genome sequence of bread wheat, initially rice was
tried as a model system because of its small genome size and due to the availability of the whole
genome sequences for rice genome. However, recently Brachypodium distachyon (purple false
brome, has later emerged as a better model system for the study of temperate grasses. This was
particularly, due to several of its desirable biological features and its phylogenetic position (Huo et al.
2008). It is postulated that relative to rice genome, brachypodium genome may exhibit a much higher
level of colinearity and synteny to the genomes of temperate cereal crops. In the past few years,
considerable efforts have gone into developing brachypodium as a model system and large numbers
of genomic resources have been created (Kumar et al. 2009).
During the past decade, International Wheat Genome Sequencing Consortium (IWGSC) has
adopted chromosome-based strategy for sequencing the entire 21 wheat chromosome. The
Consortium utilized flow-cytometry approach in which an individual chromosome or chromosome
arm was isolated and constructed bacterial artificial chromosome (BAC) libraries (Dolezel et al.
2007; Safar et al. 2010) followed by generating physical maps and gap filling by sequencing the
minimum tilling path (MTP). Following different strategies for ordering the contigs/scaffolds along
the chromosome, reference genome sequences are being completed. Mapped molecular markers
played an essential to anchor and orient contigs/scaffolds.
Available chromosome scaffolds can now be used to order the wheat ESTs mapped to
deletion bins. As mentioned above, using a set of nullisomic-tetrasomic, ditelosomic and deletion
lines, 16,000 EST loci were bin-mapped (Qi et al. 2004). So far, the order of these EST within
deletion bin is not known. This problem can now be overcome by in silico ordering of these EST
against the scaffold sequences of respective chromosome. Therefore, present study was planned on
group 3 chromosome bin maps of wheat (Munkvold et al. 2004) with the following objective.

 In silico ordering of wheat ESTs mapped within deletion bins of group 3 chromosomes (3A, 3B
and 3D) using scaffold sequences available in Gramene database.
2. REVIEW OF LITERATURE
Wheat is a one of the most important stable food of just about two billion people ( 36% of the world
populations).Wheat is belong to a cereal grass of the Gramineae family but now day’s known as
(Poaceae) and the genus Triticum have many species as like, monococum, durum, eastivum etc.
Poaceae includes the other cereal crops such as Barley, Rice, Sorghum, Maize, Oat, Rye, Ragi etc.
and after the discovery of polyploid series in wheat (Sakamura,1918), the wheat genome analysis and
its wild relative were undertaken (Kihara,1954). After the establishment of agriculture cereals are
providing foods for mankind. Historians believed that wheat has been growing since Paleolithic times
and cultivated since 6000 years. I would like to current study, we reviewed the wheat ESTs; its origin
and utilization in crop improvement in several research programmes in future.
2.1. Taxonomical Classification of Wheat
Kingdom: Planate – Plants
Subkingdom: Tracheobionta – Vascular plants
Super division: Spermatophyta – Seed plants
Division: Magnoliophyta – Flowering plants
Class: Liliopsida – Monocotyledons
Subclass: Commelinidae
Order: Cyperales
Family: Poaceae – Grass family
Genus: Triticum L.
Species: aestivum
2.2. Construction of Expressed Sequence Tags ( ESTs)
The term expressed sequence tags (ESTs) first time given by Anthony Kerlavage (1991) at the
Institute for Genomic Research and later Mark Adams used EST in gene identification as well as in
Human Genome project. As we know that cDNA clones are derived from expressed genes (mRNA)
therefore after many studies of cDNA were realized that the partial sequence of cDNA clones can
also be used for identification of a particular region of DNA or new genes and that partial sequence

called as Expressed sequence tag (EST). Following are the important steps to generate EST
sequences.
1. Isolation of mRNA from the targeted tissue or plant.
2. Synthesis of first and second strand of cDNA.
3. Integration of cDNA into a suitable vector.
4. Cloning of cDNA in a suitable vector.
5. Selection of contigs randomly from the colony.
6. Sequencing of either one end of contigs (3’ or 5’) or both.
2.2.1. Isolation of messenger RNA: Sequences of cDNA are types of DNA molecules which are
synthesized from mRNA templates. For production of cDNA libraries are constructed by synthesis
of cDNA from purified cellular mRNA. In case of eukaryotic genes these libraries as alternative
strategy for gene isolation. Basic characteristics of eukaryotic mRNAs is that, it carry 3′-poly(A)
tails and 5’ cap, with the help of these features mRNA can be selectively isolated from preparations
of total cellular RNA by oligo(dT)-cellulose chromatography.
2.2.2. Isolation of eukaryotic mRNA via oligo (dT): cellulose chromatography. Steps for mRNA
isolation are as follows (A) In this step the poly (A) tail of eukaryotic mRNA will anneal with short
oligo (dT) chain which is covalently to an insoluble chromatographic matrix for instance cellulose, by
adding total RNA into 0.5 M Nacl. As we know that there are other RNAs also present which will
pass right through the chromatography column. (B) There will be other contaminants and for
removing it we have to wash the column with 0.5 M NacCl. (C) By washing the column with water
we can recover the poly (A) mRNA, because as we know that base pairing between oligo dT and poly
(A) tail is unstable in low ionic strength. (http://www.biologydiscussion.com/ gene/gene-
libraries/dna-gene-libraries-construction-genomic-libraries-and-cdna-libraries/12419).
2.2.3. Synthesis of first and second strand of cDNA: It is known that mRNA cannot be cloned and
also not a substrate for DNA ligase, therefore it is required to convert mRNA into cDNA before
insertion into a suitable vector with the help of reverse transcriptase (RNA-dependent DNA
polymerase) obtained from avian myeloblastosis virus. The process of constructing cDNA is as
follows and presented in (Fig.2.1).
i. First short Oligo (dT) primer is annealed to the Poly (A) tail on the mRNA, which is the basic
characteristics of mRNA.

ii. After that reverse transcriptase will come and bind with olio dT primer and extends the 3´-end
of the primer and construct mRNA and cDNA hybrid.
iii. After that there will an enzyme called RNase H or Alkaline hydrolysis which will remove
the mRNA strand, and result ss-cDNA molecule.
iv. Now ss-cDNA serves as its own primer generating a short hairpin loop at the end. As DNA
polymerase will come, it start the synthesis of next strand of cDNA and the single stranded ss-
cDNA is then converted into double stranded (ds) cDNA.
Figure 2.1. Synthesis of first and second strand of cDNA.
2.2.4. Integration of cDNA into a suitable vector: Double stranded cDNA will trimmed with S1
nuclease to make blunt–ended ds-cDNA molecule and the blunt-ended cDNA obtained are next
modified to ligate into a vector to prepare ds-cDNA for cloning. So far study gives idea that blunt-
end ligation is ineffective, short restriction-site linkers are first ligated to both ends. Linker is a
double-stranded DNA segment has a recognition site for a particular restriction enzyme. Linker is 10-
12 base pairs long prepared by hybridizing chemically synthesized complementary oligonucleotides

(Fig.2.2). Blunt ended ds-cDNAs are ligated with the linkers by the DNA ligase from T4
Bacteriophage.
Figure 2.2. Modification of cDNA termini using linkers.
Double-stranded cDNA with linkers at both ends are treated with a restriction enzyme specific for the
linker generating cDNA molecules produce sticky ends. Ligation of the digested ds-cDNA into a
vector is the final step. The vectors should be restricted with the same that was used for linkers.
The transformed bacteria are plated and grown on nutrient media and it will construct cDNA library
and after it plasmids are isolated from randomly selected individual’s clones. The cloned cDNA can
then be sequenced either from 5’ or 3’ end or from both ends simultaneously. Curetted ESTs are a
collection of random cDNA sequences of different lengths and many are derived from identical
transcripts.
2.3. Applications of Expressed Sequence Tags
ESTs (expressed sequence tags) can be used as functional DNA arrays for the analysis of whole
genome of a species.
1. ESTs are most commonly used to locate a gene rapidly and accurately.
2. ESTs are use as genome searching tool.
3. For identification of position of genes.
4. For to find out gene responsible for disease.

5. ESTs used in similarity searches.
6. For identification of new genes.
ESTs commonly used as a source of Sequence Tagged Sites (STSs) because of their uniqueness in an
individual’s genome. The most powerful technique for genome mapping is STS mapping.
2.4. EST Databases
Generally anonymous ESTs are each a single-pass (either from 5’ or 3’) sequence 200-700 bp long
(Adams et al. 1991). For development of molecular markers belonging to the transcribed region of a
genome, EST databases represent one of the valuable resources, so that they are likely to be
conserved across a broader taxonomic range (Gupta and Rustgi 2004). EST analysis has also good
approach for annotation, comparative genomics and gene discovery in all organisms, irrespective of
their genome size (Ewing et al. 1999; Fernandes et al. 2002). In plants total 25476503 ESTs and out
of them, wheat has 1407485 ESTs generated and deposited in the National Center for Biotechnology
Information (NCBI) databases (http://www.ncbi.nlm.nih.gov) (Table2.1). For development of
molecular marker, wheat ESTs which are available in databases constitutes an essential resource
(Gupta and Rustgi 2004). Lots of SSRs and SNPs have been identified in the EST sequences via in
silico approaches and leading to the development of EST-SSR and EST-SNP markers (Rafalski
2002a, b; Gupta and Rustgi 2004; Rustgi et al. 2009; Kumar S, P.hD, Thesis, 2012).
Table 2.1. A summary of the number of ESTs belonging to genomes of some important plant
species available in NCBI database (updated on June 12, 2018)
Common name (Scientific name) Family Number of ESTs
Einkorn wheat (Triticum monococcum) Poaceae 11,190
Durum wheat (T. turgidum) Poaceae 20013
Bread wheat (T. aestivum) Poaceae 1407485
Barely (Hordeum vulgare) Poaceae 94117
Rice (Oryza sativa) Poaceae 1260567
Maize (Zea mays) Poaceae 2020455
Sorghum (Sorghum bicolor) Poaceae 210892
Mustard (Brassica rapa) Brassicaceae 106811
Potato (Solanum tuberosum) Solanaceae 256010
Tomato (Solanum lycopersicon) Solanaceae 300665
Oats (Avena sativa) Poaceae 25368

Soybean (Glycine max) Fabaceae 1474265
Rye (Secale cereale) Poaceae 9311
Onion (Allium cepa) Liliaceae 20204
Cotton (Gossypium hirsutum) Malvaceae 338644
Takacs et al. (2008) Provided a simplified procedure of complementary DNA (cDNA) cloning, easily
scalable to very different sizes of plant tissue. They extracted the mRNA from a single wheat kernel
with oligo DT magnetic beads, transcribed the mRNA into single-strand cDNA with the help of
reverse transcriptase enzyme (It is responsible for the reverse transcription) and then DNA tags were
incorporated into the ds cDNA fragments for proceeding to PCR amplification. The amplified DNA
was ligated to a poly (T) overhang cloning vector and some of the resulting clones were sequenced
with the help of BLASTN these sequences were identified in wheat EST databases.
Munkvold et al.(2004) The wheat homoeologous group 3 chromosomes are among the
largest in physical size (Dvorˇa´k et al. 1984; Gill et al.1991). According to earlier study gene density
has been found to be higher figat the ends of these chromosomes (Gill et al. 1993; Lukaszewski and
Curtis 1993). A number of important traits are known to be controlled by loci on these chromosomes,
including grain yield and seed weight (Berke et al. 1992a,b), seed dormancy (Osa et al. 2003) kernel
color (Sears 1944; Nelson et al.1995). Wheat homoeologous group 3 indicate that this group is the
most conserved in gene content, order and wheat group 3 chromosomes are most closely related to
barley (Hordeum vulgare L.) chromosome 3 (Devos and Gale 1993; Nelson et al 1995),rice (Oryza
sativa L.) chromosome 1 (Devos et al. 1992). Complementary DNA (cDNA) clones from expressed
sequence tags (ESTs) representing unigenes were used for mapping in the wheat genome using a set
of the wheat deletion stocks. Homoeologus group 3 distribution of EST loci among chromosomes.
The total number of loci 2266 were mapped on the homoeologous group 3 chromosomes. The
mapped EST 322,193,429,274, and 361,231 chromosomes were mapped to 3AL,3AS, 3BL, 3BS, and
3DL, 3DS and these respectively identified 634, 884 and 748 loci. An overall average of 2.28 EST
loci were mapped to each group 3 chromosomes with independently calculated average of 1.23 for
3A, 1.26 for 3B, and 1.26 for 3D. On the basis of value of Chi-Square analyses, significantly fewer
ESTs and loci mapped to 3A (P< 0.001) than would be expected on the basis of physical size of
chromosome and significantly more ESTs were mapped to 3D (P <10-5
). The EST distributions
followed similar patterns within chromosomes 3A and 3B On the basis of physical size of the
deletion bins. The 996 ESTs mapped to the group 3 chromosomes accounted for 765 additional loci

located in the remaining group 6 chromosomes. In case of comparison study between wheat and rice
analysis of the BLASTN results from the mapped group 3 unigenes against the rice genome indicated
that the group 3 chromosomes share the highest level of homoeology with rice chromosome 1 and
another comparison between wheat and arabidopsis BLASTN comparison of the 5655 mapped-EST
unigenes against the Arabidopsis coding region database revealed 1182 (21%) significant matches.
When only mapped-EST unigenes for group 3 were considered, 204 out of 988 (20.6%) significantly
matched coding region of Arabidopsis thaliana.
Devos et al. (1992) Construct the genetic maps of chromosomes group 3 of wheat and
chromosomes group 3 of rye were developed using 22 DNA probes, two isozyme marker systems
and all techniques of DNA extraction, restriction enzyme digestion, gel electrophoresis, southern
transfer, probe labelling and filter hybridization were as described by Sharp et al. (1988) and their
modification. Analysis of the 49 loci mapped showed extreme clustering around the centromere in all
four maps, with large 'gaps' in the distal chromosome regions, which is interpreted as being due to
strong localisation of recombination towards the ends of the wheat and rye chromosomes. A
comparison of cDNA and genomic probes showed the latter to be much more efficient for revealing
RFLP. In addition to anonymous DNA clones, the locations of known function clones,
sedoheptulose-l,7-bisphosphatase (XSbp), carboxypeptidase I (XCxpl) and a bZIP protein (XEmbp),
were ascertained along with those for two isozyme loci, Mal-1 and Est-5.controlled by genes located
on the homoeologous group 3 chromosomes. One of the most important traits, red grain colour, is
controlled by genes on the long arms of chromosomes 3A, 3B and 3D (Sears 1944). These R genes
are particularly important because of their association with dormancy, and thus pre-harvest sprouting,
which is the most serious constraint to consistent grain quality in northern Europe and other
temperate wheat growing areas. Other important genes located on 3D include sl, which defines the
sphaerococcum spike type characterising 'shot' wheat, on the long arm and ph2, the second most
potent chromosome pairing control gene, on the short arm (Sears 1982). Several isozyme loci are also
located on the homoeologous group 3 chromosomes. Est-5 (Ainsworth et al. 1984) and Per-3 are
highly polymorphic and are hence of potential value in intervarietal comparisons, while the Est-1,
Est-2, Got-3, Hk-2, Pde-1, Tpi-l, Mal-1, Ndh-3, and Ndh-4 isozyme loci have potential for use in
inter-genomic chromosome manipulation. The development of extensive genetic maps in wheat has
been hampered by the large genome size, the large number of linkage groups, and the relatively low
levels of variation shown in restriction fragment length polymorphism (RFLP) analysis (Chao et al.
1989).

Osa et al. (2003) As we know that PHS (Pre-harvest sprouting is the premature germination
of wheat seeds so that the embryo starts growing while still on the head in the field) is a most
important problem in many wheat growing areas, downgrading of quality of seed and several
limitations in end use application. Seed dormancy in wheat is governed by many genes, and in a few
cases these genes have been mapped to specific chromosome regions. It is also known that the seed-
color R genes are located as homoeologous loci on the long arms of group 3 chromosomes (Sears
1954; Nelson et al. 1995). Using NILs (Near-isogenic lines) for the R genes (Flintham et al. 2000)
and (Watanabe and Ikebata, 2000) found that these genes have direct effects on dormancy. Several
quantitative trait locus (QTL) have been detect for PHS which are co-localized with the R genes
(Nelson et al. 1995; Groos et al. 2002). The chromosome 3A map was constructed on the basis of the
genotypic classifications for the RIL population. Nineteen marker loci covering approximately 250
cM were mapped. RFLP analyses of ditelosomic stocks available in Chinese Spring demonstrated
that the centromere was assigned within the marker interval between Xgwm5 on the short arm and
Xpsr394 on the long arm. There are five loci consisting of four RFLP markers and a SSR locus were
mapped on the short arm, and ten RFLP and three SSR markers were assigned together with taVp1
on the long arm. Map position of taVp1 using a wheat cDNA clone taVp1, isolated by Dr. N.
Kawakami (unpublished data), was used as a probe to determine the chromosomal location of the
taVp1 locus. When DNAs from CS and Zen were digested with multiple restriction enzymes, taVp1
hybridized to three fragments in most cases, indicating that the taVp1 gene is present as a single copy
in each of the A, B and D genomes. When digested with HindIII, CS had a marker band of about 20
kbp, whereas Zen lacked it. Nullisomic and ditelosomic analyses indicated that this marker band was
encoded by the gene located on 3AL. taVp1 was mapped in the middle of the long arm of
chromosome 3A 84.8 cM from the centromere. Using qgene analysis we deduced one putative QTL
associated with seed dormancy. The QTL, designated QPhs.ocs-3A.1, was identified within the
marker intervals between Xbcd1380 and Xfbb370 (GC’00), Xfbb370 and Xbcd907 (GC’01) in the
terminal region of the short arm. The Zen alleles at the QPhs.ocs-1 contributed to keeping seed
dormancy.
Ogihara et al.(2004) Constructed 24056 expressed sequence tags (ESTs), from young
spikelets of Chinese Spring wheat. They grouped these ESTs into 3605 contigs and 1902 gene
clusters. In addition, they pooled the RNAs extracted from the 17 different tissues of Chinese Spring
wheat and constructed new full-length cDNA library, and they sequenced the 19,968 clones from
both ends (5’ and 3’) and classified these sequences into 25,502 contigs with the help of phrap

method, and 15,197 gene clusters with the BLASTN. Then, they assembled these gene clusters into
the 7,149 unigene clusters, and they sequenced 4,168 cDNAs entirely, out of the 7,149 genes, and
ultimately they found that 18.7 % of the full-length cDNAs were unique against 32,881 EST database
of common wheat. In addition, when they searched the homology against the rice full-length cDNA
databases, (KOME) then, 8.9 % of wheat cDNAs were unique. This result depicts that full-length
cDNA library of common wheat might provide an efficient source to study the comparative
functional genomics of cereal crops.
Gupta and Rustgi (2004), EST Databases represent potentially valuable resource for the
development of molecular markers related to the written area of the genome so that they can be
preserved in the broad taxonomic range. In the databases wheat ESTs are available an essential
resource for the development of molecular marker. Using in silico approaches, SSRs and SNPs have
been identified in the EST sequences leading to the development of EST-SSR and EST-SNP markers
(Rafalski 2002; Gupta and Rustgi 2004; Rustgi et al. 2009).
2.5. DNA Based Molecular Marker
A DNA marker is a small piece of DNA which can be used to detect the polymorphism of particular
sequences among DNA samples. DNA-based molecular markers have a number of desirable
characteristics, which include the following: (i) molecular marker should be available in large
number, (ii) molecular marker should be highly polymorphic in nature, (iii) molecular marker should
show dominant and co-dominant inheritance (Co-dominant are most useful), (iv) molecular marker
should be randomly or frequently distributed throughout the genome, (v) molecular marker should be
simple, quick and inexpensive, (vi) molecular marker need small amount of DNA, (vii) molecular
marker should be provide adequate resolution of genetic differences, (viii) molecular marker should
not influenced by the environment, (ix) molecular marker should be detectable at all stages of plant
growth and (x) molecular marker should show high reproducibility.
2.6. Expressed sequence tag containing simple sequence repeats
Expressed sequence tags (ESTs) provided a new opportunity for gene discovery, genome annotation,
comparative genomics, gene mapping and tagging, evolutionary studies, marker assisted selection
(MAS), positional cloning of genes, etc. in all organisms, irrespective of their genome size (Adams et
al. 1992; Ewing et al. 1999; Fernandes et al. 2002). As we know that ESTs are obtained by partial
sequencing of random cDNA clones. Once it generated, we can use it in cloning the specific genes of
interest and synteny mapping of functional genes with various related organisms. There are two

programs availale at Gramene website like, MISA (MIcroSAtellites), written in Perl 5 script and
simple sequence repeat information tool (SSRIT), where we can search for SSRs in EST sequences.
For amplifying the SSR loci located within the genes, SSRs derived from ESTs (EST-SSRs) can be
used as locus specific primers. They are sorted in silico with ease, unbiased in repeat type, present in
genic regions of the genome, and are more likely to produce amplicon from the coding region of the
genome than those designed from noncoding sequences (Yu et al. 2004; Zhang et al. 2005; Parida et
al. 2006). However, the species which have sufficient numbers of ESTs in the database are the good
source of generating EST-SSRs. EST-SSR markers have been reported in several plant species
including grape, wheat, Arabidopsis, soybean, rice, maize, barley, cotton, sorghum (Scott et al. 2000;
Pillen et al. 2000; Eujayl et al. 2002; Holton et al. 2002; Kantety et al. 2002; Saha et al. 2004; Han et
al. 2006).
As we know that ESTs are constructed from expressed sequence that’s why EST-SSRs are
physically associate with coding regions of the genome, which can enhance the role of molecular
markers in mapping agronomically important loci. The frequencies of EST-SSRs vary from species
to species Cardle et al. (2000). Reported frequencies of EST-SSRs in rice (1 in 3.4 kb), maize (1 in
8.1 kb), soybean (1 in 7.4 kb), tomato (1 in 11.1 kb), poplar (1 in 14.0 kb), Arabidopsis (1 in 13.8 kb)
and cotton (1 in 20.0 kb). In bread wheat, the frequency of EST-SSRs ranged from 1 in 9.20 kb to 1
in 17.42 kb (Gupta et al. 2003; Gao et al. 2004; Parida et al. 2006). Frequencies of EST-SSRs in
different species vary because it may also depend on the criteria used to discover SSRs in the
sequence database. Since the last decade, EST-SSRs have been used for the study of genetic
diversity, transferability and mapping in a number of plant species, which include wheat, rice, maize,
oat, barley, sorghum, rye and Arabidopsis (Cardle et al. 2000; Hackauf and Wehling 2002; Holton et
al. 2002; Theil et al. 2003; Gao et al. 2004; Nicot et al. 2004; Bandopadhyay et al. 2004; Yu et al.
2004; Zhang et al. 2005; Peng and Lapitan, 2005; Mohan et al. 2007). In case of wheat, EST-SSR
based genetic maps have been developed by (Gao et al. 2004; Nicot et al. 2004; Yu et al. 2004; Xue
et al. 2008) and physical maps have been developed by (Yu et al. 2004; Qi et al. 2004; Peng and
Lapitan 2005; Mohan et al. 2007).
EST-SSRs were also used to study the impact of modern plant breeding on the allelic
diversity in wheat suggesting that allelic diversity has reduced in the transcribed portion of wheat (Fu
et al. 2005). EST-SSRs originated from coding region that’s why show higher level of transferability
(relative to gSSRs) across closely related genera (Holton et al. 2002) which implies their significant

potential for comparative mapping (Scott et al. 2000; Eujayl et al. 2002; Bandopadhyay et al. 2004).
In view of this, EST-SSRs were used for comparative mapping in rice and wheat (Yu et al. 2005).
Genes for important agronomic traits can be locate on chromosome map with the EST-SSRs mapping
(Holton et al.2002). Those EST-SSR markers, which are obtained from the non-coding portion of the
genome, they are less polymorphic than the genomic SSR (Eujayl et al. 2001
2.7. Uses of Molecular Marker
Molecular markers have been extensively used for a variety of purposes of genetic studies both in
animal and plant systems. During the last four decades (starting from 1980), In all these cases, the
ability of these markers to detect DNA polymorphism has been utilized For example (1) germplasm
characterization, (2) genetic/physical mapping DNA-based markers have also been used for
construction of genetic, cytogenetic and physical maps of genomes in a number of animal and plant
systems, (3) diversity analysis, gene tagging, (4) genome-wide QTL mapping, (5) association
analysis, (6) marker-assisted selection, (7) map based cloning, (8) study of evolutionary relationships
among genotypes of the same species or among different related species and genera.

3. MATERIALS AND METHODS
MATERIALS
3.1. Wheat ESTs Sequences
A total of 8,210 wheat ESTs representing deletion bin-mapped ESTs (Table 3.1) belonging to all the
seven homoeologous groups of wheat were retrieved from GrainGenes-SQL database
(http://wheat.pw.usda.gov/cgi-bin/westsql/map_locus_rev.cgi). The allocation of these mapped wheat
ESTs in deletion bins was also obtained from the same database and from wEST-SQL
(https://wheat.pw.usda.gov/wEST/binmaps/). Of the 8,210 bin-mapped wheat ESTs, 1,283 those
belonged to chromosomes 3A, 3B and 3D (See Table 3.1) were used in the present study to determine
their order within bins of these chromosomes.
Table 3.1. Distribution of ESTs among the homeologous group of wheat
Homoeologous
group
Homoeologous
chromosome
Number of ESTs bin-mapped
1 1A, 1B, 1D 1123
2 2A, 2B, 2D 1288
3 3A, 3B, 3D 1283
4 4A, 4B, 4D 1190
5 5A, 5B, 5D 1247
6 6A, 6B, 6D 945
7 7A, 7B, 7D 1134
Total 8210
3.2. Sequence database

Above 1,283 bin-mapped wheat ESTs of homoeologous group 3 were used for nucleotide BLAST
(BLASTN) in Gramene database (http://ensembl.gramene.org/Multi/Tools/Blast) containing
sequenced scaffold of wheat chromosomes. The alignment of each mapped wheat EST with scaffold
sequences of wheat chromosomes was carried out by using independently each mapped wheat EST as
a query sequence in BLASTN analysis.
METHODS
3.3. Criteria used for sequence alignment
The bin-mapped wheat ESTs (1,283) belonging to chromosomes of homoeologous group 3 were
subjected to sequence comparisons following BLASTN in ensemble Gramene database
(http://ensembl.gramene.org/Multi/Tools/Blast) containing whole genome sequences of wheat.
Default BLASTN search parameters [cut-off E (expectation) value of e-15] and bit score 100 were
used. ESTs showing top single hit from the alignments were allocated to specific bin of wheat
chromosomes 3A, 3B and 3D. (Fig. 3.1) In many cases of sequence alignment, we observed that one
EST sequence as query often contain many high scoring segment pairs (HSPs) may be due to
sequence redundancy or presence of duplication in the database. In such cases when many HSP in a
single alignment were observed, we carefully examined the sequence alignments of each BLAST
output and determined the perfect order of constitutive HSPs between the alignments of query and
subject sequences. An example of our approach, where a bin-mapped wheat EST sequence aligned
with several HSPs of its matching sequence in consecutive manner, is presented in (Fig. 3.2) A High-
scoring Segment Pair (HSP) is a local alignment (The alignment of a high-scoring region of two
nucleic acid or protein sequences) parameter of BLAST, which shows one of the highest alignment
scores in a given search without having any gap. When we BLAST the query sequence against any
genomic sequence then there are possibilities that our query sequence may aligned in more than one
part, that’s called HSP, it may be due to presence of introns because we blasted against the genomic
sequences which have both introns and exons, but on the other hand our query sequence has only
exons and exons will always match with exons.

Figure. 3.1. ESTs showing top single hit from the alignments were allocated to specific bins of wheat
chromosomes 3A, 3B and 3D.
Figure. 3.2. A query sequence subject to BLAST (for instance, EST ID No: BF145392) against the
wheat genomic sequence in ensemble Gramene, it splits into 4 different segments (1, 2, 3 and 4) as
per matching found in wheat genomic sequence and considered as HSPs. These HSPs covers the
query sequence as following, 1' HSP cover 53bases, 2' cover 185bases, 3' HSP cover 161bases and 4'

HSP cover 29bases. There are three gaps, one bet segments 1' and 2', second between 2' and 3' and
third one between 3' and 4' which is due to the presence of introns between the exons. The query
segments (1, 2, 3 and 4) of wheat EST sequence matching with segments (1' 2' 3' and 4') of wheat
genome sequence make longest consecutive HSP in correct order.
3.4. Comparison of our results with the published results by Munkvold et al (2004)
The results obtained in the present study was also compared with the results published by Munkvold
et al (2004) in relation to the EST mapping in the deletion bins of chromosomes 3A, 3B and 3D.
4. RESULTS AND DISCUSSION
4.1 Analysis of group 3 chromosome bin-mapped ESTs that matched scaffold sequences
Of the 1283 previously bin-mapped wheat EST sequences used for BLAST search, as many as 2168
EST loci were matched to the scaffold sequences of group 3 chromosomes. The summary of these
results are presented in Table 4.1 and Figure 4.1 and detailed information of the results are given in
Appendix I, II and III. Many of ESTs had loci mapping to more than one chromosome that were
considered duplicated. Similar results have also been reported earlier (Dubcovsky et al. 1996;
Akhunov et al. 2003; Qi et al. 2004). Out of 1283, 390 previously bin-mapped wheat ESTs did not
match to any scaffold of group 3 chromosomes and 38 did not match in the entire wheat genome
(Table 4.1). Generally such anomaly may result from chromosome rearrangements and segmental
duplication, but other reasons may be due to (i) different approaches used for mapping in previous
study (Munkvold et al. 2004) and in the present study, (ii) availability of scaffold sequences which
was not available earlier.
Table 4.1. Summary of BLAST results of bin-mapped wheat EST with scaffold sequences
Homoeologous
group 3
(Chromosome)
No. of wheat
ESTs used in
BLAST
No. of ESTs matched No. of ESTs not
matched to
group 3
chromosome
Not matched
in wheat
genome
3A, 3B and 3D 1,283 3AL 448
97 17
3AS 259

3BL
741 178 11
3BS
3DL 457
115 6
3DS 263
Total 1,283 2,168 390 38
Figure 4.1. Distribution pattern of EST loci on deletion-bins of group 3 chromosome. The bin
fraction is indicated to the right of each chromosome. Numbers (red font) indicate EST loci; numbers
(green font) inside parenthesis are number of scaffolds matched. This figure is based on only those
ESTs having bin-mapped position and matched to scaffold sequences of group 3 chromosomes.
4.2 Order of bin-mapped EST
The availability of scaffold sequences of group 3 chromosomes in Gramene database has revealed
that a substantial number of physically mapped ESTs can be linearly ordered within deletion-bins.
Therefore, we thought that alignment of bin-mapped ESTs with scaffold sequences can be an
3AL3-0.42-0.78
3A
3AS2-0.23-0.45
C-3AS2-0.23
C3AL3-0.42
C-3BL2-0.22
3BL2-0,22-0.50
C-3BS1- 0.33
3BS9-0.57-0.78
3BS10.33-0.57
3BL10-0.50-0..63
3D
C-3DS3-0.24
3DL2-0.27-0.81
3DS3-0.24-0.55
C-3DL2-0.27
3B
91(81)
129(116)
46(42)
22(21)
36(33)
106(95)
145(133)
82(77)
66(62)
11(11)
67(56)
87(74)
6(6)
6(6)
11(11)
2(2)
6(6)
3(3)
39(35)
2(2)
79(74)
143(135)
58(55)
51(47)
49(45)
2(2)
14(14)
52(48)
1(1)
49(40)
2(2)
S
4(4)
L

effective way to linearly order the ESTs mapped in deletion-bins earlier by Munkvold et al. (2004).
Ninety one (91) ESTs previously mapped in deletion bin 3AL3-0.42-0.78 (fraction length 0.36) were
matched to 81 scaffolds sequences of long arm of chromosome 3A (3AL). Matching results indicated
that the majority of ESTs were matched to different scaffold sequences and therefore order of such
ESTs cannot be determined unless we know the order of scaffolds along chromosome 3A. In an
instance, we found that three ESTs {BE494219 (528 bases), BE406587 (347 bases), BE489130 (520
bases)} were matched to a single scaffold (Scaffold_3A_194186_96323-117325) at a certain interval.
Based on the alignment between EST and scaffold, order of these EST were determined following
sequence coordinates (start to end) of scaffold and the results are presented in Figure 4.2
sequence of chromosome 3A. The bin fraction is indicated to the left of chromosome 3A (green).
Scaffold (Scaffold_3 A_194186_96323-117325) is shown as vertical bar (blue) and aligned ESTs
3AS2- 0.23-0.45
C-3AS2- 0.23
3AL3-0.42-0.78
3A
S
C-3AL3- 0.42
L
Scaffold_3A_194186
91(81)
Coordinate_(96332-117325)
347b
520b
528b
113794
115155
116659
117112
96632
97250
(BE406587)
(BE489130)
(BE494219)

Therefore, alignment of previously bin-mapped ESTs with scaffolds sequence allowed the order of
EST within bin and results suggested the reliability of our approach. Interestingly, results of the
present study also allowed the assignment of scaffolds to deletion-bins. Following the same approach,
bin-mapped ESTs of chromosomes 3B and 3D were also ordered using matched scaffold sequence
and their results presented in Figure 4.3 and Figure 4.4, respectively.
sequence of chromosome 3B. The bin fraction is indicated to the left of chromosome 3B
(green). Scaffold (Scaffold_3B_220619_140901-365343) is shown as vertical bar (blue) and
aligned ESTs (BE443132, BE497749, BF429274, BM138221) are shown in red colour boxes.
Name and size of aligned ESTs and their sequence coordinates (start-end) are given to the right
of scaffold.
3BS9-0.57-0.78
3BS10-0.33-0.57
3BL10-0.50-0.63
3B
S
3BL2-0.22-0.50
L
scaffold_3B_220619
39(35)
coordinate_(140901-365343)
396
433
678
225397
281597
282073
365043
141113
224525
(BE497749)
(BF429274)
(BE443132)
C-3BS1-0.33
C-3BL2-0.22
141791
364692
294 (BM138221)

sequence of chromosome 3D. The bin fraction is indicated to the left of chromosome 3D (green).
Scaffold (Scaffold_3D_249102_8066-30149) is shown as vertical bar (blue) and aligned ESTs
4.3 Comparison to previous deletion bin mapping of group 3 chromosomes
In the present study, we detected more EST loci than the previous study by Munkvold et al. (2004) in
all the six arms of group 3 chromosomes (Table 4.2). The differences between both the studies may
be due to the different approaches {probe genotyping using deletion lines (Munkvold et al. 2004) and
in silico (present study)} employed and also due to the availability of scaffold sequence in database.
Table 4.2. Differences in mapping results between present study and earlier study by Munkvold et al.
(2004) using 1,283 ESTs of group 3 chromosomes.
Chromosome arm 3AL 3AS 3BL 3BS 3DL 3DS Total
Present study 448 259 741 457 263 2,168
Previous study
(Munkvold et al. 2004)
322 193 429 274 361 231 1,810
We have also detected the ESTs those did not match to the scaffold sequence of group 3
chromosomes. Such ESTs were matched to the scaffolds of other groups and their number is given in
Table 4.3. We found that the chromosome 3B had greater number of EST loci than did the
chromosomes 3A and 3D. Such differences have also been reported in earlier studies (Qi et al. 2004)
3DS3-0.24-0.55
3DL-0.27-0.81
C-3DL2-0.27
C-3DS3-0.24
3D
L
(BE445328)
(BE585734)
(BE489603)
7413
9242
12750
13954
28420
30014
Coordinate_8066-30149
scaffold_3D_249102
527
664
336
1 EST
2 EST
3EST
145(133)

and most suitable explanations for this number difference relates to the evolutionary history of each
of the hexaploid wheat genome.
Table 4.3. Number of ESTs mapped earlier in the deletion bins of group 3 chromosome but matched
to other groups of wheat chromosomes in the present study.
Group 3
chromosome
Group of wheat chromosomes
other than group 3
No. of wheat EST
matched to other groups
Total
3A
Group 1 18
99
Group 2 21
Group 4 18
Group 5 12
Group 6 10
Group 7 20
3B
Group 1 34
178
Group 2 36
Group 4 22
Group 5 34
Group 6 22
Group 7 30
3D
Group 1 14
101
Group 2 26
Group 4 13
Group 5 18
Group 6 16
Group 7 14
In subsequent analysis, we observed that 68 ESTs could not be mapped to any of the deletion bins of
chromosome 3A using southern hybridization (Munkvold et al. 2004). In the present study, we were
able to assign these 68 ESTs to their arms; 21 assigned to 3AS and 47 assigned to 3AL (Fig. 4.5)
using in silico approach. Similarly for chromosome 3D, 9 ESTs were assigned to 3DS and 24 ESTs
were assigned to 3DL (Fig. 4.6).

Figure 4.5: Diagram represented assignment for 68 EST to chromosome arms 3AS (21) and 3AL
(47). These EST were only assigned to chromosome 3A previously by Munkvold et al. (2004).
3AS2- 0.23-0.45
3AL3-0.42-0.78
3A
S
C-3AL3- 0.42
L
C-3AS2- 0.23
Munkvoldet al. (2004)
BE500759 BE494474
BE494539 BE494807
BE636913 BG312618
BG312690 BG314270
BE424246 BE446445
BE398519 BE438263
BG263696 BE606319
BE444162 BE443862
BE443753 BG313557
BG607141 BF428807
BF202341 BF202528
BE498378 BE405552
BF485480 BF292612
BE445966 BF485381
BG263661 BF293491
BF200872 BE426370
BG605323 BE497398
BE404971 BE637251
BF428637 BE591811
BF145244 BE604959
BE406507 BM134520
BM136936 BM137404
BM137965 BQ280814
BE442599 BE423249
BE424862 BF473626
BG312609 BG312729
BM138225 BG314507
BF483390 BF474859
BF429193 BF201604
BE499665 BG274890
BE494662 BF484678
BF483101 BE404610
BF145587 BE426763
BE490739 BG263585
3AS2- 0.23-0.45
3AL3-0.42-0.78
C-3AL3- 0.42
C-3AS2- 0.23
BE500759 BE494474 BE494539
BE494807 BE636913 BG312618
BG312690 BG314270 BE424246
BE446445 BE398519 BE438263
BG263696 BE606319 BE444162
BE443862 BE443753 BG313557
BG607141 BF428807 BF202341
BF202528 BE498378 BE405552
BF485480 BF292612 BE445966
BF485381 BG263661 BF293491
BF200872 BE426370 BG605323
BE497398 BE404971 BE637251
BF428637 BE591811 BF145244
BE604959 BE406507 BM134520
BM136936 BM137404 BM137965
BQ280814 BG263585
BE442599 BE423249 BE424862
BF473626 BG312609 BG312729
BM138225 BG314507 BF483390
BF474859 BF429193 BF201604
BE499665 BG274890 BE494662
BF484678 BF483101 BE404610
BF145587 BE426763 BE490739
BF200712 BE488609 BF482491
BE637806 BF482626 BF483469
BE604541
presentStudy
L
3A
68 ESTs
21 ESTs
47 ESTs
S
3DS3-0.24-0.55
3DL-0.27-0.81
C-3DL2-0.27
C-3DS3-0.24
3D
L
3DS3-0.24-0.55
3DL-0.27-0.81
C-3DL2-0.27
C-3DS3-0.24
3D
L
BE500759 BE636913
BF473231 BE606319
BF483299 BG313801
BE495195 BG263929
BG263661
BG262582 BE500739
BM134520
BE517656 BF200746
BE444545 BE445508
BE494805 BF292883
BM137808
BE591339 BF478815
BE498837 BF482436
BG314507 BF482626
BG314551 BE406646
BG604730 BE398275
BF483194 BF200860
BE500759 BE636913
BF473231 BE606319
BF483299 BG313801
BE495195 BG263929
BG263661 BG262582
BE500739 BM134520
BE517656 BF200746
BE444545 BE445508
BE494805 BF292883
BM137808 BE591339
BF478815 BE498837
BF473034
BG263585
BF482436 BG314507
BF482626 BG314551
BE406646 BG604730
BE398275 BF483194
BF200860
33 ESTs
24 ESTs
9 ESTs
Munkvoldet al. (2004) presentStudy

Figure 4.6. Diagram showed assignment for 33 EST to chromosome arms 3DS (9) and 3DL (24).
These EST were only assigned to chromosome 3D previously by Munkvold et al. (2004).
Further, we have successfully assigned the chromosome arm for the EST those were failed to
hybridize to any of the chromosome of group 3 in previous study by Munkvold et al. (2004). A total
of 179 unmapped wheat ESTs assigned to 3AS (69) and 3AL (110) through BLAST search against
scaffold sequences (Fig. 4.7). As many as 149 EST correspond to chromosome 3B and 165 ESTs
correspond to chromosome 3D did not hybridize to the deletion lines of 3B and 3D, respectively in
previous study by Munkvold et al. (2004). The present study assigned the above unmapped ESTs;
149 were assigned to 3B (Fig.4.8) Of the 165 unmapped ESTs, 56 were assigned to 3DS and 109
were assigned to 3DL (Fig. 4.9)
Using in silico approach, we predicted the linear order of mapped ESTs with in deletion-bins
by aligning them to corresponding scaffold sequences of group 3 chromosomes. However,
assignment of scaffold to the deletion-bins were determined, order of scaffolds (by end to end
matching) along the chromosome will need to be established. The linear order of mapped ESTs
within chromosome bins of 3A, 3B and 3D in the present study may provide useful information for
fine mapping, map-based cloning of QTL/gene(s) located on group 3 chromosomes.

Figure 4.7. Diagram represented assignment for 179 ESTs to chromosome arms 3AS (69) and 3AL
(110). These ESTs were failed to hybridize with chromosome 3A in previous study by Munkvold et
al. (2004).
S
3AS2- 0.23-0.45
3AL3-0.42-0.78
C-3AL3- 0.42
C-3AS2- 0.23
L
3A
BE422971 BE444736 BE445136 BE405374 BE404841
BF429128 BE636807 BG606803 BG607322 BE424492
BE425126 BE445607 BE446590 BE499209 BE500648
BG263409 BE422922 BQ280603 BQ280603
BE403395 BE403619 BE403637 BE403647 BE404434
BE406903 BF429416 BM138632 BF200746 BE607113
BE442759 BE488783 BE489603 BE494805 BE442882
BE443276 BE496144 BE495175 BE494067 BG607279
BE604857 BF478499 BE404125 BE445996 BE494270
BF483829 BF483086 BF483675 BE489841 BE425919
BF482977 BF292744 BF293968 BG263769 BF473034
BG262775 BF293652 BF292883 BF291728 BF292654
BE403910 BF474438 BE497053 BE518276 BE442638
BF483506 BE443349 BE591725 BG604501 BF428874
BE637668 BE471045 BM135469 BM136889
BM134606 BM137808 BE497136 BI479637 BE517923
BF200549 BF292758 BE490187 BF485214 BF429272
BF482223 BE445348 BG607326 BE407052 BE490700
BM138210 BE591864 BF428820 BF202303 BE471312
BG314311 BG263758 BE496852 BE497524 BF428535
BM138163 BE637832 BE403960 BE517962 BI479636
BG607212 BE445579 BE497804 BE490085 BF202765
BF485029 BG274635 BE494807 BG263696 BE425222
BE443397 BM138223 BG604859 BE442617
BE494921 BE500863 BE446628 BF202635 BE636816
BG314172 BE424589 BG604730 BE591959 BE444474
BE352587 BE403496 BE403509 BE398275 BE399500
BQ280546 BE403439 BE443082 BE445559 BF291720
BE490765 BE498447 BE444822 BE488921 BE495304
BG262527 BF203070 BG313208 BE495066 BG607411
BE605213 BF474937 BF292874 BE426680 BG312802
BF292454 BE517875 BM138070 BE517681 BE518003
BE499141 BG605144 BE488378 BE517655 BF473786
BE499387 BE637640 BE637640 BF292295 BF146069
BE424538 BE444171 BE442782 BE489185 BE590709
BE495866 BF202464 BF484021 BE442715 BF484790
BE443955 BE499742
BE422971 BE444736 BE445136 BE405374 BE404841
BF429128 BE636807 BG606803 BG607322 BE424492
BE425126 BE445607 BE446590 BE499209 BE500648
BG263409 BE422922 BQ280603 BQ280603 BE403395
BE403619 BE403637 BE403647 BE404434 BE406903
BF429416 BM138632 BF200746 BE607113 BE442759
BE488783 BE489603 BE494805 BE442882 BE443276
BE496144 BE495175 BE494067 BG607279 BE604857
BF478499 BE404125 BE445996 BE494270 BF483829
BF483086 BF483675 BE489841 BE425919 BF482977
BF292744 BF293968 BG263769 BF473034 BG262775
BF293652 BF292883 BF291728 BF292654 BE403910
BF474438 BE497053 BE518276 BE442638 BF483506
BE443349 BE591725 BG604501 BF428874 BE637668
BE471045 BM135469 BM136889 BM134606 BM137808
BE497136 BI479637 BE517923 BF200549 BF292758
BE490187 BF485214 BF429272 BF482223 BE445348
BG607326 BE407052 BE490700 BM138210 BE591864
BF428820 BF202303 BE471312 BG314311 BG263758
BE496852 BE497524 BF428535 BM138163 BE637832
BE403960 BE517962 BI479636 BG607212 BE445579
BE497804BE490085BF202765BF485029BG274635
BE494807 BG263696 BE425222 BE443397 BM138223
BG604859 BE442617 BE494921 BE500863 BE446628
BF202635 BE636816 BG314172 BE424589 BG604730
BE591959 BE444474 BE352587 BE403496 BE403509
BE398275 BE399500 BQ280546 BE403439 BE443082
BE445559 BF291720 BE490765 BE498447 BE444822
BE488921 BE495304 BG262527 BF203070 BG313208
BE495066 BG607411 BE605213 BF474937 BF292874
BE426680 BG312802 BF292454 BE517875 BM138070
BE517681 BE518003 BE499141 BG605144 BE488378
BE517655 BF473786 BE499387 BE637640 BE637640
BF292295 BF146069 BE424538 BE444171 BE442782
BE489185 BE590709 BE495866 BF202464 BF484021
BE442715BF484790BE443955BE499742
Unassigned ESTs (179)
69 ESTs
110 ESTs
Munkvoldet al. (2004) PresentStudy
3BS9-0.57-0.78
3BS10-0.33-0.57
3BL10-0.50-0.63
3B
3BL2-0.22-0.50
L
C-3BS1-0.33
C-3BL2-0.22
BE426356 BE446610 BE446824 BE442658 BE500759
BF478742 BE637190 BE637127 BF145392 BG606809
BG312705 BE422983 BE422971 BE424200 BE426452
BE517989 BG262634 BE490662 BE490744 BE405775
BF474516 BF483477 BF483494 BF484945 BE398519
BE438263 BE399612 BE399812 BG607914 BG606095
BQ280482 BE443995 BE585557 BE442694 BE636993
BE499049 BF482769 BE403721 BE406998 BE517736
BF429350 BF482462 BE445328 BM134469 BF202364
BF201705 BF201723 BE606319 BE606354 BE606719
BG604859 BE405089 BE500348 BE442761 BE443203
BE444162 BE443862 BE444664 BG314536 BE445539
BE497571 BE490596 BE497664 BF201776 BF428994
BF483259 BF483299 BE494750 BE495766 BG607424
BG314548 BF202341 BE403757 BE446425 BE591222
BE498100 BG314551 BF482939 BF484250 BF473725
BG262705 BG604870 BF292023 BE500739 BE442531
BE638019 BE591738 BF201670 BF485127 BM138086
BE604959 BE637868 BE490807 BM134557 BM134558
BM137912 BE497013 BI479628 BE591154 BE607045
BE517719 BF484475 BF293500 BF292343 BE498624
BE426287 BE490752 BF482385 BG274146 BG274485
BQ280440 BQ280546 BQ280603 BE442924 BE585764
BE444380 BE445348 BG607326 BE407052 BE490700
BE444171 BE442782 BE590709 BE591864 BE489538
BE495866 BF428820 BF202303 BF202464 BE498395
BE471312 BG314311 BF292434 BG263758 BE517709
BF484790 BE496852 BF428535 BE591684 BE637832
BE403960 BE517962 BI479636 BG607212 BE497804
BE499742 BF202765 BF485029 BG274635
BE426356 BE446610 BE446824 BE442658
BE500759 BF478742 BE637190 BE637127
BF145392 BG606809 BG312705 BE422983
BE422971 BE424200 BE426452 BE517989
BG262634 BE490662 BE490744 BE405775
BF474516 BF483477 BF483494 BF484945
BE398519 BE438263 BE399612 BE399812
BG607914 BG606095 BQ280482
BE443995 BE585557 BE442694 BE636993
BE499049 BF482769 BE403721 BE406998
BE517736 BF429350 BF482462 BE445328
BM134469 BF202364 BF201705
BF201723 BE606319 BE606354 BE606719
BG604859 BE405089 BE500348 BE442761
BE443203 BE444162 BE443862 BE444664
BG314536 BE445539 BE497571 BE490596
BE497664 BF201776 BF428994 BF483259
BF483299 BE494750 BE495766 BG607424
BG314548 BF202341 BE403757 BE446425
BE591222 BE498100 BG314551 BF482939
BF484250 BF473725 BG262705 BG604870
BF292023 BE500739 BE442531 BE638019
BE591738 BF201670 BF485127
BM138086 BE604959 BE637868
BE490807 BM134557 BM134558
BM137912 BE497013 BI479628 BE591154
BE607045 BE517719 BF484475 BF293500
BF292343 BE498624 BE426287 BE490752
BF482385 BG274146 BG274485
BQ280440 BQ280546 BQ280603
BE442924 BE585764 BE444380 BE445348
BG607326 BE407052 BE490700 BE444171
BE442782 BE590709 BE591864 BE489538
BE495866 BF428820 BF202303 BF202464
BE498395 BE471312 BG314311 BF292434
BG263758 BE517709 BF484790 BE496852
BF428535 BE591684 BE637832 BE403960
BE517962 BI479636 BG607212 BE497804
BE499742 BF202765 BF485029 BG274635
149 ESTs
Munkvold et al. (2004) PresentStudy
S

Figure 4.8. Diagram represented assignment for 149 ESTs to chromosome 3B. These ESTs were
failed to hybridize with chromosome 3B in previous study by Munkvold et al. (2004).
Figure 4.9. Diagram represented assignment for 165 ESTs to chromosome arms 3DS (56) and 3DL
(109). These ESTs were failed to hybridize with chromosome 3D in previous study by Munkvold et
al. (2004).
3DS3-0.24-0.55
3DL-0.27-0.81
C-3DL2-0.27
C-3DS3-0.24
L
3D
BF291928 BE494807 BF478742 BE637127 BF145392
BG606809 BE422971BE424229 BE424246 BE499016
BE517989 BE490662 BE405775 BE637664 BF474516
BF483477 BE398585 BE438263 BG263696 BG312756
BG606095 BQ280438 BE443995 BE585557 BE496857
BE445556 BE445803 BE445328 BM138223 BF201928
BF201723 BE606719 BE405089 BE443203 BE444162
BG314536 BE497571 BE494750 BG607234 BF202341
BF202528 BE403757 BE494622 BE591222 BG604568
BE446043 BE446650 BF483799 BF483930 BF485381
BF482939 BF484964 BE442531 BE638019 BF201670
BM140368 BE490807 BM134555 BM136914
BM137965 BI479628 BE517312 BF293500 BF291485
BE498624 BE500330 BE471309 BF482385 BF485117
BF429274 BE405374 BE500863 BF429128 BG607322
BE445607 BE499209 BE500648 BQ280603 BE403395
BE403637 BE404434 BE488992 BE637490 BE607113
BE443053 BE442882 BE443276 BG607279 BF483829
BF482977 BF293968 BG263769 BE403910 BF474438
BE497053 BE518276 BE591725 BF428874 BE471045
BE426188 BM136889 BM134606 BE497136 BI479637
BE517923 BF292758 BE490187 BE489612 BE406967
BE426356 BE446824 BG274134 BE442599 BE442658
BE494807 BG312705 BE424862 BE500201 BF483494
BE398279 BG263696 BE425222 BM134469 BF201705
BG604859 BE443862 BE470921 BF483259 BF483390
BF428807 BF429193 BE637850 BF483770 BF484250
BF292023 BG605127 BM138086 BM134557
BE497013 BQ282235 BE492524 BE517719 BF484475
BG275060 BF292343 BF292479 BG274485 BE442617
BE494921 BF202385 BF202635 BG314172 BE398268
BQ280546 BE403439 BF473483 BE444822 BF203070
BE517875 BE517681 BE517919 BE518003 BE517655
BF473786BE471236
BF291928 BE494807 BF478742 BE637127
BF145392 BG606809 BE422971 BE424229
BE424246 BE499016 BE517989 BE490662
BE405775 BE637664 BF474516 BF483477
BE398585 BE438263 BG263696 BG312756
BG606095 BQ280438 BE443995 BE585557
BE496857 BE445556 BE445803 BE445328
BM138223 BF201928 BF201723 BE606719
BE405089 BE443203 BE444162 BG314536
BE497571 BE494750 BG607234 BF202341
BF202528 BE403757 BE494622 BE591222
BG604568 BE446043 BE446650 BF483799
BF483930 BF485381 BF482939 BF484964
BE442531 BE638019 BF201670 BM140368
BE490807 BM134555 BM136914 BM137965
BI479628 BE517312 BF293500 BF291485
BE498624 BE500330 BE471309 BF482385
BF485117 BF429274 BE405374 BE500863
BF429128 BG607322 BE445607 BE499209
BE500648 BQ280603 BE403395 BE403637
BE404434 BE488992 BE637490 BE607113
BE443053 BE442882 BE443276 BG607279
BF483829 BF482977 BF293968 BG263769
BE403910 BF474438 BE497053 BE518276
BE591725 BF428874 BE471045 BE426188
BM136889 BM134606 BE497136 BI479637
BE517923 BF292758 BE490187 BE489612
BE406967
BE426356 BE446824 BG274134 BE442599
BE442658 BE494807 BG312705 BE424862
BE500201 BF483494 BE398279 BG263696
BE425222 BM134469 BF201705 BG604859
BE443862 BE470921 BF483259 BF483390
BF428807 BF429193 BE637850 BF483770
BF484250 BF292023 BG605127 BM138086
BM134557 BE497013 BQ282235 BE492524
BE517719 BF484475 BG275060 BF292343
BF292479 BG274485 BE442617 BE494921
BF202385 BF202635 BG314172 BE398268
BQ280546 BE403439 BF473483 BE444822
BF203070 BE517875 BE517681 BE517919
BE518003BE517655BF473786BE471236
109 ESTs
56 ESTs
Munkvoldet al. (2004) PresentStudy
S

5. SUMMARY
In the present study, we linearly ordered the majority of mapped ESTs of wheat with in deletion bins
by aligning them to corresponding scaffold sequences of group 3 chromosomes. However,
assignment of scaffold to the deletion-bins were determined, order of scaffolds (by end to end
matching) along the chromosome will need to be established in near future. The linear order of
mapped ESTs within chromosome bins of 3A, 3B, and 3D in the present study may provide useful
information for fine mapping, map-based cloning of QTL/gene(s) located on group 3 chromosomes.

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Breeding, 15(1), 1-10.

APPENDIX - I
Details of bin-mapped wheat ESTs of chromosome 3A and their matching to 3A scaffolds with
sequence coordinates. Duplicate loci of ESTs are also presented.
Wheat
EST
Size
(bases)
Mapped location Scaffold name Cordinate
Start
Cordinate
end
Duplicate
Position
BF478742 528 3AL3-0.42-0.78 scaffold_195024_3AL 31303 32097 3B,3DL
BG606778 430 3AL3-0.42-0.78 scaffold_196221_3AL 23891 24739 3B,3DL
BE424200 569 3AL3-0.42-0.78 scaffold_195431_3AL 28671 29816 3B,3DL
BE490678 565 3AL3-0.42-0.78 scaffold_199052_3AL 2780 3704 3DL
BF484945 212 3AL3-0.42-0.78 scaffold_194277_3AL 112496 113307 3B,3DL
BE399869 340 3AL3-0.42-0.78 scaffold_194635_3AL 52793 53517 3B
BG607914 364 3AL3-0.42-0.78 scaffold_194875_3AL 63288 64251 3B,3DL,7BL
BQ280515 570 3AL3-0.42-0.78 scaffold_194677_3AL 53120 54095 3DL
BE443995 593 3AL3-0.42-0.78 scaffold_194377_3AL 47687 48458 3AL,3B,3DL
BE585797 594 3AL3-0.42-0.78 scaffold_195459_3AL 20656 21425 3AL,3DL
BE636993 446 3AL3-0.42-0.78 scaffold_194092_3AL 29551 30248 3AL,3B,3DL,1AL
,1DL,5DL
BF485179 517 3AL3-0.42-0.78 scaffold_199460_3AL 2236 3039 3AL,3DL,5AL,5D
L
BE497323 341 3AL3-0.42-0.78 scaffold_195250_3AL 34609 35451 3AL,3B

BF483255 405 3AL3-0.42-0.78 scaffold_197242_3AL 17947 18696 3AL,3B,3DL,4AS
,4B
BE443318 572 3AL3-0.42-0.78 scaffold_196741_3AL 437 1403 3AL,1AL,1BL,2A
L,5BL
BM134414 390 3AL3-0.42-0.78 scaffold_194468_3AL 82171 82949 3AL,3B,3DL
BF473016 684 3AL3-0.42-0.78 scaffold_196342_3AL 35776 36542 3AL,3DL
BF201151 315 3AL3-0.42-0.78 scaffold_194468_3AL 87051 87772 3AL,3B,3DL
BG313152 650 3AL3-0.42-0.78 scaffold_193883_3AL 96294 97048 3AL,3B,3DL
BE495195 436 3AL3-0.42-0.78 scaffold_198317_3AL 11722 12587 3AL,3B,3DL,7BL
BG607861 599 3AL3-0.42-0.78 scaffold_193760_3AL 75439 76377 3AL,3B
BG607811 385 3AL3-0.42-0.78 scaffold_196014_3AL 19136 20120 3AL,3DL,U
BG607064 535 3AL3-0.42-0.78 scaffold_196719_3AL 20202 21269 3AL
BE637760 384 3AL3-0.42-0.78 scaffold_194586_3AL 82555 83538 3AL,7AL
BE446754 438 3AL3-0.42-0.78 scaffold_196616_3AL 19474 20289 3AL

BM137912 298 3AL3-0.42-0.78 scaffold_195212_3AL 25375 26183 3AL,3B
BQ280724 661 3AL3-0.42-0.78 scaffold_194734_3AL 72359 73244 3AL
BI479628 416 3AL3-0.42-0.78 scaffold_195297_3AL 41460 42263 3AL,3B,3DL
BE489472 530 3AL3-0.42-1.00* scaffold_199219_3AL 4838 5620 3AL,3B,3DL
BE497749 396 3AL3-0.42-1.00* scaffold_194192_3AL 100959 101658 3AL,3B,3DL
BG604870 137 3AL3-0.42-1.00* scaffold_193934_3AL 13864 14555 3AL,3B,3DL
BF146198 297 3AL3-0.42-1.00* scaffold_194412_3AL 89501 90254 3AL,3B,3DL
BE424229 455 3AL5-0.78-1.00 scaffold_193615_3AL 136613 137564 3AL3DL
BF474841 393 3AL5-0.78-1.00 scaffold_194524_3AL 63252 63893 3AL
BQ280438 522 3AL5-0.78-1.00 scaffold_197009_3AL 11517 12412 3AL,3B,3DL
BE442875 529 3AL5-0.78-1.00 scaffold_194691_3AL 52927 53669 3DL

BE499049 671 3AL5-0.78-1.00 scaffold_197007_3AL 29351 30525 3AQL,3B,3DL,7A
S,7DS,4AL
BF482769 556 3AL5-0.78-1.00 scaffold_195106_3AL 63176 64331 3AL,3B,3DL,7BL
,6BS,6AS,6DS
BF485004 316 3AL5-0.78-1.00 scaffold_194856_3AL 36934 37723 3AL,3B,3DL,5AL
,1DL
BF429350 323 3AL5-0.78-1.00 scaffold_197007_3AL 28821 29736 3AL,3B,3DL,4AL
,7AS,7DS
,5BL
BG607613 113 3AL5-0.78-1.00 scaffold_196932_3AL 26696 27401 3AL,5AL,5AS,5D
L,7DL

BE490596 531 3AL5-0.78-1.00 scaffold_195523_3AL 17462 18289 3AL,3B,3DL,1A,1
BL,1DL
BE494750 539 3AL5-0.78-1.00 scaffold_193618_3AL 153091 153843 3AL,3B,DL,7BL
BG607234 362 3AL5-0.78-1.00 scaffold_194733_3AL 46317 47033 3AL,3DL,6AS,7B
S
BE498100 471 3AL5-0.78-1.00 scaffold_193626_3AL 89264 90008 3AL,3B,2AL,4AS
,5AL,6AL,7BL
BF485440 110 3AL5-0.78-1.00 scaffold_197747_3AL 19073 19771 3AL,3B,3DL,4BL
4DL,5AL
BF483129 257 3AL5-0.78-1.00 scaffold_193755_3AL 45513 46249 3AL,3B,5BL,5DL
,7AL,7DL
BE426274 466 3AL5-0.78-1.00 scaffold_195745_3AL 1424 2161 3AL,1BS,5BS,7A
L
BF484767 521 3AL5-0.78-1.00 scaffold_195325_3AL 43175 44168 3AL,3B,3DL,U
BG262705 438 3AL5-0.78-1.00 scaffold_195304_3AL 9175 10072 3AL,3B,U,2AS,6
AS,6BL,6DS,7AL
,7AS,7DS,
BF291831 620 3AL5-0.78-1.00 scaffold_198610_3AL 7411 8280 3AL,4BL,2AS,7A
L7DS

BF201670 465 3AL5-0.78-1.00 scaffold_196062_3AL 12308 13171 3AL,3B.3DL.6BL
BE518446 617 3AL5-0.78-1.00 scaffold_196753_3AL 25895 26664 3AL,3B,U
BF293500 558 3AL5-0.78-1.00 scaffold_196429_3AL 22918 23971 3AL,3B,3DL,5BS
BF291966 475 3AL5-0.78-1.00 scaffold_193717_3AL 184506 185230 3AL,2AL,2BL,2D
L
BF483375 116 3AL5-0.78-1.00 scaffold_194097_3AL 47661 48323 3AL,3DL,7BS
BE426452 474 3AS2-0.23-0.45 scaffold_193608_3AL 49734 50807 3AL,3B,3DL
BE637127 399 3AS4-0.45-1.00 scaffold_195377_3AL 50979 51882 3AL,3B.3DL,U
BG606809 587 3AS4-0.45-1.00 scaffold_194420_3AL 27648 28534 3AL,3B,3DL
BF483477 186 3AS4-0.45-1.00 scaffold_196729_3AL 14849 15593 3AL,3B,3DL
BM138223 312 3AS4-0.45-1.00 scaffold_195574_3AL 11584 12322 3AL,3AS,3DL,2B
L,5DL,5DS,6BL,7
AL,7BS
BE446425 306 3AS4-0.45-1.00 scaffold_194589_3AL 91855 92714 3AL,3B.1AS,1DS,
4DS,7BL,7DL
BF293108 194 3AS4-0.45-1.00 scaffold_194993_3AL 39905 40698 3AL
BM134558 193 3AS4-0.45-1.00 scaffold_193607_3AL 163218 163937 3AL,3B
BG263585 312 C3A scaffold_196423_3AL 34621 35374 3AL,3B,3DL
BE500460 377 C-3AL3-0.42 scaffold_195795_3AL 46243 47054 3AL,3B,3DL,6DL
,5BL,5DS,4DL
BE423472 605 C-3AL3-0.42 scaffold_196333_3AL 14199 15101 3AL,3B,3DL
BG262899 269 C-3AL3-0.42 scaffold_195209_3AL 39385 40173 3AL,3B

BE405776 526 C-3AL3-0.42 scaffold_193599_3AL 283837 284805 3AL,3B,U
BG263667 372 C-3AL3-0.42 scaffold_194109_3AL 121306 122084 3AL,3B,3DL
BE403721 540 C-3AL3-0.42 scaffold_194285_3AL 102945 103631 3AL,3B.3DL,4DS
,4AL,4BS
BE517931 601 C-3AL3-0.42 scaffold_196646_3AL 19148 20099 3AL,3B
BF201723 293 C-3AL3-0.42 scaffold_193648_3AL 191215 192038 3AL,3B,3DL
BE500510 429 C-3AL3-0.42 scaffold_194450_3AL 86044 86792 3AL,3B
BE442595 650 C-3AL3-0.42 scaffold_194295_3AL 97962 98834 3AL,4BS,2BL
BG313297 471 C-3AL3-0.42 scaffold_194658_3AL 9916 10986 3AL,3B,3DL,1DL
BG607570 468 C-3AL3-0.42 scaffold_196414_3AL 29674 30450 3AL,3B
BM138094 242 C-3AL3-0.42 scaffold_194496_3AL 50718 51559 3AL,1AL,2DL,6A
S

BE499024 382 C-3AL5-0.78* scaffold_196812_3AL 27998 28924 3AL,3DL
BF482930 108 C-3AL5-0.78* scaffold_194675_3AL 28004 28662 3AL,3B,3DL
BG313636 512 C-3AL5-0.78* scaffold_194961_3AL 50072 50864 3AL,3B,3DL
BE446650 451 C-3AL5-0.78* scaffold_196147_3AL 24882 25640 3AL,3B,3DL
BM140368 559 C-3AL5-0.78* scaffold_194068_3AL 63935 64990 3AL,3B,3DL
BE637307 265 C-3AL5-0.78* scaffold_195232_3AL 18476 19233 3AL,3B,3DL
BG274146 409 C-3AS2-0.23 scaffold_194245_3AL 113745 114543 3AL,3B,3DL
BF473725 481 3AL3-0.42-0.78 scaffold_212620_3AS 22442 23350 3AS,B,1AL,BS,A
S,2AL,AS,AL,5A
S,6AL,6AS,6BS,7
AL
BF482436 345 3AS2-0.23-0.45 scaffold_210678_3AS 137729 138418 3AS,3B,3DS
BF473348 526 3AS2-0.23-0.45 scaffold_210626_3AS 84026 84970 3AL,3B,3DL
BG262634 542 3AS2-0.23-0.45 scaffold_210504_3AS 241581 242633 3AL,3B,3DL
BE500201 643 3AS2-0.23-0.45 scaffold_212272_3AS 25816 27058 3AS,3DS
BF201310 152 3AS2-0.23-0.45 scaffold_211381_3AS 56656 57371
BE488644 373 3AS2-0.23-0.45 scaffold_210432_3AS 351189 351984
BE638043 375 3AS2-0.23-0.45 scaffold_210726_3AS 21000 21754 3AS,3DS,4BS,4D
S
BF484960 623 3AS2-0.23-0.45 scaffold_210762_3AS 89554 90536 5Al,5BS,6BL,6DL
BE399952 396 3AS2-0.23-0.45 scaffold_211331_3AS 69325 70047 3AS,3B,3DS
BF482462 527 3AS2-0.23-0.45 scaffold_213407_3AS 2640 3633 3AS,3B,3DL
BM134371 585 3AS2-0.23-0.45 scaffold_212656_3AS 23985 25112 3AS,3B,3DS
BG263949 416 3AS2-0.23-0.45 scaffold_210479_3AS 87208 87998
BE496996 594 3AS2-0.23-0.45 scaffold_211492_3AS 13580 14564 3AS,U,6DS,
BQ282235 458 3AS2-0.23-0.45 scaffold_210454_3AS 280567 281405 3AS,3B,3DS
BG274851 546 3AS2-0.23-0.45 scaffold_211361_3AS 40581 41339 3AS,3DS,U

BE406567 242 3AS4-0.45-1.00 scaffold_211316_3AS 34177 34316 3AS,3B,3DS,1DS,
1BS
BE426356 507 3AS4-0.45-1.00 scaffold_211194_3AS 18063 18924 3AS,3B,3DS,7DS,
7BS
BE446610 550 3AS4-0.45-1.00 scaffold_211988_3AS 15625 16427 3AS,3B.3DS.1BS
BE490440 348 3AS4-0.45-1.00 scaffold_212091_3AS 22454 23306 3AS,3B,3DS,1AS,
1BS,1DS
BE591226 511 3AS4-0.45-1.00 scaffold_213233_3AS 11588 12698 3AS,3B,3DS,5DL
BE405260 624 3AS4-0.45-1.00 scaffold_210989_3AS 74837 75643 3AS,3DS,5BL,5A
L,5DL
BG274134 250 3AS4-0.45-1.00 scaffold_210783_3AS 19975 20704 3AS,3B,3DS
BG312705 197 3AS4-0.45-1.00 scaffold_211949_3AS 31664 32376 3B,3DS
BE423484 458 3AS4-0.45-1.00 scaffold_212447_3AS 10043 11084 3AS
BE406607 341 3AS4-0.45-1.00 scaffold_213408_3AS 7309 8216 3DS.U
BE500231 271 3AS4-0.45-1.00 scaffold_211563_3AS 61581 62243 3DS
BF483494 633 3AS4-0.45-1.00 scaffold_211087_3AS 31323 32240 3B,3DS
BE398279 498 3AS4-0.45-1.00 scaffold_212515_3AS 14755 15523 3B,3DS
BI479183 267 3AS4-0.45-1.00 scaffold_213550_3AS 13695 14561 3B,3DS
BI479242 474 3AS4-0.45-1.00 scaffold_212276_3AS 18682 19601 3B,3DS
BG606190 632 3AS4-0.45-1.00 scaffold_210989_3AS 73657 74486 3DS
BQ280482 412 3AS4-0.45-1.00 scaffold_210983_3AS 18135 18938 3B,3DS
BE444576 341 3AS4-0.45-1.00 scaffold_210716_3AS 2447 3217 3B,3DS,2BL,2DL
BE405200 573 3AS4-0.45-1.00 scaffold_210800_3AS 53763 54577 5BS,6AL
BE407082 462 3AS4-0.45-1.00 scaffold_212044_3AS 36264 37206 3B,3DL,4DL,2BL
,

BE490150 513 3AS4-0.45-1.00 scaffold_210691_3AS 145760 146754 3B,3DS,6AL,
BE591845 212 3AS4-0.45-1.00 scaffold_211647_3AS 42593 43288
BE605225 378 3AS4-0.45-1.00 scaffold_212877_3AS 16019 16984 3B,5AL,5DL,5BL
BE494004 380 3AS4-0.45-1.00 scaffold_211275_3AS 54525 55291 2DL
BF482885 489 3AS4-0.45-1.00 scaffold_210963_3AS 20038 21102 3B,U
BG274303 131 3AS4-0.45-1.00 scaffold_211122_3AS 41747 42476 3B
BE442933 533 3AS4-0.45-1.00 scaffold_210646_3AS 36966 37787 3B,3DS,U,6AS,6
BS,
BE405496 562 3AS4-0.45-1.00 scaffold_212062_3AS 18256 19058 3B,U
BE591948 517 3AS4-0.45-1.00 scaffold_211981_3AS 15970 16795
BM138086 417 3AS4-0.45-1.00 scaffold_212152_3AS 30832 31700 3B,3DS
BF428898 616 3AS4-0.45-1.00 scaffold_212641_3AS 7894 8893 3B
BF428900 399 3AS4-0.45-1.00 scaffold_211917_3AS 14562 15329 1AL,1DL,1DS,4A
S,5AL,5BL,

BG275060 461 3AS4-0.45-1.00 scaffold_210989_3AS 91053 91728 3AS,3B,3DS,6AS,
6BS.6DS
BE499309 597 3AS4-0.45-1.00 scaffold_211206_3AS 8903 9593 3B
BE446824 441 C-3AS2-0.23 scaffold_211294_3AS 59069 59808 3B,3DS
BE637190 359 C-3AS2-0.23 scaffold_211780_3AS 30167 30912 3B,U
BE446462 509 C-3AS2-0.23 scaffold_210432_3AS 269795 270711 33B,3DS,6AS,U
BG274933 397 C-3AS2-0.23 scaffold_212293_3AS 12848 13737 3B,3DS
BF478475 390 C-3AS2-0.23 scaffold_211779_3AS 56981 57970 3DS,1BL,2BL,2D
L,5BL,6DS
BF483751 308 C-3AS2-0.23 scaffold_211328_3AS 63389 64218 3B,3DS
BG263578 422 C-3AS2-0.23 scaffold_210455_3AS 8964 9985
BF292023 549 C-3AS2-0.23 scaffold_213185_3AS 10261 11131 3B,3DS
BE426298 216 C-3AS2-0.23 scaffold_211121_3AS 12920 13735
BM135339 629 C-3AS2-0.23 scaffold_212092_3AS 16090 16896 3B,3DS
BM136734 269 C-3AS2-0.23 scaffold_212695_3AS 26543 27411 U
BE443960 618 C-3AS4-0.45* scaffold_211462_3AS 59250 60076 3B,3DS
BF478841 356 C-3AS4-0.45* scaffold_210599_3AS 32780 33531 3B,3DS
BG604567 380 C-3AS4-0.45* scaffold_211594_3AS 24412 25243 3B,3DS

BE497864 493 C-3AS4-0.45* scaffold_210581_3AS 182826 183914 U
BF485348 382 C-3AS4-0.45* scaffold_210641_3AS 153315 154273 3B,3DS
BG605127 641 C-3AS4-0.45* scaffold_211054_3AS 21665 22520 3B,3DS

APPENDIX - II
Details of bin-mapped wheat ESTs of chromosome 3B and their matching to 3B scaffolds with
Wheat
EST
Size
(bases)
Mapped location Scaffold name
Cordinate
Start
Cordinate
end
Duplicate Position
BF291928 303 3BL10-0.50-0.63 scaffold_222513_3B 51761 52491 3AL,3DL
BE443747 571 3BL10-0.50-0.63 scaffold_221109_3B 210860 211649 3AL,3DL
BE497323 341 3BL10-0.50-0.63 scaffold_223053_3B 38578 39278 3AL
BF478406 493 3BL10-0.50-0.63 scaffold_225011_3B 15162 16006 3DL,1AS
BF478414 606 3BL10-0.50-0.63 scaffold_224719_3B 19565 20770
BG313152 650 3BL10-0.50-0.63 scaffold_222072_3B 127430 128184 3AL,3DL
BM140325 534 3BL10-0.50-0.63 scaffold_221814_3B 81059 82146 3AL,3DL
BE403697 139 3BL10-0.50-0.63 scaffold_230966_3B 4253 4991 1BL,4bs,7BS
BE488783 641 3BL10-0.50-0.63 scaffold_227609_3B 19257 20204
3AL,3B,3DL,1AS,1B
L1DL,7DS
BE517914 524 3BL10-0.50-0.63 scaffold_220802_3B 165163 165899
BF291729 566 3BL10-0.50-0.63 scaffold_224591_3B 40388 41194 3DL

BF484141 503 3BL10-0.50-0.63 scaffold_223017_3B 45976 46792 2BL
BM134414 390 3BL10-0.50-1.00* scaffold_222607_3B 99662 100442 3AL,3DL
BE591450 538 3BL10-0.50-1.00* scaffold_222281_3B 102934 103805 7BS,7DS,
BE490734 443 3BL2-0.22-0.50 scaffold_222369_3B 97058 97959 3DL
BE405776 526 3BL2-0.22-0.50 scaffold_221268_3B 53461 54429 3AL,U
BF483255 405 3BL2-0.22-0.50 scaffold_223037_3B 9876 10625 3AL,3DL,4AS,4B
BF478698 596 3BL2-0.22-0.50 scaffold_224894_3B 47588 48783
BG313297 471 3BL2-0.22-0.50 scaffold_224886_3B 40081 41151 3AL,3DL,1DL
BG607861 599 3BL2-0.22-0.50 scaffold_220896_3B 149926 150861 3AL
BG607570 468 3BL2-0.22-0.50 scaffold_221520_3B 11755 12531 3AL
BF484767 521 3BL2-0.22-0.50 scaffold_222276_3B 23902 25022 3AL,3DL,U
BG604766 291 3BL2-0.22-0.50 scaffold_225301_3B 8041 8813

BE406507 475 3BL2-0.22-0.50 scaffold_223057_3B 85995 87069
3AL,2DS,4DS,5AL,5
BL,5DL,
BF484783 612 3BL2-0.22-0.50 scaffold_226236_3B 6550 7345 4AL,4BS,4DS
BG263580 453 3BL2-0.22-0.50 scaffold_226456_3B 28691 29667 2BS,2DS
BI479128 587 3BL2-0.22-0.50 scaffold_221905_3B 43643 44576
BI479128 587 3BL2-0.22-0.50 scaffold_221905_3B 43643 44576
BE585764 632 3BL2-0.22-0.50 scaffold_222062_3B 107689 108892 4AL,4BS,4DS
BE403439 464 3BL2-0.22-0.50 scaffold_221940_3B 94368 95069
3AL,3DL,1AS,1BS,1
DS,
BE489323 514 3BL2-0.22-0.50 scaffold_222871_3B 55519 56609 4BS,5BL,7BL
BE590689 508 3BL2-0.22-0.50 scaffold_224699_3B 3413 4207 5BL,6AS,6DS
BE605119 447 3BL2-0.22-0.50 scaffold_221924_3B 58423 59253
BG313765 478 3BL2-0.22-0.50 scaffold_227342_3B 4183 5101 5BL,5BS,7BL,7BS
BE606723 352 3BL2-0.22-0.50 scaffold_221963_3B 86541 87328 4AS,4BL,4DL
BI479637 562 3BL2-0.22-0.50 scaffold_222761_3B 20657 21815 3AL,3DL
BF485214 334 3BL2-0.22-0.50 scaffold_226235_3B 26714 27384 3AL
BF485118 497 3BL2-0.22-0.50 scaffold_222788_3B 92069 92777

BE500460 377 3BL7-0.63-1.00 scaffold_220915_3B 48956 49796
3AL,3DL,6DL,5BL,5
DS,4DL
BG312756 240 3BL7-0.63-1.00 scaffold_221732_3B 94403 95242
3AL,3DL,7BS,6AS,2
BL,4AS
BQ280438 522 3BL7-0.63-1.00 scaffold_221313_3B 64947 65842 3AL,3DL
BE444473 388 3BL7-0.63-1.00 scaffold_221246_3B 113987 114736
3AL,3DL,4AL,4BL,5
AL
BF485004 316 3BL7-0.63-1.00 scaffold_221870_3B 110015 110804 3AL,3DL,5AL
BE403428 551 3BL7-0.63-1.00 scaffold_222483_3B 55479 56359 3AL,3DL,1AL,1DL

BF484536 408 3BL7-0.63-1.00 scaffold_223057_3B 61195 62202
BE495195 436 3BL7-0.63-1.00 scaffold_224042_3B 50530 51294 3AL,3DL,7BL
BE498322 557 3BL7-0.63-1.00 scaffold_228420_3B 11846 12985 3DL,U
BF485440 110 3BL7-0.63-1.00 scaffold_221246_3B 113334 114031
3AL,3DL,4BL4DL,5
AL
BF483129 257 3BL7-0.63-1.00 scaffold_225283_3B 42917 43609
3AL,5BL,5DL,7AL,7
DL
BM137713 421 3BL7-0.63-1.00 scaffold_221409_3B 78377 79074 3DL

BF291485 544 3BL7-0.63-1.00 scaffold_227311_3B 24496 25215
3AL,3DL,1AL,1BL.1
DL,
BG314183 694 3BL7-0.63-1.00 scaffold_221160_3B 185016 186059 1DL,5AL,5BL,7DL
BE446590 413 3BL7-0.63-1.00 scaffold_221368_3B 118123 118902 3AL,U,1DL,5DS
BQ280440 625 3BL7-0.63-1.00 scaffold_224897_3B 34346 35182 5DL
BQ280603 435 3BL7-0.63-1.00 scaffold_220646_3B 357363 358388 3AL,3DL
BE403395 574 3BL7-0.63-1.00 scaffold_220697_3B 223087 224256
3AL,3DL,4AL,4BL,5
BL,5DL,7AL,7BL,7D
L
BE488364 475 3BL7-0.63-1.00 scaffold_224283_3B 38560 39502 7AS
BM134384 378 3BL7-0.63-1.00 scaffold_221745_3B 72456 73424 2BS,7BL,
BM138221 294 3BL7-0.63-1.00 scaffold_220619_3B 364517 365343 5AS,
BM138418 460 3BL7-0.63-1.00 scaffold_225478_3B 23761 24820 U,1AS,1BS,1DS
BE517960 540 3BL7-0.63-1.00 scaffold_221013_3B 145998 146903
BF202430 438 3BL7-0.63-1.00 scaffold_222937_3B 64917 65655 1BL,4BL,5BS,
BG604623 222 3BL7-0.63-1.00 scaffold_228086_3B 17722 18543 6BL,7BS
BF474686 434 3BL7-0.63-1.00 scaffold_222137_3B 122053 122824
BG275074 544 3BL7-0.63-1.00 scaffold_224505_3B 6507 7635 6BL
BF485422 460 3BL7-0.63-1.00 scaffold_227258_3B 19294 20157
BG263421 557 3BL7-0.63-1.00 scaffold_223532_3B 48391 49368 3DL,5DL,6AS
BF483803 315 3BL7-0.63-1.00 scaffold_221975_3B 121307 122118 7DL,
BF483485 548 3BL7-0.63-1.00 scaffold_226656_3B 14153 14972 7AL,7BL

BE403910 138 3BL7-0.63-1.00 scaffold_224812_3B 4621 5354
3AL,3DL,1BL,2AL,7
BL,6BS,U,2BS,4AL,
4BS,5DL
BE637668 369 3BL7-0.63-1.00 scaffold_220912_3B 163173 164141 3AL,3DL,U
BM134504 356 3BL7-0.63-1.00 scaffold_224273_3B 33463 34249
BM136889 157 3BL7-0.63-1.00 scaffold_223032_3B 60450 61206
3AL,3DL,1AL,1BL,1
DL
BE590950 465 3BL7-0.63-1.00 scaffold_221800_3B 61478 62353
BG274339 198 3BL7-0.63-1.00 scaffold_220677_3B 241640 242349 2AS,2BS
BG274676 350 3BL7-0.63-1.00 scaffold_224749_3B 41343 42099 3DL
BG274655 567 3BL7-0.63-1.00 scaffold_225280_3B 19522 20334
BE443955 528 3BL7-0.63-1.00 scaffold_220765_3B 287569 288264 3AS
BE490440 348 3BS1-0.33-0.57 scaffold_221971_3B 34193 35045 1AS,1BS,1DS
BF473626 337 3BS1-0.33-0.57 scaffold_221176_3B 200762 201532 3AS,3DS
BE446462 509 3BS1-0.33-0.57 scaffold_222076_3B 76867 77827 3AS,3DS.6AS,U
BI479242 474 3BS1-0.33-0.57 scaffold_225588_3B 37121 38040 3AS,3DS
BE443960 618 3BS1-0.33-0.57 scaffold_223351_3B 50847 51769 3AS,3DS
BM134371 585 3BS1-0.33-0.57 scaffold_222280_3B 4545 5672 3AS,3DS
BE490150 513 3BS1-0.33-0.57 scaffold_223537_3B 48430 49309 3AS,DS,6AL,
BG606936 378 3BS1-0.33-0.57 scaffold_220765_3B 48440 49219 3AS,3DS
BF429193 526 3BS1-0.33-0.57 scaffold_226398_3B 12779 13566 3AS,3DS,U,

BF482885 489 3BS1-0.33-0.57 scaffold_225488_3B 29372 30438 3AS,U
BG275060 461 3BS1-0.33-0.57 scaffold_223692_3B 17101 17775
3AS,3DS,6AS,6BS.6
DS
BF478445 627 3BS1-0.33-0.57 scaffold_225602_3B 29825 30787 1DS,2DL,7AS
BE445559 475 3BS1-0.33-0.57 scaffold_224833_3B 15569 16606 3AS
BE490765 531 3BS1-0.33-0.57 scaffold_246418_3B 210 1075 3AS,3DS,4BS,6AL
BF201454 364 3BS1-0.33-0.57 scaffold_227307_3B 6280 7219
BF485469 380 3BS1-0.33-0.57 scaffold_220827_3B 239479 240401 7AS
BF475136 113 3BS1-0.33-0.57 scaffold_223834_3B 27505 28175 3DS
BF291779 513 3BS1-0.33-0.57 scaffold_225471_3B 35580 36690 1BL,6AL,7BL
BG275104 341 3BS1-0.33-0.57 scaffold_223901_3B 27308 28230
BF291911 560 3BS1-0.33-0.57 scaffold_221925_3B 140566 141581
BE403326 488 3BS1-0.33-0.57 scaffold_223900_3B 66281 67368
BG605144 679 3BS1-0.33-0.57 scaffold_221937_3B 143740 144524
BF428968 349 3BS1-0.33-0.57 scaffold_224342_3B 45705 46653
3AS,3DS,1BS,2BS,5
BL,6AS,
BE471236 375 3BS1-0.33-0.57 scaffold_225840_3B 31308 32065 3DS
BE399515 216 3BS8-0.78-1.00 scaffold_221405_3B 115836 116628 3DS,4AL
BE444576 341 3BS8-0.78-1.00 scaffold_220626_3B 105929 106720 3AS,3DS,2BL,2DL

BF428807 511 3BS8-0.78-1.00 scaffold_221049_3B 22044 22809 3AS,3DS,1AL
BE442933 533 3BS8-0.78-1.00 scaffold_220651_3B 158102 158818
3AS,3DS,U,6AS,6BS
,
BG314067 328 3BS8-0.78-1.00 scaffold_224058_3B 49176 49957 3DS
BE446642 530 3BS8-0.78-1.00 scaffold_222378_3B 59318 60116 1AS,5AL,7DL
BF484268 590 3BS8-0.78-1.00 scaffold_225383_3B 43881 44656 3DS,U
BE398268 155 3BS8-0.78-1.00 scaffold_222664_3B 43312 43984 3DS,U
BG607967 575 3BS8-0.78-1.00 scaffold_222391_3B 33753 34446 3DS
BE422466 317 3BS8-0.78-1.00 scaffold_221719_3B 31053 31749 5AL,7DS,U
BE517903 536 3BS8-0.78-1.00 scaffold_226978_3B 22477 23612
BM134413 416 3BS8-0.78-1.00 scaffold_221277_3B 121380 122143
BM138503 689 3BS8-0.78-1.00 scaffold_223464_3B 76332 77219
BF473483 578 3BS8-0.78-1.00 scaffold_225631_3B 35639 36813 3DS,2BS,7DS,
BE499320 386 3BS8-0.78-1.00 scaffold_221573_3B 83983 84819
BE444122 309 3BS8-0.78-1.00 scaffold_222519_3B 21479 22294 U
BF292499 518 3BS8-0.78-1.00 scaffold_224848_3B 21049 21772
BE518285 574 3BS8-0.78-1.00 scaffold_221310_3B 142290 143240 6BL,7BL,7DS
BE499327 471 3BS8-0.78-1.00 scaffold_220791_3B 168603 169408 5AS,1BS

BF292335 480 3BS8-0.78-1.00 scaffold_222139_3B 59429 60333 7BL
BG274122 204 3BS8-0.78-1.00 scaffold_233500_3B 816 1539 2BS,2AS,1BL
BE406567 242 3BS9-0.57-0.78 scaffold_225328_3B 45479 46218 3AS,3DS,1DS,1BS
BE591226 511 3BS9-0.57-0.78 scaffold_223280_3B 65774 66884 3AS,3DS,5DL
BI479183 267 3BS9-0.57-0.78 scaffold_221861_3B 108676 109542 3AS,3DS
BE605225 378 3BS9-0.57-0.78 scaffold_221696_3B 75389 76354 3AS,5AL,5DL,5BL
BG274303 131 3BS9-0.57-0.78 scaffold_222178_3B 46482 47148 3AS
BF428674 497 3BS9-0.57-0.78 scaffold_224002_3B 22135 23231 1BL,6BL,7DS,
BE403624 696 3BS9-0.57-0.78 scaffold_224569_3B 6699 7873
5AS,5Bl,5DS.7AL,7
BL,7DL
BE498470 514 3BS9-0.57-0.78 scaffold_221705_3B 67765 68821 2BL,7BL
BE403373 397 3BS9-0.57-0.78 scaffold_224569_3B 6753 7603
7AL,7BL,7DL,5AS.5
BS,5DS
BF478743 422 3BS9-0.57-0.78 scaffold_224014_3B 14055 14776 4DL
BE399103 379 3BS9-0.57-0.78 scaffold_221503_3B 81396 82184

BE445969 535 3BS9-0.57-0.78 scaffold_224325_3B 31549 32381 7DL
BE499687 568 3BS9-0.57-0.78 scaffold_221666_3B 38976 40143
BF474937 568 3BS9-0.57-0.78 scaffold_234034_3B 146 1313 3AS
BF482960 594 3BS9-0.57-0.78 scaffold_223451_3B 26890 27661 4BS,4DS
BG312802 332 3BS9-0.57-0.78 scaffold_223692_3B 21048 21815 6AS,6BS,6DS
BF291701 516 3BS9-0.57-0.78 scaffold_221319_3B 50365 51319
BF483276 449 3BS9-0.57-0.78 scaffold_221067_3B 52514 53562
BE494662 454 3BS9-0.57-1.00* scaffold_223578_3B 45475 46504 3AS,4AS,6BL,6BS,
BE518257 435 3BS9-0.57-1.00* scaffold_220881_3B 54989 56023
BG263585 312 C3B scaffold_225733_3B 21150 21903 3AS,3DS
BF473034 609 C3B scaffold_220972_3B 151800 152703 3AS,3DS
BF473231 379 C-3BL10-0.50* scaffold_221488_3B 133226 134164
3AS,3DS,6BS,6DS,4
BL,5Al
BE498378 541 C-3BL10-0.50* scaffold_224757_3B 43633 44656 3AL,U,7AS,7BS,7DS
BE497979 605 C-3BL10-0.50* scaffold_225805_3B 9793 10605 3AS,3DS
BF484631 687 C-3BL10-0.50* scaffold_221561_3B 164717 165568 3AS,3DS
BG313636 512 C-3BL10-0.50* scaffold_223874_3B 19017 19809 3AS,3DS
BG604620 124 C-3BL10-0.50* scaffold_223823_3B 19680 20403 5BL,5BS,7BS
BF483829 406 C-3BL10-0.50* scaffold_221127_3B 129685 130672 3AL,3DL,
BF482924 450 C-3BL10-0.50* scaffold_222810_3B 51975 52778 5AL
BE494474 560 C-3BL2-0.22 scaffold_221723_3B 22503 23211 3AL,3DL,
BG262899 269 C-3BL2-0.22 scaffold_222785_3B 79902 80690 3AL
BE517931 601 C-3BL2-0.22 scaffold_222136_3B 40392 41305 3AL

BE500510 429 C-3BL2-0.22 scaffold_221506_3B 155541 156289 3AL
BG313654 427 C-3BL2-0.22 scaffold_223321_3B 11499 12281 3AL,3DL,
BG607408 542 C-3BL2-0.22 scaffold_222565_3B 52066 52848 3DL,7DS
BE446403 535 C-3BL2-0.22 scaffold_221917_3B 51538 52354 3AL,3DL
BF485348 382 C-3BL2-0.22 scaffold_221803_3B 25555 26513 3AS,3DS
BF291730 697 C-3BL2-0.22 scaffold_227720_3B 8603 9422 3AL,3DL,
BE637251 381 C-3BL2-0.22 scaffold_221715_3B 35519 36261 3AL,4BL,
BF428637 465 C-3BL2-0.22 scaffold_221225_3B 122608 123672
3AL,3DL,1AL,1B,1D
L
BE591590 520 C-3BL2-0.22 scaffold_224302_3B 31420 32533 U
BM140477 546 C-3BL2-0.22 scaffold_224416_3B 43240 44082 3AL,3DL,3DL,4AS
BF474023 605 C-3BL2-0.22 scaffold_221231_3B 47893 48598 3AL,3DL
BG274556 558 C-3BL2-0.22 scaffold_226374_3B 869 1626 3AL,3DL
BE405374 597 C-3BL2-0.22 scaffold_221037_3B 210367 211210 3AL,3DL,U
BE500863 469 C-3BL2-0.22 scaffold_221894_3B 75797 76651 3AS,3DL
BE399500 342 C-3BL2-0.22 scaffold_226901_3B 23036 23828 3AS,3DS
BE442924 653 C-3BL2-0.22 scaffold_224743_3B 5391 6211 2BL,5BS no hits
BE403637 541 C-3BL2-0.22 scaffold_220697_3B 223453 224559
3AL,3DL,4AL,5BL,5
DL,7AL,7BL,7DL
BE404434 678 C-3BL2-0.22 scaffold_220697_3B 222673 223802
3AL,3DL,4AL,5BL,5
DL,7BL,U
BE443082 612 C-3BL2-0.22 scaffold_223995_3B 67460 68343 3AS,5BL,6BL
BE443053 608 C-3BL2-0.22 scaffold_220995_3B 60737 61634 3DL
BF478559 462 C-3BL2-0.22 scaffold_222297_3B 122871 123672 3DL
BG313367 243 C-3BL2-0.22 scaffold_220816_3B 223774 224525 1BL,1DL,2BS
BE495066 509 C-3BL2-0.22 scaffold_230427_3B 2433 3487 3AS,3DL
BF291713 496 C-3BL2-0.22 scaffold_224591_3B 40388 41296
BF292654 403 C-3BL2-0.22 scaffold_220622_3B 144696 145566 3AL,3DL
BF202776 541 C-3BL2-0.22 scaffold_221884_3B 106570 107710 3DL,U,4BL
BF429272 551 C-3BL2-0.22 scaffold_221122_3B 161870 162730 3AL
BF482930 108 C-3BL7-0.63* scaffold_221509_3B 97627 98285 3AL,3DL
BE442599 654 C-3BS1-0.33 scaffold_225266_3B 33424 34327 3AS,3DS
BE494807 603 C-3BS1-0.33 scaffold_221059_3B 55135 55959 3AL,3DL

BG274933 397 C-3BS1-0.33 scaffold_224701_3B 26138 27134 3AS,3DS
BM138225 551 C-3BS1-0.33 scaffold_222327_3B 13280 14400 3AS,3DS
BF200587 441 C-3BS1-0.33 scaffold_221829_3B 80630 81461 3AS,3DS
BG313557 127 C-3BS1-0.33 scaffold_221364_3B 100547 101211 3AL,3DL
BE405131 498 C-3BS1-0.33 scaffold_223975_3B 70739 71474 7AL,7BL,7DL
BE446126 142 C-3BS1-0.33 scaffold_221829_3B 65950 66654
BE405496 562 C-3BS1-0.33 scaffold_226213_3B 29617 30543 3AS,U
BM138019 498 C-3BS1-0.33 scaffold_220956_3B 246936 247714 3AS,3DS
BF202385 362 C-3BS1-0.33 scaffold_223909_3B 63000 63762 3DS,1BL
BG606803 434 C-3BS1-0.33 scaffold_221145_3B 174804 175694 1DL,1DS,5AS,7DS
BE444280 520 C-3BS1-0.33 scaffold_221077_3B 75813 76682 3DS,U
BE638004 194 C-3BS1-0.33 scaffold_221510_3B 90540 91333 4BS,6DL
BM138680 488 C-3BS1-0.33 scaffold_221208_3B 50113 51200
1AL,2BS,2DS,4BL,4
DS,5BL,5DS,6AS,6D
L,7BL,7DL
BE498447 421 C-3BS1-0.33 scaffold_223225_3B 39922 40942 3AS,U
BE499349 545 C-3BS1-0.33 scaffold_225484_3B 26844 27988
BE591258 540 C-3BS1-0.33 scaffold_222170_3B 15213 16025 3DS
BF482977 239 C-3BS1-0.33 scaffold_221643_3B 58646 59349 3AL,3DL

BE591725 616 C-3BS1-0.33 scaffold_222040_3B 96309 97412
3AS,3DS,2BL,4BL,5
AL
BE637525 460 C-3BS1-0.33 scaffold_221510_3B 82602 83324 1DS,2AL,5BL,U
BF482223 563 C-3BS1-0.33 scaffold_221106_3B 62492 63586 3AL
BF291384 622 C-3BS1-0.33 scaffold_220956_3B 177125 177965
BF478745 519 C-3BS9-0.57* scaffold_220591_3B 74740 75569 3AS,3DS
BE637806 537 C-3BS9-0.57* scaffold_221087_3B 25613 26488 3AS,3DS

APPENDIX - III
Details of bin-mapped wheat ESTs of chromosome 3D and their matching to 3D scaffolds with
Wheat EST Size
(bases)
Mapped location Scaffold name Coordinate
Start
Coordinate
end
Duplicate
Position
BE500460 377 3DL2-0.27-0.81 scaffold_250627_3DL 37587 38427 3AL,3B
BF429203 500 3DL2-0.27-0.81 scaffold_249309_3DL 40354 41090 3AL,3B
BE490734 443 3DL2-0.27-0.81 scaffold_252077_3DL 16438 17156 3B
BG263667 372 3DL2-0.27-0.81 scaffold_249279_3DL 61006 61785 3AL,3B
BG607914 364 3DL2-0.27-0.81 scaffold_251186_3DL 7148 8103 3AL,3B,7BL
BQ280515 570 3DL2-0.27-0.81 scaffold_251459_3DL 26056 26859 3AL
BE585797 594 3DL2-0.27-0.81 scaffold_250807_3DL 4095 4864 3AL
BE404385 709 3DL2-0.27-0.81 scaffold_253909_3DL 10201 11089 U
BE636993 446 3DL2-0.27-0.81 scaffold_249777_3DL 68030 68727 3AL,3B,1AL,1DL,
5DL
BF485179 517 3DL2-0.27-0.81 scaffold_252022_3DL 24201 24998 3AL,5AL,5DL
BE403721 540 3DL2-0.27-0.81 scaffold_249105_3DL 10261 10942 3AL,3B,4DS,4AL,
4BS

BF483255 405 3DL2-0.27-0.81 scaffold_249702_3DL 81967 82716 3AL,3B,4AS,4B
BM134414 390 3DL2-0.27-0.81 scaffold_250855_3DL 25946 26726 3AL,3B
BE490596 531 3DL2-0.27-0.81 scaffold_249556_3DL 87160 87987 3AL,3B,
1A,1BL,1DL
BE500112 502 3DL2-0.27-0.81 scaffold_251513_3DL 34310 35411
BF201874 467 3DL2-0.27-0.81 scaffold_249085_3DL 34890 35795 3B
BF478406 493 3DL2-0.27-0.81 scaffold_249611_3DL 74805 75586 3B,1AS
BF478932 499 3DL2-0.27-0.81 scaffold_249301_3DL 56626 57549 3B,1AS
BG313152 650 3DL2-0.27-0.81 scaffold_250301_3DL 22000 22859 3B,1AS
BG313297 471 3DL2-0.27-0.81 scaffold_249061_3DL 31457 32518 3B,3AL,1DL

BF484767 521 3DL2-0.27-0.81 scaffold_252146_3DL 29461 30369 3AL,3B,U
BF200872 379 3DL2-0.27-0.81 scaffold_249054_3DL 238053 238894 5BL
BM137713 421 3DL2-0.27-0.81 scaffold_249716_3DL 71775 72479 3B
BF483399 115 3DL2-0.27-0.81 scaffold_250475_3DL 58100 58814
BE443829 697 3DL2-0.27-0.81 scaffold_249600_3DL 98334 99235 3AS,3B,7BS
BE488783 641 3DL2-0.27-0.81 scaffold_249996_3DL 48376 49323 3AL,3B,1AS,1BL
1DL,7DS
BF482582 474 3DL2-0.27-0.81 scaffold_251496_3DL 18055 19008 3AL

BG604501 376 3DL2-0.27-0.81 scaffold_251561_3DL 21393 22161 3AL
BG263786 522 3DL2-0.27-0.81 scaffold_252574_3DL 2212 3314
BM138209 485 3DL2-0.27-0.81 scaffold_250547_3DL 41909 42831
BM138364 614 3DL2-0.27-0.81 scaffold_251887_3DL 6157 6922 2BL,6AL
BE591159 371 3DL2-0.27-0.81 scaffold_250140_3DL 35227 36003 6BL
BE591705 555 3DL2-0.27-0.81 scaffold_251001_3DL 31214 32026
BE490085 448 3DL2-0.27-0.81 scaffold_249075_3DL 39705 40665 3AL,2AS
BG607408 542 3DL2-0.27-1.00* scaffold_259756_3DL 1298 2080 3B,7DS
BG607811 385 3DL2-0.27-1.00* scaffold_250239_3DL 49490 50471 3AL,U
BG607141 574 3DL2-0.27-1.00* scaffold_249314_3DL 125527 126257 3AL,3B
BF485331 446 3DL2-0.27-1.00* scaffold_249494_3DL 69826 70586 3AL
BE494219 528 3DL2-0.27-1.00* scaffold_249241_3DL 132022 132878 3AL,3B
BE426370 425 3DL2-0.27-1.00* scaffold_251823_3DL 9107 9888 3AL,3B,4BL
BE426763 658 3DL2-0.27-1.00* scaffold_249616_3DL 28071 29143 3AS,3B
BE425126 286 3DL2-0.27-1.00* scaffold_250864_3DL 48969 49826 3AL,3B
BG607781 422 3DL2-0.27-1.00* scaffold_250515_3DL 40038 40863 1AL,2DS,7BS
BF428820 493 3DL2-0.27-1.00* scaffold_251638_3DL 22928 23725 3AL,3B
BG263758 382 3DL2-0.27-1.00* scaffold_249740_3DL 31174 31875 3AL,3B
BG312618 170 3DL3-0.81-1.00 scaffold_250913_3DL 23981 24750 3AL,3B,U
BE444473 388 3DL3-0.81-1.00 scaffold_251482_3DL 10135 10851 4AL,4BL,5AL
BE442818 549 3DL3-0.81-1.00 scaffold_249516_3DL 111251 112075 3AL,1AL

BE443397 600 3DL3-0.81-1.00 scaffold_249172_3DL 82498 83300 3AS,3B
BE499049 671 3DL3-0.81-1.00 scaffold_250453_3DL 48662 49932 3AL,3B,7AS,7DS,
4AL
BF482769 556 3DL3-0.81-1.00 scaffold_249256_3DL 34595 35750 3AL,3B,7BL,6BS,
6AS,6DS
BF485004 316 3DL3-0.81-1.00 scaffold_252677_3DL 8724 9513 3AL,3B,5AL
BE403428 551 3DL3-0.81-1.00 scaffold_249665_3DL 24887 25748 3AL,3B,1AL,1DL
BF429350 323 3DL3-0.81-1.00 scaffold_250453_3DL 49544 50459 3AL,3B,4AL,7AS,
7DS
BE498322 557 3DL3-0.81-1.00 scaffold_249101_3DL 133919 135058 3B,U
BF485440 110 3DL3-0.81-1.00 scaffold_251482_3DL 9221 9922 3AL,3B,4B,L4DL,
5AL

BE591914 472 3DL3-0.81-1.00 scaffold_249523_3DL 15680 16533
BF483375 116 3DL3-0.81-1.00 scaffold_249555_3DL 19638 20300 3AL,7BS
BQ280603 435 3DL3-0.81-1.00 scaffold_250135_3DL 24263 25175 3AL,3B
BE443242 525 3DL3-0.81-1.00 scaffold_249263_3DL 48479 49603
BM138221 294 3DL3-0.81-1.00 scaffold_249615_3DL 45966 46810 3B
BG274676 350 3DL3-0.81-1.00 scaffold_251754_3DL 29992 30759 3B
BE443305 523 3DL3-0.81-1.00 scaffold_251509_3DL 36689 37685 4DL,5DL,6AS
BM135213 409 3DL3-0.81-1.00 scaffold_253427_3DL 13590 14408 5DL,7DS
BG313589 383 3DL3-0.81-1.00 scaffold_251115_3DL 26515 27320
BG605374 450 3DL3-0.81-1.00 scaffold_251189_3DL 35720 36543 6DS,
BE405038 627 3DL3-0.81-1.00 scaffold_250184_3DL 39147 40001
BI479636 558 3DL3-0.81-1.00 scaffold_251038_3DL 7802 8622 3AL,3B
BE495766 539 3DS3-0.24-0.55 scaffold_251993_3DL 17360 18258 3AL,3B
BF473016 684 3DS3-0.24-1.00* scaffold_249494_3DL 8364 9130 3AL
BG604661 472 3DS6-0.55-1.00 scaffold_249832_3DL 33137 34044 3AL,3B
BF292434 364 3DS6-0.55-1.00 scaffold_252826_3DL 15692 16365 3B
BG263585 312 C3D scaffold_249369_3DL 85309 86062 3AL,3B
BF473034 609 C3D scaffold_249183_3DL 81725 82628 3AL,3B
BE494474 560 C-3DL2-0.27 scaffold_249037_3DL 65571 66279 3AL,3B,4DL
BE423472 605 C-3DL2-0.27 scaffold_250996_3DL 39179 40154 3AL,3B

BF474720 520 C-3DL2-0.27 scaffold_251860_3DL 27314 28314 3AL,3B
BF482462 527 C-3DL2-0.27 scaffold_249549_3DL 42971 43964 3AS,3B
BE489326 599 C-3DL2-0.27 scaffold_253300_3DL 12061 13173 3AS,3B
BF201691 388 C-3DL2-0.27 scaffold_249236_3DL 152004 152736 3B
BF201776 447 C-3DL2-0.27 scaffold_249314_3DL 80102 80917 3B
BF201439 474 C-3DL2-0.27 scaffold_250375_3DL 11873 12920 3B,4AL
BF478475 390 C-3DL2-0.27 scaffold_253601_3DL 9663 10652 3AS,1BL,2BL,2D
L,5BL,6DS
BG313557 127 C-3DL2-0.27 scaffold_249774_3DL 70569 71233 3AS,3B
BG313654 427 C-3DL2-0.27 scaffold_252287_3DL 22708 23490 3AS,3B
BE495748 163 C-3DL2-0.27 scaffold_251969_3DL 20071 20746 5BL
BF428637 465 C-3DL2-0.27 scaffold_253481_3DL 15104 16135 3AL,3B,1AL,1B,1
DL
BM140477 546 C-3DL2-0.27 scaffold_249124_3DL 178635 179477 3B,4AS
BG274556 558 C-3DL2-0.27 scaffold_250633_3DL 53367 54124 3AL,3B

BG263421 557 C-3DL2-0.27 scaffold_249676_3DL 67285 68213 3B,5DL,6AS
BF202776 541 C-3DL2-0.27 scaffold_249734_3DL 72869 73966 3B,U,4BL
BF484106 533 C-3DL2-0.27 scaffold_254663_3DL 5432 6562 5BL,4DL
BE444380 558 C-3DL2-0.27 scaffold_252453_3DL 14677 15573 3B
BF202211 257 C-3DL2-0.27 scaffold_254283_3DL 2881 3728 4DL
BG263699 596 C-3DL2-0.27 scaffold_251735_3DL 1443 2504 5AL,5DL
BM135222 168 C-3DL2-0.27 scaffold_249034_3DL 204530 205220 1DL,2DS,5AS,7A
S
BE517709 534 C-3DL2-0.27 scaffold_250589_3DL 21367 22190 3B,2BL
BM138163 488 C-3DL2-0.27 scaffold_249159_3DL -99 706 3AL,U
BE403960 665 C-3DL2-0.27 scaffold_250000_3DL 17449 18713 3AL,3B,2BS
BE445579 453 C-3DL2-0.27 scaffold_249865_3DL 71903 72846 3AL,1BL,1DL
BF474318 388 C-3DL2-0.27 scaffold_249039_3DL 25090 25841 1AL,5DS
BF202765 378 C-3DL2-0.27 scaffold_251720_3DL 19446 20133 3AL
BE443747 571 C-3DL3-0.81* scaffold_251414_3DL 6508 7297 3AL,3B
BG313636 512 C-3DL3-0.81* scaffold_252943_3DL 13122 13914 3AL,3B
BF146076 416 C-3DL3-0.81* scaffold_249968_3DL 63586 64438 3AL,3B
BE636807 354 C-3DL3-0.81* scaffold_251950_3DL 27268 28069 3AL,3B
BE422511 273 C-3DL3-0.81* scaffold_249228_3DL 148660 149419 3AL
BE637638 383 C-3DL3-0.81* scaffold_249288_3DL 9416 10226
BE490678 565 3DL2-0.27-0.81 scaffold_272441_3DS 54977 55721 3AL,1AL,1DL
BE444171 515 3DL2-0.27-0.81 scaffold_273348_3DS 8233 9347 3AS
BE490440 348 3DS3-0.24-0.55 scaffold_273416_3DS 7382 8234 3AS,3B,1AS,1BS,
1DS
BE422983 428 3DS3-0.24-0.55 scaffold_273156_3DS 20804 21599 3AS,3B
BF473348 526 3DS3-0.24-0.55 scaffold_273138_3DS 16464 17408 3AS,3B
BE403480 486 3DS3-0.24-0.55 scaffold_272031_3DS 29633 30491 3B
BE638043 375 3DS3-0.24-0.55 scaffold_272614_3DS 26616 27370 3AS
BG312609 288 3DS3-0.24-0.55 scaffold_273371_3DS 28504 29391 3AS,3B
BI479242 474 3DS3-0.24-0.55 scaffold_272047_3DS 63607 64526 3AS,3B
BQ280482 412 3DS3-0.24-0.55 scaffold_272540_3DS 17727 18527 3AS,3B

BM134371 585 3DS3-0.24-0.55 scaffold_271900_3DS 75856 77040 3AS,3B
BG274851 546 3DS3-0.24-0.55 scaffold_273371_3DS 13185 13943 3AS,U
BE399489 110 3DS3-0.24-0.55 scaffold_272035_3DS 11862 12502

BQ280546 575 3DS3-0.24-0.55 scaffold_272090_3DS 43986 44769 3AS,3B,4AS,4BL,
4DL
BE490765 531 3DS3-0.24-0.55 scaffold_285889_3DS 141 1006 3AS,3B,4BS,6AL
BG607200 391 3DS3-0.24-0.55 scaffold_272671_3DS 54338 55180 1AL,2DL,6DS,6B
L,7AL,7BS,
BF475136 113 3DS3-0.24-0.55 scaffold_272429_3DS 39379 40049 3B
BE585537 663 3DS3-0.24-0.55 scaffold_271659_3DS 10194 11398 5AL,5DL,6AL,
BE443269 309 3DS3-0.24-0.55 scaffold_271907_3DS 7950 8815 4AS,6AS
BE404647 655 3DS3-0.24-0.55 scaffold_271574_3DS 146576 147749 7BL,7BS,
BM140479 499 3DS3-0.24-0.55 scaffold_273416_3DS 30117 31002
BM137369 467 3DS3-0.24-0.55 scaffold_271934_3DS 8178 9244
BF200712 149 3DS3-0.24-1.00* scaffold_272016_3DS 60194 60917 3AS
BE406567 242 3DS6-0.55-1.00 scaffold_273364_3DS 18703 19442 3AS,3B,1DS,1BS
BE591226 511 3DS6-0.55-1.00 scaffold_271619_3DS 48936 50046 3AS,3B,
BE405260 624 3DS6-0.55-1.00 scaffold_271746_3DS 53347 54083 3AS,5AL,5DL,5B
L
BF203138 210 3DS6-0.55-1.00 scaffold_271464_3DS 314911 315581 3AS,3B,1BL
BG263754 426 3DS6-0.55-1.00 scaffold_273058_3DS 20529 21258 U
BE406607 341 3DS6-0.55-1.00 scaffold_273467_3DS 17816 18723 3AS,U
BE399515 216 3DS6-0.55-1.00 scaffold_271859_3DS 80729 81455 3B,4AL
BI479183 267 3DS6-0.55-1.00 scaffold_273919_3DS 12059 12925 3AS,3B
BG606190 632 3DS6-0.55-1.00 scaffold_271746_3DS 54179 55008 3AS
BE444576 341 3DS6-0.55-1.00 scaffold_272169_3DS 31459 32233 3AS,2BL,2DL

BE407082 462 3DS6-0.55-1.00 scaffold_272882_3DS 20815 21757 3AS,3B4DL,2BL,
U
BE490150 513 3DS6-0.55-1.00 scaffold_273425_3DS 5679 6558 3AS,3B,6AL,
BF483469 614 3DS6-0.55-1.00 scaffold_272632_3DS 32029 32790 3AS
BE497169 646 3DS6-0.55-1.00 scaffold_272327_3DS 53919 55137 3B,4AL,
BE442933 533 3DS6-0.55-1.00 scaffold_272069_3DS 81517 82338 3AS,3B,U,6AS,6B
S,
BE636816 454 3DS6-0.55-1.00 scaffold_272319_3DS 15030 15752 3AS,1AL,1BL,1D
L
BG314067 328 3DS6-0.55-1.00 scaffold_271613_3DS 75312 76064 3B
BE444280 520 3DS6-0.55-1.00 scaffold_272265_3DS 29043 29923 3B,U

BF484268 590 3DS6-0.55-1.00 scaffold_272766_3DS 34708 35568 3B,U
BG607967 575 3DS6-0.55-1.00 scaffold_271614_3DS 52052 52745 3B
BG607411 320 3DS6-0.55-1.00 scaffold_272300_3DS 33595 34492 3AS
BG312802 332 3DS6-0.55-1.00 scaffold_271746_3DS 34587 35354 3AS,3B,6AS,6BS,
6DS
BF484355 370 3DS6-0.55-1.00 scaffold_272566_3DS 20069 20886
BG604761 443 3DS6-0.55-1.00 scaffold_272525_3DS 20706 21463 U
BF292295 554 3DS6-0.55-1.00 scaffold_271794_3DS 100376 101112 3AS,7BL,
BE499719 530 3DS6-0.55-1.00 scaffold_272896_3DS 4294 5338
BE497463 331 3DS6-0.55-1.00 scaffold_272933_3DS 32120 32876 4BS
BE497524 494 3DS6-0.55-1.00 scaffold_272361_3DS 28201 29294 3AL,1AL,4AS,4D
S,5AL,6AL,6BL,7
BL,U
BF201008 343 3DS6-0.55-1.00 scaffold_271546_3DS 105934 106788
BE399500 342 C-3DL2-0.27 scaffold_271449_3DS 245430 246341 3AS,3B

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