Lecture 3.pptx lecture on Monday evening

Lecture 1. Genetics (February 18)
Lecture 2: Molecular Genetics (February 18)
Lecture 3 Recent Advances in Plant Breeding (February 19)
Madan K. Bhattacharyya, Ph.D.
Professor, Iowa State University
Adjunct Prof., Assam Agricultural University
mbhattac@iastate.edu

http://aau.ac.in/NAHEP/
Website for the presentations and some of the resources used

Lecture 3: Recent Advances in Plant Breeding (February 19)
 Molecular Markers & Marker Assisted Selection
 Speed Breeding
 Doubled-haploid
 TILLING Genome
 CRISPR Cas9
 Fixing Heterosis in Rice

RFLP gel showing DNA fragment length polymorphisms.

Polymerase Chain Termination Reaction (PCR)

RFLP: Restriction Fragment Length Polymorphism
RAPD: Random Amplified Polymorphic DNA
SSR: Simple Sequence Repeat
AFLP: Amplified Fragment Length Polymorphism
SNP: Single Nucleotide Polymorphism
GBS: Genotype by Sequencing
CAPS: Cleaved Amplified Polymorphic Sequences
SBP: Sequenced-based Polymorphic marker
Some of the popular markers

Restriction Fragment Length Polymorphism (RFLP)

RFLPs among three Arabidopsis ecotypes

Segregation of two RFLP markers in F3

RFLP linkage map in Arabidopsis ecotypes

Random Amplified Polymorphic DNA (RAPD)

Random Amplified Polymorphic DNA (RAPD)
 A single 10 nucleotide oligo anneal in opposite orientation and
amplifies DNA.

Two SSR alleles differing in repeat numbers produce PCR
products that can be separated on an agarose gel.

SSR markers are usually co-dominant.

Lane 10 and 25 carry the allele linked to the soybean aphid
resistance Rag1 gene in homozygous condition.

P1: CGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGG
P2: CGGCGGCGGCGGCGGCGGCGG (15 nt shorter)
SSR: Type and their frequencies in rice
Miah et al. 2013

AFLP: Amplified Fragment Length Polymorphism

EcoRI MseI
EcoRI MseI
AFLP Technology

An AFLP Gel: Radio active label is used to detect the PCR
amplified fragments.

Single Nucleotide Polymorphism (SNP)

Heterozygote
Homozygote
Homozygote
An example of SSR marker

Types of single-nucleotide polymorphism (SNPs)

SBP: Sequenced-based Polymorphic marker

Comparison of sequences from two Arabidopsis ecotypes.

SBP Markers that are polymorphic between Columbia -0 and Neiderzenz ecotypes.

Rapid Identification of Linked Molecular Markers

Bulked segregant Analysis
Michilemore et al. 1991

SHORE mapping to identify genetic loci (BSA)

Molecular marker assisted selection

Molecular marker linked tightly to the fruit size trait.

Foreground and Background Selection

Recover the Double Recombinant to Eliminate any Linkage Drag

Comparison of cultivar ‘Zak’ derivatives carrying stripe rust resistance
gene Yr15developed with (WA8059) and without (WA8046) MABS.

 In this study Randhawa et al. 2009 identified a BC2F2:3 plant with
97% of the recurrent parent genome through marker-assisetd
background selection (MABS).
 In contrast, only 82% of the recurrent parent genome was
recovered in phenotypically selected BC4F7 plants developed
without MABS.
 Marker-assisted selection can also be applied to expedite
pedigree or single seed descent method of breeding, if most
desirable trait loci linked markers are known.
Marker-assisted Selection

Speed breeding accelerates generation time of major
crop plants for research and breeding
Speed Breeding Greenhouse Control

1. Lights Quality: Light that produces a spectrum covering the PAR region (400–700 nm),
with particular focus on the blue, red and far-red ranges, is suitable to use for SB.
2. Light Quantity: Intensity should very high: ~450–500 μmol/m2/s at plant canopy height
effective for a range of crop species.
3. Photoperiod: We recommend a photoperiod of 22 h with 2 h of darkness in a 24-h
diurnal cycle. The dark period slightly improves plant health.
4. Temperature: The optimal temperature regime (maximum and minimum temperatures)
should be applied for each crop. A higher temperature should be maintained during the
photoperiod, whereas a fall in temperature during the dark period can aid in stress
recovery. A 12-h 22 °C/17 °C temperature cycling regime with 2 h of darkness occurring
within 12 h of 17 °C has proven successful. A temperature cycling regime of 22 °C/17 °C
for 22 h of light and 2 h of dark, respectively also work fine.
5. Humidity: Most controlled-environment chambers have limited control over humidity,
but a reasonable range of 60–70% is ideal. For crops that are more adapted to drier
conditions, a lower humidity level may be advisable
Steps to follow in Speed Breeding

Harvesting of immature spikes and drying them in an
oven/dehydrator saves 12 days (3 vs. 15 days)
~ 3 Days
~ 15 Days

Accelerated plant growth and development under speed
breeding (left) compared to control conditions (right).

Peas mature in 8 instead of 12 weeks in greenhouse
under normal condition.
Pea plants grown in limited media and nutrition (“flask method”) in order
to achieve rapid generation advancement

Pods harvested from Brassica napus RV31 grown in LED-
supplemented glasshouses at the John Innes Centre, UK.
22-hour photoperiod
16-hour photoperiod

Single-seed descent sowing densities of spring wheat (bread
and durum) and barley.

Fig. 3: Adult plant phenotypes in wheat and barley
under speed breeding conditions.
Adult plant phenotypes in wheat and barley under speed
breeding conditions

Speed Breeding Expedites the Development of
Novel Cultivars
One can now generate novel cultivars very rapidly. Four to six crops a
year!
Single seed descent (SSD) method can be pursued under speed
breeding without any trade off. In fact, becomes less expensive to grow
thousands of lines densely under greenhouse condition for SSD.
Selection can be made for disease resistance in adult plants.
 General methodologies work for most if not all crop plants; but
modification can help.

Doubled-haploid to Expedite the Breeding Program
We need to fix the inbred lines for heterosis breeding.
Doubled-haploid approach fix the genome in one
generation.
Process is labor-intensive.
 Recombination in one step as opposed to additional
recombination in selfing generations of the pedigree/SSD
method.

Targeting Induced Local Lesions IN Genomes (TILLING)

TILLING Results for A Target Gene

Targeting Induced Local Lesions IN Genomes (TILLING)
1.Intended for reverse genetics – means we look for
mutations in the target gene.
2.The resource can also be screened/phenotyped for traits
of interest and apply positional gene cloning – forward
genetics.
3.Applied extensively across crop species.
4.One can create desirable mutants for a trait gene instead
of gene silencing or knockout or editing – GMO free.

CRISPR-Cas9 mediated gene editing

https://www.youtube.com/watch?v=TdBAHexVYzc&t=26s
Please watch this video:

Innate Immunity in Prokaryote
The Clustered Regularly Interspaced Short Palindromic Repeats, or CRISPR

 The Clustered Regularly Interspaced Short Palindromic Repeats, or CRISPR was
first discovered in 1993 through sequence analyses.
 Significance of CRISPR was unknown until 2007, when immunity function of this
element was uncovered.
 The mechanism used by the element to confer immunity became known after five
years
The bacteria and archaea use CRISPR to defend against the invading viruses termed
as bacteriophages. Following viral infection, they employ a special CRISPR-
associated nuclease 9 (Cas9) to generate a double-strand break (DSB) in its target
loci of the bacteriophages’ DNA molecules. Thus, viruses become ineffective. Cas9
is directed to the target sequence by a short RNA fragment known as a guide RNA
(gRNA), complementary to a segment of the viral genome for generating DSB.
Parallel to viral DNA cleavage, a short viral DNA is stored between the palindromic
CRISPR sequences. This sequence is being used to generate the gRNA for rapid
activation of this defense mechanism against any subsequent infection by the same
bacteriophage. This system is kind of similar to antibody production in humans.

The CRISPR-Cas9 system comprises a guide RNA (gRNA) and Cas9 nuclease, which together form
a ribonucleoprotein (RNP) complex. The gRNA binds to the genomic target upstream of a
protospacer adjacent motif (PAM), enabling the Cas9 nuclease to make a double-strand break in the
DNA (denoted by the scissors). Adopted from: https://www.synthego.com/resources/crispr-101-ebook
CRISPR-Cas9 System

Two steps to consider in designing a CRISPR-Cas9 system for editing a
gene:
(i) The design of guide RNA (gRNA)
(ii) Choice of the nuclease depends on the desired application – Cas9 for plant
work.
The gRNA that targets specifically to your gene of intertest should be designed.
Best scenario would be 0 non-specific cut and highly specific to the target site in
exons. You can edit members of a gene family simultaneously. Following double
stranded breaks (DSB), cells repair the DNA by non-homologous end joining
(NHEJ) mechanism. During this process indels (insertions and deletions) are
created leading to frameshift mutations and gene knockouts (KO).

 We can also conduct knock-in (KI) mutation by repairing the DSB through
homology directed repair (HDR) mechanism.
 To facilitate or induce HDR-mediated repair, copies of homologous DNA
molecules with a desirable mutation are provided to use as a template. The
mutation can be a single point mutation to change an amino acid.
 It can be used to correct a disease-causing mutation in humans and
generating herbicide resistance in plants.
 For example in plants, we can replace an amino acid in the gene encoding
acetolactate synthase (ALS) involved in biosynthesis of branched-chain
amino acids to make the enzyme resistant to several herbicides, including
imidazolinones and sulfonylureas. Out come herbicide resistant plants.

 You can also generate gRNA and Cas9 protein in test tubes and apply the two
as ribonucleoprotein (RNP) complexes into the cells; this approach has recently
been reported to be the most effective strategy (Liang et al. 2015). The complex
is unstable and does not continue to function to cause additional off-target
mutations.
 Alteration of function through homologous recombination can also be
accomplished through Crispr/Cas9 system.
 Point or deletion mutations through Crispr/Cas9 is predictable. The only
weakness is the mutations caused by the system in non-targeted genomic
regions. There are many sequences similar to 16 bp target sequence in
complex genome. Therefore, we have to investigate the genome sequence for
target sequence just to make sure that the target site is either absent or is not
present in coding sequences. One can always breed the desirable Crispr/Cas9-
induced mutations through backcrossing.

Will There be a CRISPR Nobel Prize?
A CRISPR research project or experiment has not yet won a Nobel Prize, but given its popularity, it sure seems to be on the path to one.
CRISPR is a novel DNA editing tool that is faster, more cost-efficient, and more accurate than any previous gene editing techniques. CRISPR has
proven to be a powerful research tool contributing significantly to genetic research by allowing scientists to better understand biological processes
associated with certain diseases. Given these significant breakthrough raises the obvious question: “Will there be a Nobel Prize for CRISPR
research in the future?”
One thing is sure- if there were to be one, many CRISPR scientists, who played a vital role in the development of this technology, are strong
contenders for the award. Listed below are some of the big names in CRISPR that would be the likely front runners for the prize.
Jennifer Doudna: The most celebrated name in CRISPR
Jennifer Doudna is one of the biggest names in CRISPR, as she is credited as the co-inventor of CRISPR. She was also the first to propose that
enzymes from bacteria that control microbial immunity (CRISPR-Cas9) could be used for programmable editing of genomes. This is considered
one of the most significant discoveries in recent history, as this technique is much faster and more accurate than any of the previous gene editing
tools. Many people believe that Jennifer Doudna would be a top contender for a Nobel Prize for CRISPR.
Emmaneulle Charpentier: The co-founder of CRISPR
Emmanuelle Charpentier is the co-founder of CRISPR, along with Doudna. Charpentier first began biochemical characterization of CRISPR with
her colleague in Vienna. She met Doudna in 2011, and they began working together soon after on what would go on to become one of the
greatest inventions in the history of genetics.
Feng Zhang: The man who showed CRISPR could work in mammalian systems
Feng Zhang was the first to successfully adapt CRISPR-Cas9 for gene editing in eukaryotic cells. He further expanded his research beyond the
technology itself to show how versatile it was, and demonstrated that it could be used in mammalian cells for the first time. His current focus is on
developing tools that can be applied to study genetic diseases, and develop diagnostics and therapeutics. His team was also the first to show
CRISPR systems that can target RNA.
Virginijus Šikšnys: The overshadowed independent CRISPR inventor
Virginijus Šikšnys was also one of the first researchers to show how CRISPR works. Šikšnys is biochemist from Lithuania who independently
figured out how certain bacteria are able to cut and paste specific genes from other organisms. He and his colleagues also found a way to control
the process.
Luck played a huge role in his research not getting as much attention as Doudna’s did. The paper he submitted to Cell in April 2012 was rejected,
while Doudna’s paper was published in Science two months later, fetching her celebrity status in the CRISPR field.

Establishing a CRISPR–Cas-like immune system conferring DNA
virus resistance in plants
Ji et al. 2015

Ali et al. 2015
CRISPR/Cas9-mediated viral interference in plants

The knockout mutations in all three homoeologous copies
of one of the target genes, TaGW2, resulted in a substantial
increase in seed size and thousand grain weight.
Wang et al. 2018

Efficient DNA-free genome editing of bread wheat using CRISPR/Cas9
ribonucleoprotein complexes

 The avoidance of transgene integration and reduction of off-target mutations are two
most important issues in gene editing.
 Liang et al. (2017) described an efficient genome editing method for bread wheat
using CRISPR/Cas9 ribonucleoproteins (RNPs).
 The whole protocol takes only seven to nine weeks, with four to five independent
mutants produced from 100 immature wheat embryos. Delivery system was a gun.
 Deep sequencing revealed no off-target mutations in wheat cells in RNP mediated
genome editing method.
 Because no foreign DNA is used in CRISPR/Cas9 RNP mediated genome editing, the
mutants obtained are completely transgene free.
 This method may be widely applicable for producing genome edited crop plants and
has a good prospect of being commercialized.
Efficient DNA-free genome editing of bread wheat using
CRISPR/Cas9 ribonucleoprotein complexes

Lecture 3: Recent Advances in Plant Breeding (February 14)
 Speed Breeding
 Marker Assisted Selection
 Doubled-haploid
 TILLING Genome
 CRISPR Cas9
 Fixing Heterosis in Rice

Fixation of Heterozygosity in Rice Through
Editing Four Genes.

Heterosis or hybrid vigor enhances crop yield. Example; maize
Unfortunately, most staple food and legume crops are self-pollinated.
Generation and identification of male sterility gene have been long attempted with a
view to exploit heterosis.
Clonal propagation through seeds would enable self-propagation of F1 hybrids in self
or cross pollinated crop species.
Wang et al. (2019) reported a strategy to enable clonal reproduction of F1 rice hybrids
through seeds.
Conducted multiplex CRISPR–Cas9 genome editing of the REC8, PAIR1 and OSD1
meiotic genes to produce clonal diploid gametes and tetraploid seeds.
Next, they editing the MATRILINEAL (MTL) gene (involved in fertilization) to induce
formation of haploid seeds in hybrid rice.
Finally, simultaneous editing of all four genes (REC8, PAIR1, OSD1 and MTL) in
hybrid rice led them to propagate F1s clonally through seeds.

a, The structure of CRISPR–
Cas9 vector
targeting OSD1, PAIR1 and
REC8.
b, The chromosomes of
CY84 and Mitosis instead of
Meiosis (MiMe) were probed
by digoxigenin-16-dUTP-
labeled 5 S rDNA (red signal,
indicated with a white arrow)
in spores, showing one
signal in wild-type CY84 and
two signals in MiMe. The
DNA is stained with 4′,6-
diamidino-2-phenylindole
(DAPI, blue signal). Scale
bars, 5 μm.

c, Panicles of wild-type CY84 and MiMe. The fertility
of MiMe was as high as that of wild-type CY84.
d, Ploidy analysis of CY84 (left) and the progeny
of MiMe (right) by flow cytometry, which were found
to be diploid and tetraploid, respectively.
e, Genotype analysis of the paternal C84, maternal
Chunjiang 16A (16A), hybrid variety CY84 and the
progeny siblings of MiMe. Ten indel markers
distributed on chromosomes 1 and 8 were used to
identify the genotype of the offspring of MiMe.
Positions of markers (brown) and centromeres
(black) are indicated along the chromosomes. For
each marker, plants carrying the C84 allele are in
red, plants carrying the 16 A allele are in blue, and
plants with both C84 and 16 A alleles appear in
yellow. Each row represents one plant, and each
column indicates a locus.
f, Panicles and grain shape of CY84 and the progeny
of MiMe. The progeny of MiMe displayed reduced
fertility, increased glume size and elongated awn
length. Scale bars, 2 cm.
Turning meiosis into mitosis in hybrid rice variety CY84.

Generation of a haploid inducer line by editing the MTL
gene involved in fertilization in hybrid rice variety CY84.

a, Schematic diagram of the structure of the CRISPR–Cas9 vector
targeting MTL.
b, Panicles of the WT and mtl in the CY84 background. The fertility was
decreased in mtl; a white arrow indicates an aborted seed and a red arrow
shows a fertile seed. Scale bars, 2 cm.
c, Cropped gels indicate the genotype of haploids, doubled haploids (DH) and
recombinant inbred diploids (RID) using 12 indel markers (1 per chromosome).
Plants homozygous at all markers in the progeny siblings of mtl were identified
as haploid or DH.
d, Ploidy analysis of the haploid and DH by flow cytometry (Table 1); PI,
propidium iodide.
e, Whole-genome sequencing of the haploid, DH and RID plants. Twelve blocks
represent 12 chromosomes. The SNPs of C84 allele are in red, the SNPs of 16
A allele are in blue, and the coexistence of both alleles is in yellow.
f, Panicles of wild-type CY84 and mtl progeny, including RID, haploid and DH
plants. Scale bars, 2 cm.

a, A model for fixation of heterozygosity of the hybrid. In normal sexual reproduction (left),
recombinant inbred embryos are generated by fusion of recombined haploid gametes. The clonal
reproduction strategy (right) is based on two components: meiosis is turned into mitosis to
produce clonal diploid gametes (MiMe), and the genome of the male gamete is eliminated by
knocking out the MTL gene. The progeny of self-pollinated Fix are genetically identical to the
hybrid parent.
b, The CRISPR–Cas9 vector simultaneously targeting OSD1, PAIR1, REC8 and MTL.
c, Comparison of the plant morphology and panicles of CY84 and Fix (osd1 pair1 rec8 mtl) grown
in paddy fields. The Fix plant exhibited a low seed-setting rate (Table 1). An aborted seed is
indicated with a white arrow and a normally developed seed with a red arrow. Scale bars, 5 cm.
d, Ploidy analysis of the progeny of Fix by flow cytometry, including tetraploid (left) and diploid
(right) examples; PI, propidium iodide.
e, Whole-genome sequencing of the diploid and tetraploid progeny of Fix and the diploid progeny
of clonal Fix. The SNPs of the C84 allele are in red, the SNPs of the 16 A allele are in blue, and
the coexistence of both alleles is in yellow. Twelve blocks represent 12 chromosomes. The diploid
and tetraploid progeny of Fix and the diploid progeny of clonal Fix are heterozygous and identical
to CY84.
f, Comparison of the plant morphology and panicles of wild-type CY84 and the diploid progeny
of Fix (clonal Fix) grown in paddy fields. The clonal Fix displayed a low seed-setting rate that was
similar to that of parent Fix plant. An aborted seed is indicated with a white arrow and a normally
developed seed with a red arrow. Scale bars, 5 cm.

Fixation of Heterozygosity in Rice Through Editing Four Genes.
1. Two biological steps were modified to fix heterozygosity in rice.
2. In step 1, three genes edited to generate a mutant known as “Mitosis instead of
Meiosis (MiME).”
3. In the Step 2, a single mutation to avoid fertilization is generated.
4. Gene editing for all four genes resulted in seeds that carry the genotype of the F1.
5. You end up two copies of the haploid F1 genome; without going through meiosis
(crossing over, etc.).
6. The gametes are as a result diploids.
7. Mutation in the fertilization gene suppressed the fusion of male gamete with the
novel diploid ovum.
8. The diploid ovum generates the embryo and then the seeds as in apospory.
9. Poor seed setting of these novel F1s will require some more work to improve
fertility. Okay to use in fodder crops grown for foliage only.

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