Presented By

Sampath

Why…?

Wheat – Important cereal crop

Food- 30% of the world population, Rich in nutrients

Challenges : Increasing population, Climatic changes

Need for increasing the productivity

Explore the genome content to understand molecular basis for Agronomic traits – accelerate them

1. Wheat genome – Introduction

2. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

3. Structural and functional partitioning of bread wheat chromosome 3B

4. Ancient hybridizations among the ancestral genomes of bread wheat

5. Genome interplay in the grain transcriptome of hexaploid bread wheat

The International Wheat Genome Sequencing Consortium (IWGSC)

What…? Content

1. Wheat genome – Introduction

Modern Bread Wheat (T. aestivum)

Hexaploid (AABBDD) 2n=6x=42

Genome Size of 17 Gb

>80% repeats, 2% coding sequence

High sequence similarity within sub genomes –A/B/D

IWGSC

Ancestral Wheat varieties and species –believed to be the closest living relatives of modern bread wheat

1. Wheat genome – Introduction

2. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

3. Structural and functional partitioning of bread wheat chromosome 3B

4. Ancient hybridizations among the ancestral genomes of bread wheat

5. Genome interplay in the grain transcriptome of hexaploid bread wheat

The International Wheat Genome Sequencing Consortium (IWGSC)

What…? Content

2. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

17 Gb draft sequence – Individual chromosome arms

123 201 gene loci – Evenly distributed

Comparative analysis –diploid relatives – high conservation and very limited gene loss

Gene gain and duplication after speciation

No sub genome dominance – Adopted very well

Wheat - The complex genome

Wild emmer wheat for pasta

Modern bread wheat

4.9 Gb6.2 Gb5.7 Gb

17 Gb

Flow cytometric chromosome analysis and sorting in bread wheat from ditelosomic lines

Physical map, CSS, and Reference sequence of the Wheat chromosome

Total length: 9.2 /17 Gb (61%)

L50: 1-9 Kb

A genome

B genome

Total length: 9.2 /17 Gb (61%)

L50: 1-9 Kb

C genome

Total length: 9.2 /17 Gb (61%)

L50: 1-9 Kb

Pipeline for the detection of potential gene structures from spliced alignments of wheat transcripts and reference grass proteins.

Genes are evenly distributed throughout the A,B,D subgenome

44%

High conservation of the gene family A,B,D subgenome

High confidence inter genome cluster analysis

Inversion translocation

23.6% genes duplicated

Comparative analysis – Gene conservation/ loss/gain) and the wheat pan- and core genes

(kb)

Very limited gene loss –genome stabilized

Molecular evolution of the wheat lineage – Haploid adoptation based on SNV of ABD Vs diploid relatives

• 11143 SNV at B subgenome – variations happened after poliploidization

• SS has both B and D genome

• Pseudogenization was observed with HC-1 genes (introduced stop codon)

• Chr Seq similarity 97-99.5%

• Chr4 deviation (inversion translocation)

Subgenome transcription profiling – cluster analysis

• Individual subgenome exhibit high regulatory and transcriptional autonomy

• Overall very similar expression in all 3 genome

• Rape seed/cotton –genome dominance

• Recent polyplodization- balance the expression

Gene family size variation – Gene loss/gain

Chapter 2 : summary

17 Gb draft sequence – Individual chromosome arms

123 201 gene loci – Evenly distributed

Comparative analysis –diploid relatives – high conservation and very limited gene loss

Gene gain and duplication after speciation

No sub genome dominance – Adopted very well

1. Wheat genome – Introduction

2. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

3. Structural and functional partitioning of bread wheat chromosome 3B

4. Ancient hybridizations among the ancestral genomes of bread wheat

5. Genome interplay in the grain transcriptome of hexaploid bread wheat

The International Wheat Genome Sequencing Consortium (IWGSC)

What…? Content

The 3B

• The biggest (892 Mb)

• 774.4 Mb (93%) – 8452 BAC

• 5326 genes & 1938 pseudogenes

• 85% TEs

• Meiotic recombination responsible for partitioning of functional n regulatory genes

• Genome adaptation – inter-intra chromosomal duplication and TEs

• NTR (novel transcribe regions)

• Encode- functional ncRNA

• 485 TE family

Statistics of 3B

Putative location of centromere

Meiotic recombination rate

Recombination hotspot

Gene density

Gene expression

Alternate splicing transcripts

TE content

Partitioning the 3B

• Comparative analysis –syntonic relationship with grass genome

• 35% non syntenic genes

• Substantial rearrangement of gene space

Evolution of genes after divergence

Distribution of syntenic and non-syntonic genes

Inter-chromosomal duplication

Origin and Evolution of non- syntenic genes

Dispersed (uniform)Tandem (variation at telomere)Singletons

• The non-syntonic genes are under strong selection pressure

• Process to become pseudogenization

• TEs in the vicinity of the non-syntenic genes regulates its expression (CACTA)

• TE activity leads to duplications – Interchromosomal duplication by ds DNA break and repair mechanisms

• Estimation of time of duplication by Ks confirms that 31% of the species –specific duplicates were recently happened

Origin and Evolution of non- syntonic genes

TE superfamilies associated with syntenic and nonsyntenic genes

• Characterization of 3B (93%)

• Gene density, expression, function and evolution of the genes

• Wheat genome plasticity by adaptation of genes – limited gene loss

• Gaining new genes by TEs and intra chromosomal duplication found

• Improve understanding the wheat genome and helps to manipulate it

Chapter 3 : summary

1. Wheat genome – Introduction

2. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

3. Structural and functional partitioning of bread wheat chromosome 3B

4. Ancient hybridizations among the ancestral genomes of bread wheat

5. Genome interplay in the grain transcriptome of hexaploid bread wheat

The International Wheat Genome Sequencing Consortium (IWGSC)

What…? Content

Phylogenetic history of the wheat genome

• Orthologs from bread wheat and its diploid relatives

• AB subgenome more closely related to D then each other (80% anchored genes)

• Equal contribution of parents observed – model of hybrid origin

Topological analysis based on 275 orthologs

Distribution of lineage topologies – hybrid gene model for D sub genome

Coalescent-based genome divergence analyses - pairwise ortholog distributions 2269 genes

Divergence tree based on coalescent times consistent with topology analysis

Topology and Coalescent-based genome divergence analyses

Chapter 4: Summary - Phylogenetic history of the wheat genome

1. Wheat genome – Introduction

2. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

3. Structural and functional partitioning of bread wheat chromosome 3B

4. Ancient hybridizations among the ancestral genomes of bread wheat

5. Genome interplay in the grain transcriptome of hexaploid bread wheat

The International Wheat Genome Sequencing Consortium (IWGSC)

What…? Content

Wheat Kernel…

• Rich in nutrients –carbohydrates, proteins, vitamins and minerals

• 20% of the calories consumed by humans & need of quality improvement

• Grain transcriptome analysis – distinct co-expression clusters

• Observed tissue-specific homeologous gene expression

• No global dominance but cell type and stage dependent dominance

• Asymmetric expressions in gene families related to baking quality

The global landscape of endosperm gene expression

• Endosperm composed of 3 main tissues

• Various tissues were analyzed from different developmental stages

• 85173 total genes found

• Equal contribution of no. of genes from all three genome

• Preferential expression of genes based on tissues (2 cluster) and similar expression b/w subgenomes

Spatiotemporal gene expression pattern – Tissue and Time

• Endosperm developmental stages

• Seven co-expressed gene clusters

• Partitioning of gene expression

• Sub functionalization but not functionalization was observed

The cell-type specific genome dominance

• Co-expression network with 25 gene modules

• Spatiotemporal analysis – transcripts grouped according to genomes not cell types

• No global dominance

• Functional complementation from subgenomes

Local regulatory divergence at chromosomal domains

• SE expression analysis has strong correlation between subgenome

• Very few domain has produced Asymmetric expression

• Gene copy number

variation – epigenetically controlled

Local regulatory divergence at chromosomal domains

• Protein associated with grain protein

• Domination by B and D- SPA, LMW, HMW, PIN

• Alpha-Gli D-genome deletion

• Asymmetric expression in genes families

1. Wheat genome –Towards completion –sustainable production

2. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome – the shortgun sequencing

3. Structural and functional partitioning of bread wheat chromosome 3B – for completion of remaining chromosomes

4. Ancient hybridizations among the ancestral genomes of bread wheat – history of wheat origin and phylogeny

5. Genome interplay in the grain transcriptome of hexaploid bread wheat – Improvement of wheat grain quality

SummaryContent

References

Thank you for your kind attention

Having a segment missing from two chromosomes

https://www.jstage.jst.go.jp/article/ggs/88/5/88_311/_html

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HMW glutenin

-gliadins albumins globulinsLMW glutenins (B subunits)

, ,-gliadins LMW glutenins (C subunits)

albumins

A-PAGE fractionation of

gliadins

Wheat Gluten Proteins

Monomeric

gliadins

Polymeric

glutenin

-gliadins

-type gliadins

-type gliadin

s

LMW subunit

s

HMW subunit

s

SDS-PAGE fractionation of

polymeric protein (Singh et al. 1991)

SDS-PAGE fractionation of total endosperm

protein

Wheat Gluten Proteins