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
12
7
8
12 10
5
9
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
Top Related