1. The document discusses the genome sequencing of bread wheat (Triticum aestivum). It summarizes that the 17 Gb draft sequence was organized by individual chromosome arms and identified over 123,000 gene loci that were evenly distributed. Comparative analysis with diploid relatives found high conservation with limited gene loss. 2. Characterization of chromosome 3B found it contained over 5,300 genes, with gene density, expression and function partitioning along the chromosome. Wheat genome plasticity was demonstrated through gene adaptation involving intra-chromosomal duplication and transposable elements. 3. Analysis of the wheat grain transcriptome identified distinct co-expression clusters in the endosperm with some tissue-specific and stage-dependent

1. Presented By
Sampath

2. 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

3. 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
What…?
Content

4. 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

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

6. 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
What…?
Content

7. 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

8. Wheat - The complex genome
Wild emmer
wheat for pasta
Modern bread wheat
4.9 Gb6.2 Gb5.7 Gb
17 Gb

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

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

11. Total length: 9.2 /17 Gb (61%)
L50: 1-9 Kb
A genome

12. B genome
Total length: 9.2 /17 Gb (61%)
L50: 1-9 Kb

13. C genome
Total length: 9.2 /17 Gb (61%)
L50: 1-9 Kb

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

17. Genes are evenly distributed throughout the A,B,D subgenome
44%

18. High conservation of the gene family A,B,D subgenome
High confidence inter genome cluster analysis
Inversion
translocation
23.6% genes
duplicated

19. Comparative analysis –
Gene conservation/ loss/gain) and the wheat pan- and core genes
(kb)
Very limited gene loss –genome stabilized

20. 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)

21. 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

22. Gene family size variation – Gene loss/gain

23. 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

24. 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
What…?
Content

25. 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

26. • NTR (novel transcribe regions)
• Encode- functional ncRNA
• 485 TE family
Statistics of 3B

27. Putative location of centromere

28. Meiotic
recombination rate
Recombination
hotspot
Gene density
Gene expression
Alternate splicing
transcripts
TE content
Partitioning the 3B

30. • Comparative analysis –
syntonic relationship with
grass genome
• 35% non syntenic genes
• Substantial rearrangement
of gene space
Evolution of genes after divergence

31. Distribution of syntenic and non-
syntonic genes
Inter-chromosomal duplication
Origin and Evolution of non- syntenic genes
Dispersed (uniform)
Tandem (variation at telomere)
Singletons

32. • 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

33. • 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

34. 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
What…?
Content

35. Phylogenetic history of the wheat genome

36. • 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

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

38. Coalescent-based genome divergence analyses
- pairwise ortholog distributions 2269 genes
Divergence tree based on coalescent times consistent with topology analysis

39. Topology and Coalescent-based genome divergence analyses

40. Chapter 4: Summary - Phylogenetic history of the wheat genome

41. 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
What…?
Content

42. 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

43. 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

44. 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

45. 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

46. 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

47. 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

48. 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
Summary
Content

49. References

51. Having a segment missing from two chromosomes
https://www.jstage.jst.go.jp/article/ggs/88/5/
88_311/_html

53. 12
7
8
12 10
5
9
HMW glutenin
-gliadins
albumins
globulins
LMW glutenins (B
subunits)
, ,-gliadins
LMW glutenins
(C subunits)
albumins
A-PAGE
fractionation of
gliadins
Wheat
Gluten
Protein
s
Monomeri
c gliadins
Polymeri
c
glutenin
-
gliadins
-type
gliadins
-type
gliadins
LMW
subunits
HMW
subunits
SDS-PAGE fractionation
of polymeric protein
(Singh et al. 1991)
SDS-PAGE fractionation
of total endosperm
protein
Wheat Gluten Proteins