The genome and transcriptome of

Triticeae genomes and the impact

of polyploidization

“The genomes of civilization (and their molecular

linguistics)”

The domestication of cereals und the cradle of western agriculture and civilisation

The domestication of cereals und the cradle of western agriculture and civilisation

Driscoli et al., PNAS, 2009

The fertile crescent („fruchtbarer Halbmond“)

Rapid spread of wheat after domesticationRapid spread of wheat after domestication

“[…] societies will have to almost double the existing rate of

agricultural productivity growth while minimizing the associated environmental damage.”

(The World Bank, World Development Report 2010. 2009)

“The identification of genes […] will […] lead to

improved varieties with improved yield and quality, tolerance to unfavourable environmental conditions and

resistance to disease.”(Edwards et al., Plant genome sequencing: applications for crop improvement. 2010)

• Staple food for 30% of the worlds population

• ~20% of calories consumed daily

• 620 Million Tons harvested (2012)Global crop production (%)

2050

2006

+69%

Demand in food calories

(Figure and data sources: FAO Stat 2012, Ray et al. 2013, Alexandratos and Bruinsma 2012)

Yield increase – a Challenge for Agricultural Research (and for BioGreenformatics)

Yield increase – a Challenge for Agricultural Research (and for BioGreenformatics)

(Figure source: Li et al., 2014)

• 21 Chromosomes (haploid)

• Impressing genome size(17 Gigabases)• Highly repetetive genome sequence

(>80% repetitive sequences)

• Allohexaploid Genome(>97% similarity in corresponding “homeologous” gene sequences)

TaBB

TaDD

TaAA

The genome of bread wheat (Triticum aestivum)The genome of bread wheat (Triticum aestivum)

The Genealogy of WheatThe Genealogy of Wheat

Marcussen et al. 2014

Breen et al., 2010

The wheat genome is rererererererererererepetitiveThe wheat genome is rererererererererererepetitive

Reduction of Complexity by Chromosome SortingReduction of Complexity by Chromosome Sorting

Geninformation für >90% der Weizengene

“Divide et impera” using Chromosome Sorting“Divide et impera” using Chromosome Sorting

changed cellular architecture irregularities in cell divisionaltered regulatory mechanisms(novel intra- and intergenome interactions)

Compensating negative and deleterious effects

Development of novel traits through positive interactions

or buffering effects

Genomic restructuring

Polyploidization – a “Genome Shock”Polyploidization – a “Genome Shock”

grain hardness

genome asymmetry

morphologicaltraits

differences in genome composition

favoured expressionof genes of particular genomes

Genome-level analysis of the consequence of polyploidization

Genome dynamics

retention and elimination of genes(gene loss / pseudogenization)

Regulatory patterns

homoeologous gene expression(genome bias)

gene expression divergence(sub- and neofunctionalization)

disease resistance

Implications of polyploidy on the bread wheat genome and transcriptome

Implications of polyploidy on the bread wheat genome and transcriptome

Transfer Cells (TC): Connecting plant and the endosperm

Starchy endosperm (SE): 75% of tissue; contains the carbohydrates

Aleurone (AL): Conatins vitamins and lipids as well as enzymes fpor the mobilisation of starch and storage

(Figure and data source: Dupont et al., 2003)

The Grain Transcriptome of Bread WheatThe Grain Transcriptome of Bread Wheat

Major fraction of flour;dough qualityMajor fraction of flour;dough quality

LMW-Glutenins

HMW-Glutenins

Puroindoline (pin) hardness

Storage Protein Activator crucial role in orchestrating the grain storage protein expression; A& D corr. with grain

hardness

Grain Softness ProteinGrain Softness Protein

Grain Quality GenesGrain Quality Genes

Major fraction of flour;dough quality

25 Koexpressionsmodule

Network Analysis of homeologous Gene ExpressionNetwork Analysis of homeologous Gene Expression

The Topology of the Wheat Transcriptome NetworkThe Topology of the Wheat Transcriptome Network

Expression domains and chromosomal landscape of subgenome dominance

Expression domains and chromosomal landscape of subgenome dominance

Both regulation on individual gene level as well as on chromatin level seem to contribute to transcriptional dominance of individual genes

• Even large genomes can now be done by economic means• Polyploids can be attacked and separated (improved assembly methods; chromosome sorting...)• Fundamental for rapid and improved breeding• The crosstalk in a polyploid is far from random and chaotic

SummarySummary

Franz MarcHaystacks in the snow