Deciphering structural variation in wheat genome using resequencing data
2018
De Oliveira, Romain
Structural variations (SVs) such as copy number and presence-absence variations (CNVs, PAVs) are polymorphisms that are known to be involved in the expression of phenotypes. In the absence of a reference genome sequence, their study has long been hampered in wheat. The recent advent of new wheat genomic resources has led to a paradigm shift, making possible to investigate the extent of SVs among cultivated and wild populations. Our project aims at characterizing SVs in a Triticeae diversity panel of 44 accessions from seven tetraploid and hexaploid Triticeae species. To cope with the wheat genome complexity, we developed strategies combining shotgun sequencing of sorted chromosomes 3B with bioinformatics tools and we studied SVs affecting not only genes but also transposable elements (TEs). Our results show that 14% of the genes are variable within this panel. In addition, they reveal a very high level of intra- and interspecific variability affecting TEs, contrasting with the weak polymorphism rate usually reported with SNPs. Chromosomal extremities are the regions where we see most of the variability, confirming previous hypotheses made when comparing wheat with the other grasses.
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