From Genes to Phenotypes in Wheat – Towards Breeder Friendly Markers

Modern selection technologies, mainly marker assisted selection (MAS), are used by our spring wheat (Triticum aestivum L.) and durum (Triticum turgidum var. durum) breeding programs to improve selection efficiency. However, most agronomically important traits are associated with quantitative trait loci (QTL) and only a few studies have defined genes associated with these in wheat.  Next-generation sequencing strategies and high density single nucleotide polymorphism (SNP) arrays have allowed improved resolution of QTL in well phenotyped bi-parental mapping populations and the recent availability of physical maps, and chromosomal/whole genome shot gun assemblies of the wheat genome promises the possibility to associate functional genes with these QTL. However, only a single wheat chromosome has been sequenced to reference quality (chromosome 3B) and current whole genome assemblies are still highly fragmented. This has slowed our map-based cloning efforts because much of the assembled scaffolds lack genetic position and order. Here we will report on our efforts to improve the current whole genome assembly of wheat that, in combination with transcriptome/exome sequencing and digital phenotyping, are aiding in marker development and postional cloning of a gene for insect resistance in both spring and durum wheat.  Detailed genetic studies in both wheat species have identified two putative candidate genes, but it appears that SNPs within these do not capture all the phenotypic variation.  Current data suggests that larger structural variants, coupled with gene silencing in some genetic backgrounds, may play an important role in trait expression.