Genome-wide association study for disease traits in wheat and its wild relatives

Wheat is the most widely grown crop in the world and as such, is an essential source of energy
and nutrition. The challenges that breeders presently face is to increase production to feed the
rising population of the world, while also accounting for climate change, pollution, water and
environmental stresses. As genetic uniformity of modern cultivars has increased vulnerability to
pests and diseases, the wild relatives of wheat offer a rich source of genetic diversity and stress
tolerance traits, that can be harnessed and transferred in to modern wheat.
In this study, we used array-based genotyping to explore genetic diversity in 385
domesticated and non-domesticated lines of wheat and their wild relatives. Genetic
characterization using the wheat 90K array, and subsequent filtering and validation mapped 9,570
single nucleotide polymorphic markers onto the wheat reference genome. Phylogenetic analyses
illustrated four major clades, clearly separating the wild species from the domesticated, and the
ancient Triticum turgidum species from modern T. turgidum cultivars.
Using this diverse germplasm, a genome-wide association study (GWAS) was performed
for leaf rust, the most widespread rust disease of wheat. Identification of novel sources of
resistance is necessary to maintain disease resistance and stay ahead in the plant-pathogen
evolutionary arms race. GWAS was conducted using eight statistical models for infection types
against six leaf rust isolates and leaf rust severity rated in field trials for 3-4 years at 2-3 locations
in Canada. Functional annotation of genes containing significant quantitative trait nucleotides
(QTNs) identified 96 disease-related nucleotide associated with leaf rust resistance. A total of 21
QTNs were in haplotype blocks or within flanking markers of at least 16 known leaf rust (Lr)
resistance genes. The remaining significant QTNs were considered loci that putatively harbor new
Lr resistance genes. Future efforts to validate these loci will help understand their role in disease
resistance and promote their utility for marker-assisted selection in pre-breeding.