Genome-wide association mapping identifies yellow rust resistance loci in Ethiopian durum wheat germplasm

Abstract

Durum wheat is an important cereal grown in Ethiopia, a country which is also its center for genetic diversity. Yellow (stripe) rust caused by Puccinia striiformis fsp tritici is one of the most devastating diseases threatening Ethiopian wheat production. To identify sources of genetic resistance and combat this pathogen, we conducted a genome wide association study of yellow rust resistance on 300 durum wheat accessions comprising 261 landraces and 39 cultivars. The accessions were evaluated for their field resistance using a modified Cobb scale at Meraro, Kulumsa and Chefe Donsa in the 2015 and 2016 main growing seasons. Analysis of the 35K Axiom Array genotyping data of the panel resulted in a total of 8,797 polymorphic SNPs of which 7,093 were used in subsequent analyses. Population structure analysis suggested two groups in which the cultivars clearly stood out separately from the landraces. Eleven SNPs significantly associated with yellow rust resistance were identified on four chromosomes (1A, 1B, 2B, and 5A) which defined at least five genomic loci. Six of the SNPs were consistently identified on chromosome 1B singly at each and combined overall environments which explained 62.6–64.0% of the phenotypic variation (R2). Resistant allele frequency ranged from 14.0–71.0%; Zooming in to the identified resistance loci revealed the presence of disease resistance related genes involved in the plant defense system such as the ABC transporter gene family, disease resistance protein RPM1 (NBS-LRR class), Receptor kinases and Protein kinases. This study has provided SNPs for tracking the loci associated with yellow rust resistance and a diversity panel which can be used for association study of other agriculturally important traits in durum wheat.

Genome-Wide Association Study Reveals Novel Genetic Loci for Quantitative Resistance to Septoria Tritici Blotch in Wheat (Triticum aestivum L.)

“…26-105.61 Mbp in all the chromosomes, with an overall mean of 31.44 Mbp. This is much lower than the average physical distance (69.1 Mbp) for LD decay in Ethiopian durum wheat at the critical threshold of r 2 = 0.2 (Alemu et al, 2021). The marker distances at which the LD decayed across the older sub-genomes (A and B) were relatively lower than those for the D sub-genome, most likely because of the long evolutionary history of the A and B genomes as compared with the D genome.…”

Genetic approaches to exploit landraces for improvement of Triticum turgidum ssp. durum in the age of climate change

“…GWAS studies, based on highthroughput genotyping tools, helped in defining genomic regions affecting such agronomic traits in landraces highlighting available superior alleles. Among others, the contribution to the yield of root system architecture traits and phenology were highlighted (Mengistu et al, 2016;Kidane et al, 2017a;Desiderio et al, 2019;Gupta et al, 2020;Alemu et al, 2021;A ́vila et al, 2021;Royo et al, 2021).…”

Discovery of stripe rust resistance with incomplete dominance in wild emmer wheat using bulked segregant analysis sequencing

“…A number of wheat Yr genes including Yr15/YrH52/YrG303 8,31 , Yr24/Yr26 32 , Yr10 13 , YrC142 33 , YrAlp 34 , Yr64 35 , and Yr65 35 , have been previously mapped on chromosome arm 1BS. Many genomewide association studies have also shown marker-trait associations for stripe rust resistance on 1BS that could overlap with the positions of these Yr loci [36][37][38][39][40][41][42][43][44] . Of these genes, only Yr15/YrH52/YrG303 has been cloned as Wheat Tandem Kinase 1 (WTK1) and here we show that Yr84 localizes ∼86 Mb distal to WTK1, and that PI 487260 lacks Wtk1 based on genotyping with functional markers.…”