Novel stripe rust all‐stage resistance loci identified in a worldwide collection of durum wheat using genome‐wide association mapping

Abstract

Durumwheat [Triticum turgidum L. ssp. durum (Desf.)] production is constrained by fungal diseases including stripe rust caused by Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst). Continuous mining of germplasm for the discovery and deployment of stripe rust resistance (Yr) genes is needed to counter the impact of this disease. In this study, we evaluated a worldwide collection of 432 durum wheat accessions to seven U.S. Pst races that carry diverse virulence and avirulence combinations on wheat Yr genes. We found that 47–82% of the durum wheat accessions were susceptible to each of the tested Pst races. A total of 32 accessions were resistant to all seven races. Genome‐wide association studies (GWAS) using over 97,000 single‐nucleotide polymorphism markers generated from genotyping‐by‐sequencing of 364 accessions identified 56 quantitative trait loci (QTL) associated with all‐stage stripe rust resistance located on all 14 durum wheat chromosomes. Six of these QTL were associated with resistance to 2–4 Pst races, and none were associated with resistance to all seven races. The remaining 50 QTL were race specific. Eighteen of the 56 identified QTL had relatively large effects against at least one of the races. A map‐based comparison of the discovered QTL in this study with previously published Yr genes and QTL showed that 29 were previously identified, whereas the remaining 27 QTL appeared to be novel. This study reports effective sources of stripe rust resistance to contemporary races in the United States and shows that this durum wheat collection is abundant in novel resistance loci that can be transferred into adapted durum cultivars.

Identification of Disease Resistance Parents and Genome-Wide Association Mapping of Resistance in Spring Wheat

“…Previous mapping studies conducted in diverse types of biparental populations and association mapping panels reported numerous genes and QTLs that confer resistance to stripe rust on all wheat chromosomes, including 1B (33 QTLs), 2B (48 QTLs), 4B (19 QTLs), 5A (15 QTLs), and 7D (22 QTLs) [ 35 ]. Recently, for example, Aoun et al [ 45 ] reported the physical positions of 56 QTLs that confer stripe rust resistance in a global durum wheat collection, including four on chromosomes 1B, one on 2B, three on 4B, and five on 5A; however, none of these QTLs were located close to the QTLs identified in the present study. The long arm of chromosome 2B harbors several race-specific stripe rust resistance genes, including Yr5, Yr7 , Yr43 , Yr44 , Yr53 , and Yr72 [ 46 ].…”

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.…”

Wheat end-use quality: State of art, genetics, genomics-assisted improvement, future challenges, and opportunities

“…An effective strategy is to study the G×E interaction for end-use quality traits. Traits highly influenced by environment, such as GPC and FPC, should be tested in multiple environments to allow breeders to get a better estimation of the value of a particular genotype ( Aoun et al, 2021 ). Traits not as affected by environment can be tested in fewer environments which saves resources to test additional lines in the breeding program ( Aoun et al, 2021 ).…”

“…Traits highly influenced by environment, such as GPC and FPC, should be tested in multiple environments to allow breeders to get a better estimation of the value of a particular genotype ( Aoun et al, 2021 ). Traits not as affected by environment can be tested in fewer environments which saves resources to test additional lines in the breeding program ( Aoun et al, 2021 ). In addition, the G×E interaction provides information on genotype stability across environment and identifies the target environment for maximizing genetic gain ( Dias et al, 2018 ).…”

“…Based on the results of these studies, a few reviews were published that summarized the QTLs/genes and their diagnostic markers to be used for marker-assisted breeding of wheat end-use quality ( Gale, 2005 ; Liu et al, 2012 ). More recently, studies on genomic selection and translational genomics for end-use quality traits are being carried out which still warrants exhaustive efforts across wheat breeding programs to achieve satisfactory results as is the case for grain yield or disease resistance ( Kristensen et al, 2019 ; Nigro et al, 2019 ; Aoun et al, 2021 ). There are limited reviews that capture these modern genetic and genomic studies on diverse end-use quality traits.…”