TCAP FAC‐WIN6 Elite Barley GWAS Panel QTL. I. Barley Stripe Rust Resistance QTL in Facultative and Winter Six‐Rowed Malt Barley Breeding Programs Identified via GWAS

Abstract

The fungal disease barley stripe rust (BSR, causal agent Puccinia striiformis f. sp. hordei) can greatly reduce yield and quality of malt barley (Hordeum vulgare L.), a valuable crop in the distilling and brewing industries. Yield losses of up to 70% have been reported. Resistant cultivars are the most sustainable defense against BSR, especially those cultivars with pyramids of quantitative disease resistance (QDR) genes. The Oregon State University (OSU) barley breeding program has selected for BSR resistance for decades and has released cultivars with BSR resistance. We wanted to determine the number and effect of the loci underlying that resistance, as well as whether it was conferred by QDR or race‐specific qualitative loci. To test these, we used BSR resistance quantitative trait loci (QTL) mapping via genomewide association studies (GWAS) in adult‐plant field trials (3 yr, one location) and race‐specific seedling greenhouse trials (five races). The FAC‐WIN6, a GWAS panel composed of 300 lines that represent the OSU and University of Minnesota facultative and winter six‐rowed malt barley breeding programs, was used in genotyping and phenotyping. The FAC‐WIN6 was developed as part of the USDA‐ARS Triticeae Coordinated Agricultural Project but was not developed specifically for BSR resistance. In total, we detected three race‐specific QTL in greenhouse trials (one of which was also significant in field trials) and 14 QTL significant in field trials only with 2.3 to 20.7% additive reduction in percentage disease severity. At least five QTL were considered novel. These results indicated that the OSU breeding program had both QDR and race‐specific loci for BSR resistance. We suspected that its BSR resistance distributions in the FAC‐WIN6 might align with the major population structure patterns in ways that would be difficult to account for with a GWAS model alone. Therefore, based on post hoc diagnostics, we report a qualitative “usability” level for each QTL.

Genome Wide Association Mapping of Seedling and Adult Plant Resistance to Barley Stripe Rust (Puccinia striiformis f. sp. hordei) in India

“…Out of the 45 QTL identified for resistance at SRT, 15 were coincident with prior reports Those QTL were reported from different barley germplasm and different Psh races (Thomas et al, 1995 ; Toojinda et al, 2000 ; Vales et al, 2005 ; Rao et al, 2007 ; Verhoeven et al, 2011 ; Gutiérrez et al, 2015 ; Dracatos et al, 2016 ; Esvelt Klos et al, 2016 ; Belcher et al, 2018 ). For Psh resistance at the APS stage using different germplasm and races, only 3 out of the 18 QTL detected, shown in Table 5 , are coincident with previous reports (Vales et al, 2005 ; Rao et al, 2007 ; Verhoeven et al, 2011 ; Gutiérrez et al, 2015 ; Dracatos et al, 2016 ; Belcher et al, 2018 ).…”

TCAP FAC‐WIN6 Elite Barley GWAS Panel QTL. II. Malting Quality QTL in Elite North American Facultative and Winter Six‐Rowed Barley Identified via GWAS

“…These five cultivars were also used with the FAC‐WIN6 in evaluating resistance to barley stripe rust (caused by Puccinia striiformis f. sp. hordei ) disease (Belcher et al, 2017 [companion paper]).…”

Introgression Breeding in Barley: Perspectives and Case Studies

“…The disease spread throughout the Americas, arriving in the United States in 1991. A long-term collaboration with the late Dr. Hugo Vivar, who led the former ICARDA barley program based at CIMMYT in Mexico, resulted in extensive literature on mapping resistance genes and QTLs (most recently reviewed by Belcher et al, 2018). Parallel to these efforts we conducted ongoing stripe resistance breeding efforts based primarily on phenotypic selection because (1) mapping efforts were conducted in spring growth habit barley and our breeding program is directed primarily at winter and facultative growth habit barley and (2) phenotypic selection is generally effective at our test sites due to high heritability and consistent natural disease epidemics.…”

“…Parallel to these efforts we conducted ongoing stripe resistance breeding efforts based primarily on phenotypic selection because (1) mapping efforts were conducted in spring growth habit barley and our breeding program is directed primarily at winter and facultative growth habit barley and (2) phenotypic selection is generally effective at our test sites due to high heritability and consistent natural disease epidemics. Periodically, however, QTL alleles were characterized in germplasm derived from phenotypic selection in our winter and facultative barley program (Belcher et al, 2018). We added stem rust to our resistance breeding efforts due to the threat posed by race TTKSK of this disease, which has yet to be reported in the Americas.…”