Genome-wide Association Studies and Candidate Gene Identification for Leaf Scald and Net Blotch in Barley (Hordeum vulgare L.)

Abstract

We report genomic regions that significantly control resistance to scald, net form (NFNB) and spot form net blotch (SFNB) in barley. Barley genotypes from Ethiopia, ICARDA, and the United States were evaluated in Ethiopia and North Dakota State University (NDSU). Genome-wide association studies (GWAS) were conducted using 23,549 single nucleotide polymorphism (SNP) markers for disease resistance in five environments in Ethiopia. For NFNB and SFNB, we assessed seedling resistance in a glasshouse at NDSU. A large proportion of the Ethiopian landraces and breeding genotypes were resistant to scald and NFNB. Most of genotypes resistant to SFNB were from NDSU. We identified 17, 26, 7, and 1 marker-trait associations (MTAs) for field-scored scald, field-scored net blotch, greenhouse-scored NFNB, and greenhouse-scored SFNB diseases, respectively. Using the genome sequence and the existing literature, we compared the MTAs with previously reported loci and genes for these diseases. For leaf scald, only a few of our MTAs overlap with previous reports. However, the MTAs found for field-scored net blotch as well as NFNB and SFNB mostly overlap with previous reports. We scanned the barley genome for identification of candidate genes within 250 kb of the MTAs, resulting in the identification of 307 barley genes for the 51 MTAs. Some of these genes are related to plant defense responses such as subtilisin-like protease, chalcone synthase, lipoxygenase, and defensin-like proteins.

Identification of QTLs conferring resistance to scald (Rhynchosporium commune) in the barley nested association mapping population HEB-25

“…In the same region two QTLs linked to the marker Bmac0213 [42,47] and a meta-QTL [40] were identified. Another QTL (Qsc-1H), distinct from Rrs14, was detected by Daba et al [60]. However, none of the mentioned resistance loci corresponds to QRs.1H from this study.…”

Recent insights into barley and Rhynchosporium commune interactions

“…So far, overall 13 QTLs from three GWAS analysis for scald resistance have been detected under natural field conditions at adult plant stage (Table 2 and Figure 2) (Gawenda et al, 2015;Looseley et al, 2018;Daba et al, 2019). GWAS analysis suggested Rrs1 is the most significant effect QTL among European spring barley germplasm under natural field conditions in Europe (Looseley et al, 2018).…”

Research advances in the Pyrenophora teres–barley interaction

“…A total of seven conventional genome‐wide association studies (GWAS) have been performed to investigate P. teres f. teres resistance in barley (Adhikari et al , ; Amezrou et al , ; Daba et al , ; Novakazi et al , ; Richards et al , ; Rozanova et al , ; Wonneberger et al , ). Investigation of resistance to a set of diverse global isolates was performed on the Barley Core Collection (Muñoz‐Amatriaín et al , ; Richards et al , ), Nordic Barley Panel (Wonneberger et al , ), ICARDA AM‐2014 Panel (Amezrou et al , ), Ethiopian, ICARDA and NDSU Barley Panel (Daba et al , ), Siberian Barley Panel (Rozanova et al , ), Ethiopian and Eritrean Barley Collection (Adhikari et al , ) and Vavilov Research Institute Collection (Novakazi et al , ). Between 7 and 31 unique genomic loci were identified in each GWAS (Fig.…”

“…Four studies have used GWAS to investigate barley resistance to P. teres f. maculata (Burlakoti et al , ; Daba et al , ; Tamang et al , ; Wang et al , ) . Evaluations of resistance to diverse global (Tamang et al , ), Australian (Wang et al , ) and single American isolates (Burlakoti et al , ; Daba et al , ) were performed on the Barley Core Collection (Muñoz‐Amatriaín et al , ; Neupane et al , ; Tamang et al , ), Northern Region Barley Breeding Program of Australia (Wang et al , ), Upper Midwest Breeding Programs (Burlakoti et al , ) and Ethiopian, ICARDA and NDSU Barley Panel (Daba et al , ), respectively. A total of 27 (Tamang et al , ), 29 (Wang et al , ), 11 (Burlakoti et al , ) and 1 (Daba et al , ) unique genomic loci were identified in each GWAS, respectively (Fig.…”

“…The most significant QTL identified was novel, mapped to chromosome 2H and accounted for 4.3–6.6% of the phenotypic variation (Burlakoti et al , ). Daba et al () identified a single novel QTL on chromosome 6H, but this is attributed to most lines being susceptible to P. teres f. maculata. The association mapping studies of Tamang et al (), Wang et al () and Burlakoti et al () indicated that the genetic interaction of P. teres f. maculata and barley was more complex than originally hypothesized.…”