Abstract
Spot blotch (SB) caused by Cochliobolus sativus (anamorph: Bipolaris sorokiniana) is an economically important disease of wheat worldwide. Under a severe epidemic condition, the disease can cause yield losses up to 70%. Previous approaches like bi-parental mapping for identifying SB resistant genes/QTLs exploited only a limited portion of the available genetic diversity with a lower capacity to detect polygenic traits, and had a lower marker density. In this study, we performed genome-wide association study (GWAS) for SB resistance in hard winter wheat association mapping panel (HWWAMP) of 294 genotypes. The HWWAMP was evaluated for response to B. sorokiniana (isolate SD40), and a range of reactions was observed with 10 resistant, 38 moderately resistant, 120 moderately resistant- moderately susceptible, 111 moderately susceptible, and 15 susceptible genotypes. GWAS using 15,590 high-quality SNPs and 294 genotypes we identified six QTLs (p = <0.001) on chromosomes 2D, 3A, 4A, 4B, 5A, and 7B that collectively explained 30% of the total variation for SB resistance. Highly associated SNPs were identified for all six QTLs, QSb.sdsu-2D.1 (SNP: Kukri_c31121_1460, R2 = 4%), QSb.sdsu-3A.1 (SNP: Excalibur_c46082_440, R2 = 4%), QSb.sdsu-4A.1 (SNP: IWA8475, R2 = 5.5%), QSb.sdsu-4B.1 (SNP: Excalibur_rep_c79414_306, R2 = 4%), QSb.sdsu-5A.1 (SNP: Kukri_rep_c104877_2166, R2 = 6%), and QSb.sdsu-7B.1 (SNP: TA005844-0160, R2 = 6%). Our study not only validates three (2D, 5A, and 7B) genomic regions identified in previous studies but also provides highly associated SNP markers for marker assisted selection. In addition, we identified three novel QTLs (QSb.sdsu-3A.1, QSb.sdsu-4A.1, and QSb.sdsu-4B.1) for SB resistance in wheat. Gene annotation analysis of the candidate regions identified nine NBS-LRR and 38 other plant defense-related protein families across multiple QTLs, and these could be used for fine mapping and further characterization of SB resistance in wheat. Comparative analysis with barley indicated the SB resistance locus on wheat chromosomes 2D, 3A, 5A, and 7B identified in our study are syntenic to the previously identified SB resistance locus on chromosomes 2H, 3H, 5H, and 7H in barley. The 10 highly resistant genotypes and SNP markers identified in our study could be very useful resources for breeding of SB resistance in wheat.
Highlights
Wheat (Triticum aestivum L) is an important cereal crop grown worldwide and remains a vital source for human food (FAO, 2017)
Seedlings showed a range of infection types (Supplementary Figure 1) within 294 hard winter wheat genotypes when inoculated with B. sorokiniana (Figure 1 and Supplementary Table 1)
Our analysis indicated that mixed linear model (MLM), compressed mixed linear model (CMLM), and enhanced compressed mixed linear model (ECMLM) reduced the type-I error and increased power when compared to others
Summary
Wheat (Triticum aestivum L) is an important cereal crop grown worldwide and remains a vital source for human food (FAO, 2017). Helminthosporium sativum, teleomorph Cochliobolus sativus) is one of the destructive fungal diseases that affects wheat and several other small grains worldwide (Dubin and Rajaram, 1996; Duveiller and Dubin, 2002; Joshi and Chand, 2002; Sharma et al, 2007b; Singh and Singh, 2007; Gurung et al, 2009; Chowdhury et al, 2013) It has a wide range of hosts within wild and cultivated Poaceae species (Kumar et al, 2002; Pandey et al, 2005; O’Boyle et al, 2014). Average yield loss of 15–20% due to SB has been reported from several countries, but under suitable climatic conditions the losses in yield can reach up to 70% in susceptible genotypes, in addition to the reduction in seed quality (Mehta et al, 1992; Lemerle et al, 1996; Fernandez et al, 1998, 2014; Wang et al, 2002; Fernandez and Jefferson, 2004; Sharma et al, 2004, 2007b; Siddique et al, 2006; Sharma and Duveiller, 2007; Acharya et al, 2011)
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