Multiple-race stem rust resistance loci identified in durum wheat using genome-wide association mapping

Authors: MEGERSSA, SHITAYE - Cornell University; AMMAR, KARIM - International Maize & Wheat Improvement Center (CIMMYT); ACEVEDO, MARICELIS - Cornell University; Brown-Guedira, Gina; Ward, Brian; DEGETE, ASHENAFI - Ethiopian Institute Of Agricultural Research; RANDHAWA, MANDEEP - International Maize & Wheat Improvement Center (CIMMYT); SORRELLS, MARK - Cornell University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/1/2020
Publication Date: 12/17/2020
Citation: Megerssa, S.H., Ammar, K., Acevedo, M., Brown Guedira, G.L., Ward, B.P., Degete, A.G., Randhawa, M.S., Sorrells, M.E. 2020. Multiple-race stem rust resistance loci identified in durum wheat using genome-wide association mapping. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2020.598509.
DOI: https://doi.org/10.3389/fpls.2020.598509

Interpretive Summary: Stem rust of wheat is the most damaging fungal disease of both common and durum wheat. Continuously emerging races virulent to many of the commercially deployed resistance genes have caused remarkable loss worldwide and threaten global wheat production. The objectives of this study were to evaluate the response of a panel of 280 durum wheat lines assembled by the International Maize and Wheat Improvement Center (CIMMYT) to multiple races of stem rust in East Africa at the adult plant stage and to identify genes associated with field resistance. The lines were evaluated in Debre Zeit, Ethiopia and Njoro, Kenya from 2018 to 2019 in five environments (year x season). Using 26,439 Single Nucleotide Polymorphism (SNP) DNA markers, genome-wide association analysis (GWAS) was conducted to identify significant DNA markers for resistance. GWAS analysis detected a total of 160 significant marker trait associations representing 42 quantitative trait loci. Of those, 21 were potentially novel and 21 were mapped to the same regions as previously reported genes. Known stem rust resistance genes/alleles postulated as present in the panel included Sr8a, Sr8155B1, SrWeb/Sr9h, Sr11, Sr12, Sr13/Sr13 alleles, Sr17, Sr28/Sr16, Sr22 and Sr49. Lines resistant to multiple races in East Africa can be utilized as parents in durum wheat breeding programs. Further studies are needed to determine if there are new alleles at the Sr13 locus in this panel and to validate potential markers for the known Sr13 alleles.

Technical Abstract: Stem rust of wheat caused by Puccinia graminis Pers.f.sp. trtici Eriks and E. Henn., is the most damaging fungal disease of both common (Triticum aestivum L.) and durum (Triticum turgidum L., ssp. Durum) wheat. Continuously emerging races virulent to many of the commercially deployed qualitative resistance genes have caused remarkable loss worldwide and threaten global wheat production. The objectives of this study were to evaluate the response of a panel of 283 durum wheat lines assembled by the International Maize and Wheat Improvement Center (CIMMYT) to multiple races of stem rust in East Africa at the adult plant stage and map loci associated with field resistance. The lines were evaluated in Debre Zeit, Ethiopia and Njoro, Kenya from 2018 to 2019 in five environments (year x season). The panel was genotyped using genotyping-by-sequencing. After filtering, 26,439 Single Nucleotide Polymorphism (SNP) markers and 280 lines and three checks were retained for analysis. Population structure was assessed using principal component analysis. Genome-wide association analysis (GWAS) was conducted using Genomic Association and Prediction Integrated Tool (GAPIT). The broad-sense heritability of the phenotype data revealed that 64% to 83% of the variation in stem rust response explained by the genotypes and lines with multiple race resistance were identified. GWAS analysis detected a total of 160 significant marker trait associations representing 42 quantitative trait loci. Of those, 21 were potentially novel and 21 were mapped to the same regions as previously reported loci. Known stem rust resistance genes/alleles were postulated including Sr8a, Sr8155B1, SrWeb/Sr9h, Sr11, Sr12, Sr13/Sr13 alleles, Sr17, Sr28/Sr16, Sr22 and Sr49. Lines resistant to multiple races in East Africa can be utilized as parents in durum wheat breeding programs. Further studies are needed to determine if there are new alleles at the Sr13 locus and potential markers for the known Sr13 alleles.