Genetic dissection of resistance to gray leaf spot by genome-wide association study in a multi-parent maize population

Abstract

Background Understanding the genetic mechanisms underlying gray leaf spot (GLS) resistance in maize is crucial for breeding GLS-resistant inbred lines and commercial hybrids. Genome-wide association studies (GWAS) and gene functional annotation are valuable methods for identifying potential SNPs (single nucleotide polymorphism) and candidate genes associated with GLS resistance in maize. Results In this study, a total of 757 lines from five recombinant inbred line (RIL) populations of maize at the F7 generation were used to construct an association mapping panel. SNPs obtained through genotyping-by-sequencing (GBS) were used to perform GWAS for GLS resistance using a linear mixture model in GEMMA. Candidate gene screening was performed by analyzing the 10 kb region upstream and downstream of the significantly associated SNPs linked to GLS resistance. Through GWAS analysis of multi-location phenotypic data, we identified ten candidate genes that were consistently detected in two locations or from one location along with best linear unbiased estimates (BLUE). One of these candidate genes, Zm00001d003257 that might impact GLS resistance by regulating gibberellin content, was further identified through haplotype-based association analysis, candidate gene expression analysis, and previous reports. Conclusions The discovery of the novel candidate gene provides valuable genomic resources for elucidating the genetic mechanisms underlying GLS resistance in maize. Additionally, these findings will contribute to the development of new genetic resources by utilizing molecular markers to facilitate the genetic improvement and breeding of maize for GLS resistance.

Identification of candidate gene associated with maize northern leaf blight resistance in a multi-parent population

“…The inbred line YML226 was selected from the CATETO related germplasm originating from tropical regions in Brazil and Argentina (Fan et al 2018 ). Hu et al ( 2024 ) demonstrated that YML226 showed high resistance to maize gray spot disease. Subedi et al ( 2015 ) conducted a survey of maize lines used in Nepal and found that maize derived from the CATETO germplasm imported from Yunnan Province, China showed high leaf spot resistance and yield.…”

“…Therefore, the tropical maize germplasm retained more favorable variations during domestication, conferring stronger resistance to diseases than temperate maize. The CATETO germplasm, originating in South America, has been proven to exhibit high general combining ability and disease resistance in both temperate and tropical-subtropical environments, thus, it has been widely used in breeding programs (Santos et al 2001 ; Subedi 2015 ; Fan et al 2018 ; Hu et al 2024 ). Therefore, identifying NLB resistant genes against maize NLB in populations derived from the tropical germplasm may be a good strategy for marker-assisted breeding.…”