Identification of genetic loci associated with rough dwarf disease resistance in maize by integrating GWAS and linkage mapping. (February 2022)

• Record Type: Journal Article
• Authors: Zhao, Meiai; Liu, Shuangshuang; Pei, Yuhe; Jiang, Xuwen; Jaqueth, Jennifer S.; Li, Bailin; Han, Jing; Jeffers, Daniel; Wang, Jiabo; Song, Xiyun
• Is Part Of: Plant science. Volume 315(2022)
• Publication Date: 2022-02
• Subjects: Maize -- MRDD -- GWAS -- Linkage mapping -- Candidate genes; Botany -- Periodicals; Botanique -- Périodiques; 580
• DOI: 10.1016/j.plantsci.2021.111100
• Languages: English
• ISSNs: 0168-9452

Abstract

Highlights: In this study, 292 maize inbred lines and a F6 linkage population were investigated across multiple environments for two years. Using the genotypes obtained from the Maize SNP 50 K chip, GWAS was performed with four analytical models. Results showed that 22 SNPs distributed on chromosomes 1, 3, 4, 6, 7 and 8 were found to be significantly associated with resistance to MRDD (P < 0.0001). The SNPs on chromosomes 3, 6 and 8 were consistent with the quantitative trait locus (QTL) regions from linkage mapping in a RIL population. Candidate genes identified by GWAS include an LRR receptor-like serine/threonine-protein kinase ( GRMZM2G141288 ) and a DRE-binding protein ( GRMZM2G006745 ). In addition, we performed allele variation analysis on the SNP loci selected by GWAS and linkage mapping. We found that the main alleles of the two SNP loci PZE_101170408 and PZE_106082685 on chromosome 1 were different in disease-resistant materials and disease-susceptible materials. These SNPs and genes identified provide useful information for MRDD-related gene cloning, an understanding of the underlying disease resistance mechanisms, and can be used in marker assisted breeding to develop MRDD resistant maize. Abstract: Maize rough dwarf disease (MRDD) is a viral disease that causes substantial yield loss, especially in China's summer planted maize area. Discovery of resistance genes would help in developing high-yielding resistant maize hybrids. Genome-wide association studies (GWASs) have advanced quickly and are now a powerful tool for dissecting complex genetic architectures. In this study, the disease severity index (DSI) of 292 maize inbred lines and an F6 linkage population were investigated across multiple environments for two years. Using the genotypes obtained from the Maize SNP 50K chip, a GWAS was performed with four analytical models. The results showed that 22 SNPs distributed on chromosomes 1, 3, 4, 6, 7 and 8 were significantly associated with resistance to MRDD (P<0.0001). The SNPs on chromosomes 3, 6 and 8 were consistent with the quantitative trait locus (QTL) regions from linkage mapping in an RIL population. Candidate genes identified by GWAS included an LRR receptor-like serine/threonine-protein kinase ( GRMZM2G141288 ), and a DRE-binding protein ( GRMZM2G006745 ). In addition, we performed an allele variation analysis of the SNP loci selected by GWAS and linkage mapping and found that the main alleles of the two SNP loci PZE_101170408 and PZE_106082685 on chromosome 1 differed in terms of disease-resistant materials and disease-susceptible materials. The identified SNPs and genes provide useful information for MRDD-related gene cloning and insights on the underlying disease resistance mechanisms, and they can be used in marker-assisted breeding to develop MRDD-resistant maize.