Identification of significant single nucleotide polymorphisms for resistance to maize rough dwarf disease in elite maize (Zea mays L.) inbred lines

Maize rough dwarf disease (MRDD) is a devastating viral disease that causes considerable yield losses in maize worldwide. Identifying quantitative trait loci underlying resistance to MRDD is important for genetic improvement of maize. In this study, 184 elite maize inbred lines from modern breeding programs were evaluated in three years to identify QTLs for MRDD resistance using 3072 single-nucleotide polymorphisms (SNPs) via genome-wide association analysis. The analysis revealed abundant phenotypic diversity in the studied population. All tested maize inbred lines were divided into two subpopulations based on a Bayesian model, and the linkage disequilibrium (LD) level differed among chromosomes, with an intra-chromosomal average of 1,000-1,500 kb. After correction for multiple testing, 21 SNPs were identified for MRDD resistance in different years as well as for BLUPs (the best linear unbiased predictions) of MRDD resistance based on the MLM model, one SNP of PZE-101245575 was stably possessed the most promising association. Several SNPs were located in or close to previously reported quantitative trait loci for MRDD resistance. The significant SNPs identified in this study will be helpful for further understanding the genetic basis of MRDD resistance, and might facilitate the pyramiding of favorable alleles for high resistance to MRDD in future marker-assisted selection schemes in maize.