Identification of Major QTL for Waterlogging Tolerance Using Genome-Wide Association and Linkage Mapping of Maize Seedlings

To investigate the genetic basis of maize seedling response to waterlogging, we performed a genome-wide association study in 144 maize inbred lines, measuring length, fresh and dry weight of roots and shoots under normal and waterlogged conditions using 45,868 SNPs. This panel was divided into three subgroups based on the population structure results and the LD decay distance was 180 kb. A biparental advanced backcross (AB) population was also used to detect quantitative trait loci (QTL). In a comparison of 16 different models, principal components analysis (PCA/top PC3) + K was found to be best for reduction of false-positive associations for further analysis. A whole-genome scan detected four strong peak signals (P < 2.18 × 10−5) significantly associated with the waterlogging response on chromosomes 5, 6 and 9. SNP4784, SNP200, SNP298, and SNP6314 showed significant association with corresponding traits under waterlogging and explained 14.99–19.36 %, 15.75–17.64 %, 16.08 % and 15.44 % of the phenotypic variation, respectively. The identified SNPs were located in GRMZM2G012046, GRMZM2G009808, GRMZM2G137108 and GRMZM2G369629 (AGPV1). SNP4784 (GRMZM2G012046) was colocalized with the major QTL that was identified with the same traits in the AB population. Forty-seven SNPs significantly associated (P < 2.18 × 10−4) with six traits in association mapping were identified and, among these, 33 SNPs were already reported in literature as waterlogging-related traits. These results will help elucidate the genetic basis of differential responses and tolerance to waterlogging stress among maize inbred lines, and provide novel loci for improvement of waterlogging tolerance of maize inbred lines using marker-assisted selection.