Abstract
Waterlogging significantly restricts growth and production of crops, and natural genetic variation associated with waterlogging tolerance is controlled by quantitative trait loci (QTL). Here, two sibling inbred maize (Zea mays L.) lines, A3237 and A3239, with contrasting phenotypes in response to waterlogging were used to analyze genetic polymorphism via global simple sequence repeat markers and specific-locus amplified fragment sequencing. We mapped a novel QTL associated with root-related traits, qWT5.04, from the cross between A3237 and A3239. The key candidate gene GRMZM2G179981, located within the target QTL, showed differential expression between A3237 and A3239 at the transcriptional and proteomic levels. Thirty-seven variations located within the 1.5-kb promoter region of GRMZM2G179981 were detected in parental lines. Re-sequencing this 1.5-kb region in 110 randomly selected inbred lines identified 13 variants significantly associated with root-related phenotypes; these showed complete linkage disequilibrium and overlapped with variations in A3237 and A3239, indicating that this haplotype was the causal functional locus. Furthermore, favorable alleles of GRMZM2G179981 in natural populations enhanced survival rate and decreased leaf injury after waterlogging, strongly suggesting that GRMZM2G179981 is a key gene for waterlogging tolerance. Functional markers derived from this locus could be applied for marker-assisted selection to enhance waterlogging tolerance in maize.
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