QTL mapping and transcriptome analysis reveal genetic loci and candidate genes associated with drought-related traits in maize (Zea mays L.)

Drought is a major abiotic constraint on maize growth and productivity worldwide. Elucidating the genetic basis of drought-related traits is essential for developing drought-tolerant maize cultivars. In this study, a recombinant inbred line (RIL) population derived from a cross between the drought-sensitive inbred line ZhengA88 and the drought-tolerant line ZhengT22, was used to identify quantitative trait loci (QTLs) for plant height (PH), ear height (EH), plant-to-ear height ratio (PEH), ear tip-barrenness length (ETL), and kernel ratio (KR) under well-watered (WW) and water deficit (WD) conditions at the flowering stage over two summer maize growing seasons. A total of 125 QTLs were detected, each explaining 1.55%–19.65% of the phenotypic variation. Of these QTLs, 78 (62.4%) were associated with drought tolerance and 5 showed significant QTL-by-environment interactions (QEI) effects. Fifty-one QTLs were located in overlapping genomic regions, forming 18 QTL clusters. Integrating QTL mapping with transcriptome profiling of the parental lines under drought stress identified 235 drought-responsive differentially expressed genes (DEGs) within nine genomic regions encompassing seven QTL clusters and two major-effect QTLs. Based on these genes expression patterns and reported functional annotations, eleven genes were predicted as candidate genes for drought tolerance: Zm00001d005748 ( ZmCIPK16 ), Zm00001d042088 ( si605032h02 ), Zm00001d024800 , Zm00001d024804 , Zm00001d024778 ( NAC1 ), Zm00001d025055 ( ZmPP2C37 ), Zm00001d024531 ( THX43 ), Zm00001d026139 ( CDPK30 ), Zm00001d024786 , Zm00001d024798 , and Zm00001d025255 . These results will advance understanding of the genetic architecture of drought tolerance and provide molecular resources for drought-tolerant maize breeding and gene cloning.