Identification of QTLs and Meta-QTLs for Seven Agronomic Traits in Multiple Maize Populations under Well-Watered and Water-Stressed Conditions

Drought is one of the most important factors contributing to crop yield loss. To develop drought-tolerant maize (Zea mays L.) varieties, it is important to explore the genetic mechanism and genes involved. In this study, we identified 69 quantitative trait loci (QTLs) for plant height, ear height, anthesis-silking interval, ear weight, cob weight, 100-kernel weight, and ear length in two F-2: 3 populations in both drought-stressed and unstressed conditions. These QTLs explained 4.0 to 17.2% of phenotypic variation in a single watering condition. Approximately 52 of the 69 QTLs were identified under water-stressed conditions. Moreover, 21 stable QTLs were validated in one or two F-2: 3 populations under multiple water-stressed conditions. Remarkably, bin 4.09 (umc2287-umc2011) had two stable QTLs for ear height and anthesis-silking interval; bin 1.07_1.08 (bnlg1025-mmc0041) identified three stable QTLs for ear, cob, and 100-kernel weights; bin 4.08_4.09 (umc2041-umc2287) validated four stable QTLs for ear weight, cob weight, 100-kernel weight, and ear length; and bin 9.04_9.06 (umc1120-umc2134) mapped three stable QTLs for ear weight, cob weight, and ear length that were consistent with phenotypic correlations among traits, supporting pleiotropy of QTLs and playing important roles in conferring growth and yield advantages under drought stress. Additionally, we identified 36 meta-QTLs across 26 populations under 52 well-watered and 38 water-stressed conditions using a meta-analysis, and we predicted 39 candidate genes in the corresponding meta-QTL intervals. These results provide valuable information for further mapping quantitative traits and revealing the genetic basis of drought tolerance.