Numerous genetic loci identified for drought tolerance in the maize nested association mapping populations

BACKGROUND: Maize requires more water than most other crops; therefore, the water use efficiency of this crop must be improved for maize production under undesirable land and changing environmental conditions. RESULTS: To elucidate the genetic control of drought in maize, we evaluated approximately 5000 inbred lines from 30 linkage-association joint mapping populations under two contrasting water regimes for seven drought-related traits, including yield and anthesis-silking interval (ASI). The joint linkage analysis was conducted to identify 220 quantitative trait loci (QTLs) under well-watered conditions and 169 QTLs under water-stressed conditions. The genome-wide association analysis identified 365 single nucleotide polymorphisms (SNPs) associated with drought-related traits, and these SNPs were located in 354 candidate genes. Fifty-two of these genes showed significant differential expression in the inbred line B73 under the well-watered and water-stressed conditions. In addition, genomic predictions suggested that the moderate-density SNPs obtained through genotyping-by-sequencing were able to make accurate predictions in the nested association mapping population for drought-related traits with moderate-to-high heritability under the water-stressed conditions. CONCLUSIONS: The results of the present study provide important information that can be used to understand the genetic basis of drought stress responses and facilitate the use of beneficial alleles for the improvement of drought tolerance in maize. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-3170-8) contains supplementary material, which is available to authorized users.