Identification of the drought tolerance involved candidate genes in foxtail millet through an integrated meta-analysis approach

Drought stress is one of the most important factors limiting production in the agricultural sector. Due to the need to use smart agriculture adapted to climate change, the use of drought-tolerant alternative plants with high water use efficiency is of great importance. Foxtail millet (Setaria italica L.) is one of the important drought tolerant fodder and food grains in semi-arid regions. In this study, drought stress associated QTLs were collected and located on the integrated genetic map of millet chromosomes. From a total of eight studies, 386 QTLs associated with yield controlling traits including plant height, water use efficiency, plant biomass, root length and panicle length were collected in foxtail millet. Under drought stress and normal irrigation conditions, 96 and 287 QTLs were collected and projected on the reference consensus genetic map, respectively. The meta-analysis of QTLs was conducted using BioMercator software V4.2. A total of 32 meta-QTLs (MQTLs) were detected on 9 foxtail millet chromosomes with a confidence interval of 3.4 times lower than the average of the original QTLs. In order to investigate the pattern of gene expression in the MQTL regions, available microarray and RNA-seq data sets in the databases were analyzed. Based on the achieved results, 95 and 2172 differentially expressed genes with at drought conditions were identified in 4 MQTLs with a CI of less than 1 Mbp and in all MQTL regions, respectively. Also, eight key genes were identified by the hub analysis which belonged to transcription factors and regulatory elements. We hope that the results of this study would be useful for marker assisted selection (MAS) and foxtail millet breeding programs with the aim of development of new high yielding drought-tolerant genotypes.