The genomic regions and candidate genes associated with drought tolerance and yield-related traits in foxtail millet: an integrative meta-analysis approach

Abstract Drought stress is one of the most significant limiting factors affecting crop products. Foxtail millet ( Setaria italica ) is one of the superior drought-tolerant crop plants, comprising high collinearity with other staple cereals. The present study used a meta-analysis approach to identify genomic regions and candidate genes associated with drought tolerance and yield-related traits in foxtail millet. Meta-analysis using all 448 collected original quantitative trait loci (QTLs) lead to detection of 41 meta-QTLs (MQTLs) on the nine chromosomes of foxtail millet. The confidence interval (CI) of the identified MQTLs was determined to be 0.31–14.47 cM (5.23 cM average), which was 3.5 times narrower than the mean CI of the original QTLs. Based on the available RNA-seq and microarray data, 1631 differentially expressed genes (DEGs) were detected in 41 MQTLs. Through synteny analysis, 8, 4, and 2 ortho-MQTLs were recognized within co-linear regions of foxtail millet with rice, barley, and maize, respectively. To detect the most important genome regions involved in the genetic control of yield maintenance and drought tolerance of foxtail millet, 10 MQTLs with physical intervals of below 1 Mb and seven hotspot regions with high-value QTL-overview index were distinguished. Several candidate genes involved in sensing and signaling, transcription regulation, ROS inhibition, and adaptation to abiotic stress of foxtail millet were detected by seeking drought-responsive genes in MQTL regions with CI < 1 Mb. We hope that the achieved results will aid in developing new high-yielding drought-tolerant genotypes.