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

Drought stress is one of the most significant limiting factors limiting crop productions. Foxtail millet (Setaria italica) is among the most drought-tolerant crop plants, with a high degree of 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. A meta-analysis employing all 448 collected original quantitative trait loci (QTL) identified 41 meta-QTL (MQTL) on the nine foxtail millet chromosomes. The confidence interval (CI) of the identified MQTL 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 QTL. Based on the available RNA-seq and microarray data, 1631 differentially expressed genes (DEGs) were detected in 41 MQTL. Furthermore, through synteny analysis, 8, 4, and 2 ortho-MQTL were recognized within co-linear regions of foxtail millet with rice (Oryza sativa), barley (Hordeum vulgare), and maize (Zea mays), respectively. To detect the most significant genome regions involved in the genetic control of drought tolerance and yield maintenance in foxtail millet, 10 MQTL with physical intervals of less than 1 Mb and seven hotspot regions with a high QTL-overview index were identified. Several candidate genes involved in foxtail millet sensing and signaling, transcription regulation, ROS inhibition, and adaptation to abiotic stress were detected by seeking drought-responsive genes in MQTL regions with a CI < 1 Mb. We hope that the achieved results would aid in developing new high-yielding drought-tolerant genotypes.