Genome-wide investigation on transcriptional responses to drought stress in wild and cultivated rice

• Published in: Environmental and experimental botany 2021-09, Vol.189, p.104555, Article 104555
• Main Authors: Geng, Mu-Fan, Wang, Xiu-Hua, Wang, Mei-Xia, Cai, Zhe, Meng, Qing-Lin, Wang, Xin, Zhou, Lian, Han, Jing-Dan, Li, Ji-Long, Zhang, Fu-Min, Guo, Ya-Long, Ge, Song
• Format: Article
• Language: English
• Subjects: Cultivated and wild rice; Drought stress; Genomic hotspot; RNA-seq; WGCNA
• ISSN: 0098-8472; 1873-7307
• DOI: 10.1016/j.envexpbot.2021.104555

•Drought-tolerant and drought-sensitive accessions of cultivated and wild rice were used to investigate the mechanisms of drought tolerance.•Differentially expressed genes (DEGs) between the drought-treated and control samples and their co-expression patterns were analyzed.•Specific transcript factors and genes were identified to be associated with drought tolerance, with some of them being unique to wild rice.•There were clusters or hotspots of DEGs in which overrepresentation of the QTLs published previously were observed. Whole transcriptomic sequencing of the drought-tolerant (DT) and drought-sensitive (DS) accessions of cultivated and wild rice under drought treatments was performed to uncover the mechanism of plant adaptation to drought and to facilitate the development of drought-tolerant cultivars in crops. By analyzing the differentially expressed genes (DEGs) between the drought-treated and untreated samples and their co-expressed pattern, we revealed distinct susceptibilities of different samples to the stress treatments and identified some specific transcription factors (TFs) and genes that play critical roles in rice adaptation to drought. Some drought-responsive genes or pathways unique to the wild rice were also detected, highlighting the importance of wild rice resources in developing elite cultivars. Furthermore, we showed that the DEGs in the DT accessions were enriched in the genome as clusters or hotspots in which previously identified drought-associated quantitative trait loci (QTLs) were overrepresented. The finding that a single hotspot contained up to 52 QTLs and involved as many as 20 traits implicates the complicated genetic architecture underlying the DT traits. These results provide new insights into the understanding of plant adaptation to drought and help effective manipulation of specific genes or gene cluster in crop breeding.