Genome-wide analysis of gene expression provides new insights into waterlogging responses in Barley (Hordeum vulgare L.)
Citation
Borrego-Benjumea, A., Carter, A., Tucker, J.R., Yao, Z., Xu, W., Badea, A. (2020). Genome-wide analysis of gene expression provides new insights into waterlogging responses in Barley (Hordeum vulgare L.). Plants, [online] 9(2), http://dx.doi.org/10.3390/plants9020240
Plain language summary
Waterlogging is a major abiotic stress that affects numerous crops, including barley, and results in significant yield losses. Two barleys, one waterlogging moderately-tolerant and one waterlogging tolerant, were grown in controlled conditions and exposed to waterlogging at seedling stage (about two-week-old seedlings). The roots were sampled for further molecular analysis such as RNA-Sequencing which is a powerful method that provides information on the ribonucleic acid (RNA-is an essential molecule that has different attributes) in a sample at a given time. Our study revealed common genes and pathways that respond to a variety of abiotic stress conditions in different crops as well as it discovered a few new genes and pathways in barley under waterlogging. The findings provide new insights into the molecular mechanisms underlying the response to waterlogging in barley. These will be of benefit for future studies of molecular responses to waterlogging and will greatly assist barley genetic research and breeding for barley with inbuilt waterlogging tolerance.
Abstract
Waterlogging is a major abiotic stress causing oxygen depletion and carbon dioxide accumulation in the rhizosphere. Barley is more susceptible to waterlogging stress than other cereals. To gain a better understanding, the genome-wide gene expression responses in roots of waterlogged barley seedlings of Yerong and Deder2 were analyzed by RNA-Sequencing. A total of 6736, 5482, and 4538 differentially expressed genes (DEGs) were identified in waterlogged roots of Yerong at 72 h and Deder2 at 72 and 120 h, respectively, compared with the non-waterlogged control. Gene Ontology (GO) enrichment analyses showed that the most significant changes in GO terms, resulted from these DEGs observed under waterlogging stress, were related to primary and secondary metabolism, regulation, and oxygen carrier activity. In addition, more than 297 transcription factors, including members of MYB, AP2/EREBP, NAC, WRKY, bHLH, bZIP, and G2-like families, were identified as waterlogging responsive. Tentative important contributors to waterlogging tolerance in Deder2 might be the highest up-regulated DEGs: Trichome birefringence, α/β-Hydrolases, Xylanase inhibitor, MATE efflux, serine carboxypeptidase, and SAUR-like auxin-responsive protein. The study provides insights into the molecular mechanisms underlying the response to waterlogging in barley, which will be of benefit for future studies of molecular responses to waterlogging and will greatly assist barley genetic research and breeding.