Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/10/2021
Publication Date: 8/26/2021
Citation: Medina, C., Samac, D.A., Yu, L. 2021. Pan-transcriptome identifying master genes and regulation network in response to drought and salt stresses in Alfalfa (Medicago sativa L.). Scientific Reports. 11:17203. https://doi.org/10.1038/s41598-021-96712-x.
Interpretive Summary: Alfalfa is an important forage crop grown worldwide. Drought and salt stresses are the most important factors affecting crop production in arid locations. This study described gene expression in three alfalfa germplasms with different levels of tolerance to drought and high salt. This work identified sets of genes in leaves, stems and roots that were influenced by salt and drought stress treatments. Most of the genes we identified had reduced activity in the presence of these stresses. We were able to identify key genes that appear to be involved in resistance to drought and salt stress. This work improves understanding of how drought and salt stress effect gene action in alfalfa. The genes we identified can be used to develop enhanced alfalfa varieties with improved tolerance to these stresses that impact alfalfa production throughout the Western USA.
Technical Abstract: In this work, three alfalfa germplasms: Wilson (drought tolerant), Saranac (nontolerance to drought and salt), PI467895 (salt tolerant) were used for unraveling the alfalfa response to drought and salt stresses through full-length transcriptome analysis. Twenty-one different RNA samples were extracted from three tissue sources (leaf, stem and root) of plants subjected to salt, drought and control nonstress treatments. These samples were sequenced using PacBio SMRT technology and the Illumina HiSeq platform to obtain comparative transcriptional profiles in response to drought and salt stresses. A total of 20 and 710 million raw reads were obtained from PacBio and Illumina sequencing, respectively. The long reads from PacBio were corrected using a hybrid approach with short reads from Illumina to improve the quality of transcriptomes, resulting in 91,378 unique transcripts with 1,124,275 unique isoforms among all treatments. Transcriptomic analysis identified the transcriptional and post-transcriptional differences among germplasms, tissue sources, and stress conditions. Post-transcriptional modifications including alternative splicing (AS) events, fusion genes, and nonsense-mediated mRNA decay (NMD) events were found. More than half of total AS events were intron retention. Additionally, we were able to predict 13,468 long non-coding RNAs (lncRNAs) among different treatments, which was the most complete catalog in M. sativa to date. The analyses of gene ontology and weighted gene co-expression network allowed us to identify key genes that play important roles in drought and salt stress tolerance in alfalfa.