Submitted to: Plant and Cell Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/4/2013
Publication Date: 4/15/2013
Citation: Postnikova, O.A., Shao, J.Y., Nemchinov, L.G. 2013. Analysis of alfalfa root transcriptome in response to salinity stress. Plant And Cell Physiology. 54(7):1041-1055.
Interpretive Summary: Salinity is one of the major abiotic factors affecting alfalfa productivity. Identifying genes that control the trait of salt tolerance will provide critical insights for alfalfa breeding programs. At present, the genomics of alfalfa is in the early stages of development primarily due to a complex genetic structure of this species and the genomic resources available for crop improvement through molecular breeding are not comprehensive. In this study we address salinity-related issues in alfalfa by applying high-throughput sequencing technologies to elucidate the role of genes associated with salt tolerance and to identify genetic markers that are linked to adaptation to salt stress. It is expected that results of this work will be of interest to the researchers in academia and government organizations that are involved in alfalfa studies as well as to the breeders and alfalfa producers and representatives of industry.
Technical Abstract: Illumina RNA-sequencing was performed in two alfalfa genotypes, AZ-88NDC and AZ-GERM SALT-II in order to estimate a broad spectrum of genes affected by and/or involved in adaptation to salt stress. Both accessions were considered susceptible due to the stage at which samples were collected. A total of 184,596,972 and 183,022,614 short reads were generated from cDNA libraries originated from roots of AZ-88NDC and AZ-GERM SALT-II, respectively. More than 60,000 Tentative Consensus sequences (TCs) were obtained and among them 44922 (74.5%) had a significant similarity with genes in protein database. Mining of simple sequence repeats from all assembled TCs (60,290) revealed 6,496 SSR belonging to 4,479 annotated unigenes. Out of the 44922 assembled TCs, 90% had hits in M. truncatula genome. Bioinformatics analysis showed that 762 and 1028 genes significantly changed their expression in AZ-88NDC and AZ-GERM SALT-II, respectively. Seventy one transcription factor changed their expression under salt stress in AZ-88NDC and 77 in AZ-GERM SALT-II. All differentially expressed genes were annotated and assigned to known functional groups, biological processes and regulatory networks using Arabidopsis gene ontology. Random check of the genes by quantitative real-time PCR confirmed the validity of RNA-seq data. Expression of selected gene-candidates was screened in salt-tolerant line AZ-90NDC-ST to assess their roles in adaptation to salt stress. Alfalfa-specific data on salt-responsive genes obtained in this work will be useful in understanding the molecular mechanisms of salinity tolerance in alfalfa needed to maximize yield and economic return.