Bogazici University Department of Molecular Biology and Genetics, Istanbul, Turkey.
PLoS One. 2014 Mar 20;9(3):e92598. doi: 10.1371/journal.pone.0092598. eCollection 2014.
Salinity is one of the important abiotic stress factors that limit crop production. Common bean, Phaseolus vulgaris L., a major protein source in developing countries, is highly affected by soil salinity and the information on genes that play a role in salt tolerance is scarce. We aimed to identify differentially expressed genes (DEGs) and related pathways by comprehensive analysis of transcriptomes of both root and leaf tissues of the tolerant genotype grown under saline and control conditions in hydroponic system. We have generated a total of 158 million high-quality reads which were assembled into 83,774 all-unigenes with a mean length of 813 bp and N50 of 1,449 bp. Among the all-unigenes, 58,171 were assigned with Nr annotations after homology analyses. It was revealed that 6,422 and 4,555 all-unigenes were differentially expressed upon salt stress in leaf and root tissues respectively. Validation of the RNA-seq quantifications (RPKM values) was performed by qRT-PCR (Quantitative Reverse Transcription PCR) analyses. Enrichment analyses of DEGs based on GO and KEGG databases have shown that both leaf and root tissues regulate energy metabolism, transmembrane transport activity, and secondary metabolites to cope with salinity. A total of 2,678 putative common bean transcription factors were identified and classified under 59 transcription factor families; among them 441 were salt responsive. The data generated in this study will help in understanding the fundamentals of salt tolerance in common bean and will provide resources for functional genomic studies.
盐度是限制作物生产的重要非生物胁迫因素之一。普通菜豆（Phaseolus vulgaris L.）是发展中国家主要的蛋白质来源，它对土壤盐度高度敏感，而关于在耐盐性中发挥作用的基因的信息却很少。我们旨在通过在水培系统中对耐盐基因型的根和叶组织在盐胁迫和对照条件下进行转录组的综合分析，鉴定差异表达基因（DEGs）和相关途径。我们总共生成了 1.58 亿条高质量的reads，这些 reads 被组装成 83774 个全长基因，平均长度为 813bp，N50 为 1449bp。在全长基因中，经过同源性分析后，有 58171 个被赋予了 Nr 注释。结果表明，叶片和根组织在盐胁迫下分别有 6422 个和 4555 个全长基因差异表达。通过 qRT-PCR（定量逆转录 PCR）分析对 RNA-seq 定量（RPKM 值）进行了验证。基于 GO 和 KEGG 数据库的 DEGs 富集分析表明，叶片和根组织均通过调节能量代谢、跨膜转运活性和次生代谢物来应对盐胁迫。总共鉴定出 2678 个普通菜豆假定转录因子，并分为 59 个转录因子家族；其中 441 个对盐响应。本研究产生的数据将有助于理解普通菜豆耐盐性的基础，并为功能基因组研究提供资源。
