Mirdar Mansuri Raheleh, Shobbar Zahra-Sadat, Babaeian Jelodar Nadali, Ghaffari Mohammad Reza, Nematzadeh Ghorban-Ali, Asari Saeedeh
Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), PO Box 31535-1897, Karaj, Iran.
Department of Plant breeding and Biotechnology, Faculty of Crop Science, Sari Agricultural Science and Natural Resources University, Sari, Mazandaran, 578, Iran.
Rice (N Y). 2019 Mar 4;12(1):13. doi: 10.1186/s12284-019-0273-2.
Salinity expansion in arable land is a threat to crop plants. Rice is the staple food crop across several countries worldwide; however, its salt sensitive nature severely affects its growth under excessive salinity. FL478 is a salt tolerant indica recombinant inbred line, which can be a good source of salt tolerance at the seedling stage in rice. To learn about the genetic basis of its tolerance to salinity, we compared transcriptome profiles of FL478 and its sensitive parent (IR29) using RNA-seq technique.
A total of 1714 and 2670 genes were found differentially expressed (DEGs) under salt stress compared to normal conditions in FL478 and IR29, respectively. Gene ontology analysis revealed the enrichment of transcripts involved in salinity response, regulation of gene expression, and transport in both genotypes. Comparative transcriptome analysis revealed that 1063 DEGs were co-expressed, while 338/252 and 572/908 DEGs were exclusively up/down-regulated in FL478 and IR29, respectively. Further, some biological processes (e.g. iron ion transport, response to abiotic stimulus, and oxidative stress) and molecular function terms (e.g. zinc ion binding and cation transmembrane transporter activity) were specifically enriched in FL478 up-regulated transcripts. Based on the metabolic pathways analysis, genes encoding transport and major intrinsic proteins transporter superfamily comprising aquaporin subfamilies and genes involved in MAPK signaling and signaling receptor kinases were specifically enriched in FL478. A total of 1135 and 1894 alternative splicing events were identified in transcripts of FL478 and IR29, respectively. Transcripts encoding two potassium transporters and two major facilitator family transporters were specifically up-regulated in FL478 under salt stress but not in the salt sensitive genotype. Remarkably, 11 DEGs were conversely regulated in the studied genotypes; for example, OsZIFL, OsNAAT, OsGDSL, and OsELIP genes were up-regulated in FL478, while they were down-regulated in IR29.
The achieved results suggest that FL478 employs more efficient mechanisms (especially in signal transduction of salt stress, influx and transport of k, ionic and osmotic homeostasis, as well as ROS inhibition) to respond to the salt stress compared to its susceptible parent.
耕地盐碱化对农作物构成威胁。水稻是世界上多个国家的主食作物；然而，其对盐敏感的特性在盐分过高时会严重影响其生长。FL478是一个耐盐籼稻重组自交系，在水稻苗期可作为耐盐性的良好来源。为了解其耐盐性的遗传基础，我们使用RNA测序技术比较了FL478及其敏感亲本（IR29）的转录组图谱。
与正常条件相比，在盐胁迫下，FL478和IR29中分别发现共有1714个和2670个基因差异表达（DEG）。基因本体分析揭示了两种基因型中参与盐胁迫响应、基因表达调控和转运的转录本的富集。比较转录组分析表明，1063个DEG共表达，而分别有338/个252和572/908个DEG在FL478和IR29中特异性上调/下调。此外，一些生物学过程（如铁离子转运、对非生物刺激的响应和氧化应激）和分子功能术语（如锌离子结合和阳离子跨膜转运活性）在FL478上调的转录本中特异性富集。基于代谢途径分析，编码转运蛋白和主要内在蛋白转运体超家族（包括水通道蛋白亚家族）的基因以及参与MAPK信号传导和信号受体激酶的基因在FL478中特异性富集。在FL478和IR29的转录本中分别鉴定出1135个和1894个可变剪接事件。编码两种钾转运体和两种主要促进剂家族转运体的转录本在盐胁迫下在FL478中特异性上调，但在盐敏感基因型中未上调。值得注意的是，11个DEG在研究的基因型中呈相反调节；例如，OsZIFL、OsNAAT、OsGDSL和OsELIP基因在FL478中上调，而在IR29中下调。
所获得的结果表明，与其敏感亲本相比，FL478采用了更有效的机制（特别是在盐胁迫信号转导、钾离子流入和转运、离子和渗透稳态以及ROS抑制方面）来应对盐胁迫。
