Zhu Yongqun, Wang Xia, Huang Linkai, Lin Chaowen, Zhang Xinquan, Xu Wenzhi, Peng Jianhua, Li Zhou, Yan Haidong, Luo Fuxiang, Wang Xie, Yao Li, Peng Dandan
Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural UniversityChengdu, China.
Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural SciencesChengdu, China.
Front Plant Sci. 2017 May 4;8:687. doi: 10.3389/fpls.2017.00687. eCollection 2017.
Sudan grass () is an annual warm-season gramineous forage grass that is widely used as pasture, hay, and silage. However, drought stress severely impacts its yield, and there is limited information about the mechanisms of drought tolerance in Sudan grass. In this study, we used next-generation sequencing to identify differentially expressed genes (DEGs) in the Sudan grass variety Wulate No.1, and we developed simple sequence repeat (SSR) markers associated with drought stress. From 852,543,826 raw reads, nearly 816,854,366 clean reads were identified and used for analysis. A total of 80,686 unigenes were obtained via assembly of the clean reads including 45,065 unigenes (55.9%) that were identified as coding sequences (CDSs). According to Gene Ontology analysis, 31,444 unigenes were annotated, 11,778 unigenes were identified to 25 categories in the clusters of orthologous groups of proteins (KOG) classification, and 11,223 unigenes were assigned to 280 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Additionally, there were 2,329 DEGs under a short-term of 25% polyethylene glycol (PEG) treatment, while 5,101 DEGs were identified under the long-term of 25% PEG treatment. DEGs were enriched in pathways of carbon fixation in photosynthetic organisms and plant hormone signal transduction which played a leading role in short-term of drought stress. However, DEGs were mainly enriched in pathway of plant hormone signal transduction that played an important role under long-term of drought stress. To increase accuracy, we excluded all the DEGs of all controls, specifically, five DEGs that were associated with high PEG concentrations were found through RNA-Seq. All five genes were up-regulated under drought stress, but the functions of the genes remain unclear. In addition, we identified 17,548 SSRs obtained from 80,686 unigenes. The newly identified drought tolerance DEGs will contribute to transgenic breeding efforts, while SSRs developed from high-throughput transcriptome data will facilitate marker-assisted selection for all traits in Sudan grass.
苏丹草（）是一种一年生暖季型禾本科牧草，广泛用作牧场、干草和青贮饲料。然而，干旱胁迫严重影响其产量，关于苏丹草耐旱机制的信息有限。在本研究中，我们使用下一代测序技术来鉴定苏丹草品种乌拉特1号中的差异表达基因（DEG），并开发与干旱胁迫相关的简单序列重复（SSR）标记。从852,543,826条原始读段中，鉴定出近816,854,366条clean读段并用于分析。通过对clean读段进行组装，共获得80,686个单基因，其中45,065个单基因（55.9%）被鉴定为编码序列（CDS）。根据基因本体分析，31,444个单基因得到注释，11,778个单基因在蛋白质直系同源簇（KOG）分类中被鉴定到25个类别，11,223个单基因被分配到280条京都基因与基因组百科全书（KEGG）通路。此外，在25%聚乙二醇（PEG）短期处理下有2,329个DEG，而在25% PEG长期处理下鉴定出5,101个DEG。DEG在光合生物的碳固定和植物激素信号转导途径中富集，这些途径在短期干旱胁迫中起主导作用。然而，DEG主要富集在植物激素信号转导途径中，该途径在长期干旱胁迫下发挥重要作用。为了提高准确性，我们排除了所有对照的所有DEG，具体而言，通过RNA-Seq发现了5个与高PEG浓度相关的DEG。所有5个基因在干旱胁迫下均上调，但其功能仍不清楚。此外，我们从80,686个单基因中鉴定出17,548个SSR。新鉴定的耐旱DEG将有助于转基因育种工作，而从高通量转录组数据开发的SSR将促进苏丹草所有性状的标记辅助选择。
