Huang Xin, Peng Xianjun, Zhang Lexin, Chen Shuangyan, Cheng Liqin, Liu Gongshe
Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, People's Republic of China.
BMC Genomics. 2014 Dec 17;15(1):1126. doi: 10.1186/1471-2164-15-1126.
Sheepgrass (Leymus chinensis) is an important perennial forage grass across the Eurasian Steppe and is adaptable to various environmental conditions, but little is known about its molecular mechanism responding to grazing and BSA deposition. Because it has a large genome, RNA sequencing is expensive and impractical except for the next-generation sequencing (NGS) technology.
In this study, NGS technology was employed to characterize de novo the transcriptome of sheepgrass after defoliation and grazing treatments and to identify differentially expressed genes (DEGs) responding to grazing and BSA deposition. We assembled more than 47 M high-quality reads into 120,426 contigs from seven sequenced libraries. Based on the assembled transcriptome, we detected 2,002 DEGs responding to BSA deposition during grazing. Enrichment analysis of Gene ontology (GO), EuKaryotic Orthologous Groups (KOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways revealed that the effects of grazing and BSA deposition involved more apoptosis and cell oxidative changes compared to defoliation. Analysis of DNA fragments, cell oxidative factors and the lengths of leaf scars after grazing provided physiological and morphological evidence that BSA deposition during grazing alters the oxidative and apoptotic status of cells.
This research greatly enriches sheepgrass transcriptome resources and grazing-stress-related genes, helping us to better understand the molecular mechanism of grazing in sheepgrass. The grazing-stress-related genes and pathways will be a valuable resource for further gene-phenotype studies.
羊草是欧亚草原一种重要的多年生牧草，能适应各种环境条件，但关于其对放牧和牛血清白蛋白（BSA）沉积响应的分子机制知之甚少。由于其基因组庞大，除了新一代测序（NGS）技术外，RNA测序成本高昂且不切实际。
在本研究中，采用NGS技术对羊草进行去叶和放牧处理后的转录组进行从头测序，并鉴定对放牧和BSA沉积有响应的差异表达基因（DEG）。我们从7个测序文库中组装了超过4700万个高质量读段，形成了120426个重叠群。基于组装的转录组，我们检测到2002个在放牧期间对BSA沉积有响应的DEG。基因本体（GO）、真核直系同源组（KOG）和京都基因与基因组百科全书（KEGG）通路的富集分析表明，与去叶相比，放牧和BSA沉积的影响涉及更多的细胞凋亡和氧化变化。对放牧后DNA片段、细胞氧化因子和叶痕长度的分析提供了生理和形态学证据，表明放牧期间BSA沉积改变了细胞的氧化和凋亡状态。
本研究极大地丰富了羊草转录组资源和与放牧胁迫相关的基因，有助于我们更好地理解羊草放牧的分子机制。与放牧胁迫相关的基因和通路将为进一步的基因-表型研究提供宝贵资源。
