State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
School of Agricultural Science, Zhengzhou University, Zhengzhou, 450001, Henan, China.
Genes (Basel). 2019 Feb 6;10(2):119. doi: 10.3390/genes10020119.
Upland cotton () is grown for its elite fiber. Understanding differential gene expression patterns during fiber development will help to identify genes associated with fiber quality. In this study, we used two recombinant inbred lines (RILs) differing in fiber quality derived from an intra- population to explore expression profiling differences and identify genes associated with high-quality fiber or specific fiber-development stages using RNA sequencing. Overall, 72/27, 1137/1584, 437/393, 1019/184, and 2555/1479 differentially expressed genes were up-/down-regulated in an elite fiber line (L1) relative to a poor-quality fiber line (L2) at 10, 15, 20, 25, and 30 days post-anthesis, respectively. Three-hundred sixty-three differentially expressed genes (DEGs) between two lines were colocalized in fiber strength (FS) quantitative trait loci (QTL). Short Time-series Expression Miner (STEM) analysis discriminated seven expression profiles; gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation were performed to identify difference in function between genes unique to L1 and L2. Co-expression network analysis detected five modules highly associated with specific fiber-development stages, especially for high-quality fiber tissues. The hub genes in each module were identified by weighted gene co-expression network analysis. Hub genes encoding actin 1, Rho GTPase-activating protein with PAK-box, TPX2 protein, bHLH transcription factor, and leucine-rich repeat receptor-like protein kinase were identified. Correlation networks revealed considerable interaction among the hub genes, transcription factors, and other genes.
陆地棉（）因其优质纤维而被种植。了解纤维发育过程中的差异基因表达模式将有助于鉴定与纤维品质相关的基因。本研究利用来自群体内的两个纤维品质不同的重组自交系（RIL），通过 RNA 测序探索表达谱差异，鉴定与优质纤维或特定纤维发育阶段相关的基因。总体而言，在开花后 10、15、20、25 和 30 天，优质纤维系（L1）相对于劣质纤维系（L2）分别有 72/27、1137/1584、437/393、1019/184 和 2555/1479 个差异表达基因上调/下调。两个系之间的 363 个差异表达基因（DEGs）在纤维强度（FS）数量性状位点（QTL）中发生共定位。短时间序列表达挖掘器（STEM）分析区分了七个表达谱；基因本体论（GO）和京都基因与基因组百科全书（KEGG）注释用于鉴定 L1 和 L2 特有基因之间功能的差异。共表达网络分析检测到五个与特定纤维发育阶段高度相关的模块，特别是与高质量纤维组织相关的模块。通过加权基因共表达网络分析鉴定了每个模块中的枢纽基因。鉴定出编码肌动蛋白 1、含 PAK 框的 Rho GTP 酶激活蛋白、TPX2 蛋白、bHLH 转录因子和富含亮氨酸重复受体样蛋白激酶的枢纽基因。关联网络揭示了枢纽基因、转录因子和其他基因之间存在相当多的相互作用。
