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Abstract：
To determine the genes associated with the fiber strength trait in cotton, three different cotton cultivars were selected: Sea Island cotton (Xinhai 32, with hyper-long fibers labeled as HL), and upland cotton (17-24, with long fibers labeled as L, and 62-33, with short fibers labeled as S). These cultivars were chosen to assess fiber samples with varying qualities. RNA-seq technology was used to analyze the expression profiles of cotton fibers at the secondary cell wall (SCW) thickening stage (20, 25, and 30 days post-anthesis (DPA)). The results showed that a large number of differentially expressed genes (DEGs) were obtained from the three assessed cotton cultivars at different stages of SCW development. For instance, at 20 DPA, Sea Island cotton (HL) had 6,215 and 5,364 DEGs compared to upland cotton 17-24 (L) and 62-33 (S), respectively. Meanwhile, there were 1,236 DEGs between two upland cotton cultivars, 17-24 (L) and 62-33 (S). Gene Ontology (GO) term enrichment identified 42 functions, including 20 biological processes, 11 cellular components, and 11 molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis identified several pathways involved in SCW synthesis and thickening, such as glycolysis/gluconeogenesis, galactose metabolism, propanoate metabolism, biosynthesis of unsaturated fatty acids pathway, valine, leucine and isoleucine degradation, fatty acid elongation pathways, and plant hormone signal transduction. Through the identification of shared DEGs, 46 DEGs were found to exhibit considerable expressional differences at different fiber stages from the three cotton cultivars. These shared DEGs have functions including REDOX enzymes, binding proteins, hydrolases (such as GDSL thioesterase), transferases, metalloproteins (cytochromatin-like genes), kinases, carbohydrates, and transcription factors (MYB and WRKY). Therefore, RT-qPCR was performed to verify the expression levels of nine of the 46 identified DEGs, an approach which demonstrated the reliability of RNA-seq data. Our results provided valuable molecular resources for clarifying the cell biology of SCW biosynthesis during fiber development in cotton.
摘要：
为了确定与棉花纤维强度性状相关的基因，选择了三个不同的棉花品种:海岛棉(新海32号，超长纤维标记为HL)，和陆地棉（17-24，长纤维标记为L，和62-33，短纤维标记为S）。选择这些品种来评估具有不同质量的纤维样品。RNA-seq技术用于分析次生细胞壁（SCW）增厚阶段（花后20、25和30天（DPA））棉纤维的表达谱。结果表明，在SCW发育的不同阶段，从三个被评估的棉花品种中获得了大量的差异表达基因（DEGs）。例如,在20DPA，海岛棉（HL）与陆地棉17-24（L）和62-33（S）相比有6,215和5,364度，分别。同时,两个陆地棉品种之间有1236个DEG，17-24（L）和62-33（S）。基因本体论(GO)术语富集确定了42个功能，包括20个生物过程，11个细胞成分，和11个分子功能。京都基因和基因组百科全书（KEGG）富集分析确定了参与SCW合成和增稠的几种途径，如糖酵解/糖异生，半乳糖代谢，丙酸代谢，不饱和脂肪酸的生物合成途径，缬氨酸,亮氨酸和异亮氨酸降解，脂肪酸延伸途径，和植物激素信号转导。通过共享DEG的识别，发现46个DEGs在三个棉花品种的不同纤维阶段表现出相当大的表达差异。这些共享的DEG具有包括氧化还原酶在内的功能，结合蛋白，水解酶（如GDSL硫酯酶），转移酶，金属蛋白（细胞染色质样基因），激酶，碳水化合物,和转录因子（MYB和WRKY）。因此,进行RT-qPCR以验证46个鉴定的DEGs中的9个的表达水平，一种证明RNA-seq数据可靠性的方法。我们的结果为阐明棉花纤维发育过程中SCW生物合成的细胞生物学提供了宝贵的分子资源。
