School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, China.
Nanosphere Inc., 4088 Commercial Drive, Northbrook, IL 60062, USA.
Gene. 2014 Feb 10;535(2):273-85. doi: 10.1016/j.gene.2013.11.017. Epub 2013 Nov 23.
Ligon lintless-1 (Li1) is a monogenic dominant mutant of Gossypium hirsutum (upland cotton) with a phenotype of impaired vegetative growth and short lint fibers. Despite years of research involving genetic mapping and gene expression profile analysis of Li1 mutant ovule tissues, the gene remains uncloned and the underlying pathway of cotton fiber elongation is still unclear. In this study, we report the whole genome-level deep-sequencing analysis of leaf tissues of the Li1 mutant. Differentially expressed genes in leaf tissues of mutant versus wild-type (WT) plants are identified, and the underlying pathways and potential genes that control leaf and fiber development are inferred. The results show that transcription factors AS2, YABBY5, and KANDI-like are significantly differentially expressed in mutant tissues compared with WT ones. Interestingly, several fiber development-related genes are found in the downregulated gene list of the mutant leaf transcriptome. These genes include heat shock protein family, cytoskeleton arrangement, cell wall synthesis, energy, H2O2 metabolism-related genes, and WRKY transcription factors. This finding suggests that the genes are involved in leaf morphology determination and fiber elongation. The expression data are also compared with the previously published microarray data of Li1 ovule tissues. Comparative analysis of the ovule transcriptomes of Li1 and WT reveals that a number of pathways important for fiber elongation are enriched in the downregulated gene list at different fiber development stages (0, 6, 9, 12, 15, 18dpa). Differentially expressed genes identified in both leaf and fiber samples are aligned with cotton whole genome sequences and combined with the genetic fine mapping results to identify a list of candidate genes for Li1.
无纤维棉花突变体 Li1 的基因组测序分析
Li1 是陆地棉（Gossypium hirsutum）的单基因显性突变体，表现为营养生长受阻和短纤维。尽管多年来对 Li1 突变体胚珠组织进行了遗传图谱和基因表达谱分析的研究，但该基因仍未被克隆，棉花纤维伸长的潜在途径仍不清楚。在这项研究中，我们报告了 Li1 突变体叶片组织的全基因组深度测序分析。鉴定了突变体与野生型（WT）植株叶片组织中差异表达的基因，并推断了控制叶片和纤维发育的潜在途径和潜在基因。结果表明，与 WT 相比，突变体组织中转录因子 AS2、YABBY5 和 KANDI-like 的表达显著差异。有趣的是，在突变体叶片转录组下调基因列表中发现了几个与纤维发育相关的基因。这些基因包括热休克蛋白家族、细胞骨架排列、细胞壁合成、能量、H2O2 代谢相关基因和 WRKY 转录因子。这一发现表明这些基因参与了叶片形态决定和纤维伸长。表达数据还与先前发表的 Li1 胚珠组织的微阵列数据进行了比较。对 Li1 和 WT 胚珠转录组的比较分析表明，在不同纤维发育阶段（0、6、9、12、15、18dpa），许多与纤维伸长相关的途径在下调基因列表中富集。在叶片和纤维样本中鉴定的差异表达基因与棉花全基因组序列对齐，并结合遗传精细图谱结果，确定了 Li1 的候选基因列表。
