Chen Guoquan, Liu Zhao, Li Shengdong, Liu Le, Lu Lili, Wang Zhi, Mendu Venugopal, Li Fuguang, Yang Zuoren
Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China.
National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China.
Physiol Plant. 2023 Jul-Aug;175(4):e13972. doi: 10.1111/ppl.13972.
Cotton (Gossypium hirsutum L.) is an important economic crop, and cotton fiber is one of the longest plant cells, which provides an ideal model for the study of cell elongation and secondary cell wall synthesis. Cotton fiber length is regulated by a variety of transcription factors (TF) and their target genes; however, the mechanism of fiber elongation mediated by transcriptional regulatory networks is still unclear to a large extent. Here, we used a comparative assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) assay and RNA-seq analysis to identify fiber elongation transcription factors and genes using the short-fiber mutant ligon linless-2 (Li ) and wild type (WT). A total of 499 differential target genes were identified and GO analysis shows that differential genes are mainly involved in plant secondary wall synthesis and microtubule-binding processes. Analysis of the genomic regions preferentially accessible (Peak) has identified a number of overrepresented TF-binding motifs, highlighting sets of TFs that are important for cotton fiber development. Using ATAC-seq and RNA-seq data, we have constructed a functional regulatory network of each TF regulatory target gene and also the network pattern of TF regulating differential target genes. Further, to obtain the genes related to fiber length, the differential target genes were combined with FLGWAS data to identify the genes highly related to fiber length. Our work provides new insights into cotton fiber elongation.
棉花（陆地棉）是一种重要的经济作物，棉纤维是最长的植物细胞之一，为研究细胞伸长和次生细胞壁合成提供了理想模型。棉纤维长度受多种转录因子（TF）及其靶基因调控；然而，转录调控网络介导纤维伸长的机制在很大程度上仍不清楚。在此，我们利用转座酶可及染色质高通量测序（ATAC-seq）分析和RNA-seq分析的比较试验，以短纤维突变体ligon linless-2（Li）和野生型（WT）为材料，鉴定纤维伸长转录因子和基因。共鉴定出499个差异靶基因，GO分析表明差异基因主要参与植物次生壁合成和微管结合过程。对优先可及的基因组区域（峰）分析已鉴定出许多过度富集的TF结合基序，突出了对棉纤维发育重要的TF集。利用ATAC-seq和RNA-seq数据，我们构建了每个TF调控靶基因的功能调控网络以及TF调控差异靶基因的网络模式。此外，为获得与纤维长度相关的基因，将差异靶基因与FLGWAS数据相结合，以鉴定与纤维长度高度相关的基因。我们的工作为棉纤维伸长提供了新见解。
