Genome-wide Analysis of the HD-ZIP_N Gene Family in Gossypium hirsutum
YE Si-Hong1,*, JI Mei-Jun2,*, CHEN Qi2, FENG Qun2, WANG Dong-Mei2, SUN Meng2, DENG Xiao-Nan1, WANG Rui1, HAN Wen-Bing1, WANG Bao-Hua2,**
1 Cotton Research Institute, Anhui Academy of Agricultural Science, Hefei 230001, China; 2 School of Life Sciences, Nantong University, Nantong 226019, China
Abstract：In previous research of our research group, a cotton (Gossypium) fiber strength candidate gene Gh_D09G1210 was identified by combining transcriptome sequencing and QTL mapping, which belongs to homeodomain-leucine zipper (HD-ZIP)__N gene family. The purpose of this study was to identify HD-ZIP_N gene family members in G. hirsutum and analyze their role in the formation of cotton fiber strength. Genome-wide analysis of HD-ZIP_N gene family in G. hirsutum was carried out, and the differential expression patterns of HD-ZIP_N genes in cotton fibers at different days post anthesis were analyzed by real-time quantitative PCR (qPCR). A total of 18 genes of the HD-ZIP_N gene family were identified in G. hirsutum genome conserved motif analysis and gene-promoter analysis showed that the gene family members had highly similar gene sequences and structural domains. The phylogenetic tree showed that all the gene family members could be divided into 3 subcategories. According to the gene location, HD-ZIP_N genes were located on 10 chromosomes in G. hirsutum genome. Most of the homologous genes had been purified and selected according to the Ka/Ks results. Collinearity analysis showed that the members of the HD-ZIP_N gene family distributed on homologous chromosomes had a strong connection. Cotton fibers of 17 and 21 d post-anthesis (dpa) were used to carry out qPCR verification experiments. The results showed that 3 genes Gh_D11G0809, Gh_D04G0859 and Gh_A11G0693 had a significant down-regulation trend in 'PD94042' with average fiber quality and 'IL9' with elite fiber quality (P<0.05), while Gh_A09G1204 had a significant up-regulation trend in 'IL9' (P<0.05), indicating that HD-ZIP_N gene family members had effects on regulation of fiber strength development. The findings of this study suggest that the HD-ZIP_N gene family members participate in regulating the development of G. hirsutum fiber strength, and provide genetic resources for improving cotton fiber strength through molecular breeding.
叶泗洪, 季美君, 陈奇, 冯群, 王冬梅, 孙萌, 邓小楠, 汪睿, 韩文兵, 汪保华. 陆地棉HD-ZIP_N基因家族的全基因组分析[J]. 农业生物技术学报, 2023, 31(12): 2454-2465.
YE Si-Hong, JI Mei-Jun, CHEN Qi, FENG Qun, WANG Dong-Mei, SUN Meng, DENG Xiao-Nan, WANG Rui, HAN Wen-Bing, WANG Bao-Hua. Genome-wide Analysis of the HD-ZIP_N Gene Family in Gossypium hirsutum. 农业生物技术学报, 2023, 31(12): 2454-2465.
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