陆地棉HD-ZIP_N基因家族的全基因组分析  

Genome-wide Analysis of the HD-ZIP_N Gene Family in Gossypium hirsutum

作　　者：叶泗洪[1] 季美君 陈奇 冯群 王冬梅 孙萌 邓小楠 汪睿 韩文兵[1] 汪保华[2] YE Si-Hong;JI Mei-Jun;CHEN Qi;FENG Qun;WANG Dong-Mei;SUN Meng;DENG Xiao-Nan;WANG Rui;HANWen-Bing;WANG Bao-Hua(Cotton Research Institute,Anhui Academy of Agricultural Science,Hefei 230001,China;School of Life Sciences,Nantong University,Nantong 226019,China)

机构地区：[1]安徽省农业科学院棉花研究所,合肥230001 [2]南通大学生命科学学院,南通226019

出　　处：《农业生物技术学报》2023年第12期2454-2465,共12页Journal of Agricultural Biotechnology

基　　金：国家重点研发计划(2021YFE0101200);安徽省农业科学院棉花种质创制与利用创新团队(2023YL005);安徽省财政农业科技成果转化(2022ZH011);南通大学大学生创新训练计划(202210304024Z)。

摘　　要：本课题组在前期研究中结合转录组测序和QTL定位鉴定到1个棉花(Gossypium)纤维强度候选基因Gh_D09G1210,该基因属于同源异型域-亮氨酸拉链(homeodomain-leucine zipper,HD-ZIP)_N基因家族。为了鉴定陆地棉(G.hirsutum)HD-ZIP_N基因家族成员并分析其在棉花纤维强度形成中的作用,本研究利用生物信息学方法对陆地棉HD-ZIP_N基因家族进行了全基因组分析;利用qPCR方法分析了开花后不同时期棉纤维中HD-ZIP_N基因的表达模式。在陆地棉基因组中鉴定到了18个HD-ZIP_N基因家族成员。保守基序(motif)分析及启动子序列分析表明,该基因家族成员具有高度相似的特征序列和结构域。基因进化树结果表明,该基因家族的成员可被分为3个亚类。根据染色体位置信息,HD-ZIP_N基因家族的成员分别定位在10条不同染色体上。非同义替换率/同义替换率(nonsynonymous substitution rate/synonymous substitution rate,Ka/Ks)值表明大部分同源基因都经过了纯化选择。基因共线性分析表明,分布于同源染色体上的HD-ZIP_N基因家族成员间具有较强的连锁关系。取开花后17和21 d的棉花纤维进行qPCR验证实验,结果表明,Gh_D11G0809、Gh_D04G0859和Gh_A11G0693这3个基因在纤维品质普通的‘PD94042'和纤维品质优异的‘IL9'中具有显著下调的趋势(P<0.05),而在‘IL9'中Gh_A09G1204有着显著上调的趋势(P<0.05),表明HD-ZIP_N基因家族成员在纤维强度发育过程中具有调节作用。本研究发现,HD-ZIP_N基因家族成员在陆地棉纤维强度发育过程中有一定的调节作用,可为分子育种改良棉花纤维强度提供基因资源。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.Genomewide 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 postanthesis(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 upregulation 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.

关 键 词：陆地棉 纤维强度 同源异型域-亮氨酸拉链_N(HD-ZIP_N) 全基因组分析 

分 类 号：S562[农业科学—作物学]