欢迎访问《棉花学报》! 今天是

棉花学报 ›› 2020, Vol. 32 ›› Issue (5): 404-417.doi: 10.11963/1002-7807.zamxf.20200831

• 研究与进展 • 上一篇    下一篇

陆地棉MADS-box家族基因鉴定及组织特异性表达分析

张爱1,3,王彩香2,宿俊吉2,张先亮3,史春辉2,刘娟娟2,彭云玲1*,马雄风1,3,4*   

  1. 1.甘肃农业大学农学院,兰州 730070;2.甘肃省干旱生境作物学重点实验室/甘肃农业大学生命科学技术学院,兰州 730070;3.中国农业科学院棉花研究所,河南 安阳 455000;4.郑州大学农学院,郑州 450001
  • 收稿日期:2019-12-11 出版日期:2020-09-15 发布日期:2020-09-30
  • 通讯作者: 马雄风,maxiongfeng@caas.cn;彭云玲,pengyunlingpyl@163.com
  • 作者简介:张爱(1996―),女,在读硕士研究生,za_abzh@163.com
  • 基金资助:
    国家自然科学基金(31660409,31971986),甘肃农业大学科技创新基金(GAU-KYQD-2018-01,GAU-KYQD-
    2018-32),农业农村部“一带一路”农业资源与技术合作(125161016000180005),中国农业科学院科技创新工程农业科技走出去协同创新与集成示范研究任务“中亚优质棉花品种筛选及配套栽培技术集成研发与应用”(CAAS-
    XTCX2018020-4),中国农业科学院基本科研业务费专项院级统筹工作任务“CCIA高品质棉花产业链关键技术研究与示范”(Y2020LM01),中国农业科学院科技创新工程“乡村振兴创新团队”

Identification of MADS-box Family and Analysis of Tissue Specific Expression in Gossypium hirsutum L.

Zhang Ai1, 3, Wang Caixiang2, Su Junji2, Zhang Xianliang3, Shi Chunhui2, Liu Juanjuan2, Peng Yunling1*, Ma Xiongfeng1, 3, 4*   

  1. 1.College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; 2.Gansu Provincial Key Laboratory of Aridland Crop Science/College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; 3.Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China; 4.School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
  • Received:2019-12-11 Online:2020-09-15 Published:2020-09-30

摘要: 【目的】MADS-box蛋白是1种重要的转录因子,参与调控棉花生长发育进程。鉴定分析陆地棉MADS-box家族基因,可为研究其生物学功能奠定基础。【方法】基于2019年最新组装的陆地棉TM-1参考基因组,通过HMMER 3.0软件鉴定陆地棉Type Ⅰ型及MIKC型MADS-box基因。利用MapInspect、MEGA 7.0、MEME和TBtools软件以及omicshare网站进行染色体定位、多序列比对聚类分析、Motif预测、基因结构鉴定以及组织特异性表达分析。【结果】从全基因组水平上鉴定出181个陆地棉MADS-box基因(66个Type Ⅰ型和115个MIKC型),染色体定位发现该181个基因在陆地棉26条染色体上均有分布,其中A组染色体上分布有78个基因、D组上分布有103个基因。系统进化分析显示Type Ⅰ型MADS-box蛋白有3个亚家族,MIKC型蛋白包括MIKC*型和含有10个亚家族的MIKCC型;motif预测结果显示所有MADS-box蛋白均含有MADS结构域,基因结构分析结果显示,外显子、内含子结构和长度在各亚家族内具有同一性;组织特异性表达分析发现MADS-box家族基因中有33个在纤维组织中优势表达,103个在花器官中优势表达,41个基因在根茎中优势表达。【结论】本研究通过生物信息学方法,鉴定并获得了与陆地棉开花调控和纤维发育相关的MADS-box基因,对于揭示棉花纤维品质等重要性状的遗传调控机制及分子育种具有一定的理论意义和应用价值。

关键词: 陆地棉; MADS-box基因; 家族鉴定; 生物信息学; 表达分析

Abstract: [Objective] MADS-box is an important transcription factor regulating the growth and development processes in cotton. Identification and screening upland cotton MADS-box genes is indispensible for accelerating their studying of biological functions. [Method] This article based on the upland cotton TM-1 reference genome assembled in 2019, all members of upland cotton MADS-box family were identified through HMMER 3.0 software. MapInspect, MEGA 7.0, MEME, TBtools and omicshare website were utilized to analyze chromosome location, phylogenetic relationship, motif prediction, gene structure, and tissue-specific expression of MADS-box genes. [Result] One hundred and eighty one upland cotton MADS-box genes (66 Type Ⅰ and 115 MIKC genes) were identified in total, which located on 26 chromosomes. The Type I proteins were scattered on 3 subfamilies and the MIKC proteins were divided into MIKC* and MIKCC which contain 10 subfamilies. The prediction results of motif showed that all proteins of MADS-box family contain MADS domain and gene structure analysis revealed that the structure and length of exons and introns are similar in one subfamily. Tissue-specific expression analysis found that 33 MADS-box genes were mainly expressed in fibrous tissue, 103 genes were primarily expressed in floral organs, and 41 genes were strongly expressed in roots and stems. [Conclusion] The MADS-box genes related to flowering regulation and fiber development of upland cotton were obtained in the study, which has theoretical significance for revealing the genetic regulation mechanism of cotton fiber quality and has application value for molecular breeding.

Key words: upland cotton; MADS-box gene; family identification; bioinformatics; expression analysis