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

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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

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