谷子KNOX基因家族鉴定及组织表达模式分析  

Identification and Tissue Expression Pattern Analysis of KNOX Gene Family in Setaria italica

作　　者：施卫萍 张欣 赵媛 刘敏 代渴丽 张艾英[3] 郭二虎 史关燕 郭杰 SHI Wei-Ping;ZHANG Xin;ZHAO Yuan;LIU Min;DAI Ke-li;ZHANG Ai-Ying;GUO Er-Hu;SHI Guan-Yan;GUO Jie(College of Agronomy,Key Laboratory of Sustainable Dryland Agriculture(Co-construction by Ministry and Province),Ministry of Agriculture and Rural Affairs,Shanxi Agricultural University,Jinzhong 030801,China;Industrial Crop Institute,Shanxi Agricultural University,Taiyuan,030031,China;Millet Research Institute,Shanxi Agricultural University,Changzhi 046011,China)

机构地区：[1]山西农业大学农学院/农业农村部有机旱作农业重点实验室(部省共建),晋中030801 [2]山西农业大学经济作物研究所,太原030031 [3]山西农业大学谷子研究所,长治046011

出　　处：《农业生物技术学报》2024年第8期1742-1752,共11页Journal of Agricultural Biotechnology

基　　金：国家自然科学基金(32201857);山西省重点研发计划(2022ZDYF107);山西省基础研究计划(20210302124019);山西省现代农业产业技术体系建设专项(2023CYJSTX04);山西省高等学校科技创新(2021L120);山西农业大学科技创新基金(2020BQ60)。

摘　　要：KNOX(knotted1-like homeobox,KNOX)是植物特有的一类具有同源异型结构域的转录因子,广泛参与植物的生长发育过程。为探究谷子(Setaria italica)KONXs基因的潜在功能,本研究采用生物信息学方法,在谷子全基因组水平对SiKNOX基因家族进行了鉴定和分析,并利用RT-qPCR检测其在不同组织中的表达量。结果显示,在谷子全基因组水平上一共鉴定到11个SiKNOXs基因,系统进化分析分为classⅠ和classⅡ两组,classⅠ包含5个SiKNOXs,classⅡ包含6个SiKNOXs。亚细胞定位预测发现所有SiKNOXs蛋白均定位在细胞核。染色体定位分析发现,11个SiKNOXs基因不均等地分布在谷子的7条染色体上。基因复制分析发现,有5个SiKNOXs基因组成了4个片段复制基因对。基因结构组成分析发现,所有的SiKNOXs由5~6个外显子组成;蛋白保守结构域分析结果显示,SiKNOXs的蛋白保守结构域由10个基序组成,其中motif 2、3、5、6分别构成了KNOX1、KNOX2、ELK、HD结构域。在SiKNOXs基因的启动子区域分布着许多与生物过程密切相关的顺式作用元件。SiKNOXs基因在谷子不同组织部位(包括根,茎,叶,穗,种子)均能检测到,且大部分SiKNOXs基因具有组织特异性表达特点。本研究为深入探讨KNOX基因家族调控谷子生长发育的功能提供了基础资料。Knotted1-like homeobox(KNOX)is a transcription factor unique to plants,characterized by its homologous domain,and is widely involved in plant growth and development.To explore the potential function of the foxtail millet(Setaria italica)KONXs,bioinformatic methods were used to identify and analyze the SiKNOX gene family at the whole-genome level of foxtail millet,and the expression patterns of SiKNOXs in different tissues were also detected using RT-qPCR.The results showed that a total of 11 SiKNOXs were identified in the S.italica genome.Phylogenetic analysis classified them into 2 groups,classⅠand classⅡ.ClassⅠcontained 5 SiKNOXs and classⅡcontained 6 SiKNOXs.Subcellular localization prediction revealed that all SiKNOX proteins were predicted to be nuclear.Chromosomal localization analysis showed that they were unevenly distributed among the 7 chromosomes of S.italica.Duplication analysis showed that there were 5 SiKNOXs forming 4 segmental duplication gene pairs.Gene structure analysis revealed that all 11 SiKNOXs consisted of 5~6 exons.Protein conserved domain analysis indicated 10 motifs in SiKNOXs.Motifs 2,3,5,and 6 corresponded to the KNOX1,KNOX2,ELK,and HD domains,respectively.The promoter region of the SiKNOXs harbored numerous cis-acting elements that were closely associated with various biological processes.Expression pattern analysis revealed that all SiKNOXs were detected in different tissues(including roots,stems,leaves,tassels,and seeds),and most of them showed tissue-specific expression.This study lays the foundation for further research on KNOX genes family in the growth and development of S.italica.

关 键 词：谷子 KNOX(knotted1-like homeobox) 基因家族 组织表达模式 

分 类 号：S515[农业科学—作物学]