藜麦MADS-box基因家族的全基因组鉴定和表达分析

doi:10.13560/j.cnki.biotech.bull.1985.2024-0656

摘要/Abstract

摘要：

【目的】开展藜麦CqMADS-box基因家族鉴定和表达分析，为藜麦产量品质的提高提供优异基因资源。【方法】基于拟南芥MADS-box蛋白序列，利用BLASTP和隐马尔可夫模型文件（Hidden Markov Model, HMM）鉴定CqMADS-box基因家族成员，采用最大似然法（maximum likelihood, ML）构建系统发育树，分析MADS-box基因在染色体的位置，利用MXSCan分析CqMADS-box基因家族成员在藜麦亚基因组A/B间，及其与甜菜二倍体近缘种C. pallidicaule（A）、C. suecicum（B），六倍体近缘种中国台湾红藜（Chenopodium formosanum）中MADS-box成员的共线性，利用WoLF PSORT、PlantCARE等在线网站分析CqMADS-box转录因子的理化性质、基因结构、启动子区顺式作用元件。基于前期发表的转录组数据，分析CqMADS-box在不同组织、6个花序发育时期、种子萌发的表达模式；利用转录组数据分析在长日照和短日照下，花期和花器官相关CqMADS-box的表达情况。【结果】鉴定得到117个藜麦MADS-box基因家族成员，分布在17条染色体上。I型CqMADS-box包含Mα、Mγ两个进化分支，II型包含CqPI（CqGLO）、CqAGL17等14个进化分支。不同分支CqMADS-box基因结构、蛋白Motif组成、转录因子结合位点类型和数量存在不同程度的差异。进化分析表明，串联复制是藜麦MADS-box家族扩张的主要途径，大部分复制的时间在四倍体化之前。表达模式结果表明，CqMADS-box基因在花序中表达量相对较高，而在花序发育前期（YP1或YP2），CqSEP3、CqAP1、CqGGM13类基因呈相对高表达；种子经过ABA处理后，CqSEP3类基因表达量显著上升；不同光周期下的表达模式表明，CqAP1、CqSOC1类基因在长日照和短日照下表达量均较高。【结论】CqMADS-box基因家族成员具有组织特异性表达模式，且CqSEP3类基因在藜麦花序发育和响应ABA激素处理的过程中发挥重要作用。

关键词: CqMADS-box, 藜麦, 全基因组鉴定, 进化分析, 花序发育, 光周期

Abstract:

【Objective】Identification and expression analysis of CqMADS-box gene family in quinoa（Chenopodium quinoa）were carried out to provide excellent gene resources for improving the yield and quality of quinoa.【Method】Based on the MADS-box protein sequences of Arabidopsis thaliana, BLASTP and Hidden Markov model（HMM）were employed to identify the members of the CqMADS-box gene family, and maximum likelihood method（ML）was to construct the phylogenetic tree, and analyze the positions of MADS-box genes on the chromosomes. MXSCan was used to analyze the collinear relationships of MADS-box family members between quinoa sub-genome A/B and their relatives sugar beet（Beta vulgaris）and diploid C. pallidicaule（A）, C. suecicum（B）and hexaploid species Chenopodium formosanum. Online tools WoLF PSORT and PlantCARE were utilized to analyze the physicochemical properties, gene structure, and cis-acting elements of CqMADS-box transcription factors. Based on our previous transcriptome data, the expression patterns of CqMADS-box were analyzed in different tissues, six inflorescence development stages and during seed germination. The expression patterns of CqMADS-box related to flowering and flower organs were analyzed under long-day and short-day conditions.【Result】A total of 117 members of the MADS-box gene family were identified on 17 chromosomes. CqMADS-box genes of type I contained two subfamilies, Mα and Mγ, and type II CqMADS-box genes contained 14 subfamilies of CqPI（CqGLO）and CqAGL17. There were differences in the CqMADS-box gene structure, protein Motif composition, and transcription factor binding site types and numbers in different branches. Evolutionary analysis showed that tandem replication was the major driving force for MADS-box family expansion in quinoa, and most of the duplication events occurred before the tetraploidization. Gene expression pattern analysis showed that the overall expressions of CqMADS-box genes were relatively higher in the inflorescence, while the expressions of CqSEP3, CqAP1 and CqGGM13 genes were relatively higher in the early stage of inflorescence development（YP1 or YP2）. After ABA treatment to seeds, the expressions of CqSEP3-like genes increased significantly. The expression patterns under different photoperiods showed that the expressions of CqAP1 and CqSOC1 genes were high under both long-day and short-day conditions.【Conclusion】Most of the CqMADS-box members have tissue-specific expression patterns, and CqSEP3 genes play important roles in the process of inflorescence development and response to ABA hormone treatment in quinoa.

Key words: CqMADS-box, quinoa, genome-wide identification, evolutionary analysis, inflorescence development, photoperiod

何财林, 卢晶, 郭会会, 李小安, 吴琪. 藜麦MADS-box基因家族的全基因组鉴定和表达分析[J]. 生物技术通报, 2025, 41(1): 157-172.

HE Cai-lin, LU Jing, GUO Hui-hui, LI Xiao-an, WU Qi. Genome-wide Identification and Expression Analysis of the MADS-box Gene Family in Quinoa[J]. Biotechnology Bulletin, 2025, 41(1): 157-172.

图/表 9

图1 藜麦、水稻和拟南芥MADS-box蛋白系统发育树 A：藜麦、拟南芥和水稻的I型MADS-box蛋白系统发育树；B：藜麦、拟南芥和水稻的II型MADS-box蛋白系统发育树；红色五角星代表藜麦蛋白，紫色方框代表拟南芥蛋白，绿色圆代表水稻蛋白

Fig. 1 MADS-box protein phylogenetic tree of quinoa, rice and Arabidopsis A: Phylogenetic tree of type I MADS-box proteins in quinoa（Chenopodium quinoa）, Arabidopsis and rice（Oryza sativa）. B: Phylogenetic tree of type II MADS-box proteins in quinoa, Arabidopsis and rice. The red five-pointed star indicates quinoa protein, the purple box indicates Arabidopsis protein, and the green circle indicates rice protein

图2 藜麦MADS-box家族成员保守基序（A）、结构域（B）及基因结构（C）

Fig. 2 Conserved motifs（A）, domains（B）and gene structures（C）of the MADS-box family members of quinoa

图3 藜麦MADS-box家族基因染色体定位分布图

Fig. 3 Chromosomal mapping of MADS-box family genes in quinoa

图4 藜麦亚基因组A和亚基因组B的MADS-box之间共线性绿色表示藜麦A亚基因组，蓝色表示藜麦B亚基因组

Fig. 4 Collinearity between the MADS-box of quinoa sub-genome A and sub-genome B Green indicate quinoa A sub-genome, and blue represents quinoa B sub-genome

图5 藜麦与C. pallidicaule（A）和C. suecicum（B）的MADS-box共线性分析绿色表示藜麦染色体，紫色表示C. pallidicaule染色体，蓝色表示C. suecicum染色体

Fig. 5 Collinearity analysis of quinoa MADS-box members with that in C. pallidicaule（A）and C. suecicum（B） Green indicates quinoa chromosome, purple indicates C. pallidicaule chromosome and blue indicates C. suecicum chromosome

表1 藜麦MADS-box家族中假基因信息表

Table 1 Information of pseudogenes in the MADS-box family of quinoa

基因名称 Gene name	基因 ID Gene ID	染色体 Chromosome	起始位置 Start-end position（+/-strand）	氨基酸数 Number of amino acids/aa	类型 Type
CqSVP-1A-2	CQ048095	Cq1A	1 174 6420-11 746 605（-）	61	假基因-串联复制
CqAGL17-1A-1	CQ047997	Cq1A	10 659 725-10 659 946（-）	73	假基因-串联复制
CqAGL12-1A	CQ048800	Cq1A	22 590 418-22 590 639（-）	73	假基因-节段复制
CqAGL17-1A-2	CQ048000	Cq1A	10 725 903-10 726 115（-）	70	假基因-串联复制
CqAG-1B-2	CQ023885	Cq1B	49 507 013-49 507 303（-）	96	假基因-串联复制
CqMα-1B-1	CQ023867	Cq1B	48 895 860-48 896 081（-）	73	假基因-节段复制
CqAGL17-1B-1	CQ024731	Cq1B	64 342 030-64 342 293（+）	87	假基因-串联复制
CqAGL15-3B-2	CQ019107	Cq3B	66 834 322-66 834 510（-）	62	假基因-串联复制
CqAGL15-3B-1	CQ019105	Cq3B	66 809 225-66 812 527（-）	99	假基因-节段复制
CqSEP3-5B	CQ005895	Cq5B	67 053 435-67 053 671（+）	78	假基因-串联复制
CqAP1-5B-2	CQ005897	Cq5B	67 131 352-67 131 611（+）	64	假基因-串联复制
CqMα-6A-1	CQ025753	Cq6A	4 153 499-4 153 970（+）	74	假基因-串联复制
CqMα-6B-2	CQ000301	Cq6B	3 428 220-3 429 042（+）	75	假基因-节段复制
CqSVP-7B-1	CQ007326	Cq7B	3 310 550-3 310 735（-）	61	假基因-串联复制
CqMIKC*-7B	CQ007095	Cq7B	1 279 202-1 286 618（-）	97	假基因-串联复制
CqSVP-9A-1	CQ052433	Cq9A	51 460 017-51 462 248（+）	73	假基因-串联复制
CqAGL17-9A-1	CQ052648	Cq9A	53 340 285-53 346 018（+）	77	假基因-串联复制

图6 藜麦MADS-box家族成员启动子区域顺式作用元件预测 A：藜麦MADS-box家族成员启动子区域顺式作用元件分布图；B：藜麦MADS-box家族成员启动子区域结合的顺式作用元件数量统计

Fig. 6 Prediction of cis-acting elements in the promoter region of quinoa MADS-box family members A: The distribution map of cis-acting elements in the promoter region of quinoa MADS-box family members. B: Statistics on the number of cis-acting elements in the promoter region of quinoa MADS-box family members

图7 MADS-box在不同组织、六期花序和种子萌发中的表达分析 A：MADS-box在不同组织中的表达；表达值由FPKM值表示（下同）；B：MADS-box在藜麦花序发育中的表达；YP1-YP4表示早期发育阶段的无分枝幼穗；P1和P2表示发育后期2个阶段的分枝穗；C：MADS-box在种子萌发过程中的表达变化；BL-A-5h/-15h和BL-5h/-15h分别表示ABA处理和未处理5 h和15 h的BL材料；每个表达值由3个重复生成；同一基因在6个阶段的表达水平逐行归一化为0-1

Fig. 7 Expression analysis of MADS-box in different tissues, six-stage inflorescences, and seed germination A: Expressions of MADS-box in different tissues. The expression value is represented by the FPKM values generated from the RNA-seq data（the same below）. B: Expression of MADS-box in quinoa inflorescence development. YP1-YP4 indicates unbranched young spikelets in the early developmental stage. P1 and P2 indicate branched panicles at 2 stages of late development. C: Expression changes of MADS-box during seed germination. BL-A-5h/-15h and BL-5h/-15h indicate the ABA-treated and untreated BL materials at 5 h and 15 h after germination, respectively. Each expression value is generated from three replicates. The expressions of the same gene in the 6 stages were normalized to 0 to 1 by row

图8 短日照和长日照条件下CqMADS-box的昼夜表达模式分别于17:00、20:00、23:00、02:00、05:00、08:00、11:00和14:00采集短日照和长日照条件下生长两周的藜麦幼苗叶片样本。采用RNA-seq分析CqMADS-box的表达模式。蓝色实线为LD下的基因表达曲线，橙色实线为SD下的基因表达曲线

Fig. 8 Diurnal expression patterns of CqMADS-box under short- and long-day conditions Leaf samples of quinoa seedlings grown for two weeks under short-day and long-day conditions were collected at 17:00, 20:00, 23:00, 02:00, 05:00, 08:00, 11:00 and 14:00, respectively. RNA-seq is used to analyze the expression pattern of CqMADS-box. The solid blue line is the gene expression curve under LD, and the solid orange line is the gene expression curve under SD

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