Genome-wide Identification and Expression Analysis of the MADS-box Gene Family in Quinoa

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

Abstract

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

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.

Figures/Tables 9

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

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

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

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

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

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

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

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

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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