藜麦GRAS基因家族的鉴定及其在生殖发育中的调控功能

doi:10.3969/j.issn.1004-1524.20250081

浙江农业学报 ›› 2026, Vol. 38 ›› Issue (1): 35-53.DOI: 10.3969/j.issn.1004-1524.20250081

藜麦GRAS基因家族的鉴定及其在生殖发育中的调控功能

杨炀^a(), 张帅^a, 董陈文华^a^,^b, 曾孟琼^a, 林春^a^,^b, 毛自朝^a^,^b^,^*()

云南农业大学 a. 农业与生物技术学院;b. 特色小宗作物研究中心,云南昆明 650201

收稿日期:2025-02-07 出版日期:2026-01-25 发布日期:2026-02-11
作者简介:*毛自朝,E-mail:zmao@ynau.edu.cn
杨炀,研究方向为生物化学与分子生物学。E-mail:Yyang_ynau@163.com
通讯作者: 毛自朝
基金资助:
国家自然科学基金(32260482)

Identification of GRAS gene family members and their regulatory roles in reproductive development in Chenopodium quinoa

YANG Yang^a(), ZHANG Shuai^a, DONG Chenwenhua^a^,^b, ZENG Mengqiong^a, LIN Chun^a^,^b, MAO Zichao^a^,^b^,^*()

College of Agriculture and Biotechnology; b. Research Center of Featured Minor Crops, Yunnan Agricultural University, Kunming 650201, China

Received:2025-02-07 Online:2026-01-25 Published:2026-02-11
Contact: MAO Zichao

摘要/Abstract

摘要：

GRAS基因家族在植物生长发育与逆境响应中具有重要调控功能,但目前尚未见其在藜麦(Chenopodium quinoa)生殖发育中的相关报道。本研究基于最新藜麦基因组数据,系统鉴定并分析藜麦GRAS家族(CqGRAS)成员,重点解析其基因结构、启动子顺式作用元件,以及在营养与生殖生长阶段的表达模式与调控机制。同时,将CqGRAS成员与拟南芥、藜麦二倍体祖先Chenopodium watsonii(A基因组)和Chenopodium suecicum(B基因组)的GRAS基因进行对比分析。结果共鉴定到51个CqGRAS基因,这些基因普遍内含子数量较少,且与拟南芥及二倍体藜属物种GRAS基因具有较高同源性。启动子分析表明,该家族基因富含响应植物激素(如赤霉素、脱落酸、乙烯和茉莉酸)、生长发育与逆境胁迫的顺式作用元件。系统进化分析将CqGRAS家族划分为10个亚家族,其中HAM(CqHAM01)、PAT1(CqPAT1-06/07/08)、DELLA(CqDELLA01/02)、DLT(CqDLT01/02)和SHR(CqSHR05/06)在花序和发育种子中表达水平较高。加权基因共表达网络分析提示,这些与生殖发育相关的CqGRAS基因可能通过整合光信号与激素信号通路,调控藜麦花和种子的生长发育。本研究为阐明GRAS家族在藜麦生殖发育中的功能提供了新见解,并为深入解析其分子机制与育种应用奠定了基础。

关键词: 藜麦, GRAS基因家族, 生殖调控, 加权基因共表达网络分析, 生殖发育

Abstract:

The GRAS gene family plays an essential regulatory role in plant growth, development, and stress responses, but no relevant reports have been published on its function in the reproductive development of quinoa (Chenopodium quinoa). Based on the latest quinoa genome data, this study systematically identified and analyzed the quinoa GRAS family (CqGRAS) members, focusing on their gene structures, promoter cis-acting elements, as well as their expression patterns and regulatory mechanisms during vegetative and reproductive growth stages. Additionally, a comparative analysis was conducted between the CqGRAS members and the GRAS genes of Arabidopsis thaliana and the diploid ancestral species of quinoa, Chenopodium watsonii(A genome) and Chenopodium suecicum(B genome). A total of 51 CqGRAS genes were identified. These genes generally contained few introns and exhibited high homology with the GRAS genes of Arabidopsis and the diploid Chenopodium species. Promoter analysis revealed that these genes were enriched with cis-acting elements responsive to plant hormones (such as gibberellin, abscisic acid, ethylene, and jasmonic acid), growth and development, as well as stress signals. Phylogenetic analysis classified the CqGRAS family into 10 subfamilies, among which HAM (CqHAM01), PAT1 (CqPAT1-06/07/08), DELLA (CqDELLA01/02), DLT (CqDLT01/02), and SHR (CqSHR05/06) showed relatively high expression levels in inflorescences and developing seeds. Weighted gene co-expression network analysis (WGCNA) suggested that these CqGRAS genes associated with reproductive development might regulate the growth and development of quinoa flowers and seeds by integrating light signaling and hormone signaling pathways. This study provided novel insights into the role of the GRAS family in quinoa reproductive development and laid the foundation for further elucidation of its molecular mechanisms and breeding applications.

Key words: Chenopodium quinoa, GRAS gene family, reproductive regulation, weighted gene co-expression network analysis (WGCNA), reproductive development

中图分类号:

S519

杨炀, 张帅, 董陈文华, 曾孟琼, 林春, 毛自朝. 藜麦GRAS基因家族的鉴定及其在生殖发育中的调控功能[J]. 浙江农业学报, 2026, 38(1): 35-53.

YANG Yang, ZHANG Shuai, DONG Chenwenhua, ZENG Mengqiong, LIN Chun, MAO Zichao. Identification of GRAS gene family members and their regulatory roles in reproductive development in Chenopodium quinoa[J]. Acta Agriculturae Zhejiangensis, 2026, 38(1): 35-53.

图/表 10

表1 qRT-PCR引物序列

Table 1 Sequences of qRT-PCR primers

引物名称primer name	引物序列(5'→3') Primer sequence(5'→3')	产物大小/bp Product length/bp
1-CqDELLA01-F2	CGAAAGACACGAGCCACTAATAAA	169
1-CqDELLA01-R2	CCACCCTAGAGTCAAGCACCC
2-CqDELLA02-F2	ACTTCTAGTTCTCAATCTTTTGTTTTC	194
2-CqDELLA02-R2	AAAGTGTCTAGCACCCCCAG
3-CqPAT1-05-F2	CTTTCCCTTAGCAATGACAACA	105
3-CqPAT1-05-R2	AATGTTTAGGAAGGATGGTCGT
4-CqPAT1-06-F	AGGACTACTTCGGTGTTACTCTG	103
4-CqPAT1-06-R	CCAAGCTGAAGCCGAGATCAA
5-CqDLT01-F2	GGTATCAGGAGGGACGAAAG	166
5-CqDLT01-R2	CAGCAGCATCAACAGAACCC
6-CqDLT02-F2	CATGGATTAGTCTTTGATTTTCGAT	175
6-CqDLT02-R2	CATGCCATAAGTAGATCAAATAACAA
7-CqSHR05-F	GGCGTATAGTGAGGAGGTTTGTG	109
7-CqSHR05-R	TATTCCGGCAGTCGGAGAC
8-CqSHR06-F	CGGAGAGGAGAGAGAATGCC	137
8-CqSHR06-R	TGCCATCGACCACCCTTCT
CqActin-F2	TTGGAATCTCGCCGCCAAA	132
CqActin-R2	CCAGGTCCACCAACAATCCA

表2 藜麦GRAS基因家族信息

Table 2 Information of GRAS gene family in quinoa

基因名称 Gene name	基因ID Gene ID	染色体 Chromosome	氨基酸长度/aa Amino acid length/aa	蛋白质分子质量/u Protein molecular weight/u	等电点 Isoelectric point	亚细胞定位 Subcellular localization
CqDELLA01	CQ012679	Cq8B	459	50 811.86	5.51	溶酶体Cytolysosome
CqDELLA02	CQ040570	Cq8A	474	52 509.87	5.66	溶酶体Cytolysosome
CqDELLA03	CQ001679	Cq6B	617	67 367.76	4.90	细胞核Nuclear
CqDELLA04	CQ026984	Cq6A	618	67 500.87	4.90	细胞核Nuclear
CqDLT01	CQ004440	Cq5B	648	73 031.86	5.77	叶绿体Chloroplast
CqDLT02	CQ029757	Cq5A	657	73 968.04	5.47	叶绿体Chloroplast
CqHAM01	CQ002321	Cq6B	610	67 095.88	6.46	细胞核Nuclear
CqHAM02	CQ027701	Cq6A	602	66 232.26	6.82	细胞核Nuclear
CqHAM03	CQ003474	Cq5B	785	85 801.61	6.15	细胞核Nuclear
CqHAM04	CQ028875	Cq5A	781	85 891.76	6.12	细胞核Nuclear
CqLAS01	CQ033480	Cq9B	490	55 803.58	7.02	细胞核Nuclear
CqLAS02	CQ051297	Cq9A	484	54 848.37	6.76	细胞核Nuclear
CqLISCL01	CQ032605	Cq9B	350	41 049.14	8.10	溶酶体Cytolysosome
CqLISCL02	CQ041202	Cq7A	725	82 353.95	4.95	细胞核Nuclear
CqLISCL03	CQ032598	Cq9B	689	78 590.85	5.18	细胞核Nuclear
CqLISCL04	CQ041204	Cq7A	619	70 272.91	6.29	细胞核Nuclear
CqLISCL05	CQ032601	Cq9B	679	76 337.79	5.60	细胞核Nuclear
CqLISCL06	CQ032604	Cq9B	548	62 438.96	7.94	溶酶体Cytolysosome
CqLISCL07	CQ041201	Cq7A	662	74 879.34	6.61	细胞核Nuclear
CqLISCL08	CQ032603	Cq9B	667	75 299.73	5.23	细胞核Nuclear
CqLISCL09	CQ041200	Cq7A	686	77 311.71	4.87	细胞核Nuclear
CqLISCL10	CQ030634	Cq5A	760	86 162.35	5.50	细胞核Nuclear
CqLISCL11	CQ055311	Cq2A	780	87 684.22	7.07	溶酶体Cytolysosome
CqLISCL12	CQ025002	Cq1B	818	91 640.62	7.49	细胞核Nuclear
CqLISCL13	CQ032609	Cq9B	756	84 422.57	5.55	细胞核Nuclear
CqLISCL14	CQ041197	Cq7A	756	84 533.61	5.81	细胞核Nuclear
CqPAT1-01	CQ024284	Cq1B	545	61 454.56	4.73	叶绿体Chloroplast
CqPAT1-02	CQ048458	Cq1A	426	48 153.43	5.27	溶酶体Cytolysosome
CqPAT1-03	CQ016853	Cq3B	639	70 122.51	5.46	细胞核Nuclear
CqPAT1-04	CQ044170	Cq3A	767	84 245.91	6.39	细胞核Nuclear
CqPAT1-05	CQ022180	Cq4B	635	70 854.40	8.16	叶绿体Chloroplast
CqPAT1-06	CQ037875	Cq4A	634	70 854.39	7.57	叶绿体Chloroplast
CqPAT1-07	CQ010139	Cq8B	544	61 079.89	6.33	细胞核Nuclear
CqPAT1-08	CQ038026	Cq8A	544	61 110.88	6.51	细胞核Nuclear
CqPAT1-09	CQ013243	Cq2B	466	52 280.60	5.82	叶绿体Chloroplast
CqPAT1-10	CQ034654	Cq9B	541	60 293.76	6.56	细胞核Nuclear
CqPAT1-11	CQ050106	Cq9A	588	65 884.16	6.69	叶绿体Chloroplast
CqSCL3L01	CQ019876	Cq4B	454	50 710.01	6.51	细胞核Nuclear
CqSCL3L02	CQ035148	Cq4A	454	50 837.30	6.65	细胞核Nuclear
CqSCL4L01	CQ003361	Cq6B	557	60 789.24	4.38	细胞核Nuclear
CqSCL4L02	CQ028754	Cq6A	610	67 157.51	4.74	细胞核Nuclear
CqSCR01	CQ052618	Cq9A	872	95 159.47	6.39	细胞核Nuclear
CqSCR02	CQ007129	Cq7B	861	93 906.00	6.40	细胞核Nuclear
CqSCR03	CQ014997	Cq2B	396	43 813.31	6.99	叶绿体Chloroplast
CqSCR04	CQ054542	Cq2A	396	43 859.22	7.32	细胞核Nuclear
CqSHR01	CQ003291	Cq6B	475	53 457.35	5.88	线粒体、细胞骨架 Mitochondrion, cytoskeleton
CqSHR02	CQ028690	Cq6A	389	43 994.11	5.05	细胞骨架Cytoskeleton
CqSHR03	CQ018831	Cq3B	439	50 575.84	6.38	叶绿体Chloroplast
CqSHR04	CQ044974	Cq3A	440	50 599.98	6.73	叶绿体Chloroplast
CqSHR05	CQ003315	Cq6B	472	53 064.48	5.94	细胞核Nuclear
CqSHR06	CQ028714	Cq6A	467	52 415.84	5.86	细胞核Nuclear

表2 藜麦GRAS基因家族信息

Table 2 Information of GRAS gene family in quinoa

基因名称 Gene name	基因ID Gene ID	染色体 Chromosome	氨基酸长度/aa Amino acid length/aa	蛋白质分子质量/u Protein molecular weight/u	等电点 Isoelectric point	亚细胞定位 Subcellular localization
CqDELLA01	CQ012679	Cq8B	459	50 811.86	5.51	溶酶体Cytolysosome
CqDELLA02	CQ040570	Cq8A	474	52 509.87	5.66	溶酶体Cytolysosome
CqDELLA03	CQ001679	Cq6B	617	67 367.76	4.90	细胞核Nuclear
CqDELLA04	CQ026984	Cq6A	618	67 500.87	4.90	细胞核Nuclear
CqDLT01	CQ004440	Cq5B	648	73 031.86	5.77	叶绿体Chloroplast
CqDLT02	CQ029757	Cq5A	657	73 968.04	5.47	叶绿体Chloroplast
CqHAM01	CQ002321	Cq6B	610	67 095.88	6.46	细胞核Nuclear
CqHAM02	CQ027701	Cq6A	602	66 232.26	6.82	细胞核Nuclear
CqHAM03	CQ003474	Cq5B	785	85 801.61	6.15	细胞核Nuclear
CqHAM04	CQ028875	Cq5A	781	85 891.76	6.12	细胞核Nuclear
CqLAS01	CQ033480	Cq9B	490	55 803.58	7.02	细胞核Nuclear
CqLAS02	CQ051297	Cq9A	484	54 848.37	6.76	细胞核Nuclear
CqLISCL01	CQ032605	Cq9B	350	41 049.14	8.10	溶酶体Cytolysosome
CqLISCL02	CQ041202	Cq7A	725	82 353.95	4.95	细胞核Nuclear
CqLISCL03	CQ032598	Cq9B	689	78 590.85	5.18	细胞核Nuclear
CqLISCL04	CQ041204	Cq7A	619	70 272.91	6.29	细胞核Nuclear
CqLISCL05	CQ032601	Cq9B	679	76 337.79	5.60	细胞核Nuclear
CqLISCL06	CQ032604	Cq9B	548	62 438.96	7.94	溶酶体Cytolysosome
CqLISCL07	CQ041201	Cq7A	662	74 879.34	6.61	细胞核Nuclear
CqLISCL08	CQ032603	Cq9B	667	75 299.73	5.23	细胞核Nuclear
CqLISCL09	CQ041200	Cq7A	686	77 311.71	4.87	细胞核Nuclear
CqLISCL10	CQ030634	Cq5A	760	86 162.35	5.50	细胞核Nuclear
CqLISCL11	CQ055311	Cq2A	780	87 684.22	7.07	溶酶体Cytolysosome
CqLISCL12	CQ025002	Cq1B	818	91 640.62	7.49	细胞核Nuclear
CqLISCL13	CQ032609	Cq9B	756	84 422.57	5.55	细胞核Nuclear
CqLISCL14	CQ041197	Cq7A	756	84 533.61	5.81	细胞核Nuclear
CqPAT1-01	CQ024284	Cq1B	545	61 454.56	4.73	叶绿体Chloroplast
CqPAT1-02	CQ048458	Cq1A	426	48 153.43	5.27	溶酶体Cytolysosome
CqPAT1-03	CQ016853	Cq3B	639	70 122.51	5.46	细胞核Nuclear
CqPAT1-04	CQ044170	Cq3A	767	84 245.91	6.39	细胞核Nuclear
CqPAT1-05	CQ022180	Cq4B	635	70 854.40	8.16	叶绿体Chloroplast
CqPAT1-06	CQ037875	Cq4A	634	70 854.39	7.57	叶绿体Chloroplast
CqPAT1-07	CQ010139	Cq8B	544	61 079.89	6.33	细胞核Nuclear
CqPAT1-08	CQ038026	Cq8A	544	61 110.88	6.51	细胞核Nuclear
CqPAT1-09	CQ013243	Cq2B	466	52 280.60	5.82	叶绿体Chloroplast
CqPAT1-10	CQ034654	Cq9B	541	60 293.76	6.56	细胞核Nuclear
CqPAT1-11	CQ050106	Cq9A	588	65 884.16	6.69	叶绿体Chloroplast
CqSCL3L01	CQ019876	Cq4B	454	50 710.01	6.51	细胞核Nuclear
CqSCL3L02	CQ035148	Cq4A	454	50 837.30	6.65	细胞核Nuclear
CqSCL4L01	CQ003361	Cq6B	557	60 789.24	4.38	细胞核Nuclear
CqSCL4L02	CQ028754	Cq6A	610	67 157.51	4.74	细胞核Nuclear
CqSCR01	CQ052618	Cq9A	872	95 159.47	6.39	细胞核Nuclear
CqSCR02	CQ007129	Cq7B	861	93 906.00	6.40	细胞核Nuclear
CqSCR03	CQ014997	Cq2B	396	43 813.31	6.99	叶绿体Chloroplast
CqSCR04	CQ054542	Cq2A	396	43 859.22	7.32	细胞核Nuclear
CqSHR01	CQ003291	Cq6B	475	53 457.35	5.88	线粒体、细胞骨架 Mitochondrion, cytoskeleton
CqSHR02	CQ028690	Cq6A	389	43 994.11	5.05	细胞骨架Cytoskeleton
CqSHR03	CQ018831	Cq3B	439	50 575.84	6.38	叶绿体Chloroplast
CqSHR04	CQ044974	Cq3A	440	50 599.98	6.73	叶绿体Chloroplast
CqSHR05	CQ003315	Cq6B	472	53 064.48	5.94	细胞核Nuclear
CqSHR06	CQ028714	Cq6A	467	52 415.84	5.86	细胞核Nuclear

图1 GRAS基因家族系统进化树与共线性分析 A, C. watsonii、C. suecicum、C. quinoa和拟南芥的GRAS家族系统进化树;B,C. watsonii、C. suecicum和C. quinoa的GRAS基因共线性。

Fig.1 Phylogenetic tree and collinearity analysis of GRAS gene family A, Phylogenetic tree of the GRAS family among C. watsonii, C. suecicum, C. quinoa and Arabidopsis thaliana; B, GRAS gene collinearity analysis among C. watsonii, C. suecicum and C. quinoa.

图2 藜麦GRAS基因家族成员聚类、保守基序、保守结构域和基因结构组成分析 A,藜麦GRAS基因家族成员聚类(不同颜色区域代表不同亚家族);B,藜麦GRAS蛋白保守基序组成与分布;C,藜麦GRAS家族蛋白的保守结构域;D,藜麦GRAS基因的结构。

Fig.2 Clustering, conserved motifs, conserved domains, and gene structure composition of quinoa GRAS gene family members A, Clustering of quinoa GRAS gene family members (different colored regions represent different subfamilies); B, Composition and distribution of conserved motifs of CqGRAS; C, Conserved domains of the CqGRAS family proteins; D. Gene structure of CqGRAS.

图3 藜麦GRAS家族基因的顺式作用元件

Fig.3 Cis-acting elements of GRAS gene in quinoa

图4 藜麦GRAS基因在不同发育阶段和种子发育过程中的表达 A,不同发育阶段叶片、花序、雄蕊和雌蕊中GRAS基因的表达。样品命名规则:S,夏季;W,冬季;19,W19品种;D,短日(14 h光照/10 h黑暗);L,长日(22 h光照/2 h黑暗);V,营养期;F,开花期;S,种子形成期;P,花序;L,叶片。如S19DFL代表夏季W19短日条件下开花期叶片。B,种子发育阶段GRAS基因的表达。S1~S4代表TY-20开花后7 d(S1)、17 d(S2)、27 d(S3)和42 d(S4)的3次生物学重复(1、2、3)。

Fig.4 Expression of GRAS genes in quinoa at different developmental stages and seed development A, Expression of GRAS genes in leaves, inflorescences, stamens, and pistils at different developmental stages. Sample naming: S, Summer; W, Winter; 19, W19 variety; D, Short-day (14 h light/10 h dark) condition; L, Long-day (22 h light/2 h dark) condition; V, Vegetative stage; F, Flowering stage; S, Seed formation stage; P, Panicle sample; L, Leaf sample. e.g., S19DFL represented summer W19 flowering stage leaves under short-day conditions. B, Expression of GRAS genes during seed development. S1-S4 represent the 7 d (S1), 17 d (S2), 27 d (S3), and 42 d (S4) after flowering in the TY-20, with three biological replicates (1, 2, 3).

图5 藜麦不同组织中8个基因的相对表达水平

Fig.5 Relative expression of 8 genes in different tissues of quinoa

图6 模块与模块之间的聚类和热图红色的格子代表模块之间具有正相关性,蓝色的格子代表模块之间具有负相关性。

Fig.6 Clustering and heat map between modules Red color of each box represents the positive correlation between modules. Blue color of each box represents the negative correlation between modules.

图7 藜麦模块基因GO富集与KEGG富集 A~C分别为lightcyan、yellow和turquoise模块GO富集;D,3个模块共同KEGG富集。

Fig.7 GO enrichment and KEGG enrichment of module genes in quinoa A-C, GO enrichment module of lightcyan, yellow and turquoise, respectively; D, KEGG enrichment of three combining module genes.

图8 模块中基因与转录因子在花与种子发育相关组织中的表达热图与关系网络 A~C分别代表lightcyan、yellow和tuequoise模块中CqGRAS基因和转录因子在花与种子发育相关组织中的表达;D~F分别代表lightcyan、yellow和tuequoise模块中CqGRAS基因和该模块中相关转录因子的网络图。绿色三角形代表CqGRAS成员,蓝色三角形代表与转录因子互作的其他基因,椭圆形代表转录因子。

Fig.8 Heat map and correlation of gene and transcription factor expression in flower development related tissues within the module A-C represented the expression of CqGRAS genes and transcription factors in flower and seed development related tissues in the lightcyan,yellow and tuequoise modules; D-F represented the network diagram of CqGRAS genes and related transcription factors in the lightcyan,yellow and tuequoise modules. Green triangles represented CqGRAS members, blue triangles represented other genes that interact with transcription factors, and ellipses represented transcription factors.

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藜麦GRAS基因家族的鉴定及其在生殖发育中的调控功能

Identification of GRAS gene family members and their regulatory roles in reproductive development in Chenopodium quinoa

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