大豆持绿QTL定位及全基因组选择

doi:10.3864/j.issn.0578-1752.2026.10.002

中国农业科学 ›› 2026, Vol. 59 ›› Issue (10): 2075-2087.doi: 10.3864/j.issn.0578-1752.2026.10.002

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

大豆持绿QTL定位及全基因组选择

刘芝妤¹^,²(), 陈伊洁¹^,², 于欢¹^,², 申茂廷², 邱丽娟⁴(), 王俊²^,³()

¹ 长江大学农学院，湖北荆州 434025
² 神农种业实验室，郑州 450002
³ 河南省农业科学院作物分子育种研究院，郑州 450002
⁴ 中国农业科学院作物科学研究所/农作物基因资源与基因改良国家重大科学工程/农业农村部作物基因资源与种质创制重点实验室，北京 100081

收稿日期:2025-10-15 接受日期:2025-12-02 出版日期:2026-05-16 发布日期:2026-05-20
通信作者:
王俊，Tel：15826595646；E-mail：wjsoybean_2008@163.com。
邱丽娟，E-mail：qiulijuan@caas.cn。
联系方式: 刘芝妤，Tel：18635609316；E-mail：haas_liuzhiyu@163.com。
基金资助:
神农种业实验室一流课题项目(SN01-2024-01); 农业农村部重大农业科技项目(NK202308010302); 国家重点研发计划(2022YFE0203300)

QTL Mapping and Genomic Selection of Stay-Green in Soybean (Glycine max L.)

LIU ZhiYu¹^,²(), CHEN YiJie¹^,², YU Huan¹^,², SHEN MaoTing², QIU LiJuan⁴(), WANG Jun²^,³()

¹ College of Agriculture, Yangtze University, Jingzhou 434025, Hubei
² The Shennong Laboratory, Zhengzhou 450002
³ Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002
⁴ Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Beijing 100081

Received:2025-10-15 Accepted:2025-12-02 Published:2026-05-16 Online:2026-05-20

摘要/Abstract

摘要：

【目的】持绿（stay-green）能够延长大豆有效光合作用时间，增加干物质积累，对提高大豆产量具有重要意义。挖掘大豆持绿相关QTL，解析大豆持绿的分子机制，可为提高大豆产量提供理论依据和技术支持。【方法】通过对大豆巢式关联群体进行多环境表型鉴定，结合基因型进行全基因组关联分析，通过SNP变异分析、组织特异性表达分析、基因功能注释和单倍型分析，筛选候选基因，并对候选基因进行启动子顺式作用元件分析和蛋白结构预测分析。同时，构建并评价全基因组选择在大豆持绿性状的应用效果。【结果】共定位到6个显著QTL区间，分布于第3、4、5和16染色体。其中，qSG5-1（Chr.5：41600128..42273303，613.18 kb）在多环境中被重复定位，是大豆持绿调控新QTL。连锁不平衡分析发现，qSG5-1区间内存在2个显著关联区间，qSG5-1.1（Chr.5：41798499..41996276，197.78 kb）和qSG5-1.2（Chr.5：41996989..42273303，276.32 kb），分别包含29和37个基因。SNP变异分析发现53个基因区间内包含非同义突变、可变剪切、翻译提前终止或终止子丢失SNP，经组织特异性表达分析，其中8个基因在茎或叶中转录较为活跃。基因功能注释分析显示，Glyma.05G245200和Glyma.05G247900分别参与蛋白质折叠、氧化代谢过程，可能与细胞周期与生长代谢调控以及衰老过程中营养物质再分配有关。2个基因主要单倍型表型间存在极显著差异且均包含非同义突变，Glyma.05G245200中非同义突变分别为C617T（A206V）、C44T（P15L），并引起Glyma.05G245200蛋白三级结构发生细微改变。Glyma.05G247900中非同义突变为A275G（D92G），而Glyma.05G247900蛋白三级结构无变化。顺式作用元件分析结果显示，2个基因启动子区域均存在光响应、脱落酸响应等元件，可能通过对光、激素信号调控共同影响大豆生长与衰老，进而调控大豆持绿，可能为大豆持绿相关的候选基因。持绿性状全基因组选择分析结果在不同标记集中的预测准确度为0.27—0.36。【结论】定位到1个与持绿相关的新QTL——qSG5-1。筛选出2个与大豆持绿相关候选基因，分别为Glyma.05G245200和Glyma.05G247900。

关键词: 大豆, 持绿, QTL定位, 候选基因, 全基因组选择

Abstract:

【Objective】The “stay-green” trait can prolong the effective photosynthesis duration in soybeans and increase dry matter accumulation, thereby holding significant potential for improving yield. Mining stay-green related QTL and elucidating their molecular mechanisms can provide a theoretical basis and technical support for enhancing soybean yield.【Method】A soybean nested association mapping population was evaluated for stay-green traits across multiple environments. Genome-wide association study was conducted using genotyping data. Candidate genes were screened via SNP variation, tissue-specific expression, and functional annotation analyses, haplotype, promoter cis-acting elements, and protein structure prediction analyses were performed to characterize the candidate genes. Additionally, the application effect of genomic selection for the stay-green trait was evaluated.【Result】Six significant QTL intervals were co-localized on chromosomes 3, 4, 5, and 16. Among these, qSG5-1 (Chr.5: 41600128..42273303, 613.18 kb) was repeatedly mapped across multiple environments and represents a novel QTL for stay-green regulation in soybean. Linkage disequilibrium analysis allocated two significantly associated regions within qSG5-1: qSG5-1.1 (Chr.5: 41798499..41996276, 197.78 kb) and qSG5-1.2 (Chr.5: 41996989..42273303, 276.32 kb), containing 29 and 37 genes, respectively. SNP variation analysis identified 53 genes containing variants that cause nonsynonymous mutations, alternative splicing, stopgain, or stoploss. Of these, eight genes were transcriptionally active in stems and leaves. Functional annotation suggested that Glyma.05G245200 and Glyma.05G247900 were involved in protein folding and oxidative metabolism, respectively, which highlights they might regulate cell cycle, growth metabolism, and nutrient remobilization during senescence. Besides, two major haplotypes of these genes exhibited highly significant phenotypic differences as Glyma.05G245200 harbored nonsynonymous mutations which changed C617T into A206V and C44T into P15L, and caused subtle alterations in its protein structure. Likewise, Glyma.05G247900 also contained a nonsynonymous mutation which changed A275G into D92G that did not alter its protein conformation. Analysis of cis-acting elements revealed that the presence of light and abscisic acid (ABA)-responsive elements in their promoters hints they might regulate soybean growth, senescence, and the stay-green trait by participating in light and hormonal signaling. These genes may serve as candidate genes for soybean stay-green and the prediction accuracy of genome-wide selection for stay-green across different marker sets ranged from 0.27 to 0.36.【Conclusion】This study identified a novel QTL, qSG5-1, and two candidate genes, Glyma.05G245200 and Glyma.05G247900, associated with the stay-green trait in soybean.

Key words: soybean, stay-green, QTL mapping, candidate genes, genomic selection

刘芝妤, 陈伊洁, 于欢, 申茂廷, 邱丽娟, 王俊. 大豆持绿QTL定位及全基因组选择[J]. 中国农业科学, 2026, 59(10): 2075-2087.

LIU ZhiYu, CHEN YiJie, YU Huan, SHEN MaoTing, QIU LiJuan, WANG Jun. QTL Mapping and Genomic Selection of Stay-Green in Soybean (Glycine max L.)[J]. Scientia Agricultura Sinica, 2026, 59(10): 2075-2087.

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群体编号 Cohort number	持绿样本数量 The number of stay-green samples	非持绿样本数量 The number of no stay-green samples	持绿样本所占比例 The proportion of stay-green samples (%)
N004	53	36	59.55
N005	20	78	20.41
N006	17	50	25.37
N008	17	68	20.00
N009	18	36	33.33
N010	74	23	76.29
N011	25	41	37.88
N012	15	58	20.55
N015	16	33	32.65
N017	59	37	61.46
N018	9	69	11.54
N019	25	57	30.49
N020	7	82	7.87
N021	14	74	15.91
N022	42	51	45.16
N023	16	51	23.88
N024	7	62	10.14
N025	15	65	18.75
N026	37	48	43.53
N027	71	20	78.02
N028	21	51	29.17
N029	3	43	6.52
N030	16	18	47.06
N031	4	54	6.90
N032	25	17	59.52
N033	8	70	10.26
N034	18	55	24.66

QTL名称 QTL name	环境 Environment	染色体 Chromosome	起始/bp Start/bp	终止/bp End/bp	基因数量 Gene number
qSG5-1	23XX	5	41600128	42273303	90
qSG5-1	24JN	5	41605515	42273303	88

基因 Gene	同源拟南芥基因 Homologues in Arabidopsis	功能注释 Functional annotation
Glyma.05G244200	AT3G18050	糖基磷脂酰肌醇锚定蛋白 GPI-anchored protein
Glyma.05G245200	AT1G18170	FKBP肽基脯氨酰基顺反异构酶家族蛋白FKBP-like peptidyl-prolyl cis-trans isomerase family protein
Glyma.05G246900	AT3G17930	细胞色素b_6f复合体积累的类囊体膜蛋白 Encodes a thylakoid membrane protein involved in the accumulation of the cytochrome b_6f complex
Glyma.05G247500	AT3G02850	外向整流型钾离子通道 STELAR K⁺ outward rectifier
Glyma.05G247700	AT1G48450	未知功能蛋白 Protein of unknown function
Glyma.05G247900	AT3G17790	紫色酸性磷酸酶17蛋白 Purple acid phosphatase 17 protein
Glyma.05G248700	AT5G42710	未知功能蛋白 Protein of unknown function
Glyma.05G249000	AT3G17670	四肽重复（TPR）结构域蛋白 Tetratricopeptide repeat (TPR)-containing protein

基因 Gene	单倍型 Haplotype	基因型 Genotype	频数 Frequency
Glyma.05G245200	Hap1 Hap2 Hap3 Hap4 Hap5	CGTGGGTG TACCAACA TACCAACG TACCAGTA CGTGAACA	1248 385 3 2 1
Glyma.05G247900	Hap1 Hap2	TA CG	1461 189

分类 Classification	顺式作用元件 Cis-acting elements	生物学功能 Biological function
光响应 Light response	Box 4	参与光响应的保守DNA模块 Part of a conserved DNA module involved in light responsiveness
	I-box	光响应元件 Part of a light responsive element
	ATCT-motif	参与光响应的保守DNA模块 Part of a conserved DNA module involved in light responsiveness
	TCT-motif	光响应元件 Part of a light responsive element
胁迫响应 Stress response	MYB	MYB结合位点 MYB recognition site
	MYC	MYC识别元件 MYC recognition element
	LTR	参与低温响应的顺式作用元件 Cis-acting element involved in low-temperature responsiveness
激素响应 Hormone response	CGTCA-motif	参与MeJA反应的顺式作用调控元件 Cis-acting regulatory element involved in the MeJA-responsiveness
	TGACG-motif	参与MeJA反应的顺式作用调控元件 Cis-acting regulatory element involved in the MeJA-responsiveness
	ABRE	参与脱落酸反应的顺式作用元件 Cis-acting element involved in the abscisic acid responsiveness
	ERE	乙烯响应元件 Ethylene responsive element

大豆持绿QTL定位及全基因组选择

QTL Mapping and Genomic Selection of Stay-Green in Soybean (Glycine max L.)

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标记集 Marker sets	23XX	24JN
T1	0.27	0.36
T2	0.35	0.31
T3	0.27	0.36