大豆地方种质资源鲜籽粒可溶性糖含量的全基因组关联分析

doi:10.3864/j.issn.0578-1752.2024.11.003

中国农业科学 ›› 2024, Vol. 57 ›› Issue (11): 2079-2091.doi: 10.3864/j.issn.0578-1752.2024.11.003

• 专题：大豆抗病性、产量与品质的相关性 • 上一篇下一篇

大豆地方种质资源鲜籽粒可溶性糖含量的全基因组关联分析

张玉梅¹(), 丁文涛²^,³(), 蓝新隆¹, 李清华⁴, 胡润芳¹, 郭娜²^,³, 林国强¹(), 赵晋铭²^,³()

¹ 福建省农业科学院作物研究所/福建省特色旱作物品种选育工程技术研究中心/福建省蔬菜遗传育种重点实验室，福州 350013
² 生物育种钟山实验室，南京 210014
³ 南京农业大学农学院/国家大豆生物育种产教融合创新平台/农业农村部大豆生物学与遗传育种重点实验室/作物遗传与种质创新全国重点实验室，南京 210095
⁴ 莆田市农业科学研究所，福建莆田 351106

收稿日期:2022-11-28 接受日期:2023-01-03 出版日期:2024-06-01 发布日期:2024-06-07
通信作者:
林国强，E-mail：542057656@qq.com。
赵晋铭，E-mail：jmz3000@126.com
联系方式: 张玉梅，E-mail：zym1122@126.com。丁文涛，E-mail：wentaoding@126.com。张玉梅和丁文涛为同等贡献作者。
基金资助:
国家重点研发计划(2021YFD1201605); 福建省自然科学基金(2020J011372); 福建省属公益类科研院所基本科研专项(2022R1031006); 福建省财政专项(FJVRC2020-02); 福建省财政专项(CXTD2021011-2)

Genome Wide Association Analysis of Soluble Sugar Content in Fresh Seeds of Soybean Landraces

ZHANG YuMei¹(), DING WenTao²^,³(), LAN XinLong¹, LI QingHua⁴, HU RunFang¹, GUO Na²^,³, LIN GuoQiang¹(), ZHAO JinMing²^,³()

¹ Crop Research Institute, Fujian Academy of Agricultural Sciences/Engineering Research Center for Characteristic Dry Crop Varieties Breeding/Fujian Key Laboratory of Vegetable Genetics and Breeding, Fuzhou 350013
² Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing 210014
³ College of Agriculture, Nanjing Agricultural University/National Innovation Platform for Soybean Breeding and Industry-Education Integration/Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture and Rural Affairs/National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing 210095
⁴ Putian Agricultural Sciences Research Institute, Putian 351106, Fujian

Received:2022-11-28 Accepted:2023-01-03 Published:2024-06-01 Online:2024-06-07

摘要/Abstract

摘要：

【目的】可溶性糖含量是鲜食大豆重要的品质性状之一，研究大豆鲜籽粒可溶性糖含量的遗传变异，深入解析可溶性糖含量的遗传机制，为鲜食大豆种质创新及品质育种提供依据。【方法】利用来自东北大豆生态区、北方大豆生态区、黄淮海大豆生态区和南方大豆生态区的133份大豆地方种质，在2021年连江春季、福清春季和秋季3个环境下对鲜籽粒可溶性糖含量进行表型测定，结合82 187个高质量SNP标记，基于混合线性模型MLM（Q+K）对可溶性糖含量进行全基因组关联分析，挖掘可溶性糖含量显著相关的SNP位点，并以显著SNP位点为中心，两端各扩展119.07 kb连锁不平衡衰减距离为候选区间，根据候选区间内基因的注释和组织表达信息预测候选基因。【结果】3个环境下，鲜籽粒可溶性糖含量的变异范围为3.37—33.84 mg·g^-1，遗传变异系数为24.59%—32.69%，可溶性糖含量遗传率为68.14%。通过全基因组关联分析，连江春季、福清春季和秋季3个环境下分别检测到与鲜籽粒可溶性糖含量显著关联的SNP有6、8和22个，表型变异解释率为12.43%—29.27%，以表型变异解释率较高的9个显著SNP位点所在的候选区间进行搜索，共获得86个基因，结合基因注释和组织表达信息，进一步筛选到9个候选基因，主要涉及转录因子、糖蛋白家族和糖类合成转运等生物学过程。其中，Glyma.01g016500、Glyma.13g042100、Glyma.16g131800和Glyma.16g155300在大豆种子及荚中表达水平较高，可作为大豆鲜籽粒可溶性糖的最具潜力候选基因。【结论】通过全基因组关联分析，检测到36个与鲜籽粒可溶性糖含量显著关联的SNP，进一步筛选出9个候选基因可能参与大豆鲜籽粒可溶性糖含量的调控，其中，Glyma.01g016500、Glyma.13g042100、Glyma.16g131800和Glyma.16g155300可作为调控大豆鲜籽粒可溶性糖含量的关键目标基因。

关键词: 大豆, 鲜籽粒, 可溶性糖含量, 全基因组关联分析, 候选基因

Abstract:

【Objective】Soluble sugar content is one of the important quality traits of vegetable soybean. The genetic variation and genetic mechanism of soluble sugar content in fresh soybean seeds were studied to provide a basis for germplasm innovation and quality breeding of vegetable soybean.【Method】Using 133 soybean landraces from the Northeast region, the North region, the Huanghuaihai region and the South region, the soluble sugar content of fresh seeds was determined in the three environments of Lianjiang in spring, Fuqing in spring and autumn, in 2021. In combination with 82 187 high-quality SNP markers, the whole genome association analysis of soluble sugar content was conducted based on the mixed linear model MLM (Q+K), and the SNP loci with significantly related to soluble sugar content were identified. The candidate intervals were selected by the significant SNP loci and the extension of 119.07 kb linkage disequilibrium decay distance at both ends. The candidate genes were predicted according to the annotation and tissue expression information of the genes in the candidate intervals.【Result】The variation range of soluble sugar content in fresh seeds under three environments was 3.37-33.84 mg·g^-1, the genetic variation coefficient was 24.59%-32.69%, and the heritability of soluble sugar content was 68.14%. 6, 8 and 22 SNPs were significantly associated with the soluble sugar content of fresh seeds were detected in Lianjiang in spring, Fuqing in spring and autumn, respectively, and phenotypic variation was 12.43%-29.27%. A total of 86 genes were obtained in the candidate regions of 9 significant SNP loci with higher interpretation rate of phenotypic variation, and 9 candidate genes were further screened by gene annotation and tissue expression information. These candidate genes are mainly involved in biological processes such as transcription factors, glycoprotein families and carbohydrate synthesis and transport. Among them, Glyma.01g016500, Glyma.13g042100, Glyma.16g131800 and Glyma.16g155300 were more highly expressed in soybean seeds and pods, which can be used as the most potential candidate genes for soluble sugar in fresh soybean seeds.【Conclusion】Through genome-wide association analysis, 36 SNPs significantly associated with soluble sugar content in fresh seeds were detected, and 9 candidate genes were further screened out, which may be involved in the regulation of soluble sugar content in fresh soybean seeds. Among them, Glyma.01g016500, Glyma.13g042100, Glyma.16g131800 and Glyma.16g155300 can be the key candidate genes for regulating soluble sugar content in fresh soybean seeds.

Key words: soybean, fresh seeds, soluble sugar contents, genome wide association analysis, candidate genes

张玉梅, 丁文涛, 蓝新隆, 李清华, 胡润芳, 郭娜, 林国强, 赵晋铭. 大豆地方种质资源鲜籽粒可溶性糖含量的全基因组关联分析[J]. 中国农业科学, 2024, 57(11): 2079-2091.

ZHANG YuMei, DING WenTao, LAN XinLong, LI QingHua, HU RunFang, GUO Na, LIN GuoQiang, ZHAO JinMing. Genome Wide Association Analysis of Soluble Sugar Content in Fresh Seeds of Soybean Landraces[J]. Scientia Agricultura Sinica, 2024, 57(11): 2079-2091.

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图/表 7

表1

图1

图2

表2

表3

显著标记关联的基因信息"

标记 Marker	物理位置 Position (bp)	染色体 Chromosome	等位变异 Allelic	关联基因 Associated gene	位置与变异 Region and variant
AX-90523492	1643221	1	T>C	Glyma.01g015600	基因下游Downstream
				Glyma.01g015800	基因下游Downstream
				Glyma.01g015900	基因下游Downstream
				Glyma.01g016100	基因下游Downstream
				Glyma.01g016500	基因下游Downstream
				Glyma.01g016800	基因下游Downstream
				Glyma.01g016900	基因下游Downstream
				Glyma.01g017000	基因下游Downstream
				Glyma.01g017200	外显子，同义突变Exon, synonymous
				Glyma.01g017300	基因上游Upstream
				Glyma.01g017400	基因上游Upstream
				Glyma.01g018300	基因上游Upstream
AX-90375080	4456132	6	A>G	Glyma.06g057700	基因下游Downstream
				Glyma.06g058000	基因下游Downstream
				Glyma.06g058100	基因下游Downstream
				Glyma.06g058500	基因下游Downstream
				Glyma.06g058600	基因下游Downstream
				Glyma.06g059000	内含子突变Intron variant
				Glyma.06g059500	基因上游Upstream
				Glyma.06g059700	基因上游Upstream
				Glyma.06g060200	基因上游Upstream
				Glyma.06g060300	基因上游Upstream
AX-90399131	41556768	6	G>A	Glyma.06g245400	基因下游Downstream
AX-90414763	90414763	6	T>C	Glyma.06g245500	基因下游Downstream
AX-90521281	90521281	6	G>T	Glyma.06g245600	基因下游Downstream
				Glyma.06g245700	基因下游Downstream
				Glyma.06g245800	基因下游Downstream
				Glyma.06g245900	基因下游Downstream
				Glyma.06g246000	基因下游Downstream
				Glyma.06g246100	上游基因突变Upstream gene variant
				Glyma.06g246200	基因上游Upstream
				Glyma.06g246300	基因上游Upstream
				Glyma.06g246400	基因上游Upstream
				Glyma.06g246500	基因上游Upstream
				Glyma.06g246600	外显子，非同义突变Exon, nonsynonymous
				Glyma.06g246800	外显子，同义突变Exon, synonymous
				Glyma.06g246900	基因上游Upstream
				Glyma.06g247100	基因上游Upstream
				Glyma.06g247200	基因上游Upstream
				Glyma.06g247300	基因上游Upstream
				Glyma.06g247600	基因上游Upstream
AX-90515230	18936718	8	C>T	Glyma.08g230100	基因下游Downstream
				Glyma.08g230600	基因下游Downstream
				Glyma.08g230800	基因下游Downstream
				Glyma.08g230900	基因下游Downstream
				Glyma.08g231000	内含子突变Intron variant
				Glyma.08g231400	基因上游Upstream
				Glyma.08g231500	基因上游Upstream
				Glyma.08g231600	基因上游Upstream
				Glyma.08g231800	基因上游Upstream
AX-90350462	13577053	13	A>G	Glyma.13g042100	基因下游Downstream
				Glyma.13g042200	基因下游Downstream
				Glyma.13g042300	基因下游Downstream
				Glyma.13g042600	外显子，同义突变Exon synonymous
				Glyma.13g042700	基因上游Upstream
				Glyma.13g042800	基因上游Upstream
				Glyma.13g042900	基因上游Upstream
				Glyma.13g043000	基因上游Upstream
				Glyma.13g043500	基因上游Upstream
				Glyma.13g043600	基因上游Upstream
AX-90345551	28826370	16	C>T	Glyma.16g131800	基因下游Downstream
				Glyma.16g131900	基因下游Downstream
				Glyma.16g132000	基因下游Downstream
				Glyma.16g132100	基因间变异Intergenic region
				Glyma.16g132200	基因间变异Intergenic region
				Glyma.16g132500	基因上游Upstream
				Glyma.16g132600	基因上游Upstream
				Glyma.16g132700	基因上游Upstream
				Glyma.16g132800	基因上游Upstream
AX-90351400	31631250	16	C>T	Glyma.16g155100	基因下游Downstream
				Glyma.16g155200	基因下游Downstream
				Glyma.16g155300	基因下游Downstream
				Glyma.16g155400	基因下游Downstream
				Glyma.16g155500	基因下游Downstream
				Glyma.16g155600	基因下游Downstream
				Glyma.16g155700	基因下游Downstream
				Glyma.16g155800	基因下游Downstream
				Glyma.16g156100	外显子，非同义突变Exon, nonsynonymous
				Glyma.16g156200	基因上游Upstream
				Glyma.16g156300	基因上游Upstream
				Glyma.16g156400	基因上游Upstream
				Glyma.16g156500	基因上游Upstream
				Glyma.16g156600	基因上游Upstream
				Glyma.16g156700	基因上游Upstream
				Glyma.16g156800	基因上游Upstream
				Glyma.16g157100	基因上游Upstream

表3

表4

图3

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环境 Environments	均值 Mean (mg·g^-1)	标准差 SD (mg·g^-1)	最小值 Min. (mg·g^-1)	最大值 Max. (mg·g^-1)	变异系数 CV (%)	显著性Significance			遗传率 h² (%)
环境 Environments	均值 Mean (mg·g^-1)	标准差 SD (mg·g^-1)	最小值 Min. (mg·g^-1)	最大值 Max. (mg·g^-1)	变异系数 CV (%)	F_G	F_E	F_G_×_E	遗传率 h² (%)
2021CLJ	8.73	2.850	3.37	19.05	32.69	3.01**	4.38**	7.20**	68.14
2021CFQ	10.74	2.641	5.68	18.79	24.59
2021QFQ	11.19	3.431	4.22	33.84	30.66
平均Mean	10.31	2.161	6.03	22.10	20.96

环境 Environments	标记 Markers	染色体 Chromosome	物理位置 Position (bp)	等位变异 Allelic	显著性 -log₁₀(P)	表型变异解释率 R² (%)
2021CLJ	AX-90503091	1	51857659	G/A	3.53	14.28
	AX-90375080	6	4456132	A/G	3.72	15.15
	AX-90439820	14	7015035	C/T	3.59	14.64
	AX-90326993	16	28742781	T/C	3.66	14.68
	AX-90345551	16	28826370	C/T	3.86	15.72
	AX-90366289	16	32782857	T/G	3.69	14.92
2021CFQ	AX-90498034	3	38220637	G/A	3.71	14.08
	AX-90388849	3	38318720	C/A	3.85	14.75
	AX-90399131	6	41556768	G/A	3.99	15.32
	AX-90305393	6	41636432	T/C	3.65	13.81
	AX-90414763	6	41661485	T/C	3.90	15.08
	AX-90521281	6	41672853	G/T	3.90	15.08
	AX-90430712	6	41739316	G/A	3.56	13.43
	AX-90491158	18	833161	A/C	3.79	14.36
2021QFQ	AX-90523492	1	1643221	T/C	4.13	19.65
	AX-90471910	2	15509622	T/G	3.73	14.71
	AX-90463831	5	37457082	G/A	4.33	16.52
	AX-90337094	8	18928439	C/G	3.87	13.99
	AX-90515230	8	18936718	C/T	4.04	16.18
	AX-90318719	8	27518867	T/G	3.52	12.43
	AX-90511533	8	34944396	C/T	3.70	13.72
	AX-90474383	9	6551732	T/G	3.58	13.30
	AX-90385515	9	6624803	A/C	3.51	13.64
	AX-90358417	9	6771694	T/A	3.81	13.83
	AX-90308466	9	6801826	C/T	3.58	13.28
	AX-90423241	9	6931879	T/C	3.57	12.90
	AX-90343217	9	6940434	C/T	3.71	13.46
	AX-90409115	9	6969624	T/C	3.73	13.94
	AX-90407481	10	3759843	G/A	3.82	14.71
	AX-90467097	10	41183218	C/T	3.69	14.45
	AX-90376167	11	32722314	A/G	3.54	12.78
	AX-90350462	13	13577053	A/G	4.35	16.45
	AX-90317931	13	18042528	T/G	3.89	13.17
	AX-90364912	15	5490816	C/T	3.91	16.89
	AX-90351400	16	31631250	C/T	6.81	29.27
	AX-90304999	18	46549803	G/A	3.69	13.49

候选基因 Candidate genes	同源基因 Homologous gene	功能注释 Function annotation
Glyma.01g016100	AT1G05670.1	PPR超家族蛋白PPR superfamily protein
Glyma.01g016500	AT4G25960.1	P-糖蛋白2 P-glycoprotein 2
Glyma.06g058600	AT5G21280.1	富含羟脯氨酸的糖蛋白Glycoprotein rich in hydroxyproline
Glyma.08g231800	AT1G30320.1	Remorin家族蛋白Remorin family protein
Glyma.13g042100	AT5G53140.1	蛋白磷酸酶2C家族蛋白Protein phosphatase 2C family proteins
Glyma.16g131800	AT4G36360.1	β-半乳糖苷酶3 β-galactosidase 3
Glyma.16g155300	AT3G60530.1	GATA转录因子GATA transcription factors
Glyma.16g156800	AT1G22710.1	蔗糖质子转运体2 Sucrose proton transporter 2
Glyma.16g157100	AT1G71880.1	蔗糖质子转运体1 Sucrose proton transporter 1

大豆地方种质资源鲜籽粒可溶性糖含量的全基因组关联分析

Genome Wide Association Analysis of Soluble Sugar Content in Fresh Seeds of Soybean Landraces

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