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

Abstract

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

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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Figures/Tables 7

Table 1

Fig.1

Fig. 2

Table 2

Table 3

Gene information associated with significant markers"

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

Table 3

Table 4

Fig. 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

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

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