QTL Mapping for Seed Coat Color in Soybean

doi:10.13560/j.cnki.biotech.bull.1985.2026-0347

Abstract

Abstract:

Objective Seed coat color is a key quality trait in soybean. Through QTL mapping for seed coat color-related traits, this study aims to identify associated genetic loci, clarify the genetic effects underlying seed coat color, screen for key candidate genes, and provide a reference for breeding high-quality soybean varieties. Method A recombinant inbred line (RIL) population derived from a cross between cultivated soybean Jinda 53 (female) and wild soybean Pingnan (male) was used. Seed coat color was evaluated using three parameters: lightness (L),red-green value(a*), and blue-yellow value (b*). A genetic map previously constructed with SLAF markers was employed, and QTL analysis was performed using composite interval mapping. Candidate genes were screened against the SoyBase and SoyMD databases. Result Ten QTLs associated with seed coat color were identified. Two candidate regions were obtained: a 663 kb interval on chromosome 8 and a 370 kb interval on chromosome 9, harboring 11 and 6 candidate genes, respectively. Transcriptome analysis revealed that Glyma.08G103900, Glyma.08G104100, Glyma.09G191200, and Glyma.09G191700 were highly expressed in seeds and were associated with seed coat color, showing higher expression levels in Jinda 53 than in Pingnan. These were thus identified as key candidate genes. Conclusion Two pleiotropic QTLs and four novel QTLs were identified in soybean.

Key words: soybean, seed coat color, recombinant inbred line, QTL, candidate gene

LI Ya-qian, FENG Long-zhe, SUN Nan, ZHANG Yi-jie, ZHANG Hao, YANG Ya-qi, ZHANG Xin-yu, YUE Ai-qin, DU Wei-jun, WANG Min. QTL Mapping for Seed Coat Color in Soybean[J]. Biotechnology Bulletin, 2026, 42(11): 103-112.

Figures/Tables 9

References 39

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性状 Trait	年份 Year	亲本 Parents			群体 Population
性状 Trait	年份 Year	晋大53 Jinda53	平南 Pingnan	显著性 Significance	均值±标准差 Mean±SD	变幅 Range	变异系数 CV（%）	峰度 Kurtosis	偏度 Skewness	广义遗传率 H²（%）
光泽度 L^*	2017	57.25±2.72	25.79±1.42	**	31.45±13.26	12.08-86.76	42	2.09	1.14	0.99
光泽度 L^*	2019	47.54±1.50	21.57±1.56	**	28.04±9.60	12.91-51.77	34	-0.72	0.25	0.99
红绿值 a^*	2017	10.07±0.83	1.38±0.278	**	5.93±5.74	-6.34-21.26	97	-0.40	0.46	0.98
红绿值 a^*	2019	10.02±0.50	3.06±0.50	**	6.12±4.56	-1.56-17.79	75	-0.81	0.39	0.98
黄蓝值 b^*	2017	29.67±2.52	6.4±0.82	**	15.80±10.07	0.85-34.27	64	-1.40	-0.05	0.99
黄蓝值 b^*	2019	27.85±1.52	3.43±0.50	**	14.07±9.71	-1.21-32.31	69	-1.36	-0.12	0.99

性状 Trait	年份 Year	亲本 Parents			群体 Population
性状 Trait	年份 Year	晋大53 Jinda53	平南 Pingnan	显著性 Significance	均值±标准差 Mean±SD	变幅 Range	变异系数 CV（%）	峰度 Kurtosis	偏度 Skewness	广义遗传率 H²（%）
光泽度 L^*	2017	57.25±2.72	25.79±1.42	**	31.45±13.26	12.08-86.76	42	2.09	1.14	0.99
光泽度 L^*	2019	47.54±1.50	21.57±1.56	**	28.04±9.60	12.91-51.77	34	-0.72	0.25	0.99
红绿值 a^*	2017	10.07±0.83	1.38±0.278	**	5.93±5.74	-6.34-21.26	97	-0.40	0.46	0.98
红绿值 a^*	2019	10.02±0.50	3.06±0.50	**	6.12±4.56	-1.56-17.79	75	-0.81	0.39	0.98
黄蓝值 b^*	2017	29.67±2.52	6.4±0.82	**	15.80±10.07	0.85-34.27	64	-1.40	-0.05	0.99
黄蓝值 b^*	2019	27.85±1.52	3.43±0.50	**	14.07±9.71	-1.21-32.31	69	-1.36	-0.12	0.99

年份 Year	性状 Trait	光泽度 L*	红绿值 a*
2017	红绿值 a*	0.383**
2017	蓝绿值 b*	0.778**	0.586**
2019	红绿值 a*	0.502**
2019	蓝绿值 b*	0.949**	0.629**

年份 Year	性状 Trait	光泽度 L*	红绿值 a*
2017	红绿值 a*	0.383**
2017	蓝绿值 b*	0.778**	0.586**
2019	红绿值 a*	0.502**
2019	蓝绿值 b*	0.949**	0.629**

性状 Trait	QTL	位置 Position （cM）	位置区间 Location interval （cM）	物理距离 Physical distance （bp）	2017			2019
性状 Trait	QTL	位置 Position （cM）	位置区间 Location interval （cM）	物理距离 Physical distance （bp）	LOD	PVE （%）	Add	LOD	PVE （%）	Add
光泽度 L^*	qL-8	50	47.824‒50.404	7 905 824‒8 568 851	10.827	30.529	-6.952	15.312	39.077	-5.719
	qL-9	123	118.478‒123.476	42 399 568‒42 769 224	4.611	10.739	-4.138	5.913	12.806	-3.284
	qL-19	71	61.93‒71.689	41 102 103‒45 900 855	2.926	6.580	-3.224
红绿值 a^*	qa-1	32	25.748‒32.014	53 380 571‒52 253 404	3.024	6.980	-1.548	5.933	13.106	-1.662
红绿值 a^*	qa-9	121	118.478‒121.095	42 399 568‒42 578 104	13.459	35.021	-3.490	12.192	30.376	-2.546
蓝黄值 b^*	qb-8-1	50	47.824‒50.404	7 905 824‒8 568 851	23.403	45.822	-6.574
	qb-8-2	51	50.404‒51.033	8 568 851‒8 621 026				13.087	31.555	-5.088
	qb-9	123	118.478‒123.476	42 399 568‒42 769 224	10.129	15.674	-3.860	9.585	22.246	-4.289
	qb-17	127	126.428‒127.29	33 704 484‒34 031 005	2.556	3.257	-1.747
	qb-19	51	50.841‒51.66	37 230 018‒37 398 935	3.244	4.201	-2.008