Mining of Genetic Loci and Screening of Candidate Genes for Seed Tocopherol Content in Soybean

doi:10.13304/j.nykjdb.2021.0599

Abstract

Abstract:

Tocopherol plays important medical function for human health， such as preventing and curing the arteriosclerosis and cardiovascular diseases. Relative higher content of tocopherol exists in soybean seed， while the genetic loci and candidate genes for tocopherol are still largely unknown. In this paper， one recombinant inbred line （RIL） soybean population was used to assess the seed tocopherol content by the performance liquid chromatography method， and the genetic loci and candidate genes were identified by combining the SNP linkage map and transcriptome data of RIL population. The results showed that there was relative wide genetic variation of seed tocopherol in the RIL. The variation coefficients of α-， γ-， δ- and total-tocopherol contents were ranged from 9.24%~36.62%， and the variation coefficients of proportions of α-， γ- and δ-tocopherol to total-tocopherol were ranged from 5.05%~35.59%. In total， 7 pleiotropic QTLs were detected to control the various tocopherol contents with the phenotypic variation explained （PVE） 3.08%~21.92%. Among these QTLs， qTOC?A2， was identified to confer 5 related traits （α-tocopherol， δ-tocopherol， total-tocopherol contents， α-tocopherol proportion and γ-tocopherol proportion） with the PVEs 3.85%~6.77%. Meanwhile， qTOC?A1 was found to control the α-， γ-， total-tocopherol content， α-tocopherol proportion and γ-tocopherol proportion with the PVEs 6.34%~21.92%. Furthermore， some candidate genes participated in the biosynthesis pathway of soybean tocopherol， Glyma.12G014200， Glyma.12G014300 and Glyma.18G141100 etc.， were screened out for their different expression levels between the RIL parents. Thus， these results provided selection markers and candidate genes for the seed tocopherol molecular genetic improvement and genetic mechanism dissection in soybean.

Key words: soybean, tocopherol, genetic loci, candidate genes

摘要：

生育酚具有抗氧化、防止人体动脉硬化和心血管疾病等多种功效，在大豆籽粒中含量丰富，但有关其遗传位点与基因发掘工作开展甚少。鉴于此，利用大豆重组自交系群体，通过高效液相色谱鉴定其籽粒生育酚，结合群体SNP连锁图谱与转录组数据，发掘其遗传位点并筛选候选基因。结果表明，供试群体籽粒生育酚存在较大遗传变异，α-、γ-、δ-生育酚及总生育酚含量变异系数分布在9.24%~36.62%之间，各组分占比的变异系数分布在5.05%~35.59%之间；发掘到7个控制生育酚及其组分一因多效QTLs，表型贡献率范围3.08%~21.92%，其中8号染色体qTOC?A2可同时控制α-、δ-和总生育酚含量以及α-生育酚占比和γ-生育酚占比，表型贡献率范围3.85%~6.77%；5号染色体qTOC?A1可同时控制α-生育酚及其占比、γ-生育酚及其占比以及总生育酚含量，表型贡献率范围6.34%~21.92%；筛选到Glyma.12G014200、Glyma.12G014300和Glyma.18G141100等参与大豆生育酚合成代谢候选基因，为进一步开展生育酚分子遗传改良与遗传机制解析提供了选择标记及基因。

关键词: 大豆, 生育酚, 遗传位点, 候选基因

CLC Number:

S565.1

Ning QIN, Junru LI, Rui TIAN, Zhenqi SHAO, Xihuan LI, Caiying ZHANG. Mining of Genetic Loci and Screening of Candidate Genes for Seed Tocopherol Content in Soybean[J]. Journal of Agricultural Science and Technology, 2022, 24(3): 48-56.

秦宁, 李俊茹, 田蕊, 邵振启, 李喜焕, 张彩英. 大豆籽粒生育酚遗传位点发掘及候选基因筛选[J]. 中国农业科技导报, 2022, 24(3): 48-56.

Figures/Tables 7

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项目 Item	均值 Mean	标准差 SD	变异系数 CV/%	最大值 Max	最小值 Min	偏度 Skew	峰度 Kurt	显著性（P值） Sig. （P value）
α-生育酚 α-tocopherol/（μg·g^‒1）	7.10	2.60	36.62	15.48	0.91	0.39	0.15	2.54×10^‒10
γ-生育酚 γ-tocopherol/（μg·g^‒1）	127.86	12.19	9.53	165.23	97.34	0.33	-0.17	2.50×10^‒10
δ-生育酚 δ-tocopherol/（μg·g^‒1）	65.65	9.21	14.03	90.58	39.13	-0.06	-0.16	2.34×10^‒10
总生育酚 Total-tocopherol/（μg·g^‒1）	200.61	18.53	9.24	253.90	149.13	0.04	-0.12	1.67×10^‒10
α-生育酚占比 α-tocopherol proportion/%	3.54	1.26	35.59	7.62	0.56	0.34	-0.04	3.23×10^‒10
γ-生育酚占比 γ-tocopherol proportion/%	63.80	3.22	5.05	74.47	54.54	0.05	0.35	2.78×10^‒10
δ-生育酚占比 δ-tocopherol proportion/%	32.66	2.84	8.70	40.55	24.32	-0.07	0.09	2.52×10^‒10

项目 Item	均值 Mean	标准差 SD	变异系数 CV/%	最大值 Max	最小值 Min	偏度 Skew	峰度 Kurt	显著性（P值） Sig. （P value）
α-生育酚 α-tocopherol/（μg·g^‒1）	7.10	2.60	36.62	15.48	0.91	0.39	0.15	2.54×10^‒10
γ-生育酚 γ-tocopherol/（μg·g^‒1）	127.86	12.19	9.53	165.23	97.34	0.33	-0.17	2.50×10^‒10
δ-生育酚 δ-tocopherol/（μg·g^‒1）	65.65	9.21	14.03	90.58	39.13	-0.06	-0.16	2.34×10^‒10
总生育酚 Total-tocopherol/（μg·g^‒1）	200.61	18.53	9.24	253.90	149.13	0.04	-0.12	1.67×10^‒10
α-生育酚占比 α-tocopherol proportion/%	3.54	1.26	35.59	7.62	0.56	0.34	-0.04	3.23×10^‒10
γ-生育酚占比 γ-tocopherol proportion/%	63.80	3.22	5.05	74.47	54.54	0.05	0.35	2.78×10^‒10
δ-生育酚占比 δ-tocopherol proportion/%	32.66	2.84	8.70	40.55	24.32	-0.07	0.09	2.52×10^‒10

项目 Item	α-生育酚 α-tocopherol	γ-生育酚 γ-tocopherol	δ-生育酚 δ-tocopherol	总生育酚 Total-tocopherol	α-生育酚占比 α-tocopherol proportion	γ-生育酚占比 γ-tocopherol proportion
γ-生育酚 γ-tocopherol	‒0.018
δ-生育酚 δ-tocopherol	0.256^**	0.410^**
总生育酚 Total-tocopherol	0.256^**	0.859^**	0.803^**
α-生育酚占比 α-tocopherol proportion	0.966^**	‒0.237^**	0.064	0.011
γ-生育酚占比 γ-tocopherol proportion	‒0.515^**	0.298^**	‒0.713^**	‒0.231^**	‒0.479^**
δ-生育酚占比 δ-tocopherol proportion	0.154^**	‒0.233^**	0.780^**	0.256^**	0.098	‒0.921^**

项目 Item	α-生育酚 α-tocopherol	γ-生育酚 γ-tocopherol	δ-生育酚 δ-tocopherol	总生育酚 Total-tocopherol	α-生育酚占比 α-tocopherol proportion	γ-生育酚占比 γ-tocopherol proportion
γ-生育酚 γ-tocopherol	‒0.018
δ-生育酚 δ-tocopherol	0.256^**	0.410^**
总生育酚 Total-tocopherol	0.256^**	0.859^**	0.803^**
α-生育酚占比 α-tocopherol proportion	0.966^**	‒0.237^**	0.064	0.011
γ-生育酚占比 γ-tocopherol proportion	‒0.515^**	0.298^**	‒0.713^**	‒0.231^**	‒0.479^**
δ-生育酚占比 δ-tocopherol proportion	0.154^**	‒0.233^**	0.780^**	0.256^**	0.098	‒0.921^**

QTL	单个QTL Individual QTL	性状 Trait	染色体Chromo-some	左标记 Left marker	物理位置 Physical position	右标记 Right marker	物理位置 Physical position	遗传位置Genetic position	LOD	贡献率 PVE/%	加性效应 Additive	区间 Confidence interval
QTL	单个QTL Individual QTL	性状 Trait	染色体Chromo-some	左标记 Left marker	物理位置 Physical position	右标记 Right marker	物理位置 Physical position	遗传位置Genetic position	LOD	贡献率 PVE/%	加性效应 Additive	左Left	右Right
qTOC‑A2	qα‑TOC‑A2	α-生育酚 α-tocopherol	8	ss715602131	43 896 715	ss715602331	45 913 059	268.4	5.2	6.26	0.691	256.4	269.4
	qδ‑TOC‑A2	δ-生育酚 δ-tocopherol						258.2	3.6	6.77	2.726	244.6	269.4
	qTotal‑TOC‑A2	总生育酚Total-tocopherol						266.3	3.4	4.98	3.981	252.9	269.4
	qα‑/Total‑TOC‑A2	α-生育酚占比 α-tocopherol proportion						267.5	3.3	4.08	0.269	253.6	269.4
	qγ‑/Total‑TOC‑A2	γ-生育酚占比 γ-tocopherol proportion						255.1	2.5	3.85	-0.748	239.3	269.4
qTOC‑A1	qα‑TOC‑A1	α-生育酚 α-tocopherol	5	ss715591799	40 916 521	ss715591790	40 974 254	98.2	7.5	8.52	0.801	97.3	98.7
	qγ‑/Total‑TOC‑A1	γ-生育酚占比 γ-tocopherol proportion		ss715591799	40 916 521	ss715591790	40 974 254	98.2	6.0	6.34	-0.956	97.4	98.7
	qγ‑TOC‑A1	γ-生育酚 γ-tocopherol		ss715591790	40 974 254	ss715591780	41 007 475	98.7	18.1	21.92	-5.564	98.2	98.7
	qα‑/Total‑TOC‑A1	α-生育酚占比 α-tocopherol proportion		ss715591790	40 974 254	ss715591780	41 007 475	98.3	11.9	13.72	0.491	98.2	98.7
	qTotal‑TOC‑A1	总生育酚Total-tocopherol		ss715591954	39 886 822	ss715591831	40 684 517	94.3	9.1	12.32	-6.226	90.4	96.4
qTOC‑H	qα‑TOC‑H	α-生育酚 α-tocopherol	12	ss715611499	1 379 873	ss715613700	980 800	153.7	5.5	6.22	-0.685	147.8	153.7
	qα‑/Total‑TOC‑H	α-生育酚占比 α-tocopherol proportion						152.9	5.1	5.83	-0.320	147.5	157.9
	qγ‑/Total‑TOC‑H	γ-生育酚占比 γ-tocopherol proportion						153.8	3.9	4.10	0.769	150.0	156.7
qTOC‑F	qγ‑TOC‑F	γ-生育酚 γ-tocopherol	13	ss715616114	39 590 255	ss715616142	39 911 642	116.6	6.6	7.53	-3.272	115.7	119.2
qTOC‑F	qTotal‑TOC‑F	总生育酚Total-tocopherol	13	ss715616114	39 590 255	ss715616142	39 911 642	116.5	5.0	6.26	-4.454	115.7	119.4
qTOC‑G	qδ‑TOC‑G	δ-生育酚 δ-tocopherol	18	ss715629792	20 419 500	ss715629811	20 502 705	104.5	3.8	4.50	2.222	104.4	104.8
	qTotal‑TOC‑G	总生育酚Total-tocopherol		ss715629923	21 629 092	ss715629930	21 908 634	106.4	2.7	3.21	3.191	105.5	106.8
	qδ‑/Total‑TOC‑G	δ-生育酚占比 δ-tocopherol proportion		ss715629675	19 772 410	ss715629709	19 955 096	103.6	3.4	6.19	0.643	103.3	103.6
qTOC‑L	qα‑TOC‑L	α-生育酚 α-tocopherol	19	ss715633071	514 053	ss715636028	580 135	116.0	4.9	5.43	0.639	115.8	116.8
qTOC‑L	qα‑/Total‑TOC‑L	α-生育酚占比 α-tocopherol proportion	19	ss715636293	809 326	ss715636173	674 202	110.1	5.2	5.77	0.318	104.0	113.4
qTOC‑M	qγ‑TOC‑M	γ-生育酚 γ-tocopherol	7	ss715598313	5 265 136	ss715598195	4 429 189	99.2	3.5	4.43	2.503	92.2	107.6
qTOC‑M	qTotal‑TOC‑M	总生育酚Total-tocopherol	7	ss715597765	3 872 947	ss715597135	3 167 571	110.1	2.6	3.08	3.112	109.2	115.8