甘蓝型油菜容重及其相关性状的全基因组关联分析

doi:10.3724/SP.J.1006.2021.04245

作物学报 ›› 2021, Vol. 47 ›› Issue (11): 2099-2110.doi: 10.3724/SP.J.1006.2021.04245

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

甘蓝型油菜容重及其相关性状的全基因组关联分析

雷维¹^,²(), 王瑞莉¹, 王刘艳¹, 袁芳¹^,², 孟丽姣¹^,², 邢明礼¹^,², 徐璐¹^,², 唐章林¹^,², 李加纳¹^,², 崔翠¹^,^*(), 周清元¹^,²^,^*()

¹西南大学农学与生物科技学院, 重庆 400715
²重庆市油菜工程技术研究中心, 重庆 400715

收稿日期:2020-10-17 接受日期:2021-03-19 出版日期:2021-11-12 网络出版日期:2021-04-01
通讯作者: 崔翠,周清元
作者简介:E-mail: 1305600171@qq.com
基金资助:
国家重点研发计划项目(2018YFD0100500);国家现代农业产业技术体系建设专项(CARS-12);重庆市技术创新与应用发展项目(cstc2019jscx-msxmX0383)

Genome-wide association study of seed density and its related traits in Brassica napus L.

LEI Wei¹^,²(), WANG Rui-Li¹, WANG Liu-Yan¹, YUAN Fang¹^,², MENG Li-Jiao¹^,², XING Ming-Li¹^,², XU Lu¹^,², TANG Zhang-Lin¹^,², LI Jia-Na¹^,², CUI Cui¹^,^*(), ZHOU Qing-Yuan¹^,²^,^*()

¹College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
²Chongqing rape Engineering Technology Research Center, Chongqing 400715, China

Received:2020-10-17 Accepted:2021-03-19 Published:2021-11-12 Published online:2021-04-01
Contact: CUI Cui,ZHOU Qing-Yuan
Supported by:
National Key Research and Development Program of China(2018YFD0100500);China Agriculture Research System(CARS-12);Chongqing Technology Innovation and Application Development Project(cstc2019jscx-msxmX0383)

摘要/Abstract

摘要：

种子容重大小反映了作物光合产物在籽粒中的积累特性, 是油菜千粒重重要的组成部分, 筛选高容重种质资源, 研究容重的遗传特性在油菜遗传育种中具有非常重要的作用。本文以不同遗传背景的187份甘蓝型油菜品种(系)构成的自然群体为研究对象, 进行2年种子的容重及其相关性状(千粒重、体积)测定和资源评价, 基于最优模型对各性状进行全基因组关联分析(genome-wide association analysis, GWAS)和候选基因预测。结果显示, 187份材料在2年中容重及其关联性状在品种(系)间差异均达到显著水平(P<0.05), 筛选出3个种子千粒重较大的高容重种质资源。全基因组关联分析共检测到24个与种子容重及其相关性状显著关联的SNP位点, 可解释表型变异的8.21%~10.40%。通过单倍型分析确定关联SNP位点的Block区间, 其所在的Block覆盖了12个与容重、粒重和体积有关的候选基因, 主要编码转录因子(如WOX8、HAIKU1、AP2/ERF转录因子、Dof家族-Zinc finger超家族和BZR1转录因子)、酶类(如BKI1、KAT2、CEL1和UBP15)、DNA结合蛋白和激素响应蛋白(如ARF2和J3)。本研究结果将为进一步解析油菜千粒重的遗传机制、培育高容重油菜品种及后续基因的功能研究提供理论依据。

关键词: 甘蓝型油菜, 容重, 千粒重, 体积, 全基因组关联分析

Abstract:

Seed density reflects the accumulation characteristics of crop photosynthetic products in the grains, which plays an important role in the thousand-seed weight of rape. Selecting high seed density germplasm resources and studying the genetic characteristics of seed density are very important in the breeding of rapeseed. A natural population containing 187 Brassica napus L. varieties (lines) with different genetic backgrounds was used as plant materials to determine the seed density and its related traits (thousand-seed weight and seed volume) in the two environments. Genome-wide association study was carried out based on the optimal model and the candidate genes associated with seed density, thousand-seed weight, and seed volume was predicted. In the two years, there were significant differences in the seed density and its related traits among 187 materials at P < 0.05, and three materials with high seed density or thousand-seed weight were selected. A total of 24 SNP loci, that were significantly associated with seed density, seed weight, and seed volume, were identified by GWAS, which explained the phenotypic variation of 8.21%-10.40%. Haplotype analysis was used to determine the block interval of the SNP sites. The blocks containing 11 SNPs covered 12 candidate genes, which mainly encoded transcription factors such as WOX8, HAIKU1, AP2/ERF transcription factors, Dof family-zinc finger superfamily, BZR1 transcription factors, enzymes such as BKI1, KAT2, CEL1, UBP15, DNA binding proteins, and hormone response proteins such as ARF2 and J3. These results provide the theoretical basis for the development of high seed density rape varieties and the functional research of subsequent genes.

Key words: Brassica napus L., seed density, thousand-seed weight, seed volume, genome-wide association study (GWAS)

雷维, 王瑞莉, 王刘艳, 袁芳, 孟丽姣, 邢明礼, 徐璐, 唐章林, 李加纳, 崔翠, 周清元. 甘蓝型油菜容重及其相关性状的全基因组关联分析[J]. 作物学报, 2021, 47(11): 2099-2110.

LEI Wei, WANG Rui-Li, WANG Liu-Yan, YUAN Fang, MENG Li-Jiao, XING Ming-Li, XU Lu, TANG Zhang-Lin, LI Jia-Na, CUI Cui, ZHOU Qing-Yuan. Genome-wide association study of seed density and its related traits in Brassica napus L.[J]. Acta Agronomica Sinica, 2021, 47(11): 2099-2110.

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性状 Trait	年份 Year	最大值 Max.	最小值 Min.	均值 Average	标准差 SD	变异系数 CV (%)
籽粒容重Seed density (kg m^-3)	2018-2019	969.05	527.31	859.96^**	61.16	7.11
籽粒容重Seed density (kg m^-3)	2019-2020	946.00	433.93	804.35^**	99.47	12.37
体积Seed volume (×10^-9 m³)	2018-2019	7.30	2.58	4.60^**	0.89	19.38
体积Seed volume (×10^-9 m³)	2019-2020	11.97	1.28	3.52^**	1.27	35.93
千粒重Thousand-seed weight (×10^-3 kg)	2018-2019	5.75	1.73	3.95^**	0.76	19.24
千粒重Thousand-seed weight (×10^-3 kg)	2019-2020	7.39	0.70	2.80^**	0.89	31.79

性状 Trait	年度 Year	最大值 Max.	最小值 Min.	均值 Average	标准差 SD	变异系数 CV (%)
籽粒容重Seed density (kg m^-3)	2018-2019	969.05	860.09	901.76^**	26.41	2.93
籽粒容重Seed density (kg m^-3)	2019-2020	946.00	806.90	875.16^**	31.35	3.58
体积Seed volume (×10^-9 m³)	2018-2019	6.36	2.69	4.51^**	0.78	17.30
体积Seed volume (×10^-9 m³)	2019-2020	6.01	1.28	3.19^**	0.87	27.26
千粒重Thousand-seed weight (×10^-3 kg)	2018-2019	5.75	2.36	4.06^**	0.69	16.87
千粒重Thousand-seed weight (×10^-3 kg)	2019-2020	5.01	1.16	2.78^**	0.74	26.54

性状 Trait	容重 Seed density	体积 Seed volume	千粒重 Thousand-seed weight
容重Seed density	1	-0.29^**	0.1
体积Seed volume	-0.03	1	0.90^**
千粒重Thousand-seed weight	0.31^**	0.93^**	1

性状 Trait	环境 Environment	模型 Model	位点 SNP	染色体 Chr.	位置 Position	阈值 -log₁₀(P)	贡献率 R² (%)	基因型 Loci
容重 Seed density	2018-2019	K+PCA	Bn-A01-p6774837	A01	6194252	5.12	9.52	T/C
容重 Seed density			Bn-scaff_17067_1-p175366	C02	27613356	5.06	8.64	T/C
			Bn-A03-p8112016	C03	9899295	4.64	8.43	A/G
			Bn-scaff_16069_1-p1916253	C07	38327703	4.59	9.39	A/G
			Bn-scaff_21269_1-p313587	C08	37159594	4.53	8.54	A/G
	2019-2020	K+PCA	Bn-scaff_16394_2-p777469	C03	50479817	5.58	10.36	T/C
			Bn-scaff_16394_2-p510062	C03	50830988	4.95	9.20	T/C
体积 Seed volume	2018-2019	K+PCA	Bn-A10-p9973634	C09	40023501	4.41	8.22	A/C
体积 Seed volume	2019-2020	K+PCA	Bn-Scaffold000232-p58128	A07	826353	5.32	9.88	A/G
性状 Trait	环境 Environment	模型 Model	位点 SNP	染色体 Chr.	位置 Position	阈值 -log₁₀(P)	贡献率 R² (%)	基因型 Loci
			Bn-A07-p3618045	A07	5593584	5.32	9.88	T/C
			Bn-A10-p5210204	A10	4798717	4.43	8.25	T/G
			Bn-A10-p12933288	A10	12981101	4.88	9.07	A/C
			Bn-scaff_15838_5-p603655	C01	3432942	5.03	9.34	T/C
			Bn-scaff_17731_1-p749457	C01	7033263	4.41	8.21	A/C
			Bn-scaff_17731_1-p979512	C01	7260158	4.76	8.84	A/G
			Bn-scaff_21186_1-p36313	C04	43747053	4.65	8.65	A/G
			Bn-scaff_21566_1-p5088	C04	43859433	4.60	8.56	A/C
			Bn-scaff_16770_1-p306276	C05	35633542	5.26	9.78	T/C
			Bn-scaff_20270_1-p1211632	C05	41648492	5.04	9.37	T/C
			Bn-scaff_18439_1-p633449	C06	12752920	5.22	9.70	T/C
			Bn-scaff_15763_1-p595094	C06	20165181	4.65	8.64	T/G
			Bn-A07-p16045526	C06	26606197	4.63	8.62	A/C
千粒重Thousand-seed weight	2018-2019	K	—
	2019-2020	K	Bn-scaff_21186_1-p36313	C04	43747053	4.55	8.43	A/G
			Bn-scaff_21566_1-p5088	C04	43859433	5.62	10.40	A/C

性状 Trait	物理区间 Physical interval	甘蓝型油菜基因编号 Gene ID in B. napus	拟南芥基因 Arabidopsis gene	基因 Gene	参考文献 Reference
SD	26393356-28833356	BnaC02g28720D	AT5G42750	BKI1	[35]
	9439295-10359295	BnaC03g18470D	AT2G33150	KAT2	[36]
		BnaC03g18850D	AT5G45980	WOX8	[37]
		BnaC03g19320D	AT2G35230	IKU1	[38]
		BnaC03g19550D	AT2G35700	ERF38	[39]
	37927703-38727703	BnaC07g36540D	AT4G21030	ATDOF4.2	[40-41]
TSW	43147053-44459433	BnaC04g43460D	AT1G70710	CEL1	[42]
SV	2632942-4232942	BnaC01g06800D	AT1G17110	UBP15	[43]
	6233263-7833263	BnaC01g11380D	AT1G75080	BZR1	[35]
	43147053-44459433	BnaC04g43460D	AT1G70710	CEL1	[42]
	12082920-13422920	BnaC06g10480D	AT1G54060	ASIL1	[44]
	39083501-40963501	BnaC09g35740D	AT3G61830	ARF2	[45]
		BnaC09g36560D	AT3G44110	J3	[46]

甘蓝型油菜容重及其相关性状的全基因组关联分析

Genome-wide association study of seed density and its related traits in Brassica napus L.

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