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

Abstract

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)

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]

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

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