Genome-wide Association Study of Seed Glucosinolate Content in Brassica napus

doi:10.13560/j.cnki.biotech.bull.1985.2023-0611

Abstract

Abstract:

【Objective】To explore SNPs and candidate genes significantly associated with seed glucosinolate content in rapeseed is helpful to improving rapeseed quality and cultivating high quality rapeseed varieties. 【Method】Total 300 oilseed rapeseed inbred lines grew in the experimental field of Jiangxi Agricultural University（JXAU）and Jiangxi Institute of Red Soil and Germplasm Resources（JXIRS）, and the seed glucosinolate content（SGC）was analyzed after harvested. A total of 201 817 SNPs developed by SLAF-seq in all populations were used for genome-wide association with study（GWAS）of SGC. The 100 kb flanking regions on either side of significantly associated SNPs were used to identify candidate genes, and to perform functional annotations of these genes. 【Result】The SGC of these populations showed phenotypic variations under two environments. Based on the general linear model（GLM）the mixed linear model（MLM）, 209 SNPs were detected to have significant association with SGC, and 41 SNPs on A05（1）, A09（36）and C09（4）were detected by GLM and MLM under JXAU and JXIRS. The functional annotation of candidate genes showed that eight candidate genes participated in the glucosinolate biosynthetic process（GO:0019761）, including regulating the glucosinolate synthesis related genes MYB28（BnaC09g05290D and BnaC09g05300D）, MYB34（BnaA09g05480D）, and the glucosinolate transporter 2 related genes（BnaA09g06180D and BnaA09g06190D）. 【Conclusion】The SNPs significantly associated with SGC were detected under two environments by GLM and MLM, and the candidate genes were mined at the flanking of SNPs, which is conducive to resolving the genetic variation of SGC and providing a basis for the genetic improvement of new rapeseed varieties with low SGC.

Key words: Brassica napus, glucosinolate, GWAS, MYB transcription factor, glucosinolate transporter 2

ZHOU Hui-wen, WU Lan-hua, HAN De-peng, ZHENG Wei, YU Pao-lan, WU Yang, XIAO Xiao-jun. Genome-wide Association Study of Seed Glucosinolate Content in Brassica napus[J]. Biotechnology Bulletin, 2024, 40(1): 222-230.

Figures/Tables 6

References 45

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性状 Trait	环境 Environment	均值 Mean	标准差 SD	最小值 Min	最大值 Max	变异系数 CV/%
硫苷含量	JXAU	29.789	18.923	1.575	70.180	63.52
Glucosinolate content/（μmol·g^-1）	JXIRS	22.785	18.581	0.170	71.555	81.55

性状 Trait	环境 Environment	均值 Mean	标准差 SD	最小值 Min	最大值 Max	变异系数 CV/%
硫苷含量	JXAU	29.789	18.923	1.575	70.180	63.52
Glucosinolate content/（μmol·g^-1）	JXIRS	22.785	18.581	0.170	71.555	81.55

变异来源 Source of variation	DF	方差 Variance
区组 Block	1	166.55
环境 Environment（E）	1	14716.38**
基因型 Genotype（G）	299	1256.55**
基因×环境 G×E	299	150.11**
误差 Error	599	101.23

变异来源 Source of variation	DF	方差 Variance
区组 Block	1	166.55
环境 Environment（E）	1	14716.38**
基因型 Genotype（G）	299	1256.55**
基因×环境 G×E	299	150.11**
误差 Error	599	101.23

序号 Index	SNPs	QTLs	染色体 Chromosome	位置 Position	GLM				MLM
					JXAU		JXRIS		JXAU		JXRIS
					P值 P value	贡献率 R² /%	P值 P value	贡献率 R² /%	P值 P value	贡献率 R² /%	P值 P value	贡献率 R² /%
1	Bna_A05_11509410	qSGC.A05.1	A05	11509410	3.77E-07	4.96	1.11E-06	4.41	1.25E-06	5.72	2.63E-06	5.04
2	Bna_A09_1752479	qSGC.A09.1	A09	1752479	7.37E-09	10.10	1.74E-08	10.46	2.77E-07	11.10	1.32E-06	11.95
3	Bna_A09_2450831	qSGC.A09.2	A09	2450831	3.27E-07	6.13	5.39E-08	6.93	2.53E-06	6.89	9.11E-07	7.79
	Bna_A09_2450841	qSGC.A09.2	A09	2450841	1.68E-07	6.38	8.21E-08	6.77	1.50E-06	7.19	1.25E-06	7.60
	Bna_A09_2452752	qSGC.A09.2	A09	2452752	4.71E-09	7.23	9.60E-11	8.25	9.66E-08	7.91	7.71E-09	9.59
	Bna_A09_2464119	qSGC.A09.2	A09	2464119	2.03E-10	9.41	1.12E-10	9.05	1.57E-08	10.33	2.56E-08	10.53
	Bna_A09_2539106	qSGC.A09.2	A09	2539106	3.87E-11	9.52	8.30E-15	11.35	1.64E-09	10.76	5.67E-12	13.82
	Bna_A09_2539185	qSGC.A09.2	A09	2539185	1.45E-11	9.38	3.22E-14	10.93	9.58E-10	10.46	1.59E-11	13.23
	Bna_A09_2554018	qSGC.A09.2	A09	2554018	8.55E-13	10.57	1.20E-15	11.61	1.89E-10	11.90	3.47E-12	14.15
	Bna_A09_2554036	qSGC.A09.2	A09	2554036	7.62E-13	10.64	1.44E-15	11.62	1.67E-10	11.97	3.62E-12	14.14
	Bna_A09_2554311	qSGC.A09.2	A09	2554311	9.60E-12	9.17	1.06E-16	12.17	1.20E-09	10.19	1.01E-12	14.78
	Bna_A09_2554365	qSGC.A09.2	A09	2554365	5.74E-12	9.34	8.53E-17	12.24	8.35E-10	10.39	8.65E-13	14.87
	Bna_A09_2554384	qSGC.A09.2	A09	2554384	3.63E-12	9.49	1.82E-17	12.68	5.97E-10	10.57	3.19E-13	15.47
	Bna_A09_2554417	qSGC.A09.2	A09	2554417	3.98E-12	9.46	1.35E-17	12.76	6.34E-10	10.53	2.62E-13	15.58
	Bna_A09_2628903	qSGC.A09.2	A09	2628903	7.16E-07	6.11	1.44E-07	6.51	4.32E-06	6.85	8.45E-07	7.31
	Bna_A09_2632578	qSGC.A09.2	A09	2632578	2.80E-07	5.74	2.84E-08	6.14	1.72E-06	6.42	3.95E-07	7.50
4	Bna_A09_2943582	qSGC.A09.3	A09	2943582	2.36E-07	6.67	8.68E-09	8.03	7.87E-07	7.48	3.74E-08	9.65
	Bna_A09_2949845	qSGC.A09.3	A09	2949845	1.11E-09	8.96	6.02E-10	8.42	3.45E-08	9.93	2.80E-08	10.38
	Bnaa_A09_2950147	qSGC.A09.3	A09	2950147	8.13E-09	8.14	1.10E-09	8.20	1.06E-07	8.97	3.37E-08	10.05
	Bna_A09_3024563	qSGC.A09.3	A09	3024563	6.19E-07	5.39	1.81E-07	5.95	2.45E-06	6.20	5.18E-07	7.27
	Bna_A09_3056417	qSGC.A09.3	A09	3056417	1.18E-07	6.36	4.37E-10	8.04	5.54E-07	7.27	7.10E-09	8.98
	Bna_A09_3056427	qSGC.A09.3	A09	3056427	6.87E-08	6.56	3.42E-10	8.10	3.60E-07	7.48	5.98E-09	9.05
	Bna_A09_3065511	qSGC.A09.3	A09	3065511	5.47E-08	7.38	2.63E-10	8.55	3.89E-07	8.40	1.07E-08	10.68
	Bna_A09_3065837	qSGC.A09.3	A09	3065837	1.03E-07	7.10	1.38E-09	7.99	7.54E-07	8.02	3.74E-08	9.91
	Bna_A09_3066370	qSGC.A09.3	A09	3066370	3.85E-11	10.15	8.56E-12	10.12	1.63E-09	11.14	3.31E-09	11.91
	Bna_A09_3066514	qSGC.A09.3	A09	3066514	8.31E-09	7.71	1.42E-07	6.72	1.09E-07	8.50	2.59E-06	7.54
	Bna_A09_3095940	qSGC.A09.3	A09	3095940	8.30E-08	7.00	8.69E-12	10.05	5.25E-07	7.86	3.76E-10	11.24
	Bna_A09_3095954	qSGC.A09.3	A09	3095954	2.51E-07	6.59	1.15E-11	9.96	1.06E-06	7.39	4.63E-10	11.12
	Bna_A09_3095955	qSGC.A09.3	A09	3095955	8.18E-08	7.04	1.20E-11	9.97	4.94E-07	7.91	4.52E-10	11.14
	Bna_A09_3096314	qSGC.A09.3	A09	3096314	7.92E-07	5.57	2.70E-07	5.69	3.50E-06	6.32	1.27E-06	6.46
	Bna_A09_3096326	qSGC.A09.3	A09	3096326	2.64E-09	7.62	1.56E-11	8.46	3.74E-08	8.69	1.33E-09	10.39
5	Bna_A09_3404360	qSGC.A09.4	A09	3404360	4.08E-07	5.54	7.10E-09	6.55	3.02E-06	6.17	1.90E-07	8.05
	Bna_A09_3404402	qSGC.A09.4	A09	3404402	4.76E-07	5.49	7.07E-09	6.56	3.64E-06	6.10	1.98E-07	8.04
	Bna_A09_3404405	qSGC.A09.4	A09	3404405	3.76E-07	5.53	6.18E-09	6.56	3.02E-06	6.16	1.82E-07	8.06
6	Bna_A09_4102404	qSGC.A09.5	A09	4102404	5.66E-08	6.06	3.55E-09	7.11	3.16E-07	7.00	7.48E-08	8.09
7	Bna_A09_4616889	qSGC.A09.6	A09	4616889	8.62E-07	5.55	5.34E-08	5.95	4.48E-06	6.43	9.41E-07	7.30
	Bna_A09_4616895	qSGC.A09.6	A09	4616895	7.54E-07	5.43	3.79E-08	6.07	3.34E-06	6.18	7.82E-07	7.41
8	Bna_C09_2497414	qSGC.C09.1	C09	2497414	3.90E-07	8.12	2.35E-07	7.93	1.36E-06	8.89	1.14E-06	8.68
9	Bna_C09_3123158	qSGC.C09.2	C09	3123158	4.80E-08	8.34	1.61E-07	8.72	2.20E-06	9.11	4.01E-06	9.79
	Bna_C09_3123358	qSGC.C09.2	C09	3123358	1.05E-08	8.85	1.13E-09	9.68	6.58E-07	9.82	5.95E-08	11.60
10	Bna_C09_5569010	qSGC.C09.3	C09	5569010	2.84E-07	6.57	5.82E-07	5.93	6.77E-07	7.24	1.41E-06	7.02