芥菜型油菜苗期氮效率相关性状全基因组关联分析

doi:10.3864/j.issn.0578-1752.2023.20.003

摘要/Abstract

摘要：

【目的】通过对芥菜型油菜苗期氮效率相关性状进行全基因组关联分析，挖掘与油菜氮效率相关性状显著关联的SNP位点，预测相关候选基因，为揭示油菜氮高效分子机制和创制氮高效种质提供理论依据。【方法】以153份芥菜型油菜品系作为关联群体，设置低氮和正常氮2个处理，每个处理设置3个重复，并在2年（2021和2022年）进行2次完全重复的营养液培养试验。计算植株根冠比和地上部氮含量的相对值（低氮/正常氮），以此作为氮效率相关性状进行全基因组关联分析（genome-wide association study，GWAS），挖掘氮效率相关候选基因。【结果】芥菜型油菜氮效率相关性状表现出丰富的变异，变异幅度为0.21—2.44，变异系数为22.92%—26.19%。全基因组关联分析检测到45个显著关联的SNP位点，其中，第一次根冠比相对值（relative root-shoot ratio 1，RRSR1）和第二次根冠比相对值（relative root-shoot ratio 2，RRSR2）共同关联到的显著SNP位点有16个，这些位点可解释的表型变异率为10.69%—15.39%。第一次地上部相对氮含量（relative shoot nitrogen concentration 1，RSNC1）和第二次地上部相对氮含量（relative shoot nitrogen concentration 2，RSNC2）共同关联到的显著SNP位点共有29个，可解释的表型变异率为13.22%—23.96%。在显著SNP位点上下游200 kb范围内共筛选出15个与氮效率相关候选基因，包括5个与硝酸盐转运相关的基因（BjuNPF5.8、BjuNRT2.7、BjuNPF2.3、BjuCLCb和BjuNRT1.3）、3个与氮代谢相关的基因（BjuASN3、BjuGLU2和BjuADCS）、4个与生长发育相关的基因（BjuCOBL8、BjuPYL6、BjuSAUR72和BjuUP3）和3个与逆境响应相关的基因（BjuNTP7、BjuJUB1和BjuPYL6）。【结论】共检测到45个与氮效率相关性状显著关联的SNP位点，筛选出15个可能与芥菜型油菜氮效率相关的候选基因。

关键词: 芥菜型油菜, 氮效率相关性状, 全基因组关联分析, 候选基因

Abstract:

【Objective】The genome-wide association analysis was performed to identify SNP loci significantly associated with nitrogen use efficiency (NUE) traits in Brassica juncea at seedling stage and to predict the relevant candidate genes, providing a theoretical basis for revealing the molecular mechanism of nitrogen use efficiency in rapeseed and creating nitrogen-efficient germplasm. 【Method】The population of 153 Brassica juncea resources was used as the analysis population. Two treatments, low N and normal N, were established using three replicates for each treatment, and two replicated nutrient culture trials were conducted over a two-year period (2021 and 2022). The relative values of root-shoot ratio and shoot nitrogen concentration (low/normal N) were calculated and utilized as NUE traits for a genome-wide association study (GWAS) aimed at exploring candidate genes for NUE. 【Result】NUE traits of Brassica juncea resources exhibited abundant variation, ranging from 0.21-2.44 with coefficients of variation of 22.92%-26.19%. The GWAS identified 45 significant SNP loci, among which 16 overlapped between the first relative root-shoot ratio (RRSR1) and the second relative root-shoot ratio (RRSR2), accounting for a phenotype variance range of 10.69%-15.39%. Additionally, 29 significant SNP loci were shared between the first relative shoot nitrogen concentration (RSNC1) and the second relative shoot nitrogen concentration (RSNC2), explaining a phenotype variance range of 13.22%-23.96%. 15 candidate genes for NUE were identified within 200 kb upstream and downstream regions of significant SNP loci, including 5 genes related to nitrate transport (BjuNPF5.8, BjuNRT2.7, BjuNPF2.3, BjuCLCb and BjuNRT1.3), 3 genes associated with nitrogen metabolism (BjuASN3, BjuGLU2 and BjuADCS), 4 genes involved in plant growth and development (BjuCOBL8, BjuPYL6, BjuSAUR72 and BjuUP3) and 3 genes participated in stress response (BjuNTP7, BjuJUB1 and BjuPYL6). 【Conclusion】45 SNP loci were detected significantly associated with NUE traits and 15 candidate genes for NUE were identified in this study.

Key words: Brassica juncea, nitrogen use efficiency traits, GWAS, candidate genes

曾健, 王茹梦, 龚盼, 杨潇, 尹晓奇, 李江鹤, 陈世龙, 姚蕾, 宋海星, 康雷, 张振华. 芥菜型油菜苗期氮效率相关性状全基因组关联分析[J]. 中国农业科学, 2023, 56(20): 3946-3959.

ZENG Jian, WANG RuMeng, GONG Pan, YANG Xiao, YIN XiaoQi, LI JiangHe, CHEN ShiLong, YAO Lei, SONG HaiXing, KANG Lei, ZHANG ZhenHua. Genome-Wide Association Study of Nitrogen Efficiency Related Traits at Seedling Stage in Brassica juncea[J]. Scientia Agricultura Sinica, 2023, 56(20): 3946-3959.

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链接本文: https://www.chinaagrisci.com/CN/10.3864/j.issn.0578-1752.2023.20.003

https://www.chinaagrisci.com/CN/Y2023/V56/I20/3946

图/表 9

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表2

关联分析中同一性状检测到的共同显著SNP位点"

性状 Trait	染色体 Chr.	SNP位置 SNP site	重复1 R1			重复2 R2
性状 Trait	染色体 Chr.	SNP位置 SNP site	P值 P value	贡献率 R²	显著性 -log₁₀(P)	P值 P value	贡献率 R²	显著性 -log₁₀(P)
RSNC	A01	3299276	4.18E-06	0.156	5.379	9.57E-06	0.151	5.019
RSNC	A01	3299282	1.50E-05	0.144	4.823	1.13E-05	0.151	4.946
RSNC	A01	5764206	2.81E-05	0.133	4.551	2.44E-08	0.216	7.613
RSNC	A01	7987047	5.17E-06	0.152	5.286	3.83E-08	0.210	7.417
RSNC	A01	9879443	2.87E-05	0.137	4.542	2.66E-05	0.141	4.575
RSNC	A02	31293392	2.80E-05	0.133	4.553	1.31E-05	0.144	4.884
RSNC	A02	4783843	2.69E-05	0.147	4.570	5.37E-06	0.173	5.270
RSNC	A02	5196424	2.93E-05	0.134	4.533	2.03E-07	0.194	6.693
RSNC	A02	5197874	2.34E-05	0.137	4.630	3.02E-08	0.216	7.520
RSNC	A02	5227749	1.76E-05	0.135	4.755	1.00E-07	0.198	6.998
RSNC	A02	5227934	8.90E-06	0.147	5.050	8.55E-08	0.206	7.068
RSNC	A02	5231658	1.85E-05	0.158	4.733	2.16E-08	0.240	7.666
RSNC	A06	11733832	2.95E-05	0.137	4.531	1.36E-05	0.151	4.866
RSNC	A07	17007356	1.45E-05	0.156	4.838	1.66E-05	0.160	4.780
RSNC	A07	17010239	2.61E-05	0.132	4.584	1.62E-05	0.140	4.791
RSNC	A07	17054911	2.43E-05	0.133	4.614	2.39E-05	0.137	4.622
RSNC	A07	17055062	2.06E-05	0.136	4.687	2.81E-05	0.135	4.551
RSNC	A07	17055097	2.23E-05	0.137	4.652	2.96E-05	0.134	4.529
RSNC	A07	17055893	1.79E-05	0.144	4.747	2.69E-05	0.141	4.571
RSNC	A07	29692636	3.08E-05	0.135	4.512	6.56E-06	0.152	5.183
RSNC	A07	29692637	3.08E-05	0.135	4.512	6.56E-06	0.152	5.183
RSNC	A07	29692699	2.60E-05	0.135	4.586	2.34E-06	0.164	5.631
RSNC	A07	29693188	1.67E-05	0.142	4.778	4.45E-06	0.157	5.351
RSNC	A07	29693225	3.03E-05	0.138	4.519	4.20E-06	0.164	5.377
RSNC	A07	29693241	8.19E-06	0.153	5.086	5.89E-06	0.160	5.230
RSNC	A07	29693269	2.27E-05	0.143	4.644	2.72E-06	0.169	5.565
RSNC	B01	54208618	1.88E-05	0.139	4.727	1.95E-05	0.143	4.710
RSNC	B01	54208847	2.12E-05	0.147	4.673	1.99E-05	0.153	4.702
RSNC	B01	54208983	2.72E-05	0.141	4.566	2.28E-05	0.145	4.643
RRSR	A01	3956738	9.38E-05	0.117	4.028	1.85E-05	0.122	4.732
RRSR	A01	3956739	9.38E-05	0.117	4.028	1.85E-05	0.122	4.732
RRSR	A02	23835765	1.25E-05	0.154	4.904	3.37E-05	0.127	4.472
RRSR	A02	23853725	2.03E-05	0.135	4.693	3.14E-05	0.120	4.504
RRSR	A02	23853762	6.77E-05	0.124	4.169	4.87E-05	0.115	4.312
RRSR	A02	23853786	6.35E-05	0.124	4.197	9.25E-05	0.107	4.034
RRSR	A02	23861655	4.36E-05	0.130	4.361	3.01E-05	0.119	4.521
RRSR	A02	23864619	4.63E-05	0.131	4.335	8.63E-05	0.108	4.064
RRSR	A02	23866416	9.28E-05	0.120	4.032	6.50E-05	0.113	4.187
RRSR	A02	23868460	9.36E-05	0.140	4.029	2.85E-05	0.141	4.546
RRSR	A02	23868483	7.52E-05	0.129	4.124	9.32E-05	0.113	4.031
RRSR	A02	23868846	3.48E-05	0.136	4.459	2.20E-05	0.126	4.658
RRSR	A02	23868869	3.75E-05	0.132	4.427	3.00E-05	0.121	4.522
RRSR	A04	20292414	7.12E-05	0.122	4.148	8.15E-05	0.108	4.089
RRSR	A04	20293014	8.62E-05	0.120	4.064	1.20E-05	0.128	4.919
RRSR	A05	22237279	2.64E-05	0.140	4.578	2.80E-05	0.122	4.553

表2

图5

表3

图6

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性状 Traits	最小值 Min	最大值 Max	均值±标准差Mean±SD	变异系数 CV (%)	相关系数 Correlation coefficient
RRSR1	0.59	2.44	1.46±0.35	23.97	0.85**
RRSR2	0.66	1.83	1.16±0.27	23.28	0.85**
RSNC1	0.29	0.83	0.48±0.11	22.92	0.95**
RSNC2	0.21	0.78	0.42±0.11	26.19	0.95**

性状 Trait	SNP位置 SNP position	显著性-log₁₀(P)		芥菜型油菜基因 Brassica juncea genes	距SNP距离 Distance (kb)	基因注释或编码蛋白 Gene annotation or coding protein	其他名称 Other names
性状 Trait	SNP位置 SNP position	重复1 R1重复2 R2		芥菜型油菜基因 Brassica juncea genes	距SNP距离 Distance (kb)	基因注释或编码蛋白 Gene annotation or coding protein	其他名称 Other names
RSNC	A01:5764206	4.551	7.613	BjuA01g08460S	116.1	天冬酰胺合成酶 Asparagine synthetase	ASN3
RSNC	A01:5764206	4.551	7.613	BjuA01g08630S	3.1	COBRA-like蛋白8 COBRA-like protein 8	COBL8
RSNC	A01:9879443	4.542	4.575	BjuA01g13530S	0.4	应激反应A/B桶状结构域蛋白 Stress responsive A/B barrel domain protein	UP3
RSNC	A02:31293392	4.553	4.884	BjuA02g37890S	21.1	NRT1/PTR家族蛋白 NRT1/PTR family protein	NPF5.8
RSNC	A02:31293392	4.553	4.884	BjuA02g38070S	119.0	NRT2家族蛋白 NRT2 family protein	NRT2.7
RSNC	A02:5231658	4.733	7.666	BjuA02g07750S	10.1	氯离子通道蛋白 Chloride channel protein	CLCb
RSNC	A07:17007356	4.838	4.780	BjuA07g16440S	13.7	氨基脱氧分支酸合成酶 Aminodeoxychorismate synthase	ADCS
RRSR	A01:3956738	4.028	4.732	BjuA01g05410S	181.1	SAUR家族蛋白 SAUR family protein	SAUR72
RRSR	A01:3956738	4.028	4.732	BjuA01g05480S	133.9	NAC转录因子 NAC transcription factor	JUB1
RRSR	A02:23835765	4.904	4.472	BjuA02g26040S	3.8	BHLH转录因子 BHLH transcription factor	BHLH109
RRSR	A02:23868869	4.427	4.522	BjuA02g26100S	15.2	NRT1/PTR家族蛋白 NRT1/PTR family protein	NPF2.3
RRSR	A04:20292414	4.148	4.089	BjuA04g25540S	112.1	脱落酸受体PYR/PYL家族蛋白 Abscisic acid receptor PYR/PYL family protein	PYL6
RRSR	A04:20293014	4.064	4.919	BjuA04g26100S	165.3	Fd-GOGAT蛋白 Fd-GOGAT protein	GLU2
RRSR	A04:20293014	4.064	4.919	BjuA04g25700S	0.0	核苷酸转移酶 Nucleotidyl transferase	NTP7
RRSR	A05:22237279	4.578	4.553	BjuA05g23430S	109.0	NRT1/PTR家族蛋白 NRT1/PTR family protein	NRT1.3