Genome Wide Association Analysis of Thousand Seed Weight in Brassica napus L.

doi:10.13560/j.cnki.biotech.bull.1985.2022-0824

Abstract

Abstract:

This study aims to excavate the SNP loci and candidate genes significantly associated with the seed number per silique（SPS）in Brassica napus L. Having 300 B. napus inbreeding lines as experimental materials, we investigated the phenotypes of SPS under two locations（Jiangxi Agricultural University（JXAU）in Nanchang and Jiangxi Institute of Red Soil（JXIRS）in Jinxian in a year. Then we conducted the genome-wide association study via general linear model（GLM）and mixed linear model（MLM）combining 201 817 SNPs markers determined previously. And finally we predicted the functions of relevant candidate genes within the 100 kb region flanking trait significantly associated SNP loci. The results showed that the broad phenotypic variations of SPS in the two locations among the 300 300 B. napus samples existed, and two germplasm with more SNP were screened. Total 39 SNPs loci remarkably associated with SPS were excavated by general linear model（GLM）. Furthermore, 3 SNPs of SPS were detected severally using the mixed linear model（MLM）, and they all were detected using GLM. And 19 candidate orthologous genes to documented Arabidopsis the seed number per silique, like CIK, ERF022 and EDE1, were found near our eight SNPs loci. The results are conducive to analyzing the genetic basis of SPS of rapeseed and would lay a foundation for studying the regulation mechanism and guiding the genetic improvement of SPS.

Key words: Brassica napu, genome-wide association study, seed number per silique, SNP loci, orthologous gene

XIAO Xiao-jun, CHEN Ming, HAN De-peng, YU Pao-lan, ZHENG Wei, XIAO Guo-bin, ZHOU Qing-hong, ZHOU Hui-wen. Genome Wide Association Analysis of Thousand Seed Weight in Brassica napus L.[J]. Biotechnology Bulletin, 2023, 39(3): 143-151.

Figures/Tables 7

References 44

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性状 Trait	环境 Environment	平均值±标准差 Mean±SD	最小值 Min	50%分位数 50% quantile	最大值 Max	变异系数 CV /%	Kolmogorov-Smirnov
每角果粒数 SPS	JXAU	17.23±2.89	7.40	17.41	24.48	16.77	P=0.729 58
每角果粒数 SPS	JXIRS	15.79±3.36	5.54	15.88	27.78	21.29	P=0.346 01

性状 Trait	环境 Environment	平均值±标准差 Mean±SD	最小值 Min	50%分位数 50% quantile	最大值 Max	变异系数 CV /%	Kolmogorov-Smirnov
每角果粒数 SPS	JXAU	17.23±2.89	7.40	17.41	24.48	16.77	P=0.729 58
每角果粒数 SPS	JXIRS	15.79±3.36	5.54	15.88	27.78	21.29	P=0.346 01

变异来源Source of variation	自由度DF（degree of freedom）	方差及占总方差的比例MS（SS/SST）/%
区组 Block	1	52.12**（7.02）
处理间 Treatment	299	20.66**（2.78）
环境 Environment/E	1	621.99**（83.80）
基因型 Genotype /G	299	26.56**（3.58）
基因型×环境 G×E	299	12.75*（1.72）
误差 Error	599	8.17（1.10）

变异来源Source of variation	自由度DF（degree of freedom）	方差及占总方差的比例MS（SS/SST）/%
区组 Block	1	52.12**（7.02）
处理间 Treatment	299	20.66**（2.78）
环境 Environment/E	1	621.99**（83.80）
基因型 Genotype /G	299	26.56**（3.58）
基因型×环境 G×E	299	12.75*（1.72）
误差 Error	599	8.17（1.10）

环境Environment	染色体 Chromosome	位置 Locus	P值P value	贡献率 R²/%	GLM	MLM
JXAU	A04	11830197	2.40E-06	11.07	●
	A05	10733464	2.32E-06	8.65	●
	A09	16100373	1.11E-06	8.87	●
	A09	16100374	1.55E-06	8.60	●
	A09	16100386	1.65E-06	8.56	●
	A09	16100422	1.39E-06	8.67	●
	A09	16100439	1.35E-06	8.76	●
	A09	16299217	1.68E-06	9.45	●
	A09	16299389	1.49E-06	9.71	●
	A09	16299462	1.13E-06	9.87	●
	A09	16299495	4.31E-07	10.38	●
	A09	16299626	4.29E-08	12.92	●
	A09	16303740	3.33E-07	9.69	●
	A09	16303768	1.98E-06	8.59	●
	A09	16366473	2.84E-06	9.82	●
	A09	17453710	1.10E-07	17.80	●
	A09	17453729	1.29E-07	17.42	●
	A09	17453891	4.02E-07	16.69	●
	A09	17471305	2.81E-06	8.66	●
	A09	17581807	3.44E-06	9.45	●
	A09	17581835	3.73E-06	9.77	●
	A09	17582057	3.16E-06	8.96	●
	C02	27389727	2.58E-06	7.91	●
	C02	27389750	1.90E-06	8.06	●
	C02	27389775	2.39E-06	7.93	●
	C02	34901810	4.35E-06	8.04	●
	C03	18955107	4.53E-06	8.52	●
	C03	21284972	3.40E-08-4.29E-06	10.85-8.9	●	○
	C03	21342259	4.40E-06	7.67	●
	C07	32557367	4.69E-06	7.48	●
	C07	42323087	8.09E-07	14.77	●
	C07	42323117	2.00E-07-3.28E-06	15.23-14.05	●	○
	C07	42323137	3.24E-06	12.97	●
	C07	42323279	4.80E-06	11.83	●
	C07	42323280	4.90E-06	11.88	●
	C08	27721260	3.47E-06	8.13	●
	C08	37461613	2.43E-06	11.73	●
JXIRS	A05	659981	5.92E-07-4.95E-06	16.00-16.75	●	○
JXIRS	A07	7482038	3.89E-06	9.63	●