甘蓝型油菜角果长度性状的全基因组关联分析

doi:10.3724/SP.J.1006.2019.94021

Abstract

Abstract:

Silique length is a key agronomic trait of rapeseed. Moderately increasing silique length is conducive to high seed yield by enlarging photosynthetic area and seed volume. A collection of 496 representative rapeseed accessions was genotyped by the Illumina 60K SNP array, and phenotyped for silique length in four environments. The genome-wide association study (GWAS) of silique length was performed via the MLM (Mixed linear model) and GLM (General linear model). Seven loci and 25 loci were detected with MLM and GLM, which explained 25.01% and 41.77% of the phenotypic variance, respectively. Combining the common loci between two models, we finally got 27 unique loci, of which seven were overlapped with reported QTLs, and 20 were new one. Bn-A09-p29991443, the most effective locus, was located on chromosome A09, accounting for 13.89% and 12.86% of the phenotypic variance in MLM and GLM, respectively. Silique length of accessions with the favorable allele of Bn-A09-p29991443 was averagely 0.89 cm longer than that with the unfavorable allele. The cloned silique length genes ARF18 and BnaA9.CYP78A9 in rapeseed was found to be colocalized with Bn-A09-p29991443. Besides, five candidates including GID1b, FUL, EOD3, DOF4.4 and GA20ox1, orthologous to documented Arabidopsis silique length genes, were found near our GWAS loci. The results provide an insight into the genetic basis of silique length and lay a foundation for further mechanism exploration and breeding for this trait in B. napus.

Key words: Brassica napus L, yield, silique length, GWAS, SNP

SUN Cheng-Ming,CHEN Song,PENG Qi,ZHANG Wei,YI Bin,ZHANG Jie-Fu,FU Ting-Dong. Genome-wide association study of silique length in rapeseed (Brassica napus L.)[J].Acta Agronomica Sinica, 2019, 45(9): 1303-1310.

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环境 Environment	最小值 Min.	最大值 Max.	平均值±标准差 Mean ± SD	变异系数 CV
2013/2014 Nanjing	3.42	11.37	5.40±1.01	0.19
2013/2014 Nanjing	3.28	15.80	6.39±1.25	0.20
2014/2015 Taizhou	3.31	10.18	5.79±0.88	0.15
2015/2016 Taizhou	4.01	9.94	5.90±0.77	0.13

	2012/2013 Nanjing	2013/2014 Nanjing	2014/2015 Taizhou
2013/2014 Nanjing	0.57^***
2014/2015 Taizhou	0.64^***	0.70^***
2015/2016 Taizhou	0.56^***	0.57^***	0.75^***

标记 Marker	染色体 Chr.	位置 Position	-lg (P)	表型变异 R² (%)	环境 Environment	已报道QTL Reported QTL
Bn-A07-p8572785	A07	10,018,929	5.80	5.10	13NJ/15TZ
Bn-A09-p28925363	A09	26,858,796	5.15	4.92	13NJ/15TZ	[8, 22]
Bn-A09-p29991443	A09	27,815,620	13.59	13.89	13NJ/14NJ/15TZ	[6, 8, 22, 23]
Bn-scaff_15712_2-p492440	C02	38,697,584	4.67	3.54
Bn-scaff_17869_1-p813291	C04	9,884,407	5.41	4.73	14NJ /15TZ
Bn-scaff_20817_1-p60579	C04	48,635,772	4.56	4.27	15TZ
Bn-scaff_15576_1-p68473	C09	41,121,951	4.29	3.21	13NJ/15TZ

标记 Marker	染色体 Chr.	位置 Position	-lg (P)	表型变异 R² (%)	环境 Environment	已报道QTL Reported QTL
Bn-A02-p11454573	A02	8,166,563	4.61	3.72	13NJ/14NJ/15TZ
Bn-A03-p4408895	A03	3,938,915	4.39	2.91
Bn-scaff_16092_1-p866917	A03	18,418,252	4.74	4.66	13NJ/15TZ
Bn-scaff_27914_1-p34836	A06	15,544,511	6.21	5.30	15TZ/16TZ
Bn-A06-p23042849	A06	22,092,944	4.72	3.85	15TZ/16TZ
Bn-A07-p1228602	A07	860,252	4.51	3.76	16TZ
Bn-A10-p12099059	A07	2,762,935	5.02	3.38	15TZ/16TZ
Bn-A07-p7606228	A07	9,162,030	6.03	4.90	13NJ/15TZ/16TZ	[23]
Bn-A07-p8572785	A07	10,018,929	9.38	7.76	13NJ/15TZ/16TZ
Bn-A07-p10340211	A07	11,509,208	4.45	3.70	15TZ/16TZ
Bn-A07-p13957160	A07	15,884,413	5.18	4.20	15TZ/16TZ	[23]
Bn-A07-p18319586	A07	20,221,220	5.14	4.33	14NJ/15TZ	[6, 23]
Bn-A09-p3051349	A09	2,971,335	4.31	3.32	15TZ
Bn-A09-p28925363	A09	26,858,796	6.08	4.89	13NJ/15TZ/16TZ	[8, 22]
Bn-A09-p29991443	A09	27,815,620	16.27	12.86	13NJ/14NJ/15TZ/16TZ	[6, 8, 22, 23]
Bn-A10-p3966740	A10	885,133	6.47	4.46	13NJ/14NJ/15TZ/16TZ	[6]
Bn-A10-p15793623	A10	15,756,213	4.60	3.65
Bn-scaff_17177_1-p381225	C02	44,843,894	5.12	4.13	15TZ
Bn-A05-p4304172	C04	6,449,454	6.96	5.75	14NJ/15TZ/16TZ
Bn-scaff_27914_1-p9919	C04	28,255,420	7.06	6.09	13NJ/14NJ/15TZ/16TZ
Bn-scaff_20817_1-p60579	C04	48,635,772	7.98	6.89	13NJ/14NJ/15TZ/16TZ
Bn-scaff_16069_1-p1668600	C07	38,086,007	6.38	5.29	15TZ/16TZ
Bn-scaff_16069_1-p3731985	C07	40,142,298	5.92	4.63	13NJ/14NJ/15TZ/16TZ
Bn-scaff_16361_1-p241830	C08	27,753,144	4.34	3.48	13NJ	[9]
Bn-scaff_15576_1-p68473	C09	41,121,951	5.47	3.72	14NJ/15TZ/16TZ

标记 Marker	油菜基因 Rapeseed gene	染色体 Chr.	位置 Position	拟南芥同源基因 Ar. homolog	参考基因组 Ref. genome
Bn-A07-p13957160	BnaA07g19530	A07	15,590,253	GID1b	Darmor-bzh
Bn-A09-p3051349	BnaA09g05500	A09	2,718,832	FUL	Darmor-bzh
Bn-scaff_20817_1-p60579	BnaC04g50960	C04	48,343,005	EOD3	Darmor-bzh
Bn-scaff_16069_1-p1668600	BnaC07g36530	C07	38,575,790	DOF4.4	Darmor-bzh
Bn-scaff_16069_1-p3731985	BnaC07g39650	C07	40,392,394	GA20ox1	Darmor-bzh
Bn-A09-p29991443	BnA09g0377700	A09	36,712,502	ARF18	ZS11
Bn-A09-p29991443	BnA09g0377760	A09	36,740,578	CYP78A9	ZS11

Genome-wide association study of silique length in rapeseed (Brassica napus L.)

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