基于QTL定位和全基因组关联分析筛选甘蓝型油菜株高和一次有效分枝高度的候选基因

doi:10.3724/SP.J.1006.2020.94067

Abstract

Abstract:

Plant height (PH) and the first branch height (BH) are important agronomic traits closely related to thickness of pod canopy and harvest index of Brassica napus. There are many reports on quantitative trait locus (QTL) and genome-wide association study (GWAS) for PH, but few reports on QTL and GWAS localization and candidate gene screening for BH. In this study, QTLs for PH and BH using the 186 recombinant inbred lines (RIL) in the two environments of 2016 and 2017 were detected based on the high-density genetic linkage map. A total of eight PH QTLs located on chromosomes A03, A04, and A09 were detected in the two environments of 2016 and 2019, with the explained phenotypic variation of individual QTL range from 4.60% to 13.29%, among which overlapped QTLs (q-2017PH-A04-2 and q-BLUP-PH-A04-2) were detected both in 2017 and based on Best Linear Unbiased Prediction (BLUP). Nine BH QTLs located on chromosomes A01, A02, A05, A09, C01, and C05 were detected, in which a single QTL explained 5.12% to 19.10% of phenotypic variation. Among them, q-2017BH-A09-1, q-BLUP-BH-A09-2, and q-BLUP-BH-A09-3 were overlapped. GWAS for PH and BH was performed using 588 resequencing natural populations established by our previous study. A total of 50 SNPs associated with PH and 12 SNPs associated with BH were detected in two years. Thirteen PH candidate genes involved in cell proliferation, cell multiplication, cell cycle and cell wall activity and eleven BH candidate genes involved in the synthesis and metabolism of gibberellin and spermidine, ribosome composition, photosynthesis and germination were screened based on the physical locations of SNPs, and their expressions in extreme phenotypes by qRT-PCR. This result will provide a theoretical basis for improving plant architecture and subsequent functional studies of genes.

Key words: Brassica napus, plant height, first branch height, gene localization, candidate gene screening

HUO Qiang,YANG Hong,CHEN Zhi-You,JIAN Hong-Ju,QU Cun-Min,LU Kun,LI Jia-Na. Candidate genes screening for plant height and the first branch height based on QTL mapping and genome-wide association study in rapessed (Brassica napus L.)[J].Acta Agronomica Sinica, 2020, 46(02): 214-227.

Figures/Tables 10

Table 1

Table 2

Fig. 1

Fig. 2

Table 3

Putative QTLs for plant height and the first branch height detected in two years"

位点 QTL	染色体 Chr.	阈值 LOD score	加性效应 Additive effect	贡献率 R² (%)	标记区间 SNP interval	物理区间 Physical position (bp)	环境 Environment
株高 PH
q-2016PH-A03-1	A03	2.87	4.27	13.29	SNP6093-SNP6075	18421721-18543828	2016
q-2016PH-A09-1	A09	3.51	-3.81	11.28	KS30880-H112B21-1		2016
q-2017PH-A04-1	A04	2.79	2.71	4.92	SNP8751-SNP8781	14085289-14244618	2017
q-2017PH-A04-2	A04	3.26	2.93	5.75	SNP8596-SNP8650	13373664-13531885	2017
q-2017PH-A09-1	A09	5.20	-5.58	9.63	SNP46371-SNP20466	22590345-23259990	2017
q-2017PH-A09-2	A09	4.16	-5.81	7.55	SNP20486-SNP20487	23517031-23521212	2017
q-2017PH-A09-3	A09	4.72	-5.40	8.51	SNP20492-SNP20496	23603951-23642701	2017
q-2017PH-A09-4	A09	4.31	-4.55	7.86	KS10551-KS10551		2017
q-BLUP-PH-A04-1	A04	4.25	1.43	7.60	SNP8701-SNP8801	13798050-14401987	BLUP
q-BLUP-PH-A04-2	A04	3.45	1.31	6.27	SNP8596-SNP8650	13373664-13531885	BLUP
q-BLUP-PH-A09-1	A09	2.60	-1.36	4.60	ENA22-niab_ssr003		BLUP
一次有效分枝高度 BH
q-2016BH-A02-1	A02	4.14	6.24	13.56	SNP3957-SNP3759	22556597-23778808	2016
q-2016BH-C05-1	C05	5.26	7.49	19.10	SNP26887-SNP26897	4224409-4258940	2016
q-2017BH-A01-1	A01	4.78	-5.53	9.15	SNP1148-SNP1370	17881769-19687948	2017
q-2017BH-A01-2	A01	3.08	-4.64	6.03	SNP47359-SNP1693	20189127-21190484	2017
q-2017BH-A09-1	A09	2.69	-3.46	5.36	SNP21394-SNP46209	32375997-32618214	2017
q-2017BH-C01-1	C01	6.16	6.22	12.17	SNP38247-SNP38236	11120369-11162114	2017
q-BLUP-BH-A05-1	A05	2.76	1.25	5.12	SNP11708-SNP11713	20293807-20374178	BLUP
q-BLUP-BH-A09-1	A09	4.60	-1.66	9.32	SNP21425-SNP21477	32728408-33029776	BLUP
q-BLUP-BH-A09-2	A09	6.52	-1.95	13.09	SNP21413-SNP21402	32435925-32608817	BLUP
q-BLUP-BH-A09-3	A09	4.62	-1.64	9.48	SNP21405-SNP21415	32514368-32619386	BLUP
q-BLUP-BH-C05-1	C05	2.77	1.23	5.51	SNP44674-SNP47114	11206177-11417643	BLUP

Table 3

Fig.3

Supplementary table 1

Summary of significant SNPs for plant height and the first branch height by using the best model"

性状 Trait	环境 Env.	模型 Model	位点 SNP	染色体 Chr.	位置 Position	域值 -lg (P)	贡献率 R² (%)
PH	2016	K+PCA	S3_24415510	A03	24415510	5.69	20.05
	2017	K+PCA	S2_4664084	A02	4664084	5.84	6.72
			S7_19604035	A07	19604035	6.24	7.41
			S7_19609237	A07	19609237	6.01	6.81
			S7_19665408	A07	19665408	5.85	7.06
			S7_19781536	A07	19781536	5.87	7.36
			S7_19889261	A07	19889261	5.64	7.20
			S7_19890772	A07	19890772	5.66	6.94
			S7_19902486	A07	19902486	5.77	7.52
			S7_19993228	A07	19993228	5.63	6.59
			S7_19993448	A07	19993448	6.07	6.88
			S7_19993458	A07	19993458	5.69	6.42
			S7_19994131	A07	19994131	6.45	7.69
			S7_19997901	A07	19997901	5.71	6.67
			S7_19998470	A07	19998470	6.37	7.52
			S7_19999615	A07	19999615	6.07	7.05
			S7_19999649	A07	19999649	5.63	7.52
			S7_20000927	A07	20000927	6.31	7.47
			S7_20003694	A07	20003694	5.79	6.83
			S7_20005472	A07	20005472	6.67	7.80
			S7_20006012	A07	20006012	6.50	7.73
			S7_20006528	A07	20006528	5.87	7.09
			S7_20009397	A07	20009397	5.86	6.67
			S7_20009417	A07	20009417	6.19	7.04
			S7_20033861	A07	20033861	6.11	6.88
			S7_20050137	A07	20050137	5.96	8.10
			S7_20050232	A07	20050232	6.22	7.74
			S7_20053742	A07	20053742	6.72	7.72
			S7_20056543	A07	20056543	5.65	6.53
			S7_20079034	A07	20079034	5.76	7.36
			S7_20107214	A07	20107214	7.69	9.22
			S7_20107455	A07	20107455	6.40	7.44
			S7_20107531	A07	20107531	6.31	8.24
			S7_20108117	A07	20108117	5.75	6.74
			S7_20125834	A07	20125834	6.37	7.28
			S7_20144336	A07	20144336	6.16	7.20
			S7_20154451	A07	20154451	6.42	8.22
			S7_20160199	A07	20160199	5.84	7.20
			S7_20171415	A07	20171415	5.87	6.65
			S7_20171839	A07	20171839	6.46	7.34
			S7_20178594	A07	20178594	6.55	7.85
			S7_20178844	A07	20178844	6.23	7.54
			S7_20178851	A07	20178851	5.93	7.18
			S7_20186093	A07	20186093	5.79	6.56
			S7_20188262	A07	20188262	5.83	6.87
			S7_20207662	A07	20207662	5.72	6.70
			S7_20547520	A07	20547520	5.71	6.83
			S16_30960716	C06	30960716	6.60	7.81
			S16_30960741	C06	30960741	7.02	8.31
			S16_31108747	C06	31108747	5.89	6.78
	BLUP	K+PCA	S2_4664084	A02	4664084	6.36	7.07
			S2_5390778	A02	5390778	5.90	7.03
			S7_19604035	A07	19604035	6.64	7.71
			S7_19607230	A07	19607230	6.02	6.75
			S7_19609237	A07	19609237	5.96	6.47
			S7_19665408	A07	19665408	6.05	6.92
			S7_19749218	A07	19749218	6.29	7.29
			S7_19781536	A07	19781536	6.10	7.37
			S7_19856864	A07	19856864	5.73	6.34
			S7_19889261	A07	19889261	5.75	7.08
			S7_19902486	A07	19902486	5.92	7.19
			S7_19902495	A07	19902495	5.69	7.19
			S7_19902618	A07	19902618	5.59	6.50
			S7_19911177	A07	19911177	5.83	6.72
			S7_19923829	A07	19923829	5.68	6.33
			S7_19923850	A07	19923850	5.84	6.42
			S7_19989673	A07	19989673	5.61	6.35
			S7_19993448	A07	19993448	6.07	6.54
			S7_19993458	A07	19993458	5.61	6.01
			S7_19994131	A07	19994131	6.02	6.74
			S7_19997901	A07	19997901	6.04	6.71
			S7_19998042	A07	19998042	5.80	6.38
			S7_19998470	A07	19998470	5.88	6.50
			S7_19999615	A07	19999615	6.09	6.66
			S7_20000927	A07	20000927	6.31	7.10
			S7_20003694	A07	20003694	6.14	6.84
			S7_20005472	A07	20005472	6.76	7.50
			S7_20006012	A07	20006012	6.97	7.94
			S7_20006186	A07	20006186	5.73	6.36
			S7_20006210	A07	20006210	5.77	6.38
			S7_20006234	A07	20006234	5.81	6.73
			S7_20006528	A07	20006528	6.10	7.05
			S7_20008610	A07	20008610	5.71	6.89
			S7_20009397	A07	20009397	6.23	6.79
			S7_20009417	A07	20009417	6.59	7.15
			S7_20030774	A07	20030774	5.75	6.16
			S7_20050137	A07	20050137	6.12	7.78
			S7_20050232	A07	20050232	6.84	8.25
			S7_20050979	A07	20050979	5.61	6.24
			S7_20053742	A07	20053742	6.52	7.07
			S7_20057981	A07	20057981	5.77	7.00
			S7_20082865	A07	20082865	5.76	7.54
			S7_20107214	A07	20107214	7.94	8.87
			S7_20107455	A07	20107455	6.83	7.64
			S7_20107531	A07	20107531	7.26	9.02
			S7_20108117	A07	20108117	5.95	6.64
			S7_20125834	A07	20125834	6.23	6.77
			S7_20144336	A07	20144336	6.62	7.31
			S7_20154451	A07	20154451	6.55	7.99
			S7_20160199	A07	20160199	6.36	7.53
			S7_20171415	A07	20171415	6.24	6.68
			S7_20171839	A07	20171839	6.30	6.80
			S7_20178594	A07	20178594	6.59	7.55
			S7_20178844	A07	20178844	5.93	6.86
			S7_20186093	A07	20186093	6.22	6.69
			S7_20188262	A07	20188262	6.11	6.84
			S7_20198799	A07	20198799	5.65	6.49
			S7_20207662	A07	20207662	5.79	6.43
			S7_20429083	A07	20429083	5.63	6.38
			S7_20547520	A07	20547520	6.69	7.75
			S7_20567053	A07	20567053	5.67	6.06
			S12_38247607	C02	38247607	5.70	6.43
			S16_30166343	C06	30166343	5.96	6.92
			S16_30650628	C06	30650628	5.62	6.27
			S16_30960716	C06	30960716	6.66	7.47
			S16_30960741	C06	30960741	7.24	8.08
			S16_31108747	C06	31108747	6.36	6.99
BH	2016	K	S13_3400444	C03	3400444	5.67	16.87
			S13_12620221	C03	12620221	5.70	16.89
			S14_36535069	C04	36535069	5.76	18.36
			S19_41983822	C09	41983822	5.75	17.28
	2017	K+PCA	S2_1549097	A02	1549097	5.80	7.63
			S2_1553600	A02	1553600	6.39	7.73
			S2_5424292	A02	5424292	6.14	7.01
			S2_5503092	A02	5503092	6.19	7.32
			S2_5827516	A02	5827516	6.66	7.95
			S2_6130942	A02	6130942	5.76	7.02
			S12_10249838	C02	10249838	6.06	6.23
			S15_7059739	C05	7059739	5.92	6.80
	BLUP	K+PCA	S2_1553600	A02	1553600	5.81	6.55
			S2_5503092	A02	5503092	6.09	6.83
			S2_5827516	A02	5827516	6.81	7.69
			S2_9351215	A02	9351215	5.98	6.95
			S2_9351221	A02	9351221	5.89	6.82
			S12_10249838	C02	10249838	5.62	6.32
			S15_7059739	C05	7059739	6.00	6.49

Supplementary table 1

Table 4

Candidate genes for plant height and the first branch height"

基因 Gene	物理位置 Physical position	拟南芥同源基因 Homologs in A. thaliana	功能注释 Functional annotation
株高PH
BnaA02g09200D	A02:4555438-4557323	AT5G55180	O-Glycosyl hydrolases family 17 protein (MCO15.13)
BnaA02g09270D	A02:4576434-4582446	AT5G55120	GDP-L-galactose phosphorylase VITAMIN C DEFECTIVE 5 (VTC5)
BnaA03g47940D	A03:24664280-24664459	AT4G26320	Arabinogalactan protein 13 (AGP13)
BnaA04g17050D	A04:13894646-13897338	AT5G65940	Beta-hydroxyisobutyryl-CoA hydrolase 1 (CHY1)
BnaA04g17120D	A04:13961721-13963012	AT2G29350	Senescence-associated gene 13 (SAG13)
BnaA04g17490D	A04:14227152-14227949	AT2G30370	Allergen-like protein (CHAL)
BnaA07g27280D	A07:19859720-19860312	AT1G68590	Ribosomal protein PSRP-3/Ycf65
BnaA07g28720D	A07:20705370-20707220	AT1G70210	CYCD1;1/CYCLIN D1;1
BnaA07g28820D	A07:20767232-20773649	AT1G70710	Glycosyl hydrolase 9B1 (GH9B1)
BnaC02g35320D	C02:38070292-38074778	AT2G04030	Chaperone protein htpG family protein (CR88)
BnaC06g30260D	C06:31058017-31061313	AT1G68580	Agenet domain-containing protein / bromo-adjacent homology (BAH) domain-containing protein (F24J5.18)
BnaC06g30400D	C06:31172511-31173663	AT1G69220	Protein kinase superfamily protein (SIK1)
BnaC06g30410D	C06:31173893-31177895	AT1G69220	Protein kinase superfamily protein (SIK1)
一次有效分枝高度BH
BnaA01g25960D	A01:18111689-18112090	AT3G47370	Ribosomal protein S10p/S20e family protein (RPS20B)
BnaA01g27550D	A01:19232447-19236961	AT3G16840	P-loop containing nucleoside triphosphate hydrolases superfamily protein (RH13)
BnaA01g28120D	A01:19629034-19630394	AT3G16240	Delta tonoplast integral protein (DELTA-TIP)
BnaA01g29630D	A01:20485424-20487751	AT3G14067	Subtilase family protein (SASP)
BnaA01g30830D	A01:21042542-21043677	AT3G12145	Leucine-rich repeat (LRR) family protein (FLOR1)
BnaA02g37010D	A02:1536206-1537938	AT5G61780	TUDOR-SN protein 2 (Tudor2)
BnaA02g31980D	A02:23032463-23034656	AT5G25460	Transmembrane protein, putative (Protein of unknown function, DUF642) (DGR2)
BnaA09g48360D	A09:32409788-32410789	AT1G09580	Emp24/gp25L/p24 family/GOLD family protein (F14J9.28)
BnaA09g49220D	A09:32795595-32796344	AT1G07830	Ribosomal protein L29 family protein (F24B9.7)
BnaC02g14570D	C02:10095432-10098417	AT5G53120	Spermidine synthase 3 (SPDS3)
BnaC02g14600D	C02:10119161-10122317	AT5G53090	NAD(P)-binding Rossmann-fold superfamily protein (MFH8.1)

Table 4

Fig. 4

Fig. 5

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基因名 Gene name	引物序列 Primer sequence (5°-3°)
BnaA03g47940D	F: ATGGAGGCAATGAAGATGAAAC; R: GATAGACAAAGAAGCATCAGAG
BnaA07g28720D	F: CAGCTTCTTCGCTTACAAGATC; R: ATGCTCGATGGCTTATACTCAA
BnaA07g28820D	F: TTTTACTCGTCGTGCTTCTCTC; R: GACCTTCGAAAAACATGATGCT
BnaC06g30400D	F: ACAAGAATAATCGTTCTGCTGC; R: CCAACAGTTTCACTCTTCAAGG
BnaC06g30410D	F: TGGAAGCGTTACTGATTTGATG; R: TGAATATTGAGTGCAAGTAAGC
BnaA01g29630D	F: ATAAAGACTCTATCGCGATCGG; R: ATCCAAGGAGCGATATTAGTGG
BnaA01g30830D	F: ACTCTTTCGGTTCTTTTGTTGG; R: GTTTTGTTACGTCCGAAGAACA
BnaA02g31980D	F: GACGATGTCAAGCTTATAAGCG; R: TAACCCCTAAACAAACCTCTCC
BnaA02g37010D	F: TTCTTGAATTGGCAGAACGATC; R: CTTCCGTGACAACAACCTTTAG
BnaA09g48360D	F: CAGTCAAAGCCATCCATGAAAA; R: CGAAGCTAATAGTGTGTTGGTG
BnaA09g49220D	F: TTGCTTCTTTTGTCAACCTAGC; R: CAGAAACAGTGCATACAGCTAC
BnaC02g14570D	F: GTGTTCTCAGGGAGATATCTCG; R: CACGAGGATCTTCAAATCCAAC

性状 Trait	群体 Population	年份 Year	均值±标准差 Mean ± SD	范围 Range	变异系数 CV (%)	广义遗传力 h² (%)
ZY821父本株高	RIL	2016	190.80±6.85
ZY821♂ PH		2017	184.33±11.74
GH06母本株高	RIL	2016	217.40±5.61
GH06♀ PH		2017	187.33±10.8
ZY821父本一次有效分枝高度	RIL	2016	86.25±5.35
ZY821♂ BH		2017	68.63±11.54
GH06母本一次有效分枝高度	RIL	2016	83.00±6.70
GH06♀ BH		2017	95.14±15.67
株高PH	RIL	2016	213.82±11.20	187.0-241.6	5.24	75.45
		2017	207.26±11.91	163.0-238.4	5.75	75.45
	N	2016	211.84±18.15	162.2-259.0	8.57	87.42
		2017	204.39±20.76	127.4-262.4	10.16	87.42
一次有效分枝高度BH	RIL	2016	85.26±15.84	49.6-118.0	18.58	68.77
		2017	82.85±14.69	50.1-123.6	17.73	68.77
	N	2016	84.17±22.43	19.0-142.8	26.65	82.21
		2017	82.90±23.09	11.0-141.1	27.86	82.21

Candidate genes screening for plant height and the first branch height based on QTL mapping and genome-wide association study in rapessed (Brassica napus L.)

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