QTL Mapping and Candidate Gene Analysis of Related Traits of Broccoli

doi:10.16420/j.issn.0513-353x.2025-0186

Acta Horticulturae Sinica ›› 2025, Vol. 52 ›› Issue (12): 3189-3201.doi: 10.16420/j.issn.0513-353x.2025-0186

• Genetic & Breeding·Germplasm Resources·Molecular Biology • Previous Articles Next Articles

QTL Mapping and Candidate Gene Analysis of Related Traits of Broccoli

GAO Xu¹, HE Daogen¹^,^*(), TAN Guoyin¹, ZHU Changzhi¹, ZHANG Hongyun², XIAO Jiarui², WANG Hui³

¹ Taizhou Acadamy of Agricultural Sciences，Taizhou，Zhejiang 318014，China
² Zhejiang Wuwangnong Seeds Shareholding Co.，Ltd，Hangzhou 310020，China
³ Taizhou Key Laboratory of Agricultural Science and Technology Innovation and Extension，Taizhou，Zhejiang 318000，China

Received:2025-05-26 Revised:2025-08-25 Online:2025-12-25 Published:2025-12-20
Contact: HE Daogen

Abstract

Abstract:

Using two high-generation inbred broccoli lines（B20101 and B736）exhibiting significant differences in curd agronomic traits as parents，a test population of 228 F₂ individuals was obtained through hybridization and selfing. By mapping QTLs related to curd agronomic traits，candidate genes were identified to lay a theoretical foundation for elucidating the molecular mechanisms of curd formation in broccoli and breeding new superior varieties. Based on resequencing technology，SNP markers and constructed a genetic map consisting of 985 bin markers（comprising 6 329 SNP markers）were developed. The map spanned 788.78 cM，with an average marker interval of 0.84 cM. Through QTL mapping analysis of curd-related agronomic traits，3，3，1，4，and 8 QTLs were detected to control stem diameter，curd diameter，curd height，single curd weight，and floret size，respectively. The phenotypic variation explained（PVE）by these QTLs ranged from 4.5689% to 21.0997%. Among them，one major QTL（LOD = 10.6897，PVE = 21.0997%）controlling floret size was mapped within an approximately 58.977 kb interval defined by SNP markers mk_18639516 and mk_18698493. Analysis of this QTL interval identified four candidate genes-Bo6g067260，Bo6g067270，Bo6g067280，and Bo6g067290-that may influence floret size in the parental lines. These genes showed significant differences in expression levels between the two parents but no sequence variations in the parental lines or the F₂ population. This suggests that variations in the regulatory regions（e.g.，promoters）of these genes may lead to differences in gene expression，thereby affecting floret size.

Key words: broccoli, agronomic traits, genetic map, QTL mapping, candidate genes

GAO Xu, HE Daogen, TAN Guoyin, ZHU Changzhi, ZHANG Hongyun, XIAO Jiarui, WANG Hui. QTL Mapping and Candidate Gene Analysis of Related Traits of Broccoli[J]. Acta Horticulturae Sinica, 2025, 52(12): 3189-3201.

Figures/Tables 11

References 56

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材料 Material	茎横径/cm Bulb transverse diameter	球横径/cm Curd transverse diameter	球纵径/cm Curd longitudinal diameter	单球质量/kg Single bulb weight of curd	蕾粒大小/cm Bud grain size
B20101（♀）	4.862 ± 0.054 a	14.206 ± 0.208 b	11.872 ± 0.322 a	0.550 ± 0.021 a	0.367 ± 0.003 a
B736（♂）	4.001 ± 0.014 c	15.079 ± 0.073 a	8.973 ± 0.041 c	0.335 ± 0.014 c	0.155 ± 0.005 c
F₁	4.569 ± 0.066 b	14.927 ± 0.185 a	9.917 ± 0.104 b	0.483 ± 0.009 b	0.214 ± 0.001 b

材料 Material	茎横径/cm Bulb transverse diameter	球横径/cm Curd transverse diameter	球纵径/cm Curd longitudinal diameter	单球质量/kg Single bulb weight of curd	蕾粒大小/cm Bud grain size
B20101（♀）	4.862 ± 0.054 a	14.206 ± 0.208 b	11.872 ± 0.322 a	0.550 ± 0.021 a	0.367 ± 0.003 a
B736（♂）	4.001 ± 0.014 c	15.079 ± 0.073 a	8.973 ± 0.041 c	0.335 ± 0.014 c	0.155 ± 0.005 c
F₁	4.569 ± 0.066 b	14.927 ± 0.185 a	9.917 ± 0.104 b	0.483 ± 0.009 b	0.214 ± 0.001 b

性状 Trait	均值 ± 标准差 Mean ± standard deviation	极大值 Maximum value	极小值 Minimum value	峰度 Kurtosis	偏度 Skewness
茎横径/cm Bulb transverse diameter	4.622 ± 0.493	5.740	3.215	-0.441	-0.135
球横径/cm Curd transverse diameter	15.024 ± 1.080	20.806	13.156	7.677	2.102
球纵径/cm Curd longitudinal diameter	9.980 ± 0.950	13.609	8.014	0.926	0.718
单球质量/kg Single bulb weight of curd	0.496 ± 0.095	0.855	0.295	1.278	0.598
蕾粒大小/cm Bud grain size	0.232 ± 0.045	0.362	0.128	0.268	0.512

性状 Trait	均值 ± 标准差 Mean ± standard deviation	极大值 Maximum value	极小值 Minimum value	峰度 Kurtosis	偏度 Skewness
茎横径/cm Bulb transverse diameter	4.622 ± 0.493	5.740	3.215	-0.441	-0.135
球横径/cm Curd transverse diameter	15.024 ± 1.080	20.806	13.156	7.677	2.102
球纵径/cm Curd longitudinal diameter	9.980 ± 0.950	13.609	8.014	0.926	0.718
单球质量/kg Single bulb weight of curd	0.496 ± 0.095	0.855	0.295	1.278	0.598
蕾粒大小/cm Bud grain size	0.232 ± 0.045	0.362	0.128	0.268	0.512

性状 Trait	球横径 Curd transverse diameter	球纵径 Curd longitudinal diameter	单球质量 Single bulb weight of curd	茎横径 Bulb transverse diameter	蕾粒大小 Bud grain size
球横径Curd transverse diameter	1.000
球纵径Curd longitudinal diameter	0.740^**	1.000
单球质量Single bulb weight of curd	0.768^**	0.752^**	1.000
茎横径Bulb transverse diameter	0.359^**	0.359^**	0.716^**	1.000
蕾粒大小Bud grain size	-0.167	-0.096	-0.210^*	-0.033	1.000

QTL Mapping and Candidate Gene Analysis of Related Traits of Broccoli

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材料 Material	测序数据量/ Gb Sequence data	GC含量/% GC content	平均Q20值/% Average Q20	比对率/% Mapped ratio	平均测序深度/× Average depth	基因覆盖率 ≥ 4× /% Gene coverage
B20101（♀）	61.9	36.07	95.72	98.27	11.62	80.45
B736（♂）	62.4	36.78	95.48	98.39	11.98	82.12
F₂群体F₂population	264.7	39.67	96.75	98.48	2.09	6.62

连锁群编号 Chain group number	SNP标记数 Number of SNP markers	Bin标记数量 Bin tag quantity	遗传图谱的长度/cM Length of genetic map	标记间平均图谱长度/cM Average map length between markers	标记间最长图谱距离/cM The longest map distance between markers
LG1	247	77	66.55	0.86	3.35
LG2	765	117	92.93	0.79	6.46
LG3	1 238	192	126.23	0.66	8.49
LG4	930	128	83.55	0.65	2.22
LG5	563	83	71.65	0.86	6.83
LG6	630	95	59.60	0.63	2.58
LG7	298	73	107.26	1.47	30.90
LG8	400	88	66.49	0.76	4.50
LG9	1 258	132	114.52	0.87	7.69
平均Average	703.2	109.44	87.64	0.84	8.11
合计Total	6 329	985	788.78	-	-

性状 Trait	染色体 Chromosome	标记位置 Marker location	两侧标记 Flanking markers	标记区间/cM Mark interval	LOD值 LOD score	PVE/%	Add
茎横径 Stem diameter	3	352	mk_59329733 ~ mk_61983136	345.5 ~ 352.5	3.8040	10.6135	-0.18
	4	191	mk_44020554 ~ mk_44308972	189.5 ~ 199.5	2.6697	6.7029	0.17
	6	69	mk_26545858 ~ mk_26599781	67.5 ~ 69.5	3.2893	9.1783	-0.07
球横径 Curd diameter	3	36	mk_5133507 ~ mk_5133762	30.5 ~ 42.5	2.8679	7.1147	-0.37
	3	276	mk_51199178 ~ mk_51261577	275.5 ~ 277.5	3.4473	9.7267	0.04
	5	51	mk_4074690 ~ mk_4153019	49.5 ~ 51.5	2.6245	7.1233	-0.11
球纵径Curd height	2	9	mk_879251 ~ mk_1150731	8.5 ~ 10.5	2.6825	8.6049	0.04
单球质量 Single curd weight	2	28	mk_2674478 ~ mk_3346265	23.5 ~ 29.5	3.7562	8.4158	0
	3	188	mk_22663199 ~ mk_23470854	184.5 ~ 189.5	3.5189	8.2725	-0.01
	6	70	mk_26599781 ~ mk_26607362	68.5 ~ 72.5	3.8045	7.9787	-0.03
	8	21	mk_23131455 ~ mk_23573175	19.5 ~ 24.5	3.1646	6.5766	0.03
蕾粒大小 Flower bud size	2	52	mk_3843139 ~ mk_3943248	46.5 ~ 56.5	2.9333	4.7347	0.19
	3	3	mk_1051774 ~ mk_2492315	0 ~ 10.5	2.7691	4.8525	0.30
	3	201	mk_24187897 ~ mk_25434737	198.5 ~ 204.5	2.8913	4.5689	-0.22
	3	228	mk_33679504 ~ mk_34006830	225.5 ~ 230.5	3.0358	4.7702	-0.24
	4	266	mk_50028229 ~ mk_50093062	263.5 ~ 268.5	2.7718	4.9079	-0.29
	5	206	mk_38951768 ~ mk_42411411	202.5 ~ 208.5	5.7033	10.3851	0.35
	6	23	mk_18639516 ~ mk_18698493	20.5 ~ 23.5	10.6897	21.0997	0.64
	7	76	mk_39797891 ~ mk_44097312	66.5 ~ 86.5	3.1648	6.7780	0.36

染色体Chromosome	基因Gene	功能Function
6	Bo6g067260	小核RNA激活复合物（SNAPc），亚基SNAP43蛋白（AT3G53270），mRNA Small nuclear RNA activating complex（SNAPc），subunit SNAP43 protein（AT3G53270），mRNA
6	Bo6g067270	功能未知Unknown function
6	Bo6g067280	β-半乳糖苷酶15（BGAL15）β-galactosidase 15（BGAL15）
6	Bo6g067290	细胞色素p450 71b5（CYP71B5）Cytochrome p450 71b5（CYP71B5）

基因Gene	亲本编号Parent number	花蕾性状Flower bud characteristics	相对表达量Relative expression level
Bo6g067260	B20101（♀）	大Large	3.485 ± 0.470 aA
Bo6g067260	B736（♂）	小Small	1.020 ± 0.236 bB
Bo6g067270	B20101（♀）	大Large	0.788 ± 0.153 aA
Bo6g067270	B736（♂）	小Small	0.273 ± 0.114 bB
Bo6g067280	B20101（♀）	大Large	0.968 ± 0.219 bB
Bo6g067280	B736（♂）	小Small	3.028 ± 0.573 aA
Bo6g067290	B20101（♀）	大Large	1.097 ± 0.249 aA
Bo6g067290	B736（♂）	小Small	0.760 ± 0.105 bA

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