Association Analysis Between Background Selection InDel Markers and Important Agronomic Traits in Inbred Lines of Chinese Cabbage

doi:10.16420/j.issn.0513-353x.2021-0242

Acta Horticulturae Sinica ›› 2021, Vol. 48 ›› Issue (7): 1282-1294.doi: 10.16420/j.issn.0513-353x.2021-0242

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Association Analysis Between Background Selection InDel Markers and Important Agronomic Traits in Inbred Lines of Chinese Cabbage

ZHAO Yujing¹, LU Yin¹, FENG Daling¹, LUO Lei¹, WU Fang², YANG Rui¹, CHEN Yueqi¹, SUN Xiaoxue¹, WANG Yanhua¹, CHEN Xueping¹, SHEN Shuxing¹^,^**(), LUO Shuangxia¹^,^**(), ZHAO Jianjun¹^,^**()

¹State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory for Vegetable Germplasm Enhancement and Utilization of Hebei/Collaborative Innovation Center of Vegetable Industry in Hebei/College of Horticulture,Hebei Agricultural University,Baoding,Hebei 071001,China
²Institute of Economic Crops,Hebei Academy of agriculture and Forestry Sciences,Shijiazhuang 050051,China

Received:2021-04-27 Revised:2021-05-21 Online:2021-07-25 Published:2021-08-10
Contact: SHEN Shuxing,LUO Shuangxia,ZHAO Jianjun E-mail:shensx@hebau.edu.cn;yylsx@hebau.edu.cn;jjz1971@aliyun.com

Abstract

Abstract:

The InDel marker for genetic background selection is beneficial to the efficient selection of Chinese cabbage breeding parents. Taking 31 inbred lines of Chinese cabbage with different ecological types as materials,InDel genetic background and association of agronomic traits were analyzed in this study. The results showed that the coefficient of variation of 31 agronomic traits varied from 15.97% to 47.63%,with an average of 32.58%,indicating that the phenotypic diversity of tested population was rich. Finally,158 polymorphic primer pairs were selected from 177 InDel primer pairs. A total of 701 polymorphic alleles were detected in 31 accessions of Chinese cabbage,with an average of 4.418 alleles per primer pair,ranging from 1 to 11. The polymorphic information content（PIC）of the marker loci ranged from 0.612 to 0.963,with an average of 0.843,and the number of effective alleles（N_e）ranged from 1.656 to 3.985,averagely 2.640. The genetic similarity coefficient（GS）of tested materials of Chinese cabbage varied greatly from 0.575 to 0.910,indicating that the genetic background of the population was quite different. According to population structure analysis,tested materials were divided into three subgroups. Association analysis showed that 22 InDel molecular markers distributed in nine linkage groups related to 12 agronomic traits,including expansion spreading,whole plant weight,head leaf number,outer leaf number,leaf width,leaf length,leaf head height,leaf head width,leaf head weight,middle rib length,central column length and plant height.

Key words: Chinese cabbage, genetic diversity, InDel, association analysis, background selection

CLC Number:

S634.1

ZHAO Yujing, LU Yin, FENG Daling, LUO Lei, WU Fang, YANG Rui, CHEN Yueqi, SUN Xiaoxue, WANG Yanhua, CHEN Xueping, SHEN Shuxing, LUO Shuangxia, ZHAO Jianjun. Association Analysis Between Background Selection InDel Markers and Important Agronomic Traits in Inbred Lines of Chinese Cabbage[J]. Acta Horticulturae Sinica, 2021, 48(7): 1282-1294.

Figures/Tables 10

References 34

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编号 No.	名称 Name	类型 Type	熟性 Maturity	叶色 Leaf color
1	B14Q-101	卵圆类型Oval type	早熟Early maturity	浅绿Light green
2	B17Q-432	卵圆类型Oval type	晚熟Late maturity	浅绿Light green
3	B14Q-109	卵圆类型Oval type	中熟Middle maturity	浅绿Light green
4	B14Q-113	卵圆类型Oval type	早熟Early maturity	浅绿Light green
5	B17Q-433	卵圆类型Oval type	中晚熟Middle late maturity	浅绿Light green
6	B14Q-124	卵圆类型Oval type	中晚熟Middle late maturity	浅绿Light green
7	B17Q-435	卵圆类型Oval type	中熟Middle maturity	浅绿Light green
8	B17Q-436	卵圆类型Oval type	早熟Early maturity	浅绿Light green
9	B17Q-437	卵圆类型Oval type	中晚熟Middle late maturity	浅绿Light green
10	B17Q-442	卵圆类型Oval type	早熟Early maturity	浅绿Light green
11	B17Q-441	直筒类型Straight tube type	中晚熟Middle late maturity	绿Green
12	B17Q-443	直筒类型Straight tube type	晚熟Late maturity	深绿Dark green
13	B17Q-444	直筒类型Straight tube type	中晚熟Middle late maturity	绿Green
14	B14Q-211	直筒类型Straight tube type	中晚熟Middle late maturity	绿Green
15	B17Q-447	直筒类型Straight tube type	中熟Middle maturity	深绿Dark green
16	B17Q-448	直筒类型Straight tube type	中熟Middle maturity	深绿Dark green
17	B14Q-209	平头类型Flat head type	早熟Early maturity	绿Green
18	B17Q-445	平头类型Flat head type	早熟Early maturity	绿Green
19	B17Q-446	平头类型Flat head type	中熟Middle maturity	绿Green
20	B14Q-141	平头类型Flat head type	早熟Early maturity	浅绿Light green
21	B17Q-439	平头类型Flat head type	极早熟Very early maturity	浅绿Light green
22	B17Q-450	平头类型Flat head type	极早熟Very early maturity	绿Green
23	B17Q-452	平头类型Flat head type	早熟Early maturity	浅绿Light green
24	B17Q-453	平头类型Flat head type	早熟Early maturity	绿Green
25	B14Q-260	花心变种Flower heart variety	极早熟Very early maturity	绿Green
26	B17Q-440	花心变种Flower heart variety	极早熟Very early maturity	黄绿Yellow green
27	B14Q-159	花心变种Flower heart variety	中熟Middle maturity	绿Green
28	B17Q-449	散叶变种Loose leaf variety	晚熟Late maturity	绿Green
29	B14Q-267	散叶变种Loose leaf variety	早熟Early maturity	绿Green
30	B14Q-279	散叶变种Loose leaf variety	早熟Early maturity	绿Green
31	B17Q-455	散叶变种Loose leaf variety	早熟Early maturity	深绿Dark green

编号 No.	名称 Name	类型 Type	熟性 Maturity	叶色 Leaf color
1	B14Q-101	卵圆类型Oval type	早熟Early maturity	浅绿Light green
2	B17Q-432	卵圆类型Oval type	晚熟Late maturity	浅绿Light green
3	B14Q-109	卵圆类型Oval type	中熟Middle maturity	浅绿Light green
4	B14Q-113	卵圆类型Oval type	早熟Early maturity	浅绿Light green
5	B17Q-433	卵圆类型Oval type	中晚熟Middle late maturity	浅绿Light green
6	B14Q-124	卵圆类型Oval type	中晚熟Middle late maturity	浅绿Light green
7	B17Q-435	卵圆类型Oval type	中熟Middle maturity	浅绿Light green
8	B17Q-436	卵圆类型Oval type	早熟Early maturity	浅绿Light green
9	B17Q-437	卵圆类型Oval type	中晚熟Middle late maturity	浅绿Light green
10	B17Q-442	卵圆类型Oval type	早熟Early maturity	浅绿Light green
11	B17Q-441	直筒类型Straight tube type	中晚熟Middle late maturity	绿Green
12	B17Q-443	直筒类型Straight tube type	晚熟Late maturity	深绿Dark green
13	B17Q-444	直筒类型Straight tube type	中晚熟Middle late maturity	绿Green
14	B14Q-211	直筒类型Straight tube type	中晚熟Middle late maturity	绿Green
15	B17Q-447	直筒类型Straight tube type	中熟Middle maturity	深绿Dark green
16	B17Q-448	直筒类型Straight tube type	中熟Middle maturity	深绿Dark green
17	B14Q-209	平头类型Flat head type	早熟Early maturity	绿Green
18	B17Q-445	平头类型Flat head type	早熟Early maturity	绿Green
19	B17Q-446	平头类型Flat head type	中熟Middle maturity	绿Green
20	B14Q-141	平头类型Flat head type	早熟Early maturity	浅绿Light green
21	B17Q-439	平头类型Flat head type	极早熟Very early maturity	浅绿Light green
22	B17Q-450	平头类型Flat head type	极早熟Very early maturity	绿Green
23	B17Q-452	平头类型Flat head type	早熟Early maturity	浅绿Light green
24	B17Q-453	平头类型Flat head type	早熟Early maturity	绿Green
25	B14Q-260	花心变种Flower heart variety	极早熟Very early maturity	绿Green
26	B17Q-440	花心变种Flower heart variety	极早熟Very early maturity	黄绿Yellow green
27	B14Q-159	花心变种Flower heart variety	中熟Middle maturity	绿Green
28	B17Q-449	散叶变种Loose leaf variety	晚熟Late maturity	绿Green
29	B14Q-267	散叶变种Loose leaf variety	早熟Early maturity	绿Green
30	B14Q-279	散叶变种Loose leaf variety	早熟Early maturity	绿Green
31	B17Q-455	散叶变种Loose leaf variety	早熟Early maturity	深绿Dark green

染色体 Chromosome	InDel数 InDel number	基因组物理位置/bp Genomic physical location	扩增片段大小/bp Amplified fragment size
A01	20	1 214 145 ~ 25 476 244	80 ~ 160
A02	14	519 753 ~ 26 721 576	88 ~ 160
A03	18	1 103 584 ~ 30 532 716	91 ~ 160
A04	15	180 352 ~ 19 056 973	100 ~ 158
A05	22	1 631 177 ~ 23 981 249	96 ~ 156
A06	22	1 820 ~ 25 083 208	92 ~ 160
A07	21	166 456 ~ 25 516 427	83 ~ 160
A08	12	1 020 793 ~ 20 443 351	86 ~ 159
A09	23	228 941 ~ 38 012 377	93 ~ 159
A10	10	1 108 151 ~ 14 947 251	94 ~ 160

染色体 Chromosome	InDel数 InDel number	基因组物理位置/bp Genomic physical location	扩增片段大小/bp Amplified fragment size
A01	20	1 214 145 ~ 25 476 244	80 ~ 160
A02	14	519 753 ~ 26 721 576	88 ~ 160
A03	18	1 103 584 ~ 30 532 716	91 ~ 160
A04	15	180 352 ~ 19 056 973	100 ~ 158
A05	22	1 631 177 ~ 23 981 249	96 ~ 156
A06	22	1 820 ~ 25 083 208	92 ~ 160
A07	21	166 456 ~ 25 516 427	83 ~ 160
A08	12	1 020 793 ~ 20 443 351	86 ~ 159
A09	23	228 941 ~ 38 012 377	93 ~ 159
A10	10	1 108 151 ~ 14 947 251	94 ~ 160

性状类型 Character type	性状 Trait	最小值Minimum	最大值Maximum	极差Range	平均值Mean	标准差Deviation	变异系数/% Coefficient of variation	H’	J
连续性性状 Continuous traits	株高Plant height	17.33	56.50	39.17	37.88	10.77	28.44	1.961	0.943
	开展度Expansion diameter	41.50	83.67	42.17	62.47	12.14	19.44	2.038	0.927
	叶片长Leaf length	24.00	58.00	34.00	40.03	9.19	22.95	2.156	0.937
	叶片宽Leaf width	16.50	37.33	20.83	25.25	4.69	18.56	1.897	0.912
	中肋厚Middle rib thickness	0.65	1.20	0.55	0.92	0.15	15.97	1.794	0.922
	中肋长Middle rib length	10.00	36.33	26.33	21.98	7.12	32.40	2.238	0.972
	中肋宽Middle rib width	4.00	8.00	4.00	5.94	0.98	16.57	1.965	0.895
	外叶数Outer leaf number	6.00	17.50	11.50	10.72	3.30	30.74	1.634	0.912
	叶球高Height of leaf head	13.00	53.00	40.00	32.96	10.67	32.38	1.965	0.945
	叶球宽Leaf head width	12.00	31.50	19.50	20.57	5.22	25.38	2.035	0.926
	球叶数Heading leaf number	21.50	56.00	34.50	37.81	8.56	22.65	2.093	0.909
间断性性状 Discrete traits	叶球质量Leaf head weight	0.55	3.50	2.95	1.88	0.81	42.81	2.139	0.929
	中心柱长Central column length	1.50	6.50	5.00	4.01	1.36	33.97	2.173	0.906
	全株质量Whole plant weight	0.60	4.25	3.65	2.52	1.10	43.57	2.044	0.983
	叶色Leaf color	1	5	4	2.77	1.04	37.59	1.111	0.801
性状类型 Character type	性状 Trait	最小值Minimum	最大值Maximum	极差Range	平均值Mean	标准差Deviation	变异系数/% Coefficient of variation	H’	J
间断性性状 Discrete traits	叶片光泽Leaf luster	1	2	1	1.13	0.35	30.51	0.393	0.567
	叶缘波状Leaf margin undulate	1	4	3	3.27	0.83	25.34	1.106	0.798
	叶缘锯齿Leaf margin serrate	1	4	3	2.53	1.14	44.87	1.134	0.818
	茸毛Pubescence	1	3	2	2.13	0.97	45.62	0.882	0.803
	叶脉鲜明度Vein freshness	1	2	1	1.90	0.31	16.06	0.325	0.469
	株形Plant shape	1	2	1	1.33	0.48	35.96	0.637	0.918
	叶形Leaf shape	1	5	4	3.33	1.09	32.80	1.327	0.825
	中肋色Middle rib color	1	4	3	2.60	0.93	35.85	1.189	0.857
	中肋形状Middle rib shape	1	2	1	1.63	0.49	30.01	0.657	0.948
	叶球形状Leaf head shape	1	5	4	2.77	1.17	42.11	1.495	0.929
	抱合方式Embracing mode	1	4	3	2.80	1.27	45.37	1.089	0.991
	球顶部形状Top shape of leaf head	1	3	2	1.93	0.83	42.81	1.095	0.997
	叶球颜色Leaf head color	1	4	3	3.07	0.74	24.12	0.904	0.652
	叶球内叶颜色 Inner leaf color of leaf head	1	3	2	1.53	0.73	47.63	0.912	0.830
	中心柱形状Center column shape	1	4	3	2.70	1.15	42.56	1.301	0.939
	熟性Maturity	1	5	4	2.73	1.23	45.00	1.486	0.923

Association Analysis Between Background Selection InDel Markers and Important Agronomic Traits in Inbred Lines of Chinese Cabbage

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自交系Inbred line	特征引物Specific primer	自交系Inbred line	特征引物Specific primer
B14Q-101	A10-3	B17Q-442	A01-5
B14Q-109	A10-3	B17Q-444	A10-8
B14Q-209	A09-14、09-15	B17Q-446	A01-17、A02-3、A02-14、A03-2、A04-8、A05-1、A05-17、A06-5、A06-7、A06-8、A06-9、A07-4、A07-5、A07-7、A07-11、A09-3、A09-6、A09-9
B14Q-260	A04-10、A05-7	B17Q-448	A01-10
B14Q-279	A02-11、A06-4、A06-6、A06-18、A07-13、A09-10	B17Q-449	A07-12
B17Q-439	A07-6	B17Q-455	A05-1、A05-10、A07-6、A09-3、A09-17
B17Q-441	A10-3

序号 No.	材料编号 Code	遗传相似系数 GS coefficient			序号 No.	材料编号 Code	遗传相似系数 GS coefficient
序号 No.	材料编号 Code	平均值 Average	最大值 Max	最小值 Min	序号 No.	材料编号 Code	平均值 Average	最大值 Max	最小值 Min
1	B14Q-101	0.688	0.750 (B17Q-440)	0.609 (B14Q-279)	17	B17Q-444	0.709	0.765 (B17Q-447)	0.656 (B17Q-432)
2	B17Q-432	0.712	0.781 (B17Q-442)	0.634 (B17Q-446)	18	B14Q-209	0.663	0.854 (B14Q-113)	0.575 (B17Q-446)
3	B14Q-109	0.682	0.785 (B14Q-113)	0.616 (B17Q-455)	19	B14Q-211	0.718	0.859 (B17Q-441)	0.647 (B17Q-435)
4	B14Q-113	0.699	0.854 (B14Q-209)	0.598 (B17Q-446)	20	B17Q-445	0.713	0.796 (B14Q-211)	0.620 (B14Q-267)
5	B17Q-433	0.693	0.738 (B17Q-442)	0.619 (B17Q-446)	21	B17Q-446	0.671	0.760 (B14Q-141)	0.575 (B14Q-209)
6	B14Q-124	0.708	0.792 (B17Q-450)	0.625 (B14Q-209)	22	B17Q-447	0.716	0.844 (B17Q-442)	0.620 (B17Q-453)
7	B17Q-435	0.680	0.752 (B17Q-432)	0.630 (B14Q-260)	23	B17Q-448	0.721	0.775 (B17Q-442)	0.656 (B17Q-446)
8	B17Q-436	0.707	0.768 (B14Q-141)	0.661 (B17Q-455)	24	B17Q-449	0.681	0.740 (B17Q-452)	0.597 (B14Q-209)
9	B17Q-437	0.686	0.804 (B14Q-141)	0.615 (B14Q-209)	25	B17Q-450	0.732	0.910 (B17Q-439)	0.606 (B14Q-209)
10	B14Q-141	0.740	0.872 (B17Q-439)	0.621 (B14Q-209)	26	B14Q-260	0.701	0.779 (B17Q-450)	0.590 (B14Q-209)
11	B17Q-439	0.735	0.910 (B17Q-450)	0.605 (B14Q-209)	27	B17Q-452	0.681	0.740 (B17Q-449)	0.614 (B14Q-209)
12	B17Q-440	0.703	0.778 (B14Q-159)	0.624 (B14Q-279)	28	B14Q-267	0.661	0.715 (B17Q-432)	0.608 (B17Q-446)
13	B14Q-159	0.702	0.778 (B17Q-440)	0.650 (B17Q-435)	29	B17Q-453	0.685	0.729 (B14Q-159)	0.620 (B17Q-447)
14	B17Q-441	0.717	0.859 (B14Q-211)	0.638 (B17Q-452)	30	B14Q-279	0.672	0.739 (B17Q-455)	0.609 (B14Q-101)
15	B17Q-442	0.742	0.844 (B17Q-447)	0.676 (B14Q-209)	31	B17Q-455	0.688	0.758 (B17Q-444)	0.616 (B14Q-109)
16	B17Q-443	0.704	0.760 (B17Q-445)	0.640 (B14Q-267)	平均 Mean		0.700

变种 Variety	生态型Ecological type	自交系份数 No. of inbred lines	平均遗传相似系数 Average of GS
结球大白菜 Chinese cabbage	卵圆类型Oval type	10	0.700
	平头类型Flat head	8	0.703
	直筒类型Straight tube type	6	0.714
花心大白菜 Flower heart Chinese cabbage		3	0.702
散叶大白菜 Loose leaf Chinese cabbage		4	0.676
平均Average			0.699

引物编号 Primer ID	位置 Position	正向引物序列 Forward primer	反向引物序列 Reverse primer	产物大小/bp Product size
A01-19	24837737	AGAGAGAAGACCCATAAGCC	CACGAAGTCGAGAGGAAATA	110
A02-9	21774955	CTCCAGAGACAACTTTCAGC	TCACTTGTAATCCTTGAGCA	103
A03-5	4727108	ACCGTTTGCCATTATATACG	TCATTCTCTCCAATCACACA	91
A05-6	6340979	ACGTCGTCGTATTGAACTCT	TGCTTCTTCTGGAGTGTCTT	143
A05-14	16436310	CCTGCACATTATCCATCTTT	AATGACCCAGTAGATCAGGT	156
A05-16	18659064	GGGACAACTCAATTACACCT	ACACCACCGTCTCAGAATAC	126
A06-12	16861849	TCCTTTTCTTTGAAGTGTGG	GAACAATCACCACTAAACCC	154
A06-13	18292827	GGACCAGTTATCGTTTTGTC	CATAAGAAAAACTATCCGGC	92
A06-15	19392228	ACAAATCTGAACAACGAAGG	ACAAATAGATCGCGATAAGG	105
A07-5	4537468	GCTAGTCCACAGCAAATGAT	TTGGCTTCTTCTTCACTGAT	135
A07-13	16364142	GGGAAGCAATCTAACAGAAA	GGTGTAGACATGTTTCAAAGG	148
A07-14	17219194	CCTGAAGCAAGAAGTGCTAT	TTTCTGCTACGGGTAAGTTG	149
A07-16	20894341	CCACATGTAGTCACTGCAAC	AAGATGCTCAAGAAGTGCTC	136
A07-18	22027474	GTGAATGTAGACGACACACG	AATCTTCAAGCTTTCACTCG	149
A09-3	1283777	CTCCCACTTTTGAAGTTCTG	TGATATTTTCGATGACCTGG	129
A09-7	12459199	CGTTCTTCAGTGTGATTCAA	TATGAGTTAACACCCCTTGG	121
A09-8	16434839	TGTTAGATACTCCTCCACTCA	TGTCTCTCAACAACTTCGAG	108
A09-9	21909939	CTATGAACCATCCCAAAGAA	CAGCTTAATTTGCAACATCC	136
A10-3	3030502	AACATGATGCTGATAGGTCC	CTCTTTGATTTGAAGAGTGACC	101
A10-4	3775136	CAGCTCTCTCTCTTCAGTGG	CTATTAACCGTGGATTGGTC	145
A10-7	11696916	TTCTAATTTGTGCAGAGTCC	AACTTTGTCTGCGTGATGAT	130
A10-10	14947251	AAACAAAACAGGAAGTGGTG	AGAGATATTGAGGCCCATTT	133

引物编号 Primer ID	关联性状 associated traits	引物编号 Primer ID	关联性状 associated traits
A01-19	全株质量、叶球质量 Whole plant weight,leaf head weight	A07-14	叶片长、叶球高、中肋长、株高 Leaf length,leaf head height,middle rib length,plant height
A02-9	叶片宽Leaf width	A07-16	叶片宽Leaf width
A03-5	全株质量、叶球质量 Whole plant weight,leaf head weight	A07-18	叶片宽Leaf width
A05-6	叶片长Leaf length	A09-3	叶片长、叶球高、中肋长、株高 Leaf length,leaf head height,middle rib length,plant height
A05-14	中肋长、株高 Middle rib length,plant height	A09-7	叶片长Leaf length
A05-16	外叶数Outer leaf number	A09-8	球叶数Heading leaf number
A06-12	开展度、叶片宽 Expansion diameter,leaf width	A09-9	全株质量、叶球宽、叶球质量 Whole plant weight,leaf head width,leaf head weight
A06-13	叶球高、株高 Leaf head height,plant height	A10-3	全株质量Whole plant weight
A06-15	叶球高Leaf head height	A10-4	中心柱长Central column length
A07-5	叶球高Leaf head height	A10-7	全株质量、外叶数、叶球宽度、叶球质量 Whole plant weight,outer leaf number,leaf head width,leaf head weight
A07-13	叶球宽Leaf head width	A10-10	叶球宽Leaf head width

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