基于CAPS标记的甜瓜单果重相关性状QTL分析

doi:10.3864/j.issn.0578-1752.2019.09.011

Abstract

Abstract:

【Objective】 In our study, based on melon genome-wide resequencing technology, SNP loci were explored and CAPS markers were developed to construct a genetic linkage map. The preliminary QTL analysis of traits related to single fruit weight in melon was carried out, which laid a theoretical foundation for the detection of genes related to single fruit weight traits in melon.【Method】F_2:3 population materials were constructed from X207 and M4-130. The cultivated melon accession M4-130 was selected as female parent and wild melon accession X207 as male parent. Correlation analysis was carried out for fruit traits, including single fruit weight, fruit length, fruit width, pulp thickness, fruit shape index and soluble solids content in melon fruit. Parents were resequenced at 20× depth. SNP loci between parents were extracted in the whole genome by the use of BWA, SAMTools, VCFTools and other software. CAPS markers were developed by using SNP2CAPS software and combined with restriction endonuclease digestion sites in melon genome for genetic linkage map construction. Finally, QTLs of single fruit weight, fruit length, fruit width, pulp thickness, fruit shape index and soluble solids content in melon fruit were analyzed by composite interval mapping.【Result】In this experiment, single fruit weight significantly correlated with fruit length, fruit width and pulp thickness. 185 CAPS markers were developed and subsequently used for genetic linkage map construction. The genetic linkage map contained 12 linkage groups covering a total length of 1 600.45 cM and average distance of 8.65 cM. 7 QTLs (FW3.1, FW4.1, FW5.1, FW6.1, FW8.1, FW8.2 and FW11.1) were related to the single fruit weight. 7 QTLs (FL2.1, FL3.1, FL4.1, FL5.1, FL6.1, FL8.1 and FL11.1) were related to fruit length. 5 QTLs (FWID3.1, FWID4.1, FWID8.1, FWID10.1 and FWID11.1) were related to fruit width. 2 QTLs (FT6.1 and FT11.1) were related to pulp thickness. 1 QTLs (FS2.1) was related to fruit shape index. 2 QTLs (SS6.1 and SS12.1) were related to soluble solids content.【Conclusion】Twenty-three QTLs in total were identified. A major QTL FW8.1 was identified with phenotypic variance contribution rate of 25.8774% and the LOD value was 16.8746. It was also found that single fruit weight was closely related to fruit length, fruit width and pulp thickness. Location intervals were same or adjacent, closely concentrated on chromosomes 3, 4, 5, 6, 8 and 11.

Key words: melon, fruit weight, genetic linkage map, QTL

LIU XiangYu, ZHANG YuShu, LIU Liu, LIU Shi, GAO Peng, WANG Di, WANG XueZheng. The QTL Analysis of Single Fruit Weight Associated Traits in Melon Based on CAPS Markers[J].Scientia Agricultura Sinica, 2019, 52(9): 1601-1613.

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Figures/Tables 12

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Fig. 2

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Table 2

Fig. 4

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Table 4

QTLs and the effects of the fruit traits in melon"

性状 Trait	位点 QTL	相邻标记 Adjacent markers	图谱位置 Position	标记间距 Marker range	LOD	贡献率（%） R²	加性效应 Additive	显性效应 Dominance
单果重 Fruit weight	FW3.1	3-6670—3-0640	66	65.23—74.69	3.0173	2.7054	39.2379	32.2348
	FW4.1	4-9382—4-1311	31	27.25—31.68	3.2739	12.3435	39.6980	-14.1269
	FW5.1	5-9232—5-5773	108	105.17—108.46	2.9070	9.3215	-31.2002	23.5592
	FW6.1	6-1444—6-6615	160	106.62—160.37	3.9121	14.4755	40.7147	-20.9489
	FW8.1	8-2883—8-5972	101	98.60—104.93	16.8746	25.8774	-1.2134	184.5905
	FW8.2	8-0306—8-2169	71	65.29—72.09	3.3297	3.6869	3.6869	9.8677
	FW11.1	11-3692—11-1432	48	41.93—56.06	4.6085	18.8628	48.3023	-18.9123
果实长度 Fruit length	FL2.1	2-2347—2-1803	104	100.56—109.19	6.7436	17.0180	-1.3111	0.2646
	FL3.1	3-6670—3-0640	66	65.23—74.69	3.0160	15.1015	1.1146	0.9123
	FL4.1	4-9382—4-1311	30	27.25—31.68	4.2371	9.9603	0.9998	-0.2666
	FL5.1	5-9232—5-5773	107	105.17—108.46	2.6505	5.1442	-0.6258	0.5634
	FL6.1	6-1444—6-6615	148	106.62—160.37	3.8379	14.1998	1.1898	-0.0833
	FL8.1	8-8589—8-8413	14	00.00—14.22	2.8085	19.9334	1.3147	-0.5710
	FL11.1	11-8315—11-3692	35	30.15—41.93	6.1904	15.7421	1.2632	-0.0376
果实宽度 Fruit width	FWID3.1	3-1192—3-0090	34	18.50—46.50	3.0311	11.3927	0.6226	0.0665
	FWID4.1	4-1311—4-2962	34	31.68—42.76	3.2242	10.1598	0.7384	0.1435
	FWID8.1	8-0306—8-2169	71	65.29—72.09	5.3190	18.4669	0.7200	-0.3225
	FWID10.1	10-3838—10-0417	1	0.00—9.81	4.0028	13.2077	0.6771	0.0365
	FWID11.1	11-8315—11-3692	38	30.15—41.93	4.5617	15.8568	0.9479	-0.0865
果肉厚度 Fruit thickness	FT6.1	6-1444—6-6615	151	106.62—160.37	2.8921	12.0802	0.1414	-0.2006
果肉厚度 Fruit thickness	FT11.1	11-8315—11-3692	35	30.15—41.93	4.3730	15.2309	0.2292	-0.0031
果型指数 Fruit shape index	FS2.1	2-1803—2-2808	112	109.19—112.55	4.6355	22.0413	-0.1131	0.0923
可溶性固形物 Soluble solids	SS6.1	6-1444—6-6615	146	106.62—160.37	2.9412	16.4299	1.2740	0.2516
可溶性固形物 Soluble solids	SS12.1	12-5356—12-4957	9	0.00—19.61	3.3407	10.0947	0.1159	-1.4154

Table 4

Table 5

The table for the result of gene annotation"

GO一级类别 GO Level I Category	GO数据库二级分类编号 GO Level II Category	GO分类注释 Annotation of II level GO term	基因数量 Gene number
生物学过程 Biological process	GO: 0008152	代谢过程 Metabolic process	91
	GO: 0009987	细胞过程 Cellular process	83
	GO: 0044699	单体进程 Single-organism process	65
	GO: 0065007	生物调控 Biological regulation	31
	GO: 0050896	应激反应 Response to stimulus	20
	GO: 0071840	细胞成分组织与合成 Cellular component organization or biogenesis	19
	GO: 0051179	定位 Localization	16
	GO: 0032502	发展过程 Developmental process	11
	GO: 0032501	多细胞生物过程 Multicellular organismal process	9
	GO: 0000003	生殖过程 Reproduction	6
	GO: 0022414	再生过程 Reproductive process	6
	GO: 0023052	信号 Signaling	4
	GO: 0040007	发育过程 Growth	3
	GO: 0051704	多生物过程 Multi-organism process	3
	GO: 0022610	生物粘附 Biological adhesion	1
	GO: 0098754	去毒过程 Detoxification	1
分子功能 Molecular function	GO: 0005488	联结 Binding	95
	GO: 0003824	催化活性 Catalytic activity	81
	GO: 0005215	转运活性 Transporter activity	8
	GO: 0001071	核酸结合转录因子活性 Nucleic acid binding transcription factor activity	4
	GO: 0098772	分子功能调控 Molecular function regulator	4
	GO: 0005198	结构分子活性 Structural molecule activity	3
	GO: 0016209	抗氧化活性 Antioxidant activity	3
	GO: 0000988	蛋白质结合转录活性 Transcription factor activity, protein binding	1
	GO: 0004871	信号传感器活性 Signal transducer activity	1
	GO: 0060089	分子转导活性 Molecular transducer activity	1
细胞组分（Cellular Component）	GO: 0005623	细胞 Cell	73
	GO: 0044464	细胞组分 Cell part	73
	GO: 0043226	细胞器 Organelle	49
	GO: 0016020	细胞膜 Membrane	30
	GO: 0032991	大分子复合物 Macromolecular complex	26
	GO: 0044425	细胞膜组分 Membrane part	20
	GO: 0044422	细胞器组分 Organelle part	15
	GO: 0005576	细胞外区 Extracellular region	4
	GO: 0030054	细胞连接 Cell junction	4
	GO: 0055044	共质体 Symplast	4
	GO: 0031974	膜封闭的管腔 Membrane-enclosed lumen	3
	GO: 0019012	病毒 Virion	2
	GO: 0044423	病毒组分 Virion part	2

Table 5

Table 6

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性状 Trait	亲本及F₁均值 The mean value of and F₁ generation			F_2:3群体 Distribution in F_2:3 population
性状 Trait	母本 M4-130	父本 X207	F₁	均值 Mean	标准差 SD	范围 Range	峰度 SEK	偏度 SES
单果重 Fruit weight (g)	833.0±7.64	21.67±2.87	226.67±50.58	155.92	8.76	33.00—590.00	6.57	2.08
果实长度 Fruit length (cm)	14.20±0.40	3.63±0.23	9.83±1.27	7.87	1.92	3.80—13.30	0.09	0.43
果实宽度 Fruit width (cm)	11.40±0.20	3.30±0.17	6.57±0.31	6.01	1.42	3.00—11.00	0.79	0.74
果肉厚度 Fruit thickness (cm)	3.10±0.10	0.33±0.06	1.13±0.15	1.16	0.34	0.30—2.30	0.58	0.41
果形指数 Fruit shape index (%)	1.25±0.01	1.10±0.12	1.49±0.12	1.32	0.22	0.90—2.10	0.65	0.72
可溶性固形物含量Soluble solids (%)	8.17±0.35	10.5±0.79	10.00±2.20	9.46	1.81	5.90—14.40	-0.55	0.30

性状 Trait	单果重 Fruit weight	果实长度 Fruit length	果实宽度 Fruit width	果肉厚度 Fruit thickness	果形指数 Fruit shape	可溶性固形物含量 Soluble solids
单果重 Fruit weight	1
果实长度 Fruit length	0.873**	1
果实宽度 Fruit width	0.891**	0.832**	1
果肉厚度 Fruit thickness	0.866**	0.813**	0.854**	1
果形指数 Fruit shape	-0.018	0.284**	-0.278**	-0.065	1
可溶性固形物含量 Soluble solids	0.745**	0.706**	0.685**	0.648**	0.034	1

染色体 Chr.	标记数目 No. of Marker	长度 Genetic distance of linkage groups (cM)	标记间平均距离 Average distance of linkage groups (cM)
1	13	91.53	7.04
2	13	112.55	8.66
3	19	121.62	6.40
4	17	140.25	8.25
5	15	108.46	7.23
6	15	160.37	10.69
7	15	166.20	11.08
8	15	144.30	9.62
9	14	155.56	11.11
10	20	107.28	5.36
11	14	163.11	11.65
12	15	129.22	8.61
总计Total	185	1600.45	8.65

通路名称 Pathway	通路注释 Description of pathway	基因数目 Gene number	P值 P-value	基因 Gene
PWY-6902	几丁质降解II Chitin degradation II	6	3.70E-08	MELO3C007961, MELO3C007962, MELO3C007963, MELO3C007964, MELO3C007965, MELO3C007966
PWY-3561	胆碱生物合成III Choline biosynthesis III	2	0.0112	MELO3C007944, MELO3C007945
ASPARAGINE-DEG1-PWY	L-天冬胺酰降解I L-asparagine degradation I	1	0.0502	MELO3C008013
GLYSYN-ALA-PWY	甘氨酸生物合成III Glycine biosynthesis III	1	0.0403	MELO3C014568
PWY-6013	克螨酯生物合成Crepenynate biosynthesis	1	0.0204	MELO3C009630
PWY-6515	根皮苷生物合成 Phloridzin biosynthesis	1	0.0502	MELO3C007921
PWY-7039	磷脂代谢 Phosphatidate metabolism	2	0.0466	MELO3C007944, MELO3C007945

The QTL Analysis of Single Fruit Weight Associated Traits in Melon Based on CAPS Markers

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