Scientia Agricultura Sinica ›› 2019, Vol. 52 ›› Issue (9): 1601-1613.doi: 10.3864/j.issn.0578-1752.2019.09.011

• HORTICULTURE • Previous Articles     Next Articles

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

LIU XiangYu1,ZHANG YuShu1,LIU Liu1,LIU Shi1,GAO Peng1,WANG Di2,WANG XueZheng1()   

  1. 1 Horticulture College, Northeast Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Harbin 150030
    2 Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Daqing 163319, Heilongjiang
  • Received:2018-10-31 Accepted:2019-02-25 Online:2019-05-01 Published:2019-05-16
  • Contact: XueZheng WANG E-mail:xz6206815@163.com

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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】F2:3 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

Fig. 1

M4-130 and X207 longitudinal cut of fruit"

Table 1

Parents values of traits related to fruit of melon and distribution in F2:3 population"

性状
Trait		 亲本及F1均值
The mean value of and F1 generation		 F2:3群体
Distribution in F2:3 population
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

Fig. 2

Parent, F1 and F2:3 group fruit longitudinal cut map"

Fig. 3

Histogram for the fruit traits of F2:3 population"

Table 2

Correlation analysis of fruit traits in melon"

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

Fig. 4

DNA electrophoregram of muskmelon"

Fig. 5

Polymorphism of CAPS markers among parental materials and F1 generation M: The band of marker; P1: Band of female parent; P2: Band of male parent; F1: Band of F1 generation"

Table 3

Parameter of melon genetic linkage map"

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

Fig. 6

QTL analysis for melon fruit weight traits on genetic linkage map"

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
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
SS12.1 12-5356—12-4957 9 0.00—19.61 3.3407 10.0947 0.1159 -1.4154

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 6

Significant enrichment of metabolic pathways"

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
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