甜瓜果肉硬度KASP标记的开发与应用

doi:10.16420/j.issn.0513-353x.2023-0287

摘要/Abstract

摘要：

为提高不同果肉硬度类型甜瓜材料的选择效率，以脆肉甜瓜自交系20S11和软肉甜瓜自交系20S75为亲本，构建F₂与BC₁F₁群体，分析了果肉硬度性状的遗传规律为单基因遗传，脆肉相对于软肉为显性。根据F₂分离群体构建果肉硬度极端性状混池，利用全基因组重测序结合图位克隆技术，将果肉硬度基因CmPf1定位在10号染色体上约54.71 kb的区域内。通过重测序分析发现，软肉甜瓜20S75中编码GATL3（galacturonosyltransferase-like 3）的基因MELO3C012216（CmGATL3）存在1处终止密码突变，位于编码区第567位碱基处（C-G），导致蛋白翻译提前终止，造成转移酶蛋白结构域完全缺失。利用qRT-PCR对CmGATL3进行表达模式分析，结果显示其在脆肉甜瓜20S11中的表达量显著高于软肉甜瓜20S75。基于上述变异位点，开发PF-KASP分子标记并对56份甜瓜自交系材料进行基因型检测，其中脆肉材料均表现为C︰C型，软肉材料均表现为G︰G型，标记呈共显性。进一步利用PF-KASP对F₂群体进行基因型鉴定，与果肉硬度表型鉴定结果相比较，准确率达到100%。

关键词: 甜瓜, 果肉硬度, 基因定位, KASP标记, 辅助选择育种

Abstract:

In order to improve the selection efficiency of melon materials with different pulp firmness types. The crispy melon inbred line 20S11 and the soft melon inbred line 20S75 were used as parents to construct F₂ and BC₁F₁ populations，analyzed the fruit pulp firmness trait is inherited by a single gene，and crispy is dominant relative to soft. A mixed pool of extreme fruit flesh hardness traits was constructed based on the F₂ segregation population. Using whole genome sequencing combined with map based cloning technology，the pulp firmness gene CmPf1 was located in a region of approximately 54.71 kb on chromosome 10. Through resequencing analysis，it was found that the gene MELO3C012216（CmGATL3） encoding GATL3（galacturonosyltransferase-like 3）in 20S75 had a termination codon mutation located at the 567th base（C-G）of the coding region，leading to early termination of protein translation and resulting in complete deletion of the transferase protein domain. The expression pattern analysis of CmGATL3 using qRT-PCR showed that the expression level in crispy melon 20S11 was significantly higher than that in soft melon 20S75. Based on the above mutation sites，PF-KASP molecular marker was developed and performed genotype detection on 56 melon inbred line materials. Among them，the crisp materials were C︰C type，and the soft materials were G︰G type，and the markers were codominance. Further utilizing PF-KASP for genotype identification of F₂ population，compared with the results of pulp firmness phenotype identification，the accuracy reached 100%.

Key words: melon, pulp firmness, gene mapping, KASP marker, assisted selection breeding

李肯, 张伟, 武云鹏, 彭冬秀, 张若纬. 甜瓜果肉硬度KASP标记的开发与应用[J]. 园艺学报, 2024, 51(4): 773-786.

LI Ken, ZHANG Wei, WU Yunpeng, PENG Dongxiu, ZHANG Ruowei. Development and Utilization of KASP Marker for Identification of Pulp Firmness in Melon[J]. Acta Horticulturae Sinica, 2024, 51(4): 773-786.

图/表 10

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引物名称 Primer	正向引物（5′-3′） Forward primer	反向引物（5′-3′） Reverse primer
P1-25	CATAACCCTAATTCTAATTTCCCC	AACTGAATCTCCTATATGCGTAGC
P2-14	AGATTTAGTTGTCATTCATTCGTATT	TGAGAGACATTGCTTTTCATTTTT
P2-19	TTATCTGTGACTATTTCACCTAAAA	CATTTTTCTCTCTATTATTCACTCTG
P6-8	TTCTTGGGTCTTACTTTCTTATTT	AACCCTATCATCCATCTTATCTCT
P7-2	TAAAAAGGATAAAAAATGGTGG	AACCCTACTTTCCAAATCACTT
P9-27	TTTCTTTCTTTGTCATCCATTTA	TGAAATACGCAATGGAGGA
P12-32	AGTGCTGAAATTACTTTTTGTCG	ATTTTTTATGATTTTTTGTTATTTGA
MELO3C012216-1	TTCGTACCTCAACTACGATCAC	ATCAGCCATTGAATTACGCGA
MELO3C012216-2	CGAGAATGTACTTAGCAGAATC	TGTTGAAGGAGTTGAGCATCGA
MELO3C012216-3	ATGGAACCAACATGGGTTGGAC	TTAGCTAAGTGCCTTACGGATC
CmGATL3-q	AATTCGCATGGCAATACTCC	CGCGGTTAATCGAATCATCT
CmActin-q	CCGTTCTGTCCCTCTACGCTAGTG	GGAACTGCTCTTTGCACTCTCGAG
PF-KASP	1：GCCATGCGAATTTTACGAACTAC	AGATGCTAAGAAGCCTTGTCCACT
PF-KASP	2：TATTGCCATGCGAATTTTACGAACTAG	AGATGCTAAGAAGCCTTGTCCACT

引物名称 Primer	正向引物（5′-3′） Forward primer	反向引物（5′-3′） Reverse primer
P1-25	CATAACCCTAATTCTAATTTCCCC	AACTGAATCTCCTATATGCGTAGC
P2-14	AGATTTAGTTGTCATTCATTCGTATT	TGAGAGACATTGCTTTTCATTTTT
P2-19	TTATCTGTGACTATTTCACCTAAAA	CATTTTTCTCTCTATTATTCACTCTG
P6-8	TTCTTGGGTCTTACTTTCTTATTT	AACCCTATCATCCATCTTATCTCT
P7-2	TAAAAAGGATAAAAAATGGTGG	AACCCTACTTTCCAAATCACTT
P9-27	TTTCTTTCTTTGTCATCCATTTA	TGAAATACGCAATGGAGGA
P12-32	AGTGCTGAAATTACTTTTTGTCG	ATTTTTTATGATTTTTTGTTATTTGA
MELO3C012216-1	TTCGTACCTCAACTACGATCAC	ATCAGCCATTGAATTACGCGA
MELO3C012216-2	CGAGAATGTACTTAGCAGAATC	TGTTGAAGGAGTTGAGCATCGA
MELO3C012216-3	ATGGAACCAACATGGGTTGGAC	TTAGCTAAGTGCCTTACGGATC
CmGATL3-q	AATTCGCATGGCAATACTCC	CGCGGTTAATCGAATCATCT
CmActin-q	CCGTTCTGTCCCTCTACGCTAGTG	GGAACTGCTCTTTGCACTCTCGAG
PF-KASP	1：GCCATGCGAATTTTACGAACTAC	AGATGCTAAGAAGCCTTGTCCACT
PF-KASP	2：TATTGCCATGCGAATTTTACGAACTAG	AGATGCTAAGAAGCCTTGTCCACT

序号 No.	材料 Accession	变种 Varieties	剖面 TPA	穿刺 Puncture		类型 Type
序号 No.	材料 Accession	变种 Varieties	硬度/g Hardness	硬度/N Hardness	脆性/N · S Brittleness	类型 Type
1	20S11	var. inodorus	2 532.25 a	1.75 a	4.13 a	脆 Crisp
2	20S75	var. reticulatus	375.27 b	0.72 b	1.31 b	软 Soft
3	Sa-1	var. cantalupensis	2 486.14 a	1.69 a	4.02 a	脆 Crisp
4	Sa-2	var. inodorus	2 583.11 a	1.76 a	3.91 a	脆 Crisp
5	Sa-3	var. inodorus	2 478.58 a	1.67 a	3.87 a	脆 Crisp
6	Sa-4	var. inodorus	2 528.72 a	1.72 a	4.21 a	脆 Crisp
7	Sa-5	var. inodorus	2 393.23 a	1.64 a	3.95 a	脆 Crisp
8	Sa-6	var. inodorus	2 284.21 a	1.43 a	4.08 a	脆 Crisp
9	Sa-7	var. inodorus	2 308.44 a	1.45 a	3.85 a	脆 Crisp
10	Sa-8	var. inodorus	2 388.28 a	1.48 a	3.94 a	脆 Crisp
11	Sa-9	var. inodorus	2 420.87 a	1.64 a	3.61 a	脆 Crisp
12	Sa-10	var. cantalupensis	2 595.64 a	1.78 a	3.24 a	脆 Crisp
13	Sa-11	var. cantalupensis	2 406.85 a	1.64 a	4.11 a	脆 Crisp
14	Sa-12	var. cantalupensis	2 544.94 a	1.76 a	3.34 a	脆 Crisp
15	Sa-13	var. cantalupensis	2 222.65 a	1.46 a	4.40 a	脆 Crisp
16	Sa-14	var. cantalupensis	2 330.32 a	1.59 a	4.90 a	脆 Crisp
17	Sa-15	var. cantalupensis	2 234.62 a	1.47 a	3.31 a	脆 Crisp
18	Sa-16	var. chinensis	2 503.79 a	1.73 a	4.27 a	脆 Crisp
19	Sa-17	var. chinensis	2 381.80 a	1.65 a	4.60 a	脆 Crisp
20	Sa-18	var. chinensis	2 503.78 a	1.75 a	3.52 a	脆 Crisp
21	Sa-19	var. chinensis	2 553.73 a	1.74 a	3.33 a	脆 Crisp
22	Sa-20	var. chinensis	2 477.75 a	1.68 a	4.01 a	脆 Crisp
23	Sa-21	var. conomon	2 497.37 a	1.68 a	3.47 a	脆 Crisp
24	Sa-22	var. conomon	2 278.44 a	1.49 a	4.47 a	脆 Crisp
25	Sa-23	var. conomon	2 376.49 a	1.57 a	4.89 a	脆 Crisp
26	Sa-24	var. inodorus	1 875.73 ab	1.59 a	2.84 ab	酥脆 Crumbly
27	Sa-25	var. inodorus	1 841.34 ab	1.55 a	2.48 ab	酥脆 Crumbly
28	Sa-26	var. inodorus	1 889.78 ab	1.61 a	2.45 ab	酥脆 Crumbly
29	Sa-27	var. inodorus	1 787.89 ab	1.47 a	2.47 ab	酥脆 Crumbly
30	Sa-28	var. inodorus	1 807.25 ab	1.52 a	2.50 ab	酥脆 Crumbly
31	Sa-29	var. inodorus	1 721.63 ab	1.46 a	2.09 ab	酥脆 Crumbly
32	Sa-30	var. inodorus	1 713.83 ab	1.45 a	2.18 ab	酥脆 Crumbly
33	Sa-31	var. inodorus	1 643.27 ab	1.44 a	2.77 ab	酥脆 Crumbly
34	Sa-32	var. inodorus	1 818.11 ab	1.53 a	2.94 ab	酥脆 Crumbly
35	Sa-33	var. inodorus	1 618.49 ab	1.46 a	2.57 ab	酥脆 Crumbly
36	Sa-34	var. chinensis	1 693.06 ab	1.48 a	2.33 ab	酥脆 Crumbly
37	Sa-35	var. chinensis	1 795.75 ab	1.51 a	2.97 ab	酥脆 Crumbly
38	Sa-36	var. chinensis	1 697.48 ab	1.47 a	2.58 ab	酥脆 Crumbly
39	Sa-37	var. conomon	1 753.49 ab	1.49 a	2.83 b	酥脆 Crumbly
40	Sa-38	var. conomon	1 767.93 ab	1.44 a	2.26 b	酥脆 Crumbly
41	Sa-39	var. reticulatus	328.26 b	0.66 b	1.25 b	软 Soft
42	Sa-40	var. reticulatus	305.93 b	0.63 b	1.23 b	软 Soft
43	Sa-41	var. reticulatus	492.32 b	0.61 b	0.92 b	软 Soft
44	Sa-42	var. reticulatus	346.18 b	0.68 b	1.28 b	软 Soft
45	Sa-43	var. reticulatus	390.25 b	0.71 b	1.32 b	软 Soft
46	Sa-44	var. reticulatus	373.48 b	0.69 b	1.30 b	软 Soft
47	Sa-45	var. reticulatus	383.63 b	0.37 b	1.33 b	软 Soft
48	Sa-46	var. reticulatus	487.27 b	0.60 b	1.44 b	软 Soft
49	Sa-47	var. reticulatus	298.04 b	0.39 b	0.84 b	软 Soft
50	Sa-48	var. reticulatus	314.58 b	0.43 b	0.93 b	软 Soft
51	Sa-49	var. chinensis	346.86 b	0.48 b	0.98 b	软 Soft
52	Sa-50	var. chinensis	522.23 b	0.65 b	1.11 b	软 Soft
53	Sa-51	var. chinensis	366.96 b	0.67 b	1.27 b	软 Soft
54	Sa-52	var. conomon	334.83 b	0.65 b	1.25 b	软 Soft
55	Sa-53	var. conomon	477.69 b	0.59 b	0.89 b	软 Soft
56	Sa-54	var. conomon	415.18 b	0.63 b	1.03 b	软 Soft
57	Sa-55	var. conomon	312.23 b	0.43 b	0.92 b	软 Soft
58	Sa-56	var. conomon	338.12 b	0.67 b	1.28 b	软 Soft

序号 No.	材料 Accession	变种 Varieties	剖面 TPA	穿刺 Puncture		类型 Type
序号 No.	材料 Accession	变种 Varieties	硬度/g Hardness	硬度/N Hardness	脆性/N · S Brittleness	类型 Type
1	20S11	var. inodorus	2 532.25 a	1.75 a	4.13 a	脆 Crisp
2	20S75	var. reticulatus	375.27 b	0.72 b	1.31 b	软 Soft
3	Sa-1	var. cantalupensis	2 486.14 a	1.69 a	4.02 a	脆 Crisp
4	Sa-2	var. inodorus	2 583.11 a	1.76 a	3.91 a	脆 Crisp
5	Sa-3	var. inodorus	2 478.58 a	1.67 a	3.87 a	脆 Crisp
6	Sa-4	var. inodorus	2 528.72 a	1.72 a	4.21 a	脆 Crisp
7	Sa-5	var. inodorus	2 393.23 a	1.64 a	3.95 a	脆 Crisp
8	Sa-6	var. inodorus	2 284.21 a	1.43 a	4.08 a	脆 Crisp
9	Sa-7	var. inodorus	2 308.44 a	1.45 a	3.85 a	脆 Crisp
10	Sa-8	var. inodorus	2 388.28 a	1.48 a	3.94 a	脆 Crisp
11	Sa-9	var. inodorus	2 420.87 a	1.64 a	3.61 a	脆 Crisp
12	Sa-10	var. cantalupensis	2 595.64 a	1.78 a	3.24 a	脆 Crisp
13	Sa-11	var. cantalupensis	2 406.85 a	1.64 a	4.11 a	脆 Crisp
14	Sa-12	var. cantalupensis	2 544.94 a	1.76 a	3.34 a	脆 Crisp
15	Sa-13	var. cantalupensis	2 222.65 a	1.46 a	4.40 a	脆 Crisp
16	Sa-14	var. cantalupensis	2 330.32 a	1.59 a	4.90 a	脆 Crisp
17	Sa-15	var. cantalupensis	2 234.62 a	1.47 a	3.31 a	脆 Crisp
18	Sa-16	var. chinensis	2 503.79 a	1.73 a	4.27 a	脆 Crisp
19	Sa-17	var. chinensis	2 381.80 a	1.65 a	4.60 a	脆 Crisp
20	Sa-18	var. chinensis	2 503.78 a	1.75 a	3.52 a	脆 Crisp
21	Sa-19	var. chinensis	2 553.73 a	1.74 a	3.33 a	脆 Crisp
22	Sa-20	var. chinensis	2 477.75 a	1.68 a	4.01 a	脆 Crisp
23	Sa-21	var. conomon	2 497.37 a	1.68 a	3.47 a	脆 Crisp
24	Sa-22	var. conomon	2 278.44 a	1.49 a	4.47 a	脆 Crisp
25	Sa-23	var. conomon	2 376.49 a	1.57 a	4.89 a	脆 Crisp
26	Sa-24	var. inodorus	1 875.73 ab	1.59 a	2.84 ab	酥脆 Crumbly
27	Sa-25	var. inodorus	1 841.34 ab	1.55 a	2.48 ab	酥脆 Crumbly
28	Sa-26	var. inodorus	1 889.78 ab	1.61 a	2.45 ab	酥脆 Crumbly
29	Sa-27	var. inodorus	1 787.89 ab	1.47 a	2.47 ab	酥脆 Crumbly
30	Sa-28	var. inodorus	1 807.25 ab	1.52 a	2.50 ab	酥脆 Crumbly
31	Sa-29	var. inodorus	1 721.63 ab	1.46 a	2.09 ab	酥脆 Crumbly
32	Sa-30	var. inodorus	1 713.83 ab	1.45 a	2.18 ab	酥脆 Crumbly
33	Sa-31	var. inodorus	1 643.27 ab	1.44 a	2.77 ab	酥脆 Crumbly
34	Sa-32	var. inodorus	1 818.11 ab	1.53 a	2.94 ab	酥脆 Crumbly
35	Sa-33	var. inodorus	1 618.49 ab	1.46 a	2.57 ab	酥脆 Crumbly
36	Sa-34	var. chinensis	1 693.06 ab	1.48 a	2.33 ab	酥脆 Crumbly
37	Sa-35	var. chinensis	1 795.75 ab	1.51 a	2.97 ab	酥脆 Crumbly
38	Sa-36	var. chinensis	1 697.48 ab	1.47 a	2.58 ab	酥脆 Crumbly
39	Sa-37	var. conomon	1 753.49 ab	1.49 a	2.83 b	酥脆 Crumbly
40	Sa-38	var. conomon	1 767.93 ab	1.44 a	2.26 b	酥脆 Crumbly
41	Sa-39	var. reticulatus	328.26 b	0.66 b	1.25 b	软 Soft
42	Sa-40	var. reticulatus	305.93 b	0.63 b	1.23 b	软 Soft
43	Sa-41	var. reticulatus	492.32 b	0.61 b	0.92 b	软 Soft
44	Sa-42	var. reticulatus	346.18 b	0.68 b	1.28 b	软 Soft
45	Sa-43	var. reticulatus	390.25 b	0.71 b	1.32 b	软 Soft
46	Sa-44	var. reticulatus	373.48 b	0.69 b	1.30 b	软 Soft
47	Sa-45	var. reticulatus	383.63 b	0.37 b	1.33 b	软 Soft
48	Sa-46	var. reticulatus	487.27 b	0.60 b	1.44 b	软 Soft
49	Sa-47	var. reticulatus	298.04 b	0.39 b	0.84 b	软 Soft
50	Sa-48	var. reticulatus	314.58 b	0.43 b	0.93 b	软 Soft
51	Sa-49	var. chinensis	346.86 b	0.48 b	0.98 b	软 Soft
52	Sa-50	var. chinensis	522.23 b	0.65 b	1.11 b	软 Soft
53	Sa-51	var. chinensis	366.96 b	0.67 b	1.27 b	软 Soft
54	Sa-52	var. conomon	334.83 b	0.65 b	1.25 b	软 Soft
55	Sa-53	var. conomon	477.69 b	0.59 b	0.89 b	软 Soft
56	Sa-54	var. conomon	415.18 b	0.63 b	1.03 b	软 Soft
57	Sa-55	var. conomon	312.23 b	0.43 b	0.92 b	软 Soft
58	Sa-56	var. conomon	338.12 b	0.67 b	1.28 b	软 Soft

世代 Generations	总数 Total	脆肉 Crisp	软肉 Soft	分离比 Segregation ratio	χ²
P₁（20S11）	20	20	0
P₂（20S75）	20	0	20
F_{1（P1 × P2）}	40	40	0
F_{1（P2 × P1）}	37	37	0
BC_{1（F1 × 20S11）}	79	79	0
BC_{1（F1 × 20S75）}	80	43	37	1.16︰1	1.21
F₂（F_{1（P1 × P2）}⊗）	1 211	917	294	3.12︰1	1.37