Development of KASP Markers and Construction of Fingerprint Database in Oriental Melon

doi:10.7668/hbnxb.20196953

Abstract

Abstract:

To facilitate germplasm identification and molecular breeding applications in Oriental melon(Cucumis melo ssp.agrestis),this study screened highly polymorphic SNP(single nucleotide polymorphism)loci based on resequencing data from 27 C.melo ssp.agrestis and 5 C.melo ssp.melo core breeding accessions,and developed a set of high-quality KASP(Kompetitive Allele-Specific PCR)markers.A total of 60 KASP markers were uniformly designed across 12 chromosomes from 1 195 candidate SNPs.Validation using 32 breeding accessions revealed that 42 markers(70.0%)successfully generated clear and reliable genotyping clusters.Furthermore,28 optimal markers with distinct clustering and high stability were selected.Cluster analysis was highly consistent with traditional morphological classification,validating the population genetic structure of melon breeding materials at the molecular level.Using the optimal marker set,a digital fingerprint database was constructed for the 27 C.melo ssp.agrestis and 5 C.melo ssp.melo breeding accessions,and the fingerprint information of each accession was encoded into a QR code to facilitate rapid identification and management.In conclusion,the developed KASP marker system can efficiently distinguish the 27 C.melo ssp.agrestis core breeding accessions with high specificity and practicality,providing reliable technical support for future germplasm evaluation,variety identification,and marker-assisted breeding in C.melo ssp.agrestis.

Key words: Thin-skinned melon, KASP marker, Fingerprint, SNP, Molecular breeding, Cluster analysis

CLC Number:

LI Kexin, LIU Junsong, ZHAO Wei, LIU Li, LUO Juyue, ZHANG Teng, HUA Deping. Development of KASP Markers and Construction of Fingerprint Database in Oriental Melon[J]. Acta Agriculturae Boreali-Sinica, 2026, 41(5): 51-62. doi: 10.7668/hbnxb.20196953.

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http://www.hbnxb.net/EN/Y2026/V41/I5/51

Figures/Tables 9

References 37

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序号 No.	甜瓜材料 Accession	Pitrat 分类 Pitrat classification	类型 Type	特点 Characteristic
2-1	Wa1K	薄皮亚种C.melo ssp.agrestis	白皮橘肉类	白皮橘肉
2-16	Pa553	薄皮亚种C.melo ssp.agrestis	黄皮圆果类	黄皮白肉
2-17	Wb053	薄皮亚种C.melo ssp.agrestis	绿宝类	黄皮绿肉
2-31	Wb133	薄皮亚种C.melo ssp.agrestis	花雷类	黄皮绿斑条白肉
2-37	Tb230	薄皮亚种C.melo ssp.agrestis	花雷类	黄皮绿斑条白肉
2-38	Ua1084	薄皮亚种C.melo ssp.agrestis	花雷类	黄皮绿斑条绿肉
2-39	Ua1089	薄皮亚种C.melo ssp.agrestis	花雷类	黄皮绿斑点绿肉
2-42	Ub248	薄皮亚种C.melo ssp.agrestis	绿宝类	绿皮绿肉
2-43	Ua1094	薄皮亚种C.melo ssp.agrestis	绿宝类	绿皮绿肉
2-44	Na447	薄皮亚种C.melo ssp.agrestis	绿宝类	绿皮绿肉
2-45	Ua279	薄皮亚种C.melo ssp.agrestis	绿宝类	绿皮绿肉
2-49	Wa76	薄皮亚种C.melo ssp.agrestis	绿宝类	绿皮绿肉
2-50	Nb354	薄皮亚种C.melo ssp.agrestis	面瓜类	绿皮绿肉
2-51	Pa559	薄皮亚种C.melo ssp.agrestis	菜瓜类	绿皮绿肉
2-52	Sa452	薄皮亚种C.melo ssp.agrestis	羊角脆类	绿皮白肉
2-53	Ua278	薄皮亚种C.melo ssp.agrestis	绿宝类	绿皮绿肉
2-85	Nb356	薄皮亚种C.melo ssp.agrestis	花雷类	黄皮绿斑条
2-93	Sa247	薄皮亚种C.melo ssp.agrestis	菜瓜类	绿皮绿斑条绿肉
2-94	Qa368	薄皮亚种C.melo ssp.agrestis	羊角脆类	绿皮绿斑条橘肉
2-95	Ua1127	薄皮亚种C.melo ssp.agrestis	羊角脆类	绿皮绿斑条橘肉
2-101	Sb636	薄皮亚种C.melo ssp.agrestis	羊角脆类	绿皮绿斑条绿肉
2-102	Pa561	薄皮亚种C.melo ssp.agrestis	菜瓜类	白皮白肉
2-103	Pa554	薄皮亚种C.melo ssp.agrestis	菜瓜类	绿皮白肉
2-104	Pa562	薄皮亚种C.melo ssp.agrestis	菜瓜类	绿皮绿肉
2-105	Pa563	薄皮亚种C.melo ssp.agrestis	菜瓜类	绿皮绿肉
2-106	Ub747	薄皮亚种C.melo ssp.agrestis	蛇甜瓜类	绿皮绿肉
2-107	Nb353	薄皮亚种C.melo ssp.agrestis	马泡瓜	马泡瓜
2-108	Ua1027	厚皮亚种C.melo ssp.melo	瑞红类	黄皮白肉
2-138	Sa851	厚皮亚种C.melo ssp.melo	玉菇类	白皮绿肉
2-145	Qa842	厚皮亚种C.melo ssp.melo	网纹类	绿皮橘肉
2-161	Tb937	厚皮亚种C.melo ssp.melo	哈密瓜类	黄皮(细网)橘肉
2-162	Sa893	厚皮亚种C.melo ssp.melo	哈密瓜类	黄绿皮(细网)绿斑点橘肉

序号 No.	甜瓜材料 Accession	Pitrat 分类 Pitrat classification	类型 Type	特点 Characteristic
2-1	Wa1K	薄皮亚种C.melo ssp.agrestis	白皮橘肉类	白皮橘肉
2-16	Pa553	薄皮亚种C.melo ssp.agrestis	黄皮圆果类	黄皮白肉
2-17	Wb053	薄皮亚种C.melo ssp.agrestis	绿宝类	黄皮绿肉
2-31	Wb133	薄皮亚种C.melo ssp.agrestis	花雷类	黄皮绿斑条白肉
2-37	Tb230	薄皮亚种C.melo ssp.agrestis	花雷类	黄皮绿斑条白肉
2-38	Ua1084	薄皮亚种C.melo ssp.agrestis	花雷类	黄皮绿斑条绿肉
2-39	Ua1089	薄皮亚种C.melo ssp.agrestis	花雷类	黄皮绿斑点绿肉
2-42	Ub248	薄皮亚种C.melo ssp.agrestis	绿宝类	绿皮绿肉
2-43	Ua1094	薄皮亚种C.melo ssp.agrestis	绿宝类	绿皮绿肉
2-44	Na447	薄皮亚种C.melo ssp.agrestis	绿宝类	绿皮绿肉
2-45	Ua279	薄皮亚种C.melo ssp.agrestis	绿宝类	绿皮绿肉
2-49	Wa76	薄皮亚种C.melo ssp.agrestis	绿宝类	绿皮绿肉
2-50	Nb354	薄皮亚种C.melo ssp.agrestis	面瓜类	绿皮绿肉
2-51	Pa559	薄皮亚种C.melo ssp.agrestis	菜瓜类	绿皮绿肉
2-52	Sa452	薄皮亚种C.melo ssp.agrestis	羊角脆类	绿皮白肉
2-53	Ua278	薄皮亚种C.melo ssp.agrestis	绿宝类	绿皮绿肉
2-85	Nb356	薄皮亚种C.melo ssp.agrestis	花雷类	黄皮绿斑条
2-93	Sa247	薄皮亚种C.melo ssp.agrestis	菜瓜类	绿皮绿斑条绿肉
2-94	Qa368	薄皮亚种C.melo ssp.agrestis	羊角脆类	绿皮绿斑条橘肉
2-95	Ua1127	薄皮亚种C.melo ssp.agrestis	羊角脆类	绿皮绿斑条橘肉
2-101	Sb636	薄皮亚种C.melo ssp.agrestis	羊角脆类	绿皮绿斑条绿肉
2-102	Pa561	薄皮亚种C.melo ssp.agrestis	菜瓜类	白皮白肉
2-103	Pa554	薄皮亚种C.melo ssp.agrestis	菜瓜类	绿皮白肉
2-104	Pa562	薄皮亚种C.melo ssp.agrestis	菜瓜类	绿皮绿肉
2-105	Pa563	薄皮亚种C.melo ssp.agrestis	菜瓜类	绿皮绿肉
2-106	Ub747	薄皮亚种C.melo ssp.agrestis	蛇甜瓜类	绿皮绿肉
2-107	Nb353	薄皮亚种C.melo ssp.agrestis	马泡瓜	马泡瓜
2-108	Ua1027	厚皮亚种C.melo ssp.melo	瑞红类	黄皮白肉
2-138	Sa851	厚皮亚种C.melo ssp.melo	玉菇类	白皮绿肉
2-145	Qa842	厚皮亚种C.melo ssp.melo	网纹类	绿皮橘肉
2-161	Tb937	厚皮亚种C.melo ssp.melo	哈密瓜类	黄皮(细网)橘肉
2-162	Sa893	厚皮亚种C.melo ssp.melo	哈密瓜类	黄绿皮(细网)绿斑点橘肉

染色体号 Chromosome number	设计引物数量 Number of designed primer	筛选出引物数量 Number of screened primer	筛选成功率/% Screening success rate
1	5	3	60.0
2	5	3	60.0
3	5	3	60.0
4	5	5	100.0
5	5	3	60.0
6	5	4	80.0
7	5	4	80.0
8	5	2	40.0
9	5	3	60.0
10	5	3	60.0
11	5	4	80.0
12	5	5	100.0
合计或平均	60	42	70.0
Total or mean

染色体号 Chromosome number	设计引物数量 Number of designed primer	筛选出引物数量 Number of screened primer	筛选成功率/% Screening success rate
1	5	3	60.0
2	5	3	60.0
3	5	3	60.0
4	5	5	100.0
5	5	3	60.0
6	5	4	80.0
7	5	4	80.0
8	5	2	40.0
9	5	3	60.0
10	5	3	60.0
11	5	4	80.0
12	5	5	100.0
合计或平均	60	42	70.0
Total or mean

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