Genetic diversity analysis and variety identification using SSR and SNP markers in melon
Abstract Melon is an important horticultural crop with a pleasant aromatic flavor and abundance of health-promoting substances. Numerous melon varieties have been cultivated worldwide in recent years, but the high number of varieties and the high similarity between them poses a major challenge for v...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-01-01
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| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12870-023-04056-7 |
| _version_ | 1797946006994681856 |
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| author | Jian Zhang Jingjing Yang Yanling Lv Xiaofei Zhang Changxuan Xia Hong Zhao Changlong Wen |
| author_facet | Jian Zhang Jingjing Yang Yanling Lv Xiaofei Zhang Changxuan Xia Hong Zhao Changlong Wen |
| author_sort | Jian Zhang |
| collection | DOAJ |
| description | Abstract Melon is an important horticultural crop with a pleasant aromatic flavor and abundance of health-promoting substances. Numerous melon varieties have been cultivated worldwide in recent years, but the high number of varieties and the high similarity between them poses a major challenge for variety evaluation, discrimination, as well as innovation in breeding. Recently, simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), two robust molecular markers, have been utilized as a rapid and reliable method for variety identification. To elucidate the genetic structure and diversity of melon varieties, we screened out 136 perfect SSRs and 164 perfect SNPs from the resequencing data of 149 accessions, including the most representative lines worldwide. This study established the DNA fingerprint of 259 widely-cultivated melon varieties in China using Target-seq technology. All melon varieties were classified into five subgruops, including ssp. agrestis, ssp. melo, muskmelon and two subgroups of foreign individuals. Compared with ssp. melo, the ssp. agrestis varieties might be exposed to a high risk of genetic erosion due to their extremely narrow genetic background. Increasing the gene exchange between ssp. melo and ssp. agrestis is therefore necessary in the breeding procedure. In addition, analysis of the DNA fingerprints of the 259 melon varieties showed a good linear correlation (R2 = 0.9722) between the SSR genotyping and SNP genotyping methods in variety identification. The pedigree analysis based on the DNA fingerprint of ‘Jingyu’ and ‘Jingmi’ series melon varieties was consistent with their breeding history. Based on the SNP index analysis, ssp. agrestis had low gene exchange with ssp. melo in chromosome 4, 7, 10, 11and 12, two specific SNP loci were verified to distinguish ssp. agrestis and ssp. melon varieties. Finally, 23 SSRs and 40 SNPs were selected as the core sets of markers for application in variety identification, which could be efficiently applied to variety authentication, variety monitoring, as well as the protection of intellectual property rights in melon. |
| first_indexed | 2024-04-10T21:04:04Z |
| format | Article |
| id | doaj.art-3c9707c1998343148184e7e42830c5d3 |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-04-10T21:04:04Z |
| publishDate | 2023-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-3c9707c1998343148184e7e42830c5d32023-01-22T12:08:42ZengBMCBMC Plant Biology1471-22292023-01-0123111010.1186/s12870-023-04056-7Genetic diversity analysis and variety identification using SSR and SNP markers in melonJian Zhang0Jingjing Yang1Yanling Lv2Xiaofei Zhang3Changxuan Xia4Hong Zhao5Changlong Wen6Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for VegetablesBeijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for VegetablesInstitute of Vegetable, Liaoning Academy of Agricultural SciencesBeijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for VegetablesBeijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for VegetablesBeijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for VegetablesBeijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for VegetablesAbstract Melon is an important horticultural crop with a pleasant aromatic flavor and abundance of health-promoting substances. Numerous melon varieties have been cultivated worldwide in recent years, but the high number of varieties and the high similarity between them poses a major challenge for variety evaluation, discrimination, as well as innovation in breeding. Recently, simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), two robust molecular markers, have been utilized as a rapid and reliable method for variety identification. To elucidate the genetic structure and diversity of melon varieties, we screened out 136 perfect SSRs and 164 perfect SNPs from the resequencing data of 149 accessions, including the most representative lines worldwide. This study established the DNA fingerprint of 259 widely-cultivated melon varieties in China using Target-seq technology. All melon varieties were classified into five subgruops, including ssp. agrestis, ssp. melo, muskmelon and two subgroups of foreign individuals. Compared with ssp. melo, the ssp. agrestis varieties might be exposed to a high risk of genetic erosion due to their extremely narrow genetic background. Increasing the gene exchange between ssp. melo and ssp. agrestis is therefore necessary in the breeding procedure. In addition, analysis of the DNA fingerprints of the 259 melon varieties showed a good linear correlation (R2 = 0.9722) between the SSR genotyping and SNP genotyping methods in variety identification. The pedigree analysis based on the DNA fingerprint of ‘Jingyu’ and ‘Jingmi’ series melon varieties was consistent with their breeding history. Based on the SNP index analysis, ssp. agrestis had low gene exchange with ssp. melo in chromosome 4, 7, 10, 11and 12, two specific SNP loci were verified to distinguish ssp. agrestis and ssp. melon varieties. Finally, 23 SSRs and 40 SNPs were selected as the core sets of markers for application in variety identification, which could be efficiently applied to variety authentication, variety monitoring, as well as the protection of intellectual property rights in melon.https://doi.org/10.1186/s12870-023-04056-7Perfect SSRPerfect SNPGenetic diversityVariety identificationMelon |
| spellingShingle | Jian Zhang Jingjing Yang Yanling Lv Xiaofei Zhang Changxuan Xia Hong Zhao Changlong Wen Genetic diversity analysis and variety identification using SSR and SNP markers in melon BMC Plant Biology Perfect SSR Perfect SNP Genetic diversity Variety identification Melon |
| title | Genetic diversity analysis and variety identification using SSR and SNP markers in melon |
| title_full | Genetic diversity analysis and variety identification using SSR and SNP markers in melon |
| title_fullStr | Genetic diversity analysis and variety identification using SSR and SNP markers in melon |
| title_full_unstemmed | Genetic diversity analysis and variety identification using SSR and SNP markers in melon |
| title_short | Genetic diversity analysis and variety identification using SSR and SNP markers in melon |
| title_sort | genetic diversity analysis and variety identification using ssr and snp markers in melon |
| topic | Perfect SSR Perfect SNP Genetic diversity Variety identification Melon |
| url | https://doi.org/10.1186/s12870-023-04056-7 |
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