Construction of an SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars
Abstract Cauliflower is one of the most important vegetable crops grown worldwide. However, the lack of genetic diversity information and efficient molecular markers hinders efforts to improve cauliflower. This study aims to construct DNA fingerprints for 329 cauliflower cultivars based on SNP marke...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2022-11-01
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| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12870-022-03920-2 |
| _version_ | 1797988459073241088 |
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| author | Yuyao Yang Mingjie Lyu Jun Liu Jianjin Wu Qian Wang Tianyu Xie Haichao Li Rui Chen Deling Sun Yingxia Yang Xingwei Yao |
| author_facet | Yuyao Yang Mingjie Lyu Jun Liu Jianjin Wu Qian Wang Tianyu Xie Haichao Li Rui Chen Deling Sun Yingxia Yang Xingwei Yao |
| author_sort | Yuyao Yang |
| collection | DOAJ |
| description | Abstract Cauliflower is one of the most important vegetable crops grown worldwide. However, the lack of genetic diversity information and efficient molecular markers hinders efforts to improve cauliflower. This study aims to construct DNA fingerprints for 329 cauliflower cultivars based on SNP markers and the KASP system. After rigorous filtering, a total of 1662 candidate SNPs were obtained from nearly 17.9 million SNP loci. The mean values of PIC, MAF, heterozygosity and gene diversity of these SNPs were 0.389, 0.419, 0.075, and 0.506, respectively. We developed a program for in silico simulations on 153 core germplasm samples to generate ideal SNP marker sets from the candidates. Finally, 41 highly polymorphic KASP markers were selected and applied to identify 329 cauliflower cultivars, mainly collected from the public market. Furthermore, based on the KASP genotyping data, we performed phylogenetic analysis and population structure analysis of the 329 cultivars. As a result, these cultivars could be classified into three major clusters, and the classification patterns were significantly related to their curd solidity and geographical origin. Finally, fingerprints of the 329 cultivars and 2D barcodes with the genetic information of each sample were generated. The fingerprinting database developed in this study provides a practical tool for identifying the authenticity and purity of cauliflower seeds and valuable genetic information about the current cauliflower cultivars. |
| first_indexed | 2024-04-11T08:04:22Z |
| format | Article |
| id | doaj.art-03749f39fc88492abd2a57686e4e036f |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-04-11T08:04:22Z |
| publishDate | 2022-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-03749f39fc88492abd2a57686e4e036f2022-12-22T04:35:36ZengBMCBMC Plant Biology1471-22292022-11-0122111110.1186/s12870-022-03920-2Construction of an SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivarsYuyao Yang0Mingjie Lyu1Jun Liu2Jianjin Wu3Qian Wang4Tianyu Xie5Haichao Li6Rui Chen7Deling Sun8Yingxia Yang9Xingwei Yao10Tianjin Academy of Agricultural SciencesTianjin Academy of Agricultural SciencesNational Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural SciencesTianjin Agricultural Development Service CenterTianjin Academy of Agricultural SciencesTianjin Academy of Agricultural SciencesTianjin Academy of Agricultural SciencesTianjin Academy of Agricultural SciencesTianjin Academy of Agricultural SciencesTianjin Academy of Agricultural SciencesTianjin Academy of Agricultural SciencesAbstract Cauliflower is one of the most important vegetable crops grown worldwide. However, the lack of genetic diversity information and efficient molecular markers hinders efforts to improve cauliflower. This study aims to construct DNA fingerprints for 329 cauliflower cultivars based on SNP markers and the KASP system. After rigorous filtering, a total of 1662 candidate SNPs were obtained from nearly 17.9 million SNP loci. The mean values of PIC, MAF, heterozygosity and gene diversity of these SNPs were 0.389, 0.419, 0.075, and 0.506, respectively. We developed a program for in silico simulations on 153 core germplasm samples to generate ideal SNP marker sets from the candidates. Finally, 41 highly polymorphic KASP markers were selected and applied to identify 329 cauliflower cultivars, mainly collected from the public market. Furthermore, based on the KASP genotyping data, we performed phylogenetic analysis and population structure analysis of the 329 cultivars. As a result, these cultivars could be classified into three major clusters, and the classification patterns were significantly related to their curd solidity and geographical origin. Finally, fingerprints of the 329 cultivars and 2D barcodes with the genetic information of each sample were generated. The fingerprinting database developed in this study provides a practical tool for identifying the authenticity and purity of cauliflower seeds and valuable genetic information about the current cauliflower cultivars.https://doi.org/10.1186/s12870-022-03920-2CauliflowerSNPKASPDNA fingerprintingPopulation structure |
| spellingShingle | Yuyao Yang Mingjie Lyu Jun Liu Jianjin Wu Qian Wang Tianyu Xie Haichao Li Rui Chen Deling Sun Yingxia Yang Xingwei Yao Construction of an SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars BMC Plant Biology Cauliflower SNP KASP DNA fingerprinting Population structure |
| title | Construction of an SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars |
| title_full | Construction of an SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars |
| title_fullStr | Construction of an SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars |
| title_full_unstemmed | Construction of an SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars |
| title_short | Construction of an SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars |
| title_sort | construction of an snp fingerprinting database and population genetic analysis of 329 cauliflower cultivars |
| topic | Cauliflower SNP KASP DNA fingerprinting Population structure |
| url | https://doi.org/10.1186/s12870-022-03920-2 |
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