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Xing X, Hu T, Wang Y, Li Y, Wang W, Hu H, Wei Q, Yan Y, Gan D, Bao C, Wang J. Construction of SNP fingerprints and genetic diversity analysis of radish ( Raphanus sativus L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1329890. [PMID: 38371408 PMCID: PMC10869463 DOI: 10.3389/fpls.2024.1329890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/12/2024] [Indexed: 02/20/2024]
Abstract
Radish (Raphanus sativus L.) is a vegetable crop with economic value and ecological significance in the genus Radish, family Brassicaceae. In recent years, developed countries have attached great importance to the collection and conservation of radish germplasm resources and their research and utilization, but the lack of population genetic information and molecular markers has hindered the development of the genetic breeding of radish. In this study, we integrated the radish genomic data published in databases for the development of single-nucleotide polymorphism (SNP) markers, and obtained a dataset of 308 high-quality SNPs under strict selection criteria. With the support of Kompetitive Allele-Specific PCR (KASP) technology, we screened a set of 32 candidate core SNP marker sets to analyse the genetic diversity of the collected 356 radish varieties. The results showed that the mean values of polymorphism information content (PIC), minor allele frequency (MAF), gene diversity and heterozygosity of the 32 candidate core SNP markers were 0.32, 0.30, 0.40 and 0.25, respectively. Population structural analysis, principal component analysis and genetic evolutionary tree analysis indicated that the 356 radish materials were best classified into two taxa, and that the two taxa of the material were closely genetically exchanged. Finally, on the basis of 32 candidate core SNP markers we calculated 15 core markers using a computer algorithm to construct a fingerprint map of 356 radish varieties. Furthermore, we constructed a core germplasm population consisting of 71 radish materials using 32 candidate core markers. In this study, we developed SNP markers for radish cultivar identification and genetic diversity analysis, and constructed DNA fingerprints, providing a basis for the identification of radish germplasm resources and molecular marker-assisted breeding as well as genetic research.
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Affiliation(s)
- Xiaolin Xing
- School of Horticulture, Anhui Agricultural University, Hefei, China
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Tianhua Hu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yikui Wang
- Institute of Vegetables, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yan Li
- Institute of Vegetables, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Wuhong Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Haijiao Hu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Qingzhen Wei
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yaqin Yan
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Defang Gan
- School of Horticulture, Anhui Agricultural University, Hefei, China
| | - Chonglai Bao
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jinglei Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Huang S, Yu K, Xiao Q, Song B, Yuan W, Long X, Cai D, Xiong X, Zheng W. Effect of bio-nano-selenium on yield, nutritional quality and selenium content of radish. J Food Compost Anal 2023. [DOI: 10.1016/j.jfca.2022.104927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Sinyavina NG, Kochetov AA, Egorova KV, Kocherina NV, Chesnokov YV. Genetic-Biochemical Studies and Morphobiological Assessment of Small Radish (Raphanus sativus L.) under Artificial Light Culture Conditions. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422060102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Farid MM, Ibrahim FM, Ragheb AY, Mohammed RS, Hegazi NM, Shabrawy MOEL, Kawashty SA, Marzouk MM. Comprehensive Phytochemical Characterization of Raphanus raphanistrum L.: In Vitro Antioxidant and Antihyperglycemic Evaluation. SCIENTIFIC AFRICAN 2022. [DOI: 10.1016/j.sciaf.2022.e01154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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