Construction of SNP fingerprints and genetic diversity analysis of radish (Raphanus sativus L.)

Xiaolin Xing; Tianhua Hu; Yikui Wang; Yan Li; Wuhong Wang; Haijiao Hu; Qingzhen Wei; Yaqin Yan; Defang Gan; Chonglai Bao; Jinglei Wang

doi:10.3389/fpls.2024.1329890

Construction of SNP fingerprints and genetic diversity analysis of radish (Raphanus sativus L.)

Front Plant Sci. 2024 Feb 2:15:1329890. doi: 10.3389/fpls.2024.1329890. eCollection 2024.

Authors

Xiaolin Xing^{1

2}, Tianhua Hu², Yikui Wang³, Yan Li³, Wuhong Wang², Haijiao Hu², Qingzhen Wei², Yaqin Yan², Defang Gan¹, Chonglai Bao², Jinglei Wang²

Affiliations

¹ School of Horticulture, Anhui Agricultural University, Hefei, China.
² Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
³ Institute of Vegetables, Guangxi Academy of Agricultural Sciences, Nanning, China.

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.

Keywords: KASP; SNP; fingerprint; genetic diversity; radish.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. The authors gratefully acknowledge the financial support provided from the Major Science Technology Projects of Guangxi (Guike AA22068089), the New Variety Breeding Project of the Major Science Technology Projects of Zhejiang (2021C02065), the China Agriculture Research System (CARS-23-A09), Sannong Jiufang Technology Project of Zhejiang (2023SNJF013).