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

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.

Whole-Genome Sequencing and Analysis of Tumour-Forming Radish (Raphanus sativus L.) Line

“…To date, radish genome sequencing has previously been performed for several Asian and European cultivars and isolates [ 16 , 17 , 27 , 28 , 29 , 30 , 31 ]. Polymorphism in radish is being actively studied [ 32 , 33 ]. The Rs1.0 genome, which is a reference genome for radish, was based on the chromosome sequences of R. sativus of the Korean cultivar WK10039 [ 16 ].…”

Genetic diversity analysis and core germplasm bank construction in cold resistant germplasm of rubber trees (Hevea brasiliensis)

“…Cold-resistant germplasm resources of rubber trees are the important material basis for breeding new cold-resistant varieties and studying genetic background of rubber trees. It is very important for breeders to clarify the genetic relationship between germplasm resources and breeding materials 8 . Phenotype-based methods have been used in the past 9 , but they are prone to human error and environmental factors can cause significant deviations in analysis results.…”