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Genetic diversity and evolutionary relationship analyses within and among Raphanus species using EST-SSR markers

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Abstract

We screened 626 pairs of EST-SSR primers from the radish marker database using 37 different cultivars. Of the primer pairs, 89.3 % (559) were polymorphic. The average polymorphism information content (PIC) value per primer was 0.39, ranging from 0.07 to 0.73. Fifty EST-SSR markers were designated core markers according to PCR band reproducibility and stability, high polymorphism levels, easily discriminated alleles, and an even distribution of molecular markers over each radish chromosome. Genetic diversity and the evolutionary relationships of 93 radish accessions, representing nearly all typical Raphanus germplasms, were assessed with 50 core EST-SSR markers. A total of 254 alleles at 52 loci (4.88 alleles per locus on average), with a mean PIC value of 0.55, were detected. The wild radish had the largest range of variation, followed by the East Asian big long radish and the European small radish. Unweighted pair group method with arithmetic mean cluster analysis classified the 93 germplasms into four groups. The first group included most accessions belonging to R. sativus, while seven wild Raphanus strains were separated into the remaining groups. In the R. sativus group, the subspecies var. hortensis Becker, var. raphanistroides Makino, var. caudatus Hooker and Anderson, var. sativus L., var. niger Kerner, and var. oleiferus Metzg were sorted into separate subgroups. Population genetics structure analyses show that the accessions were attributed to three populations: (1) Asia cultivated and East Asian wild, (2) Europe cultivated, and (3) wild Raphanus species. Herein, we discuss the origin and ancestry of cultivated radishes based on these results.

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Acknowledgments

This work was funded by grants from National Key Technology R&D Program of China (2012BAD02B01, 2012BAD50G00) and the Technological Innovation Capacity Program of Beijing Academy of Agricultural and Forestry Sciences (KJCX20140111).

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Authors and Affiliations

  1. Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People’s Republic of China

    Qingbiao Wang, Li Zhang & Pengjing Zheng

  2. Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097, People’s Republic of China

    Qingbiao Wang, Li Zhang & Pengjing Zheng

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  1. Qingbiao Wang
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  2. Li Zhang
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Correspondence to Li Zhang.

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Supplementary material 1 (XLSX 45 kb)

11032_2015_261_MOESM2_ESM.jpg

Supplement Figure S1 Amplified bands of primer RSS2474 in 37 radish accessions and their patterns and codes for each allele. There were seven alleles at locus a, meanwhile, could not be detected polymorphism at locus b in this study (JPEG 187 kb)

Supplementary material 3 (PDF 79 kb)

Supplementary material 4 (PDF 140 kb)

Supplement Figure S4 Line chart of K values changing with Evanno’s Delta K (JPEG 12 kb)

11032_2015_261_MOESM6_ESM.jpg

Supplement Figure S5 Compare UPGMA cluster dendrogram in this study with Neighbor-joining tree of radish in Shen et al. (JPEG 113 kb)

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Wang, Q., Zhang, L. & Zheng, P. Genetic diversity and evolutionary relationship analyses within and among Raphanus species using EST-SSR markers. Mol Breeding 35, 62 (2015). https://doi.org/10.1007/s11032-015-0261-1

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