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Microsatellite Diversity, Population Structure, and Core Collection Formation in Melon Germplasm

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Abstract

Melon is one of the most important fruit crops in China, and has been the focus of much effort in breeding new cultivars but only limited effort in basic studies (e.g., germplasm collection, assessment, and utilization). In this study, we assessed the genetic diversity and population structure in a large melon collection (570 Chinese accessions and 42 exotic accessions) using 26 microsatellite markers distributed evenly in the genome. A total of 355 alleles, a high level of gene diversity (0.713), and a low observed heterozygosity (0.177) were detected among the whole panel. Using a model-based population structure analysis, all accessions were assigned to one of two main groups (P1 and P2), which were largely in line with their subspecies classification and geographic distribution. P1 comprised 279 accessions, most of which were from Northwest China, while P2 comprised 333 accessions, most of which were from the northeast, central, and east regions in China. Each of the two main groups was further subdivided into two subgroups that had different fruit features. Principal component analysis also gave similar results in positioning the 612 melon accessions. AMOVA, pairwise FST, and Nei’s genetic distance confirmed the differentiation between the groups and subgroups. The accessions from Northwest China revealed a high level of genetic diversity, as did accessions from Northeast, Central, and East China. Subsequently, we constructed a core collection representing 19.4 % of the whole panel and showing 100 % coverage of alleles. Our results provide an effective aid for future germplasm conservation and association genetics as well as development of appropriate breeding strategies in melon.

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Acknowledgments

We are grateful to Prof. Z.-F. Yan, College of Horticulture of Henan Agricultural University, for helpful discussions and critical reading of this manuscript. We also thank Zhengzhou Fruit Research Institute of Chinese Academy of Agriculture Sciences for providing melon germplasm resources. The research was supported by the National Natural Science Foundation of China (Grant No. 31101544).

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Authors and Affiliations

  1. College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, People’s Republic of China

    Jianbin Hu, Panqiao Wang, Yan Su, Ruijiao Wang, Qiong Li & Kaile Sun

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  1. Jianbin Hu
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Correspondence to Jianbin Hu.

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Table S1

List of the 612 melon accessions used in the present study. The groups (P1 and P2) and subgroups (G1, G2, G3, and G4) for these accessions were noted as well as the accession types. Accession type: B breeding line, C commercial hybrid or experimental hybrid, L landrace, W wild accession. Of these accessions, those chosen as the core collection were recorded as “Y” (XLS 118 kb)

Table S2

Description of the horticultural traits of 22 diverse melon accessions used for screening of SSR markers (XLS 20 kb)

Table S3

Characteristics of the 26 SSR markers in the present study (XLS 19 kb)

Fig. S1

Determination of LnP (D) and ΔK in the total panel and inferred groups. (a) the total panel; (b) the P1 group; (c) the P2 group. The blue and red curves represent LnP (D) and ΔK, respectively. The bar indicates standard deviation (GIF 77 kb)

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Hu, J., Wang, P., Su, Y. et al. Microsatellite Diversity, Population Structure, and Core Collection Formation in Melon Germplasm. Plant Mol Biol Rep 33, 439–447 (2015). https://doi.org/10.1007/s11105-014-0757-6

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