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Identification and validation of a core set of microsatellite markers for genetic diversity analysis in watermelon, Citrullus lanatus Thunb. Matsum. & Nakai

文献类型： 外文期刊

作者： Zhang, Haiying 1 ; Wang, Hui 1 ; Guo, Shaogui 1 ; Ren, Yi 1 ; Gong, Guoyi 1 ; Weng, Yiqun 2 ; Xu, Yong 1 ;

作者机构： 1.Beijing Acad Agr & Forestry Sci, Natl Engn Res Ctr Vegetables, Beijing 100097, Peoples R China

2.Univ Wisconsin, ARS, USDA, Vegetable Crops Res Unit,Hort Dept, Madison, WI 53719 USA

关键词： alleles;classification;cultivars;gene mapping;genetic diversity;genetic mapping;genetic markers;genetic variation;genomes;identification;inbred lines;linkage;microsatellites;molecular genetics;morphology;nucleotide sequences;plant breeding;polymorphism;simple sequence repeats;single nucleotide polymorphism;utilization;vegetable growing;vegetables;watermelons;Citrullus;Citrullus lanatus;Cucurbitaceae;Violales;dicotyledons;angiosperms;Spermatophyta;plants;eukaryotes;Citrullus;biochemical genetics;cultivated varieties;DNA sequences;genetic variability;genotypic variability;genotypic variation;minisatellites;pure lines;vegetable crops

期刊名称：EUPHYTICA （ 影响因子：1.895； 五年影响因子：2.181 ）

ISSN：

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收录情况： SCI

摘要： Watermelon, Citrullus lanatus Thunb. Matsum. & Nakai is an important vegetable crop worldwide. Due to its narrow genetic base, detection and utilization of the genetic variations, cultivar identification and increasing genetic diversity are some important tasks for watermelon breeders. Molecular markers, especially microsatellites or simple sequence repeats (SSRs) are playing increasingly important roles for these purposes. In the present study, a core set of 23 highly informative SSR markers was developed for watermelon genetic diversity analysis. Based on whole genome sequencing of 17 watermelon inbred lines, we identified 3.9 million single nucleotide polymorphisms (SNPs) which were used to construct a SNP-based dendrogram for the 17 lines. Meanwhile, from the sequenced genome, 13,744 SSRs were developed, of which 704 were placed on a high-resolution watermelon linkage map. To develop the core set SSR markers, 78 of the 704 mapped SSRs were selected as the candidate markers. Using the SNP-based dendrogram as calibration, 23 SSR markers evenly distributed across the genome were identified as the core marker set for watermelon genetic diversity analysis. Each marker was able to detect 2-7 alleles with polymorphism information content values ranging from 0.45 to 0.82. The dendrograms of 17 watermelon lines based on SNPs, the base set of 78 SSRs and the core set of 23 SSRs were highly consistent. The utility of this core set SSRs was demonstrated in 100 commercial watermelon cultivars and elite lines, which could be placed into six clusters that were largely consistent with previous classification based on morphology and parentage data. This core set of SSR markers should be very useful for genotyping and genetic variation analysis in watermelon.

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