Bin mapping of genomic and EST-derived SSRs in melon (Cucumis melo L.)
Bin mapping of genomic and EST-derived SSRs in melon (Cucumis melo L.)
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DOI：
10.1007/s00122-008-0883-3
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发表时间：
2008-12-01
影响因子：
5.4
通讯作者：
Monforte, Antonio Jose
中科院分区：
文献类型：
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作者：
Fernandez-Silva, I.;Eduardo, I.;Monforte, Antonio Jose
我们报告了158个引物对侧翼SSR基序的基因组（gSSR）和EST（EST-SSR）甜瓜序列，所有产生的多态性带在甜瓜种质，除了一个是多态性只在南瓜属物种的发展。在EST-SSR和gSSR之间、在二聚体和三聚体EST-SSR之间以及在开放阅读框或任何5 '或3'非翻译区中的EST-SSR之间发现了相似的多态性水平。SSR长度与多态性之间的相关性仅见于位于非翻译区的二核苷酸EST-SSR，而不包括三核苷酸EST-SSR。EST-SSR在南瓜属物种中的通用性分析表明，12.7%的引物至少在一个物种中扩增，但只有5.4%的引物具有多态性。选择来自栽培品种“Piel de Sapo”和登记号PI 161375之间的杂交的一组14个双单倍体系用于甜瓜中的bin作图方法。新定位了121个SSR标记。46个SSR位点的位置也通过对整个群体的基因分型进行了验证。最终构建了包括80个RFLPs、212个SSR、3个SNPs和Nsv基因座的分箱图，分布在122个分箱中，平均分箱长度为10.2cM，最大分箱长度为33 cM。图谱密度为4.2cM/标记或5.9cM/SSR。
We report the development of 158 primer pairs flanking SSR motifs in genomic (gSSR) and EST (EST-SSR) melon sequences, all yielding polymorphic bands in melon germplasm, except one that was polymorphic only in Cucurbita species. A similar polymorphism level was found among EST-SSRs and gSSRs, between dimeric and trimeric EST-SSRs, and between EST-SSRs placed in the open reading frame or any of the 5'- or 3'-untranslated regions. Correlation between SSR length and polymorphism was only found for dinucleotide EST-SSRs located within the untranslated regions, but not for trinucleotide EST-SSRs. Transferability of EST-SSRs to Cucurbita species was assayed and 12.7% of the primer pairs amplified at least in one species, although only 5.4% were polymorphic. A set of 14 double haploid lines from the cross between the cultivar "Piel de Sapo" and the accession PI161375 were selected for the bin mapping approach in melon. One hundred and twenty-one SSR markers were newly mapped. The position of 46 SSR loci was also verified by genotyping the complete population. A final bin-map was constructed including 80 RFLPs, 212 SSRs, 3 SNPs and the Nsv locus, distributed in 122 bins with an average bin length of 10.2 cM and a maximum bin length of 33 cM. Map density was 4.2 cM/marker or 5.9 cM/SSR.