Development of gene-based simple sequence repeat markers for association analysis in Cocos nucifera

文献类型： 外文期刊

第一作者： Xia, Wei

作者： Xia, Wei;Xiao, Yong;Liu, Zheng;Luo, Yi;Fan, Haikuo;Yang, Yaodong;Zhao, Songlin;Mason, Annaliese S.;Fan, Haikuo;Peng, Ming

作者机构：

关键词： Coconut;SSR;Transcriptome;Polymorphism;Association analysis

期刊名称：MOLECULAR BREEDING （ 影响因子：2.589； 五年影响因子：2.75 ）

ISSN： 1380-3743

年卷期： 2014 年 34 卷 2 期

页码：

收录情况： SCI

摘要： Simple sequence repeat (SSR) markers have been widely used to evaluate genetic resources and assist crop breeding in plant systems: they are codominant, easy to score and have abundant polymorphisms. In this study, we used coconut transcriptome sequences to determine the distribution characteristics of gene-based microsatellite loci in Cocos nucifera L. and to develop a series of polymorphic SSR markers. A total of 6,608 SSRs were identified across 57,304 unigenes from coconut transcripts: approximately one expressed sequence tag-derived SSR locus per 10 unigenes. We developed 309 primer pairs and characterized 191 polymorphic gene-based SSR markers across a set of ten coconut accessions from different countries. A total of 615 alleles were identified from the 191 polymorphic SSR loci, with an average of 3.22 alleles per locus. These gene-based SSR markers displayed moderate levels of polymorphism, with observed heterozygosity ranging from 0.18 to 0.695 (mean = 0.385 +/- 0.14). Subsequently, 80 polymorphic markers were selected to assay genotypes of 82 coconut accessions collected from different regions in Asia. Association analysis found a total of nine markers significantly associated with coconut height (P < 0.05) using general linear models in a selective unstructured population and mixed linear models in a mixed-structure population. Two SSR markers (from Unigene9331 and Unigene3350) were significantly associated with coconut height using both statistical methods.

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