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

被引:0
|
作者
Wei Xia
Yong Xiao
Zheng Liu
Yi Luo
Annaliese S. Mason
Haikuo Fan
Yaodong Yang
Songlin Zhao
Ming Peng
机构
[1] Chinese Academy of Tropical Agricultural Sciences,Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute
[2] Chinese Academy of Tropical Agricultural Science,Institute of Tropical Bioscience and Biotechnology
[3] The University of Queensland,School of Agriculture and Food Sciences, Centre for Integrative Legume Research
[4] Sichuan Agriculture University,College of Landscape Architecture
来源
Molecular Breeding | 2014年 / 34卷
关键词
Coconut; SSR; Transcriptome; Polymorphism; Association analysis;
D O I
暂无
中图分类号
学科分类号
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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页码:525 / 535
页数:10
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