The Development Of Genic-SSR Markers In Coconut And The Genetic Evaluation Of Coconut Germplasm Resources

Coconut is a tropical oil crop and widely cultivate in tropical regions. Due to versatile uses in tropical regions, it is also called as a tropical tree of life. In China, Coconut is distributed across south and southeast regions of China, such as Hainan province, Yunnan province, Guangxi province, Guangdong province, Taiwan province, and Fujian province. Some evidences had showed that there had been2000years history since the first coconut was introduced into China.Currently, DNA molecular markers has become an important method for evaluating genetic variation of germplasm resources, including the analysis of the genetic diversity, the Construction of core Germplasm, and QTL mapping. However, application of molecular markers in the coconut is less, and the opportunities for molecular breeding are still limited by lack of DNA sequence information for this species. Previous assessments of coconut germplasm have been conducted based solely on phenotypic data for agronomic and quality traits because of lack of available molecular markers, Therefore, it is very necessary to development a simple, efficient method for facilitating coconut breeding scheme.This study was carried out to develop Genic-SSR markers based on the transcriptome data of coconut and evaluate their polymorphism. Subsequently,80polymorphic SSR markers were selected to assess genetic variation and population structure of82coconut resources. Our study will provide basic platform for the ongoing molecular biology and genetic breeding in coconut palm. The detailed results are showed as follows:(1) Thirty-nine pairs of primer flanking microsatellite sequence were selected to amplify the DNAs from10coconut accessions. Among them, amplification fragment of191primer pairs showed polymorphism, the Shannon diversity ranged from0.3251to1.2396and the average heterozygosity varied from0to0.695.(2) These polymorphic SSRs were separated into different clusters based on repeat number, motif and GO functional classes. The polymorphic level of SSRs from different clusters was compared each other. The comparison results showed the richest level of polymorphism were detected in8repeats cluster in repeat number, AC and CAC in motif, Multicellular organismal、Developmental Process and Biological regulation in GO classes, respectively. These analyses will provide guidance suggestions for the development of more SSR markers.(3) Both structure analysis and Principal Component Analysis showed coconut population with different geographical origins could not be clear separated. But the dwarf and high coconut had a significant genetic differentiation. The genetic diversity of high coconut is richer than the dwarf kinds.(4) The software tassel was used to assess the level of linkage disequilibrium. Out of these marker pairs,13.24%were found to be significant in LD.(5) The association analysis was used to identify height-associated markers. The results showed that24markers have significant associated with height traits at a threshold of P<0.05. Of them, The marker WCYZ-121-180had the contribution to variation of height traits.