Development of microsatellite markers in Cocos nucifera and their application in evaluating the level of genetic diversity of Cocos nucifera

Xiao, Yong, Luo, Yi, Yang, Yaodong, Fan, Haikuo, Xia, Wei, Mason, Annaliese S., Zhao, Songlin, Sager, Ross and Qiao, Fei (2013) Development of microsatellite markers in Cocos nucifera and their application in evaluating the level of genetic diversity of Cocos nucifera. Plant Omics journal, 6 3: 193-200.

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Author Xiao, Yong
Luo, Yi
Yang, Yaodong
Fan, Haikuo
Xia, Wei
Mason, Annaliese S.
Zhao, Songlin
Sager, Ross
Qiao, Fei
Title Development of microsatellite markers in Cocos nucifera and their application in evaluating the level of genetic diversity of Cocos nucifera
Formatted title
Development of microsatellite markers in Cocos nucifera and their application in evaluating the level of genetic diversity of Cocos nucifera
Journal name Plant Omics journal   Check publisher's open access policy
ISSN 1836-0661
1836-3644
Publication date 2013-05
Year available 2013
Sub-type Article (original research)
Open Access Status File (Publisher version)
Volume 6
Issue 3
Start page 193
End page 200
Total pages 8
Place of publication Lismore, NSW, Australia
Publisher Southern Cross Journals
Collection year 2014
Language eng
Formatted abstract
Cocos nucifera (coconut) is an economically important tropical crop, but opportunities for molecular breeding are 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, due to lack of available molecular markers. In this study, we developed 30 novel microsatellite markers from Illumina transcriptome sequence data, and used these markers to evaluate coconut genetic diversity in 30 individuals representing accessions from China (12 samples) and Southeast Asia (18 samples). The microsatellite markers displayed low to high genetic polymorphism across the population: observed heterozygosity varied from 0.06 to 0.79, with an average of 0.39 ± 0.15. Our results indicated that the Southeast Asian population had a significantly higher number of alleles (p = 0.02), but not significantly different (p<0.05) observed heterozygosity (p = 0.08) or Shannon's diversity index score (p = 0.12) compared to the population from China. Population structure analysis showed that Chinese coconuts were genetically similar to a subset of coconut germplasm from Southeast Asia, suggesting that Chinese coconuts did not evolve independently of the Southeast Asian populations. Combining population structural analyses and historic information, we have devised a possible explanation for coconut dispersal patterns from Southeast Asia to China: sea currents could have carried coconuts into the Hainan province, while human dispersal from Southeast Asia may have brought coconuts to the Yunnan province.
Keyword Cocos nucifera
Ssr
Genetic diversity
Population Structure
Illumina sequencing
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Centre for Integrative Legume Research Publications
School of Agriculture and Food Sciences
Official 2014 Collection
 
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