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Development of genetic markers in abalone through construction of a SNP database

Citation

Kang, J-H and Appleyard, SA and Elliott, NG and Jee, Y-J and Lee, JB and Kang, SW and Baek, MK and Han, YS and Choi, T-J and Lee, YS, Development of genetic markers in abalone through construction of a SNP database, Animal Genetics, 42, (3) pp. 309-315. ISSN 0268-9146 (2011) [Refereed Article]

Copyright Statement

Copyright 2010 Stichting International Foundation for Animal Genetic

DOI: doi:10.1111/j.1365-2052.2010.02150.x

Abstract

In the absence of a reference genome, single-nucleotide polymorphisms (SNP) discovery in a group of abalone species was undertaken by random sequence assembly. A web-based interface was constructed, and 11 932 DNA sequences from the genus Haliotis were assembled, with 1321 contigs built. Of these, 118 contigs that consisted of at least ten annotation groups were selected. The 1577 putative SNPs were identified from the 118 contigs, with SNPs in several HSP70 gene contigs confirmed by PCR amplification of an 809-bp DNA fragment. SNPs in the HSP70 gene were compared across eight abalone species. A total of 129 polymorphic sites, including heterozygote sites within and among species, were observed. Phylogenetic analysis of the partial HSP70 gene region showed separation of the tested abalone into two groups, one reflecting the southern hemisphere species and the other the northern hemisphere species. Interestingly, Haliotis iris from New Zealand showed a closer relationship to species distributed in the northern Pacific region. Although HSP genes are known to be highly conserved among taxa, the validation of polymorphic SNPs from HSP70 in this mollusc demonstrates the applicability of cross-species SNP markers in abalone and the first step towards universal nuclear markers in Haliotis.

Item Details

Item Type:Refereed Article
Keywords:expressed sequence tags, Haliotis, HSP70, SNP, web database
Research Division:Biological Sciences
Research Group:Genetics
Research Field:Population, Ecological and Evolutionary Genetics
Objective Division:Animal Production and Animal Primary Products
Objective Group:Fisheries - Wild Caught
Objective Field:Wild Caught Edible Molluscs
Author:Appleyard, SA (Dr Sharon Appleyard)
Author:Elliott, NG (Dr Nick Elliott)
ID Code:119010
Year Published:2011
Web of Science® Times Cited:4
Deposited By:Ecology and Biodiversity
Deposited On:2017-07-25
Last Modified:2017-10-16
Downloads:0

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