A major SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp ('Litopenaeus vannamei')

Title
A major SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp ('Litopenaeus vannamei')
Publication Date
2010
Author(s)
Ciobanu, Daniel C
Bastiaansen, John W M
Plastow, G S P
van der Steen, H A M
Mileham, Alan
Magrin, J
Rocha, Joao
Jiang, D
Yu, Nan
Geiger, B
Deeb, Nader
Rocha, D
Kinghorn, Brian
Type of document
Journal Article
Language
en
Entity Type
Publication
Publisher
Wiley-Blackwell Publishing Ltd
Place of publication
United Kingdom
DOI
10.1111/j.1365-2052.2009.01961.x
UNE publication id
une:5015
Abstract
Bioinformatics and re-sequencing approaches were used for the discovery of sequence polymorphisms in 'Litopenaeus vannamei'. A total of 1221 putative single nucleotide polymorphisms (SNPs) were identified in a pool of individuals from various commercial populations. A set of 211 SNPs were selected for further molecular validation and 88% showed variation in 637 samples representing three commercial breeding lines. An association analysis was performed between these markers and several traits of economic importance for shrimp producers including resistance to three major viral diseases. A small number of SNPs showed associations with test weekly gain, grow-out survival and resistance to Taura Syndrome Virus. Very low levels of linkage disequilibrium were revealed between most SNP pairs, with only 11% of SNPs showing an r²-value above 0.10 with at least one other SNP. Comparison of allele frequencies showed small changes over three generations of the breeding programme in one of the commercial breeding populations. This unique SNP resource has the potential to catalyse future studies of genetic dissection of complex traits, tracing relationships in breeding programmes, and monitoring genetic diversity in commercial and wild populations of 'L. vannamei'.
Link
Citation
Animal Genetics, 41(1), p. 39-47
ISSN
1365-2052
0268-9146
Start page
39
End page
47

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