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

D. C. Ciobanu, J. W.M. Bastiaansen, J. Magrin, J. L. Rocha, D. H. Jiang, N. Yu, B. Geiger, N. Deeb, D. Rocha, H. Gong, B. P. Kinghorn, G. S. Plastow, H. A.M. Van Der Steen, A. J. Mileham

Research output: Contribution to journalArticle

33 Citations (Scopus)

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 r 2 -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.

Original languageEnglish (US)
Pages (from-to)39-47
Number of pages9
JournalAnimal genetics
Volume41
Issue number1
DOIs
StatePublished - Feb 1 2010

Fingerprint

Litopenaeus vannamei
phenotypic variation
single nucleotide polymorphism
Single Nucleotide Polymorphism
Dissection
shrimp
genetic variation
Breeding
breeding
Taura syndrome virus
Population
Linkage Disequilibrium
Virus Diseases
linkage disequilibrium
breeding lines
Computational Biology
Gene Frequency
bioinformatics
gene frequency
Economics

Keywords

  • Association study
  • SNP
  • Selection
  • Shrimp

ASJC Scopus subject areas

  • Animal Science and Zoology
  • Genetics

Cite this

A major SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei). / Ciobanu, D. C.; Bastiaansen, J. W.M.; Magrin, J.; Rocha, J. L.; Jiang, D. H.; Yu, N.; Geiger, B.; Deeb, N.; Rocha, D.; Gong, H.; Kinghorn, B. P.; Plastow, G. S.; Van Der Steen, H. A.M.; Mileham, A. J.

In: Animal genetics, Vol. 41, No. 1, 01.02.2010, p. 39-47.

Research output: Contribution to journalArticle

Ciobanu, DC, Bastiaansen, JWM, Magrin, J, Rocha, JL, Jiang, DH, Yu, N, Geiger, B, Deeb, N, Rocha, D, Gong, H, Kinghorn, BP, Plastow, GS, Van Der Steen, HAM & Mileham, AJ 2010, 'A major SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei)', Animal genetics, vol. 41, no. 1, pp. 39-47. https://doi.org/10.1111/j.1365-2052.2009.01961.x
Ciobanu, D. C. ; Bastiaansen, J. W.M. ; Magrin, J. ; Rocha, J. L. ; Jiang, D. H. ; Yu, N. ; Geiger, B. ; Deeb, N. ; Rocha, D. ; Gong, H. ; Kinghorn, B. P. ; Plastow, G. S. ; Van Der Steen, H. A.M. ; Mileham, A. J. / A major SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei). In: Animal genetics. 2010 ; Vol. 41, No. 1. pp. 39-47.
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