A gene-based SNP linkage map for pacific white shrimp, Litopenaeus vannamei

Z. Q. Du, D. C. Ciobanu, S. K. Onteru, D. Gorbach, A. J. Mileham, G. Jaramillo, M. F. Rothschild

Research output: Contribution to journalArticle

48 Citations (Scopus)

Abstract

Pacific white shrimp (Litopenaeus vannamei) are of particular economic importance to the global shrimp aquaculture industry. However, limited genomics information is available for the penaeid species. We utilized the limited public information available, mainly single nucleotide polymorphisms (SNPs) and expressed sequence tags, to discover markers for the construction of the first SNP genetic map for Pacific white shrimp. In total, 1344 putative SNPs were discovered, and out of 825 SNPs genotyped, 418 SNP markers from 347 contigs were mapped onto 45 sex-averaged linkage groups, with approximate coverage of 2071 and 2130 cm for the female and male maps, respectively. The average-squared correlation coefficient (r2), a measure of linkage disequilibrium, for markers located more than 50 cm apart on the same linkage group, was 0.15. Levels of r2 increased with decreasing inter-marker distance from ∼80 cm, and increased more rapidly from ∼30 cm. A QTL for shrimp gender was mapped on linkage group 13. Comparative mapping to model organisms, Daphnia pulex and Drosophila melanogaster, revealed extensive rearrangement of genome architecture for L. vannamei, and that L. vannamei was more related to Daphnia pulex. This SNP genetic map lays the foundation for future shrimp genomics studies, especially the identification of genetic markers or regions for economically important traits.

Original languageEnglish (US)
Pages (from-to)286-294
Number of pages9
JournalAnimal genetics
Volume41
Issue number3
DOIs
StatePublished - Jun 1 2010

Fingerprint

Litopenaeus vannamei
single nucleotide polymorphism
chromosome mapping
Single Nucleotide Polymorphism
shrimp
linkage groups
Genes
Daphnia
Daphnia pulex
genes
Genomics
sex linkage
shrimp fisheries
genomics
Aquaculture
shrimp culture
Expressed Sequence Tags
Linkage Disequilibrium
linkage disequilibrium
expressed sequence tags

Keywords

  • EST
  • Genetic Map
  • Litopenaeus vannamei
  • SNP

ASJC Scopus subject areas

  • Animal Science and Zoology
  • Genetics

Cite this

Du, Z. Q., Ciobanu, D. C., Onteru, S. K., Gorbach, D., Mileham, A. J., Jaramillo, G., & Rothschild, M. F. (2010). A gene-based SNP linkage map for pacific white shrimp, Litopenaeus vannamei. Animal genetics, 41(3), 286-294. https://doi.org/10.1111/j.1365-2052.2009.02002.x

A gene-based SNP linkage map for pacific white shrimp, Litopenaeus vannamei. / Du, Z. Q.; Ciobanu, D. C.; Onteru, S. K.; Gorbach, D.; Mileham, A. J.; Jaramillo, G.; Rothschild, M. F.

In: Animal genetics, Vol. 41, No. 3, 01.06.2010, p. 286-294.

Research output: Contribution to journalArticle

Du, ZQ, Ciobanu, DC, Onteru, SK, Gorbach, D, Mileham, AJ, Jaramillo, G & Rothschild, MF 2010, 'A gene-based SNP linkage map for pacific white shrimp, Litopenaeus vannamei', Animal genetics, vol. 41, no. 3, pp. 286-294. https://doi.org/10.1111/j.1365-2052.2009.02002.x
Du, Z. Q. ; Ciobanu, D. C. ; Onteru, S. K. ; Gorbach, D. ; Mileham, A. J. ; Jaramillo, G. ; Rothschild, M. F. / A gene-based SNP linkage map for pacific white shrimp, Litopenaeus vannamei. In: Animal genetics. 2010 ; Vol. 41, No. 3. pp. 286-294.
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