A major SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei) |
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| Authors: | 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 |
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| Affiliation: | Sygen International Plc, Franklin, KY 42134, USA;. Department of Animal Science, University of Nebraska, Lincoln, NE 68583, USA;. Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6709 PG, The Netherlands;. Genus Plc, DeForest, WI 53532, USA;. Genearch Aquacultura Ltda, Barra do Cunhau, Rio Grande do Norte 59190, Brazil;. College of Natural and Applied Sciences, University of Guam, UOG Station, Mangilao GU96923, Guam;. Genus Plc, Hendersonville, TN 37075, USA;. INRA/Universitéde Limoges, UMR1061, Animal Molecular Genetics Unit, Limoges F-87060, France;. The Institute of Genetics and Bioinformatics, University of New England, Armidale, NSW 2351, Australia;. Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada T6G 2P5;. StoneBridge Breeding Ltd, Abbotswood, Evesham WR 4NS, UK |
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| 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 . |
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| Keywords: | association study selection shrimp SNP |
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