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. ; Steen, H.A.M. van der; Mileham, A.J. - \ 2010
Animal Genetics 41 (2010)1. - ISSN 0268-9146 - p. 39 - 47.
taura-syndrome virus - pig skeletal-muscle - linkage map - glycogen-content - penaeus - markers - mutation - resistance - discovery - growth
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
|Identification of quantitative trait loci for carcass composition and meat quality traits in a commercial finishing cross
Wijk, H.J. van; Dibbits, B.W. ; Baron, E.E. ; Brings, A.D. ; Harlizius, B. ; Groenen, M.A.M. ; Knol, E.F. ; Bovenhuis, H. - \ 2006
Journal of Animal Science 84 (2006)4. - ISSN 0021-8812 - p. 789 - 799.
influencing economic traits - large white intercross - genome scan analysis - pig skeletal-muscle - sus-scrofa - meat quality - body-composition - glycogen-content - igf2 locus - qtl
A QTL study for carcass composition and meat quality traits was conducted on finisher pigs of a cross between a synthetic Pie¿train/Large White boar line and a commercial sow cross. The mapping population comprised 715 individuals evaluated for a total of 30 traits related to growth and fatness (4 traits), carcass composition (11 traits), and meat quality (15 traits). Offspring of 8 sires (n = 715) were used for linkage analysis and genotyped for 73 microsatellite markers covering 14 chromosomal regions representing approximately 50% of the pig genome. The regions examined were selected based on previous studies suggesting the presence of QTL affecting carcass composition or meat quality traits. Thirty-two QTL exceeding the 5% chromosome-wise significance level were identified. Among these, 5 QTL affecting 5 different traits were significant at the 1% chromosome-wise level. The greatest significance levels were found for a QTL affecting loin weight on SSC11 and a QTL with an effect on the Japanese color scale score of the loin on SSC4. About one-third of the identified QTL were in agreement with QTL previously reported. Results showed that QTL affecting carcass composition and meat quality traits segregated within commercial lines. Use of these results for marker-assisted selection offers opportunities for improving pork quality by within-line selection