Meta-Analysis of Results from Quantitative Trait Loci Mapping Studies on Pig Chromosome 4
Moraes Silva, K.M. De; Bastiaansen, J.W.M. ; Knol, E.F. ; Merks, J.W.M. ; Lopes, P.S. ; Guimaraes, R.M. ; Arendonk, J.A.M. van - \ 2011
Animal Genetics 42 (2011)3. - ISSN 0268-9146 - p. 280 - 292.
pietrain resource population - meat quality traits - large white-pigs - confidence-intervals - carcass composition - body-composition - glycogen-content - skeletal-muscle - complex traits - sus-scrofa
Meta-analysis of results from multiple studies could lead to more precise quantitative trait loci (QTL) position estimates compared to the individual experiments. As the raw data from many different studies are not readily available, the use of results from published articles may be helpful. In this study, we performed a meta-analysis of QTL on chromosome 4 in pig, using data from 25 separate experiments. First, a meta-analysis was performed for individual traits: average daily gain and backfat thickness. Second, a meta-analysis was performed for the QTL of three traits affecting loin yield: loin eye area, carcass length and loin meat weight. Third, 78 QTL were selected from 20 traits that could be assigned to one of three broad categories: carcass, fatness or growth traits. For each analysis, the number of identified meta-QTL was smaller than the number of initial QTL. The reduction in the number of QTL ranged from 71% to 86% compared to the total number before the meta-analysis. In addition, the meta-analysis reduced the QTL confidence intervals by as much as 85% compared to individual QTL estimates. The reduction in the confidence interval was greater when a large number of independent QTL was included in the meta-analysis. Meta-QTL related to growth and fatness were found in the same region as the FAT1 region. Results indicate that the meta-analysis is an efficient strategy to estimate the number and refine the positions of QTL when QTL estimates are available from multiple populations and experiments. This strategy can be used to better target further studies such as the selection of candidate genes related to trait variation.
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