Progress 09/15/00 to 09/14/05
Outputs
The Iowa State University (ISU) Berkshire x Yorkshire population of over 500 F2 pigs was genotyped for an additional 33 markers, complementing the initial 125 across the genome. In the University of Illinois (UoI) Berkshire x Duroc population of over 700 F2s, marker genotypes on 4 chromosomes were obtained. Both populations were phenotyped for a total of 40 growth, composition, and meat quality traits. An integrated database was developed to collate, maintain, and organize all data. Quantitative analysis of the UoI data using alternate models revealed moderate heritabilities of recorded traits and important trait relationships. Several novel statistical methods were developed and applied to increase power to detect QTL, to identify QTL for which expression depends on parental origin (imprinting), to detect and differentiate QTL that differ between breeds versus those that segregate within breeds, for joint analysis of multiple QTL experiments, and for multiple trait
analysis. Methods were applied to the two data sets and resulted in the discovery of a substantial number of additional QTL for growth, composition, and meat quality, and in better characterization of the genetic nature of the detected QTL. A paternally expressed QTL near IGF2 was confirmed, with major effects on backfat and loin-eye area in both populations. Several additional imprinted QTL and QTL with polar-overdominance imprinting were detected. Joint analysis of the two populations resulted in an increase in significance for many QTL, including 9 that were not significant in either population. Merit of multivariate techniques to identify QTL was evaluated and found to provide higher precision of parameter estimates and higher statistical significance in some cases than univariate models. Principal component analyses were consistent with uni- and multivariate analyses but identified a QTL for loin eye area not detected by other analyses. The advantage of multivariate approaches
depended on the genetic covariance between traits due to the modeled QTL effect and information contained in the data. False discovery rate was implemented and evaluated as an alternative to test significance of QTL and found to substantially reduce the chance that QTL remain undetected. QTL detected formed the basis of several positional candidate gene studies. Several tests of positional candidate genes in F2 breed cross populations were developed and evaluated. Results provided a much clearer picture of the value of candidate gene tests in F2 populations and demonstrated that they must be interpreted with caution and validated in outbred populations. In the area of using the detected QTL in selection, simulation studies showed that markers can be used to introduce multiple QTL from one breed into the other and to increase the effectiveness of development of synthetic breeds based on QTL detected in the initial cross for traits of low heritability. In the area of technology
transfer, an industry workshop was held in December 2003 to share results with the industry and to facilitate technology transfer. The workshop was attended by over 100 people from industry and academics.
Impacts
Results show that joint analysis of populations using a range of QTL models and single and multi-trait approaches increases power of QTL mapping and QTL characterization, which helps to identify genes for subsequent marker-assisted selection. The QTL that were detected in these studies for growth, composition and meat quality have formed the basis for further study of the underlying genes through positional candidate gene analysis. This has resulted in the development of several gene tests. Of these, two (CAST and PRKAG3) have been implemented in the industry and have a value of over 10 million dollars in annual improvement due to improved meat quality. In addition, as demonstrated by the simulation analyses, QTL detected in these studies can be used directly to aid breed improvement. The better characterization of the detected QTL, in terms of their genetic effects, presence of imprinting, and segregation within versus between breeds has important implications for the
use of these QTL in selection programs. Several QTL for meat quality were shown to segregate within the Berkshire and Yorkshire breeds, which enables use of detected QTL on a within-breed basis, which is the main strategy for improvement in pigs. Multiple QTL can be segregating in populations from currently available commercial pig lines and these can be exploited in selection programs.
Publications
- Kim, J.J., H.H. Zhao, H. Thomsen, M.F. Rothschild, and J.C.M. Dekkers. 2005. Combined line-cross and half-sib QTL analysis of crosses between outbred lines. Genet. Res. Camb. 85: 235-248.
- Kim, J.-J., K.S. Kim, M. Rothschild, J. beever, S. Rodriguez-Zas, and J.C.M. Dekkers. 2005. Joint analysis of two breed-cross populations in pigs to detect polar overdominance QTL. Proc. Integration of Structural and Functional Genomics conference, Sept. 22-25, Iowa State University. Abstract 19.
- Kim, J.-J., M.F. Rothschild, J. Beever, S. Rodriguez-Zas, and J.C.M. Dekkers. 2005. Joint analysis of two breed cross populations in pigs to improve detection and characterization of quantitative trait loci. J. Anim Sci. 83: 1229-1240.
- Kim, K.-S., H. Thomsen, J. Bastiaansen, N.T. Nguyen, J.C.M. Dekkers, G.S. Plastow, and M.F. Rothschild. 2004. Investigation of obesity candidate genes on porcine fat deposition quantitative trait loci regions. Obesity Research 12:1981-1994.
- Rodriguez-Zas, S. L., T. Stearns, J. Beever, J. Hartschuh, M. Ellis, and F. McKeith. 2003. Mapping of quantitative trait loci for weight, carcass and meat quality traits on pig chromosomes six and thirteen. Proceedings of the 28th Annual National Swine Improvement Federation Conference and Meeting. Dec 4-5 2003 Des Moines, IA. 59-70 pp.
- Stearns, T.M., J.E. Beever, B.R. Southey, M. Ellis, F.K. McKeith, and S.L. Rodriguez-Zas. 2004. Evaluation of approaches to detect quantitative trait loci for growth, carcass, and meat quality on swine chromosomes 2, 6, 13, and 18. II. Multivariate and principal component analyses. J. Anim Sci. 83(11):2471-2481.
- Stearns, T.M., J.E. Beever, B.R. Southey, M. Ellis, F.K. McKeith, and S.L. Rodriguez-Zas. 2004. Evaluation of approaches to detect quantitative trait loci for growth, carcass, and meat quality on swine chromosomes 2, 6, 13, and 18. I. Outbred F2 and analyses. J. Anim Sci. 83(7):1481-1493.
- Stearns, T., J. Beever, M. Ellis, F. McKeith, and S.L. Rodriguez-Zas. 2003. Mapping of loci on chromosome 6 influencing weight, carcass and meat quality characteristics in swine. Proceedings of the 28th Annual National Swine Improvement Federation Conference and Meeting. Dec 4-5 2003 Des Moines, IA.
- Stearns, T., J. Beever, M. Ellis, F. McKeith, and S.L. Rodriguez-Zas. 2004. Detection of quantitative trait loci for growth, carcass and meat quality traits in pigs. 2004 Midwest section, American Society of Animal Sciences. J. Anim. Sci. 82 (Suppl. 2): abs. 15, p. 36. http://www.asas.org/abstracts/2004sectional/S33.PDF
- Stearns, T., J. Beever, M. Ellis, F. McKeith, and S.L. Rodriguez-Zas. 2004. Detection of quantitative trait loci for growth, carcass and meat quality traits in pigs. 2004. In proceedings of the Midwest Section Meeting of the American Society of Animal Sciences, abstract 15, p5.
- Stearns, T., S.L. Rodriguez-Zas, J. Beever, J. Hartschuh, M. Ellis, F. McKeith, B.R. Southey, and R. Feltes. 2004. Identification of quantitative trait loci affecting growth, carcass and meat quality traits in SSC6 and 13. Swine Research Reports. University of Illinois, Department of Animal Sciences http://www.traill.uiuc.edu/porknet/papers.cfm.
- Thomsen H., J.C.M. Dekkers, H.K. Lee and M.F. Rothschild. 2002. Characterisation of quantitative loci for growth and meat quality in a breed cross in swine. 7th World Congress on Genetics Applied to Livestock Production, Montpellier, France, 15:05.
- Zhao, H., H. Gilbert, and J.C.M. Dekkers. 2005 Discriminant analysis for multitrait quantitative trait loci detection in a Berkshire x Yorkshire F2 population. Abstract presented at the 2005 Midwest Animal Science meeting, J. Anim. Sci. 83 (Suppl. 1).
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Progress 01/01/04 to 12/31/04
Outputs
Models were further developed and implemented for joint analysis of the ISU and UOI populations. Data on 26 growth and meat quality traits and genotypes on 39 (ISU) and 32 (UOI) markers on chromosomes 2, 6, 13 and 18 were analyzed using several least squares interval mapping models: line-cross (LC) models with Mendelian and imprinting effects, halfsib models (HS), and combined models (CB) that included LC and HS effects. At the 5% chromosome (genome)-wise level, 26 (8), 47 (18) and 53 (16) QTL were detected in the ISU, UOI and joint data. Of the 53 joint QTL, only 6 were detected in both populations and for many, allele effects differed between the two crosses. Nevertheless, joint analysis resulted in an increase in significance for many QTL, including 9 that were not significant in either population. A paternally expressed QTL near IGF2 was confirmed, with major effects on backfat and loin-eye area, as well as QTL for carcass composition in the distal arm of
chromosome 6. Merit of multivariate techniques to identify QTL was evaluated in both data sets. In the UOI data, multivariate and principal components analyses were used. Most multivariate analyses provided higher precision of parameter estimates and higher statistical significance in some cases than univariate models. Principal component analyses were consistent with uni- and multivariate analyses but identified a QTL for loin eye area not detected by other analyses. The advantage of multivariate approaches depended on the genetic covariance between traits due to the modeled QTL effect and information contained in the data. In the ISU data, discriminant analysis, which has been shown to be particularly suited to detect QTL with effects that are opposite to trait correlations, was used in an attempt to detect QTL that break the positive correlation between backfat and marbling. But for the analyzed chromosomes, QTL results were similar to those from single trait analyses, and no new
QTL that decrease average backfat but improve marbling were detected. Efficiency of marker-assisted selection on 3 marked QTL for a trait with heritability 0.1 in a line-cross program was evaluated by simulation. Responses to selection over 10 generations from alternate models for genetic evaluation were compared with regular BLUP selection: M1 = BLUP with markers as fixed effects; M2 = M1 with random QTL effects; M3 = BLUP with random QTL effects only. Selection on the number of favorable markers (M4) was evaluated also. QTL frequencies were fixed most rapidly with M4 (>0.9 in F4), followed by M1, M2, M3, and BLUP. For large QTL, genetic gain in the F4 was up to 29 and 39% greater than BLUP for M1 and M2, but only up to 2% and 15% greater for M3 and M4. Extra gain declined over generations for all models, with smaller QTL effects, and with larger marker intervals, and became negative for M4 in the F5. Based on genetic gains, M2 appeared to be the best model, although it is more
difficult to implement than M1.
Impacts
Results show that joint analysis of populations using a range of QTL models and multi- and single trait approaches increases power of QTL mapping and QTL characterization, which helps to identify genes for subsequent marker-assisted selection. Multiple QTL can be segregating in populations from currently available commercial pig lines and these can be exploited in selection programs. QTL detected in breed crosses can be used for subsequent selection within the cross, even using markers that are 20 cM apart.
Publications
- Ciobanu, D.C., J.W.M. Bastiaansen, S.M. Lonergan, H. Thomsen, J.C.M. Dekkers, G.S. Plastow and M.F. Rothschild. 2004. New alleles in calpastatin gene are associated with meat quality traits in pigs. J. Animal Sci. 82:2829-2839.
- Dekkers, J.C.M. 2004. Commercial application of marker- and gene-assisted selection in livestock: strategies and lessons. J. Anim. Sci. 82:E313-328E.
- Dekkers, J.C.M. and R. Chakraborty. 2004. Optimizing purebred selection for crossbred performance using QTL. Genet. Sel. Evol. 36:297-324.
- Gaboreanu, A.M., L. Grapes, A.M. Ramos, J.-J. Kim and M.F. Rothschild. 2004. Characterization of an X-chromosome PCR-RFLP marker associated with fat deposition and growth in the pig. Animal Genetics 35:401-403.
- Kim, J.-J. and J.C.M. Dekkers. 2004. A combined line-cross and halfsib model to detect and characterize QTL in an F2 outbred cross population. J. Anim Sci. 82 (Suppl. 1):415.
- Kim, J.-J., H. Thomsen, K.-S. Kim, M.F. Rothschild and J.C.M. Dekkers. 2004. A linear regression model to detect QTL with polar overdominance inheritance in a cross of outbred breeds. J. Anim. Sci. 82 (Suppl.2):42.
- Kim, J.-J., H.-H. Zhao, H. Thomsen, M.F. Rothschild and J.C.M. Dekkers. 2004. Detection of QTL for meat quality in an F2 cross in swine using combined line-cross and half-sib analysis. J. Anim. Sci. 82 (Suppl.2):42.
- Kim, K.S., J.J. Kim, J.C.M. Dekkers and M.F. Rothschild. 2004. Polar overdominance imprinting is associated with growth and fat deposition in pigs. PAG XII, p.240.
- Kim, K.S., J.J. Kim, J.C.M. Dekkers and M.F. Rothschild. 2004. Polar overdominant inheritance of a DLK1 polymorphism is associated with growth and fatness in pigs. Mammalian Genome 15:552-559.
- Piyasatian, N., R. Fernando and J. Dekkers. 2004. Efficiency of selection on multiple QTL in a crossbred population. J. Anim Sci. 82 (Suppl. 1):377.
- Stearns, T.M., J. Hartschuh, J.E. Beever, B.R. Southey, R.J. Feltes, M. Ellis, F. McKeith and S.L. Rodriguez-Zas. 2004. Identification of quantitative trait loci for carcass and growth traits in swine using principal components analysis. 2004 Annual Meeting of the American Society of Animal Sciences. J. Anim. Sci. 82(Suppl. 1):379.
- Stearns, T., J. Beever, M. Ellis, F. McKeith and S.L. Rodriguez-Zas. 2004. Detection of quantitative trait loci for growth, carcass and meat quality traits in pigs. J. Anim. Sci. 82(Suppl. 2):36.
- Thomsen, H., J.C.M. Dekkers, H.K. Lee, and M.F. Rothschild. 2004. Characterization of quantitative trait loci for growth and meat quality in a cross between commercial breeds of swine J. Anim. Sci. 82: 2213-2228.
- Zhao, H., J.-J. Kim , M. Perez-Enciso and J.C.M. Dekkers. 2004. Detection of quantitative trait loci segregation within pure breeds in a Berkshire x Yorkshire F2 population. J. Anim Sci. 82 (Suppl. 1):454.
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Progress 01/01/03 to 12/31/03
Outputs
Data from the Iowa State Berkshire x Yorkshire cross were further analyzed to identify QTL for growth, composition, and meat quality that segregate within the original purebred Berkshire and Yorkshire parents. Knowledge of segregating versus fixed QTL in the pure breeds is important for implementation of marker-assisted selection. New methodology was developed that combines QTL analyses using line-cross information and half-sib information. In total, 160 QTL were detected for the 39 traits evaluated. Using newly developed tests, these were classified into 1) 65 QTL that were fixed or nearly fixed for alternate alleles in the Berkshire and Yorkshire parents 2) 55 QTL that segregated within the purebred parents at similar frequencies in the two breeds, and 3) 40 QTL that segregated within the purebred parents at different frequencies between the two breeds. Individual QTL explained from 1.9 to 13.3% of the phenotypic variance and up to 51% when summed across QTL
identified for a given trait. These results demonstrate the utility of implementing a combined model to increase power to detect QTL and to better characterize their segregation within and between breeds. A method was also developed to detect QTL with polar overdominance, which is a unique mode of inheritance with parent-of-origin effects. Models and associated tests were applied to data on 16 growth and carcass composition traits in the Berkshire x Yorkshire cross. Three QTL regions with polar overdominance were detected at the genome-wise level, for lipid %, loin eye area, and tenth rib back fat in the distal regions of chromosome 6 and 10, and the proximal region of chromosome 12. These models enable detection and characterization of QTL with this unique mode of expression. In the University of Illinois population, genotyping has been completed for chromosomes 6 and 13 and partially for 2, 17 and 18. Several QTL were detected on chromosomes 6 and 13. Data on the Iowa State
Berkshire x Yorkshire and the University of Illinois Berkshire x Duroc resource populations for chromosome 6 were combined and analyzed for eight traits that were comparable in the two populations to evaluate the potential of a joint analysis. The joint analysis resulted in more QTL detected and smaller confidence intervals for QTL position, demonstrating the additional power from the joint analysis. None of the interactions between QTL and population were significant, indicating that QTL effects did not differ significantly between the two populations. Further joint analyses will be conducted in the coming year, as additional genotyping data becomes available from the Illinois population. On December 4, an industry workshop was held in Des Moines, in association with the National Swine Improvement Federation. Objectives were to facilitate technology transfer and implementation by the industry of QTL mapping procedures, QTL mapping research results, and strategies for the use of
molecular genetic data in breeding programs through marker-assisted selection. The workshop was attended by over 100 people from industry and academics and proceedings were published.
Impacts
Several QTL for meat quality were shown to segregate within the Berkshire and Yorkshire breeds, which enables use of detected QTL on a within-breed basis, which is the main strategy for improvement in pigs. These results have important implications for the use of the QTL in selection programs.
Publications
- Dekkers, J.C.M., Kim, J.J., Malek, M., Thomsen, H., Lee, H.K., Zhao, H.H. and Rothschild, M. 2003. A genome scan to detect QTL affecting growth, composition, and meat quality trait in a Berkshire x Yorkshire cross. USDA-IFAFS molecular genetics industry workshop and National Swine Improvement Federation Annual Meeting. Proc. 28th NSIF Annual Meeting, 21 pp.
- Kim. J.J., Dekkers, J., Rodriguez-Zas, S., Beever, J. and Rothschild, M. 2003. Joint analysis of the Berkshire x Yorkshire and Berkshire x Duroc crosses for QTL detection. USDA-IFAFS molecular genetics industry workshop and National Swine Improvement Federation Annual Meeting. Proc. 28th NSIF Annual Meeting, 5 pp.
- Rodriguez-Zas, S., Stearns, T., Beever, J., Hartschuh, J., Ellis, M. and McKeith, F. 2003. Mapping of quantitative of quantitative trait loci for weight, carcass and meat quality traits on pig chromosomes six and thirteen. USDA-IFAFS molecular genetics industry workshop and National Swine Improvement Federation Annual Meeting. Proc. 28th NSIF Annual Meeting, 12 pp.
- Rothschild, M.F., Ciobanu, D., Lonergan, S., Dekkers, J. and Stalder, K. 2003. Identification of Genes for Carcass Merit and Meat Quality in the Pig. USDA-IFAFS molecular genetics industry workshop and National Swine Improvement Federation Annual Meeting. Proc. 28th NSIF Annual Meeting, 5 pp.
- Southey, B.R. and Rodriguez-Zas, S.L. 2003. Meta-analysis to detect QTL in two connected F2 swine populations using simulation. J. Anim. Sci. 81 (Suppl. 1):252.
- Totir, L.R., Fernando, R.L., Dekkers, J.C.M., Fernandez, S.A. and Guldbrandtsen, B. 2003. A comparison of alternative methods to compute conditional genotype probabilities for genetic evaluation with finite locus models. Genet. Sel. Evol. 35:1-20.
- Zhao, H., Rothschild, M.F., Fernando, R.L., and Dekkers, J.C.M. 2003. Tests of candidate genes in breed cross population for QTL mappping in livestock. Mammalian Genome 14: 472-482.
- Dekkers, J.C.M. 2003. Commercial application of marker-assisted selection: strategies and lessons. J. Anim. Sci. 81 (Suppl. 1):5.
- Dekkers, J.C.M. 2003. Principles of QTL Mapping. USDA-IFAFS molecular genetics industry workshop and National Swine Improvement Federation Annual Meeting. Proc. 28th NSIF Annual Meeting, 14 pp.
- Dekkers, J.C.M. and Settar, P. 2003. Long-term Selection with Known Quantitative Trait Loci. Plant Breeding Reviews. Wiley. Plant Breeding Reviews, Volume 24, Part 1, Long Term Selection: Maize. edited by Jules Janick. John Wiley&Sons, Inc. Pp: 311-336.
- Dekkers, J.C.M. 2003. Marker-assisted Selection. USDA-IFAFS molecular genetics industry workshop and National Swine Improvement Federation Annual Meeting. Proc. 28th NSIF Annual Meeting, 28 pp.
- Dekkers, J.C.M., Thomsen, H., Lee, H.K., Malek, M. and Rothschild, M. 2003. Detection of imprinted QTL in the Berkshire x Yorkshire cross. USDA-IFAFS molecular genetics industry workshop and National Swine Improvement Federation Annual Meeting. Proc. 28th NSIF Annual Meeting, 17 pp.
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Progress 01/01/02 to 12/31/02
Outputs
Phenotypic data from the U of I population was entered into the integrated data base. Genotyping of the U of I population has been initiated and is nearly completed for chromosome six. Weight records obtained at multiple ages in the U of I population (10-11 per pig) were studied by a variety of models that provided complementary information on the impact of the genetic and environmental factors on weight at different ages. Orthogonal and non-orthogonal polynomials on age and spline models were considered. The percent of total variation explained by genetic effects (heritabilities) at specific ages ranged from 0.21 to 0.61 and for polynomial models the heritabilities fluctuated between 0.05 and 0.27 across the different fixed effect orders. Residual variance was lowest for the polynomial model of order 20 and highest for the polynomial model of order 2. Likewise, residual variance was lowest for the 10-knot spline model and highest for the 30-knot spline model. Based
on complementary indicators of model adequacy, the random polynomial and spline models provided the best fit to the weight data. The spline models required fewer parameters than the polynomial models and thus are superior in terms of model parsimony. There was general agreement across models in that genetic effects have a substantial impact on weight variability. Methods to identify QTL regions with parent-of-origin specific expression (imprinting) were applied to the ISU data. A total of 18 QTL with parent-of-origin effects were detected for growth and body composition, on chromosomes 1, 2, 4, 5, 10, 11, 12, 17, and 18, while 16 imprinted QTL were detected for meat quality traits, on chromosomes 2, 3, 5, 6, 9, 10, 14, 15, 16, and 18. Only four of these QTL were previously detected under the Mendelian models. Work is in progress to fit multiple-QTL models to the data, which will separate multiple QTL that may exist on a single chromosome. Analysis of the data as a half-sib design
further identified several QTL that were not detected using the original breed-cross analysis. This analysis enables detection of QTL that are segregating within the parental breeds. To combine information from the breed-cross and half-sib analysis, a variance component method has been implemented. This method optimally uses all QTL segregation information that is present in the data and will enable detection of additional QTL and determination of their segregation within the parental breeds. Several tests of positional candidate gene in F2 breed cross populations were developed and evaluated. Results provided a much clearer picture of the value of candidate gene tests in F2 populations and demonstrated that they must be interpreted with caution. Simulation and analysis programs were developed which will enable analysis of the extra responses that can be obtained from marker-assisted in breed crosses on QTL detected in a breed-cross analysis. In the area of technology transfer,
results were presented at several industry and scientific meetings, two extension articles were written, organization of a December 2003 industry workshop was initiated, and a website is under construction.
Impacts
Analysis of the U of I population indicate that studies aimed to detect QTL controlling weight are likely to identify significant associations. Parent-of-origin effects of QTL were shown to be important, and QTL were shown to segregate between as well as within breeds. These results have important implications for the use of the QTL in selection programs and strategies for their optimal use are under investigation.
Publications
- Chaiwong N and J Dekkers. 2002. Introgression of multiple QTL with limited population size in livestock. J. Anim. Sci. 80 (Suppl. 2):45.
- Chaiwong N, JCM Dekkers, RL Fernando and MF Rothschild. 2002. Introgressing multiple quantitative trait loci through backcross breeding programs. Swine Research Report, Iowa State University: 5pp.
- Chaiwong N, JCM Dekkers, RL Fernando and MF Rothschild. 2002. Introgressing multiple QTL in backcross breeding programs of limited size. 7th World Congress on Genetics Applied to Livestock Production, Montpellier, France, 22:08.
- Fernando RL, JCM Dekkers and M Soller. 2002. Controlling the proportion of false positive (PFP) in a multiple test genome scan for marker-QTL linkage. 7th World Congress on Genetics Applied to Livestock Production, Montpellier, France, 21:37.
- Huff-Lonergan E, TJ Baas, M Malek, JCM Dekkers, K Prusa and MF Rothschild. 2002. Correlations among selected pork quality traits. J. Anim. Sci. 80:617-627.
- Lee HK, JCM Dekkers, M Soller, M Malek, RL Fernando and MF Rothschild. 2002. Application of the false discovery rate to QTL interval mapping with multiple traits. Genetics 161:905-914.
- Li X, SL Rodriguez-Zas, JE Beever, M Ellis, F McKeith and BA Bailey. 2002. Parametric and non-parametric repeated-measure analysis of growth patterns. In: Proceedings of the American Statistical Association Annual Meeting, New York, New York.
- Li X, SL Rodriguez-Zas, JE Beever, M Ellis, F McKeith and BA Bailey. 2002. Mixed effects models to describe growth in related subjects. In Proceedings of the 2002 Bohrer workshop, Department of Statistics, University of Illinois at Urbana-Champaign.
- Thomsen H, JCM Dekkers, HK Lee and MF Rothschild. 2002. Characterisation of quantitative loci for growth and meat quality in a breed cross in swine. 7th World Congress on Genetics Applied to Livestock Production, Montpellier, France, 15:05.
- Thomsen H, M Malek, JCM Dekkers and MF Rothschild. 2002. Extended analysis of a Berkshire x Yorkshire cross to detect QTL for growth and meat quality traits. J. Anim. Sci. 80(Suppl. 2):41.
- Thomsen H, JCM Dekkers and MF Rothschild. 2002. Detection and characterization of quantitative trait loci for growth and meat quality traits in a Berkshire-Yorkshire cross. Swine Research Report, Iowa State University: 5pp.
- Zhao HH, JCM Dekkers and MF Rothschild. 2002. Tests of candidate genes in QTL mapping populations. J. Anim. Sci. 80 (Suppl. 2):41.
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Progress 01/01/01 to 12/31/01
Outputs
An integrated database was developed to collate, maintain, and organize data from the Iowa State University (ISU) and University of Illinois (U of I) resource populations and to facilitate data extraction. The ISU population was genotyped for an additional 33 markers, complementing the initial 125. Re-analysis revealed 18 additional QTL, for a total of 122, of which 20 were highly significant between the two breeds. Simulation studies showed that these QTL can be introduced from one breed into the other by marker-assisted introgression. Methods to identify QTL for which expression depends on parental origin (imprinting) were further developed and a QTL with paternal imprinting for growth and backfat was identified near IGF-2. This confirms previous results in mice and swine. Methods to implement the false discovery rate (FDR) as an alternative to test statistical significance of QTL were found to substantially reduce the chance that QTL remain undetected. The
performance of methods to track inheritance of marker alleles in complex pedigrees was compared. These are required for analysis of the joint data. Work was initiated on statistical tests for trait associations of positional candidate genes in the resource populations. These are needed to find the genes responsible. Phenotypic data collection on the U of I population has been completed and an analysis to estimate genetic parameters and evaluate the impact of systematic factors has been conducted. Heritabilities of traits related to weight, back fat, and meat quality were moderate to high. Estimates of genetic correlations revealed important trait relationships.
Impacts
Genomic regions with effects on meat quality that were identified in the initial analysis of the ISU data were confirmed and several additional regions were found. A region with imprinted effects was found on chromosome 2. Knowledge of the location and effects of genes is required for their utilization in selection programs to improve meat quality in the pig. One such utilization is through gene introgression. Initial theoretical analysis of such use showed that multiple genes can indeed be introgressed from one breed into another breed that lacks those genes. Results indicate that there is substantial genetic variation in the U of I population to grant further studies aiming to detect genomic regions that influence growth, carcass, and meat quality traits. These estimates also permit more accurate assessment of the impact of marker assisted selection on the improvement of these economically important traits.
Publications
- Dekkers JCM, MF Rothschild and M Malek. 2001. Potential and application of marker assisted selection for meat quality traits.1st International Virtual Conference on Pork Quality. Embrapa, Brazil. (13 pp.).
- Lee HK, JCM Dekkers, RL Fernando and MF Rothschild. 2001. Evaluation of statistical models and permutation tests for detecting gametic imprinting in QTL scans. J. Anim. Sci. 79 (Suppl. 1):190.
- Lee HK, JCM Dekkers, RL Fernando and MF Rothschild. 2001. Evidence of paternally imprinted QTL around IGF2 in a Berkshire-Yorkshire cross. J. Anim. Sci. 79 (Suppl. 1):340.
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Progress 10/01/00 to 12/31/00
Outputs
A meeting of the PI-s from Iowa State University and the University of Illinois was held on December 7 to discuss progress and plans. Recruiting of graduate students and post-doctoral fellows for the project is nearly complete. Forty additional genetic markers have been selected to test to eventually fill gaps in the existing marker map in the ISU population. These markers are currently being screened for informativeness in the F0 grand parents. Development of the UIUC resource population is on schedule to be completed by the end of 2001. Information about trait recording and genetic markers on the two populations has been exchanged to ensure sufficient overlap to allow joint analysis. Initial models to detect and identify QTL with gametic imprinting effects were developed. Methods to test for evidence of imprinting over Mendelian expression were developed, along with associated permutation tests to determine significance thresholds. These methods extend the models
proposed by de Koning et al. (PNAS 2000), who tested for imprinting by comparing against models in which no QTL was fitted. Testing against Mendelian models, which is what was developed here, is needed to identify significant deviations from Mendelian expression. Methods will be applied to the F2 population data following validation and evaluated by simulation, which is underway.
Impacts
The resource populations and statistical models that have been developed will enable identification of QTL for meat quality traits, as well as their mode of inheritance. This information will provide the input for subsequent stages of the project, which aim to develop strategies for the use of these QTL in selection.
Publications
- No publications reported this period
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