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Genetic Analysis of Quantitative Traits Using Domestic Animals: A Candidate Gene and Genome Scanning Approach
Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
2004 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Domestication has led to genetic changes that affect quantitative traits in farm animals. Both candidate gene analysis using association tests and genome scans based on linkage analysis have been performed to understand the molecular basis underlying quantitative genetic variation in horses, pigs and chickens. To test a possible association of polymorphisms in the PRKAG3 gene, previously found to be associated with excess glycogen content in pig skeletal muscle, with quantitative traits in the horse, the major coding part of the equine PRKAG3 sequence was identified. Bioinformatic characterization of the equine PRKAG3 gene was conducted. A single nucleotide polymorphism (SNP) causing a missense mutation (Pro258Leu) was found. Screening this SNP showed that the Leu258 allele was more frequent in breeds with heavy muscularity. To assess previously reported associations between polymorphisms in the MC4R gene and obesity-related traits further, we conducted linkage analysis between the MC4R locus and fatness-related traits using a Wild BoarxLarge White intercross. No significant association between segregation at the MC4R locus and fatness was detected in this pedigree. A genome scan of quantitative trait loci (QTLs) has been performed in an intercross between chicken lines divergently selected for growth. Divergent parental lines have been established by selecting for high and low 56-day body weight for over 40 generations. The selection has led to approximately a 9-fold difference in 56-day body weight between lines and resulted in correlated responses for a number of traits including appetite, immune response, body composition and metabolic traits. Phenotypic data on growth and other correlated traits were collected from more than 800 F2 individuals. Genome scans using 145 markers on 26 linkage groups have identified QTLs affecting growth and correlated responses to selection for 56-day body weight. No major QTL explaining a large portion of phenotypic variation in growth was revealed in this study.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis , 2004. , p. 51
Series
Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 0282-7476 ; 1378
Keywords [en]
Genetics, Domestication, horse, pig, chicken, quantitative traits, candidate gene, genome scan, PRKAG3, MC4R, selection experiment, growth, correlated response, metabolic disorders, Quantitative Trait Loci, linkage, single nucleotide polymorphisms
Keywords [sv]
Genetik
National Category
Medical Genetics
Identifiers
URN: urn:nbn:se:uu:diva-4582ISBN: 91-554-6056-9 (print)OAI: oai:DiVA.org:uu-4582DiVA, id: diva2:165212
Public defence
2004-10-28, B41, Uppsala Biomedical Centre, Husargatan 3, Uppsala, 09:15
Opponent
Supervisors
Available from: 2004-10-07 Created: 2004-10-07 Last updated: 2018-01-13Bibliographically approved
List of papers
1. Molecular characterization and mutational screening of the PRKAG3 gene in the horse
Open this publication in new window or tab >>Molecular characterization and mutational screening of the PRKAG3 gene in the horse
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2003 (English)In: Cytogenetic and Genome Research, ISSN 1424-8581, Vol. 102, no 1-4, p. 211-216Article in journal (Refereed) Published
Identifiers
urn:nbn:se:uu:diva-92214 (URN)
Available from: 2004-10-07 Created: 2004-10-07 Last updated: 2011-06-30Bibliographically approved
2. Melanocortin-4 receptor(MC4R) genotypes have no major effect on fatness in a Large White x Wild boar intercross
Open this publication in new window or tab >>Melanocortin-4 receptor(MC4R) genotypes have no major effect on fatness in a Large White x Wild boar intercross
2002 (English)In: Animal Genetics, ISSN 0268-9146, Vol. 33, no 2, p. 155-157Article in journal (Refereed) Published
National Category
Natural Sciences
Research subject
Genetics
Identifiers
urn:nbn:se:uu:diva-92215 (URN)
Available from: 2004-10-07 Created: 2004-10-07 Last updated: 2016-05-18
3. Assignment of fourteen microsatellite markers to the chicken linkage map
Open this publication in new window or tab >>Assignment of fourteen microsatellite markers to the chicken linkage map
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2004 (English)In: Poultry Science, ISSN 0032-5791, E-ISSN 1525-3171, Vol. 83, no 11, p. 1825-1831Article in journal (Refereed) Published
Abstract [en]

A large mapping population, with 874 F2 individuals, was generated by reciprocally intercrossing 2 chicken lines. A genetic map of 2,426.6 cM comprising 25 linkage groups was established based on 145 microsatellite markers. Chromosome locations were assigned for 14 previously unmapped markers. The marker ADL0132 was previously mapped to chromosome 9; however, here close linkage to the MCW0091 marker on chromosome 4 was found. With this exception, the derived linkage map was in excellent agreement with the chicken consensus map. A comparison with the chicken genome assembly (http://genome.ucsc.edu; February 2004) suggested a few minor errors in the assembly. A PCR-RFLP test was used to genotype a single nucleotide polymorphism in the melanocortin receptor 3 (MC3R) gene in the intercross, and pyrosequencing was used to map the genes for Hemopoetic Cell Kinase (HCK) and Bone Morphogenic Protein 7 (BMP7). The HCK and BMP7 genes on linkage group E32 showed significant linkage to MC3R on the distal end of linkage group E47W24, consequently joining the 2 linkage groups. A comparison between the linkage data in the current study and the physical location of markers as revealed in the chicken genome sequence assembly (February 2004) showed a 3-fold higher recombination rate on microchromosomes than on macrochromosomes.

Keywords
chicken, linkage map, microsatellite, recombination rate, single nucleotide polymorphism
National Category
Agricultural Sciences
Identifiers
urn:nbn:se:uu:diva-92216 (URN)15554057 (PubMedID)
Available from: 2004-10-07 Created: 2004-10-07 Last updated: 2017-12-14Bibliographically approved
4. Many QTLs, each with a small effect, explain a huge difference in growth between two selection lines in chicken
Open this publication in new window or tab >>Many QTLs, each with a small effect, explain a huge difference in growth between two selection lines in chicken
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Article in journal (Refereed) Submitted
Identifiers
urn:nbn:se:uu:diva-92217 (URN)
Available from: 2004-10-07 Created: 2004-10-07Bibliographically approved
5. QTL analysis of body composition and metabolic traits in an intercross between chicken lines divergently selected for growth
Open this publication in new window or tab >>QTL analysis of body composition and metabolic traits in an intercross between chicken lines divergently selected for growth
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(English)Manuscript (Other academic)
Identifiers
urn:nbn:se:uu:diva-92218 (URN)
Available from: 2004-10-07 Created: 2004-10-07 Last updated: 2011-06-30Bibliographically approved

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