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Quantitative trait locus and genetical genomics analysis identifies putatively causal genes for fecundity and brooding behavior in the chicken
Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.ORCID iD: 0000-0003-1262-4585
Department of Surgical Sciences, Orthopaedics, Akademiska Sjukhuset, Uppsala universitet.
Department of Medical Biochemistry and Microbiology, Uppsala universitet.
Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Life history traits such as fecundity are important to evolution, because they make up components of lifetime fitness.  Due to their polygenic architectures, they are difficult to investigate with genetic mapping. Therefore, little is known about their molecular basis. One possible way towards finding the underlying genes is to map intermediary molecular phenotypes, such as gene expression traits. We set out to map candidate quantitative trait genes for egg fecundity in the chicken by combining quantitative trait locus mapping in an advanced intercross of wild by domestic chickens with expression quantitative trait locus mapping in the same birds. We measured individual egg fecundity in 232 intercross chickens in two consecutive trials, the second one aimed at measuring brooding behaviour. We find 12 loci for different aspects of egg fecundity. We then combine the genomic confidence intervals of these loci with expression quantitative trait loci from bone and hypothalamus in the same intercross. Overlaps between egg loci and expression loci, and trait—gene expression correlations identify 29 candidates from bone and five from hypothalamus. The candidate quantitative trait genes include fibroblast growth factor 1 and mitochondrial ribosomal proteins L42 and L32. In summary, we find putative quantitative trait genes for egg traits in the chicken that have may have been affected by regulatory variants under chicken domestication. These represent, to the best of our knowledge, some of the first candidate genes identified by genome-wide mapping for life history traits in an avian species.

National Category
Genetics
Identifiers
URN: urn:nbn:se:liu:diva-122277OAI: oai:DiVA.org:liu-122277DiVA: diva2:865185
Available from: 2015-10-27 Created: 2015-10-27 Last updated: 2015-11-05
In thesis
1. Genomics of chicken domestication and feralisation
Open this publication in new window or tab >>Genomics of chicken domestication and feralisation
2015 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Domestication can serve as a study system of rapid evolutionary change with wide-ranging effects on traits in animals. The chicken was domesticated from the Red Junglefowl and has diverged in behaviour, morphology and life history traits. Conversely, feralisation is a more recent process when domestic animals are again exposed and respond to an environment outside of human husbandry. Linkage-based quantitative trait locus (QTL) mapping has been used to localise genetic variants that affect domestication traits in the chicken genome. Because of the limited resolution of linkage mapping, the QTL regions associated with domestication traits are often broad and contain many genes. One approach to help sort out potential causative genes is to measure gene expression as an intermediary molecular phenotype. In this dissertation, expression quantitative trait locus (eQTL) mapping of gene expression traits is used to search for potential causative genes for domestication traits in the chicken. Expression quantitative trait loci were mapped across the whole genome in bone and hypothalamus samples, and targeted at QTL regions in the base of the comb. These studies have resulted in candidate quantitative trait genes, supported by genetic and gene expression evidence, for relative comb mass, bone allocation, egg production and fearful behaviour as measured in an open field test. Secondly, a population genomics approach was used to study the molecular basis of feralisation in a free-range feral chicken population from the Pacific island of Kauai. Mitochondrial DNA sequences and phenotypic observations establish the hybrid origin of this population as a mixture of wild and domestic chickens. Genome-wide mapping of pooled heterozygosity highlight regions that may be involved in adaptation to the feral environment. The expression QTL results bring us closer to knowledge about the molecular basis of domestication traits in the chicken, suggesting plausible candidate genes and opening up for functional studies of individual loci. The population genomic study shows that feralisation has a mostly different genomic architecture than domestication, and suggests phenotypic effects, based on overlap with domestication QTL regions, for some of the identified regions.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2015. 28 p.
Series
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1708
National Category
Genetics
Identifiers
urn:nbn:se:liu:diva-122280 (URN)10.3384/diss.diva-122280 (DOI)978-91-7685-932-2 (Print) (ISBN)
Public defence
2015-12-18, Planck, Fysikhuset, Campus Valla, Linköping, 10:15 (English)
Opponent
Supervisors
Available from: 2015-11-02 Created: 2015-10-27 Last updated: 2015-11-05Bibliographically approved

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Johnsson, MartinJensen, PerWright, Dominic
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