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Genome-wide standing variation facilitates long-term response to bidirectional selection for antibody response in chickens
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. (Örjan Carlborg)ORCID iD: 0000-0001-8714-0812
Huazhong Agr Univ, Coll Anim Sci & Technol, Key Lab Agr Anim Genet Breeding & Reprod, Minist Educ, Wuhan 430070, Peoples R China..
Virginia Polytech Inst & State Univ, Dept Anim & Poultry Sci, Blacksburg, VA 24061 USA..
Virginia Polytech Inst & State Univ, Dept Anim & Poultry Sci, Blacksburg, VA 24061 USA..
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2017 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 18, article id 99Article in journal (Refereed) Published
Abstract [en]

BACKGROUND: Long-term selection experiments provide a powerful approach to gain empirical insights into adaptation, allowing researchers to uncover the targets of selection and infer their contributions to the mode and tempo of adaptation. Here we implement a pooled genome re-sequencing approach to investigate the consequences of 39 generations of bidirectional selection in White Leghorn chickens on a humoral immune trait: antibody response to sheep red blood cells.

RESULTS: We observed wide genome involvement in response to this selection regime. Many genomic regions were highly differentiated resulting from this experimental selection regime, an involvement of up to 20% of the chicken genome (208.8 Mb). While genetic drift has certainly contributed to this, we implement gene ontology, association analysis and population simulations to increase our confidence in candidate selective sweeps. Three strong candidate genes, MHC, SEMA5A and TGFBR2, are also presented.

CONCLUSIONS: The extensive genomic changes highlight the polygenic genetic architecture of antibody response in these chicken populations, which are derived from a common founder population, demonstrating the extent of standing immunogenetic variation available at the onset of selection.

Place, publisher, year, edition, pages
2017. Vol. 18, article id 99
Keyword [en]
Pooled genome sequencing, Selective sweeps, Virginia chicken lines, Sheep red blood cells, Antibody response
National Category
Immunology
Research subject
Immunology
Identifiers
URN: urn:nbn:se:uu:diva-313897DOI: 10.1186/s12864-016-3414-7ISI: 000394380200006PubMedID: 28100171OAI: oai:DiVA.org:uu-313897DiVA, id: diva2:1068390
Available from: 2017-01-25 Created: 2017-01-25 Last updated: 2018-01-18Bibliographically approved

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