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Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
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2014 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 345, no 6200, p. 1074-1079Article in journal (Refereed) Published
Abstract [en]

The genetic changes underlying the initial steps of animal domestication are still poorly understood. We generated a high-quality reference genome for the rabbit and compared it to resequencing data from populations of wild and domestic rabbits. We identified more than 100 selective sweeps specific to domestic rabbits but only a relatively small number of fixed (or nearly fixed) single-nucleotide polymorphisms (SNPs) for derived alleles. SNPs with marked allele frequency differences between wild and domestic rabbits were enriched for conserved noncoding sites. Enrichment analyses suggest that genes affecting brain and neuronal development have often been targeted during domestication. We propose that because of a truly complex genetic background, tame behavior in rabbits and other domestic animals evolved by shifts in allele frequencies at many loci, rather than by critical changes at only a few domestication loci.

Place, publisher, year, edition, pages
2014. Vol. 345, no 6200, p. 1074-1079
National Category
Genetics
Identifiers
URN: urn:nbn:se:uu:diva-232593DOI: 10.1126/science.1253714ISI: 000340870900046OAI: oai:DiVA.org:uu-232593DiVA, id: diva2:749547
Note

De två sista författarna delar sistaförfattarskapet (Andersson och Lindblad-Toh)

Available from: 2014-09-24 Created: 2014-09-22 Last updated: 2017-12-05Bibliographically approved
In thesis
1. Exploring genetic diversity in natural and domestic populations through next generation sequencing
Open this publication in new window or tab >>Exploring genetic diversity in natural and domestic populations through next generation sequencing
2017 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Studying genetic diversity in natural and domestic populations is of major importance in evolutionary biology. The recent advent of next generation sequencing (NGS) technologies has dramatically changed the scope of these studies, enabling researchers to study genetic diversity in a whole-genome context. This thesis details examples of studies using NGS data to: (i) characterize evolutionary forces shaping the genome of the Atlantic herring, (ii) detect the genetic basis of speciation and domestication in the rabbit, and, (iii) identify mutations associated with skeletal atavism in Shetland ponies.

The Atlantic herring (Clupea harengus) is the most abundant teleost species inhabiting the North Atlantic. Herring has seasonal reproduction and is adapted to a wide range of salinity (3-35‰) throughout the Baltic Sea and Atlantic Ocean. By using NGS data and whole-genome screening of 20 populations, we revealed the underlying genetic architecture for both adaptive features. Our results demonstrated that differentiated genomic regions have evolved by natural selection and genetic drift has played a subordinate role.

The European rabbit (Oryctolagus cuniculus) is native to the Iberian Peninsula, where two rabbit subspecies with partial reproductive isolation have evolved. We performed whole genome sequencing to characterize regions of reduced introgression. Our results suggest key role of gene regulation in triggering genetic incompatibilities in the early stages of reproductive isolation. Moreover, we studied gene expression in testis and found misregulation of many genes in backcross progenies that often show impaired male fertility. We also scanned whole genome of wild and domestic populations and identified differentiated regions that were enriched for non-coding conserved elements. Our results indicated that selection has acted on standing genetic variation, particularly targeting genes expressed in the central nervous system. This finding is consistent with the tame behavior present in domestic rabbits, which allows them to survive and reproduce under the stressful non-natural rearing conditions provided by humans.

In Shetland ponies, abnormally developed ulnae and fibulae characterize a skeletal deformity known as skeletal atavism. To explore the genetic basis of this disease, we scanned the genome using whole genome resequencing data. We identified two partially overlapping large deletions in the pseudoautosomal region (PAR) of the sex chromosomes that remove the entire coding sequence of the SHOX gene and part of CRLF2 gene. Based on this finding, we developed a diagnostic test that can be used as a tool to eradicate this inherited disease in horses.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2017. p. 62
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 1301
Keywords
Ecological adaptation, seasonal reproduction, Atlantic herring, domestication, speciation, rabbit, skeletal atavism, Shetland ponies, NGS, SMRT sequencing, genome, transcriptome, assembly, structural variation, genetic diversity, HCE, TSHR, SHOX, CRLF2
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-315032 (URN)978-91-554-9821-4 (ISBN)
Public defence
2017-03-30, B42, BMC, Husarg. 3, Uppsala, 13:15 (English)
Opponent
Supervisors
Funder
EU, European Research Council
Available from: 2017-03-09 Created: 2017-02-08 Last updated: 2017-04-03

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Rubin, Carl-JohanBarrio, Alvaro MartinezPielberg, GerliRafati, NimaYounis, ShadyXiong, AnqiForsberg-Nilsson, KarinLindblad-Toh, KerstinAndersson, Leif
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