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- Carneiro, Miguel, et al.
(författare)
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Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 345:6200, s. 1074-1079
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 2. |
- Rubin, Carl-Johan, et al.
(författare)
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Strong signatures of selection in the domestic pig genome
- 2012
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 109:48, s. 19529-19536
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Tidskriftsartikel (refereegranskat)abstract
- Domestication of wild boar (Sus scrofa) and subsequent selection have resulted in dramatic phenotypic changes in domestic pigs for a number of traits, including behavior, body composition, reproduction, and coat color. Here we have used whole-genome resequencing to reveal some of the loci that underlie phenotypic evolution in European domestic pigs. Selective sweep analyses revealed strong signatures of selection at three loci harboring quantitative trait loci that explain a considerable part of one of the most characteristic morphological changes in the domestic pig - the elongation of the back and an increased number of vertebrae. The three loci were associated with the NR6A1, PLAG1, and LCORL genes. The latter two have repeatedly been associated with loci controlling stature in other domestic animals and in humans. Most European domestic pigs are homozygous for the same haplotype at these three loci. We found an excess of derived nonsynonymous substitutions in domestic pigs, most likely reflecting both positive selection and relaxed purifying selection after domestication. Our analysis of structural variation revealed four duplications at the KIT locus that were exclusively present in white or white-spotted pigs, carrying the Dominant white, Patch, or Belt alleles. This discovery illustrates how structural changes have contributed to rapid phenotypic evolution in domestic animals and how alleles in domestic animals may evolve by the accumulation of multiple causative mutations as a response to strong directional selection.
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| 3. |
- Sayyab, Shumaila
(författare)
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Bioinformatic screening for candidate mutations underlying phenotypic traits in domestic animals
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Domestic animals represent excellent model organisms for gene mapping and identification of mutations underlying phenotypic traits. Humans have selected spontaneous mutations in farm and companion animals since they were domesticated and this has resulted in large phenotypic variation among different breeds. In this thesis, we evaluate the candidate mutations in domesticated animals from NGS and SNP genotype data using bioinformatic analysis. Functional significance of coding sequence polymorphisms was assessed using both available bioinformatics resources and in-house pipelines. In consequence, pig and rabbit sequencing revealed major sweeps for genes (NR6A1, LCORL and PLAG1) for body length and increased number of vertebrae in domestic pigs and genes (GRIK2 and SOX2) affecting brain and neuronal development in rabbit domestication. Genome-wide association mapping for demodicosis disease in Staffordshire Bull Terrier dog show several preliminary candidate risk loci (CFA17, 18, 28 and 29) containing interesting candidate genes providing a good basis for further evaluation. Additionally, we also highlight some opportunities and pitfalls of whole genome resequencing using the Ion Proton platform and developed a tool DevRO (using deviant read paired orientation) for detection of large structural variants for NGS data from paired-end sequencing or mate pair. This method will be useful when large numbers of populations are resequenced as compared to traditional methods that can detect the structural variants in a pair wise manner.
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