Analysis of porcine body size variation using re-sequencing data of miniature and large pigs. Reimer, C., Rubin, C., Sharifi, A. R., Ha, N., [...], Schlather, M., & Simianer, H. BMC Genomics, 19(1):687, 2018. doi abstract bibtex BACKGROUND Domestication has led to substantial phenotypic and genetic variation in domestic animals. In pigs, the size of so called minipigs differs by one order of magnitude compared to breeds of large body size. We used biallelic SNPs identified from re-sequencing data to compare various publicly available wild and domestic populations against two minipig breeds to gain better understanding of the genetic background of the extensive body size variation. We combined two complementary measures, expected heterozygosity and the composite likelihood ratio test implemented in \textquotedblSweepFinder\textquotedbl, to identify signatures of selection in Minipigs. We intersected these sweep regions with a measure of differentiation, namely FST, to remove regions of low variation across pigs. An extraordinary large sweep between 52 and 61 Mb on chromosome X was separately analyzed based on SNP-array data of F2 individuals from a cross of Goettingen Minipigs and large pigs. RESULTS Selective sweep analysis identified putative sweep regions for growth and subsequent gene annotation provided a comprehensive set of putative candidate genes. A long swept haplotype on chromosome X, descending from the Goettingen Minipig founders was associated with a reduction of adult body length by 3% in F2 cross-breds. CONCLUSION The resulting set of genes in putative sweep regions implies that the genetic background of body size variation in pigs is polygenic rather than mono- or oligogenic. Identified genes suggest alterations in metabolic functions and a possible insulin resistance to contribute to miniaturization. A size QTL located within the sweep on chromosome X, with an estimated effect of 3% on body length, is comparable to the largest known in pigs or other species. The androgen receptor AR, previously known to influence pig performance and carcass traits, is the most obvious potential candidate gene within this region.
@article{Reimer2018Analysis,
abstract = {BACKGROUND
Domestication has led to substantial phenotypic and genetic variation in domestic animals. In pigs, the size of so called minipigs differs by one order of magnitude compared to breeds of large body size. We used biallelic SNPs identified from re-sequencing data to compare various publicly available wild and domestic populations against two minipig breeds to gain better understanding of the genetic background of the extensive body size variation. We combined two complementary measures, expected heterozygosity and the composite likelihood ratio test implemented in {\textquotedbl}SweepFinder{\textquotedbl}, to identify signatures of selection in Minipigs. We intersected these sweep regions with a measure of differentiation, namely FST, to remove regions of low variation across pigs. An extraordinary large sweep between 52 and 61~Mb on chromosome X was separately analyzed based on SNP-array data of F2 individuals from a cross of Goettingen Minipigs and large pigs.
RESULTS
Selective sweep analysis identified putative sweep regions for growth and subsequent gene annotation provided a comprehensive set of putative candidate genes. A long swept haplotype on chromosome X, descending from the Goettingen Minipig founders was associated with a reduction of adult body length by 3{\%} in F2 cross-breds.
CONCLUSION
The resulting set of genes in putative sweep regions implies that the genetic background of body size variation in pigs is polygenic rather than mono- or oligogenic. Identified genes suggest alterations in metabolic functions and a possible insulin resistance to contribute to miniaturization. A size QTL located within the sweep on chromosome X, with an estimated effect of 3{\%} on body length, is comparable to the largest known in pigs or other species. The androgen receptor AR, previously known to influence pig performance and carcass traits, is the most obvious potential candidate gene within this region.},
author = {Reimer, C. and Rubin, C-J and Sharifi, A. R. and Ha, Ngoc-Thuy and {[...]} and Schlather, M. and Simianer, H.},
year = {2018},
title = {Analysis of porcine body size variation using re-sequencing data of miniature and large pigs},
keywords = {gen;postdoc},
pages = {687},
volume = {19},
number = {1},
journal = {BMC Genomics},
doi = {10.1186/s12864-018-5009-y},
file = {http://www.ncbi.nlm.nih.gov/pubmed/30231878},
file = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6146782},
howpublished = {refereed}
}
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We combined two complementary measures, expected heterozygosity and the composite likelihood ratio test implemented in \\textquotedblSweepFinder\\textquotedbl, to identify signatures of selection in Minipigs. We intersected these sweep regions with a measure of differentiation, namely FST, to remove regions of low variation across pigs. An extraordinary large sweep between 52 and 61 Mb on chromosome X was separately analyzed based on SNP-array data of F2 individuals from a cross of Goettingen Minipigs and large pigs. RESULTS Selective sweep analysis identified putative sweep regions for growth and subsequent gene annotation provided a comprehensive set of putative candidate genes. A long swept haplotype on chromosome X, descending from the Goettingen Minipig founders was associated with a reduction of adult body length by 3% in F2 cross-breds. CONCLUSION The resulting set of genes in putative sweep regions implies that the genetic background of body size variation in pigs is polygenic rather than mono- or oligogenic. Identified genes suggest alterations in metabolic functions and a possible insulin resistance to contribute to miniaturization. A size QTL located within the sweep on chromosome X, with an estimated effect of 3% on body length, is comparable to the largest known in pigs or other species. The androgen receptor AR, previously known to influence pig performance and carcass traits, is the most obvious potential candidate gene within this region.","author":[{"propositions":[],"lastnames":["Reimer"],"firstnames":["C."],"suffixes":[]},{"propositions":[],"lastnames":["Rubin"],"firstnames":["C-J"],"suffixes":[]},{"propositions":[],"lastnames":["Sharifi"],"firstnames":["A.","R."],"suffixes":[]},{"propositions":[],"lastnames":["Ha"],"firstnames":["Ngoc-Thuy"],"suffixes":[]},{"firstnames":[],"propositions":[],"lastnames":["[...]"],"suffixes":[]},{"propositions":[],"lastnames":["Schlather"],"firstnames":["M."],"suffixes":[]},{"propositions":[],"lastnames":["Simianer"],"firstnames":["H."],"suffixes":[]}],"year":"2018","title":"Analysis of porcine body size variation using re-sequencing data of miniature and large pigs","keywords":"gen;postdoc","pages":"687","volume":"19","number":"1","journal":"BMC Genomics","doi":"10.1186/s12864-018-5009-y","file":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6146782","howpublished":"refereed","bibtex":"@article{Reimer2018Analysis,\r\n abstract = {BACKGROUND\r\n\r\nDomestication has led to substantial phenotypic and genetic variation in domestic animals. In pigs, the size of so called minipigs differs by one order of magnitude compared to breeds of large body size. We used biallelic SNPs identified from re-sequencing data to compare various publicly available wild and domestic populations against two minipig breeds to gain better understanding of the genetic background of the extensive body size variation. We combined two complementary measures, expected heterozygosity and the composite likelihood ratio test implemented in {\\textquotedbl}SweepFinder{\\textquotedbl}, to identify signatures of selection in Minipigs. We intersected these sweep regions with a measure of differentiation, namely FST, to remove regions of low variation across pigs. 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