%0 Journal Article %1 Zhang20151 %A Zhang, Xinyue %A Misztal, Ignacy %A Heidaritabar, Marzieh %A Bastiaansen, John W.M. %A Borg, Randy %A Okimoto, Ron %A Sapp, Robyn L. %A Wing, Terry %A Hawken, Rachel R. %A Lourenco, Daniela A.L. %A Vitezica, Zulma G. %A Cheng, Hans H. %A Muir, William M. %D 2015 %J Livestock Science %K 2015 chicken genomics %P 1 - 11 %R http://dx.doi.org/10.1016/j.livsci.2014.11.003 %T Prior genetic architecture impacting genomic regions under selection: An example using genomic selection in two poultry breeds %U http://www.sciencedirect.com/science/article/pii/S1871141314005368 %V 171 %X AbstractBackground The objective of this study is to investigate if selection on similar traits in different populations progress from selection on similar genes. With the aid of high-density genome wide single-nucleotide polymorphism (SNP) genotyping, it is possible to directly assess changes in allelic frequencies and regions under selection and address the question. We compared the allele frequencies before and after two generations of selection on an index containing body weight at 6 wk, ultrasound measurement of breast meat, and leg score in two commercial chicken breeds with different selection histories: M breed was primarily selected for rapid growth and commonly used as a broiler breeder sire line; F breed was primarily used as dual-purposed dam line selected for both egg production and growth. Selection was performed on both lines with the same selection intensity and method (Genomic Best Linear Unbiased Prediction, GBLUP, using the single-step approach, ssGBLUP). Results After quality control, 52,742 and 52,639 \SNPs\ in M breed and F breed were kept in 4922 and 4904 animals, respectively. The average allele frequency change for both breeds on the autosomes was 0.049. Threshold value for detecting selected regions, where allele frequency changes exceeded expectations under drift were 0.140 and 0.136 for breeds M and F, respectively. According to the criterion used in this study, there were 25 and 17 selection regions detected on breeds M and F, respectively, without any overlap of regions between the breeds. Average heterozygosity change in F breed was greater compared to M breed (0.008 vs. 0.002, P<0.01). Also, there was no overlapping of selected regions with high heterozygosity change between breeds M and F. Conclusions The results indicate that in newly selected populations, even using the same criteria and selection methods, the historical selection goals and breed development determine the loci that most impact selection progress. These results are consistent with quantitative genetic theory that contribution of loci to selection progress depends on initial allele frequency. Therefore it should not be assumed that the same loci will be under selection in different populations even if similar selection goals and methods are used.

@article{Zhang20151, abstract = {AbstractBackground The objective of this study is to investigate if selection on similar traits in different populations progress from selection on similar genes. With the aid of high-density genome wide single-nucleotide polymorphism (SNP) genotyping, it is possible to directly assess changes in allelic frequencies and regions under selection and address the question. We compared the allele frequencies before and after two generations of selection on an index containing body weight at 6 wk, ultrasound measurement of breast meat, and leg score in two commercial chicken breeds with different selection histories: M breed was primarily selected for rapid growth and commonly used as a broiler breeder sire line; F breed was primarily used as dual-purposed dam line selected for both egg production and growth. Selection was performed on both lines with the same selection intensity and method (Genomic Best Linear Unbiased Prediction, GBLUP, using the single-step approach, ssGBLUP). Results After quality control, 52,742 and 52,639 \{SNPs\} in M breed and F breed were kept in 4922 and 4904 animals, respectively. The average allele frequency change for both breeds on the autosomes was 0.049. Threshold value for detecting selected regions, where allele frequency changes exceeded expectations under drift were 0.140 and 0.136 for breeds M and F, respectively. According to the criterion used in this study, there were 25 and 17 selection regions detected on breeds M and F, respectively, without any overlap of regions between the breeds. Average heterozygosity change in F breed was greater compared to M breed (0.008 vs. 0.002, P<0.01). Also, there was no overlapping of selected regions with high heterozygosity change between breeds M and F. Conclusions The results indicate that in newly selected populations, even using the same criteria and selection methods, the historical selection goals and breed development determine the loci that most impact selection progress. These results are consistent with quantitative genetic theory that contribution of loci to selection progress depends on initial allele frequency. Therefore it should not be assumed that the same loci will be under selection in different populations even if similar selection goals and methods are used. }, added-at = {2016-05-14T05:04:39.000+0200}, author = {Zhang, Xinyue and Misztal, Ignacy and Heidaritabar, Marzieh and Bastiaansen, John W.M. and Borg, Randy and Okimoto, Ron and Sapp, Robyn L. and Wing, Terry and Hawken, Rachel R. and Lourenco, Daniela A.L. and Vitezica, Zulma G. and Cheng, Hans H. and Muir, William M.}, biburl = {https://www.bibsonomy.org/bibtex/2087e65d896592a4edeb7167615c0af28/uga.abgg}, doi = {http://dx.doi.org/10.1016/j.livsci.2014.11.003}, interhash = {ebfc07bded72871cd983d3cb0e8f6850}, intrahash = {087e65d896592a4edeb7167615c0af28}, issn = {1871-1413}, journal = {Livestock Science }, keywords = {2015 chicken genomics}, pages = {1 - 11}, timestamp = {2016-05-14T18:05:46.000+0200}, title = {Prior genetic architecture impacting genomic regions under selection: An example using genomic selection in two poultry breeds }, url = {http://www.sciencedirect.com/science/article/pii/S1871141314005368}, volume = 171, year = 2015 }