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<article article-type="research-article" dtd-version="1.3" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xml:lang="ru"><front><journal-meta><journal-id journal-id-type="publisher-id">vavilov</journal-id><journal-title-group><journal-title xml:lang="ru">Вавиловский журнал генетики и селекции</journal-title><trans-title-group xml:lang="en"><trans-title>Vavilov Journal of Genetics and Breeding</trans-title></trans-title-group></journal-title-group><issn pub-type="epub">2500-3259</issn><publisher><publisher-name>Institute of Cytology and Genetics of Siberian Branch of the RAS</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="doi">10.18699/VJ17.298</article-id><article-id custom-type="elpub" pub-id-type="custom">vavilov-1223</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="section-heading" xml:lang="ru"><subject>ГЕНОМИКА И ГЕННАЯ ИНЖЕНЕРИЯ</subject></subj-group><subj-group subj-group-type="section-heading" xml:lang="en"><subject>GENOMICS AND GENE ENGINEERING</subject></subj-group></article-categories><title-group><article-title>Использование геномных данных  в селекции птицы</article-title><trans-title-group xml:lang="en"><trans-title>Evaluation of the genome  in bird breeding</trans-title></trans-title-group></title-group><contrib-group><contrib contrib-type="author" corresp="yes"><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Яковлев</surname><given-names>А. Ф.</given-names></name><name name-style="western" xml:lang="en"><surname>Yakovlev</surname><given-names>A. F.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Санкт-Петербург, Пушкин.</p></bio><bio xml:lang="en"><p>St. Petersburg, Pushkin.</p></bio><email xlink:type="simple">afyakov@mail.ru</email><xref ref-type="aff" rid="aff-1"/></contrib><contrib contrib-type="author" corresp="yes"><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Дементьева</surname><given-names>Н. В.</given-names></name><name name-style="western" xml:lang="en"><surname>Dement’eva</surname><given-names>N. V.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Санкт-Петербург, Пушкин.</p></bio><bio xml:lang="en"><p>St. Petersburg, Pushkin.</p></bio><xref ref-type="aff" rid="aff-1"/></contrib></contrib-group><aff-alternatives id="aff-1"><aff xml:lang="ru">Всероссийский научно-исследовательский институт генетики и разведения сельскохозяйственных животных.<country>Россия</country></aff><aff xml:lang="en">Russian Research Institute of Farm Animal Genetics  and Breeding.<country>Russian Federation</country></aff></aff-alternatives><pub-date pub-type="collection"><year>2017</year></pub-date><pub-date pub-type="epub"><day>23</day><month>12</month><year>2017</year></pub-date><volume>21</volume><issue>7</issue><fpage>770</fpage><lpage>777</lpage><permissions><copyright-statement>Copyright &amp;#x00A9; Яковлев А.Ф., Дементьева Н.В., 2017</copyright-statement><copyright-year>2017</copyright-year><copyright-holder xml:lang="ru">Яковлев А.Ф., Дементьева Н.В.</copyright-holder><copyright-holder xml:lang="en">Yakovlev A.F., Dement’eva N.V.</copyright-holder><license license-type="creative-commons-attribution" xlink:href="https://creativecommons.org/licenses/by/4.0/" xlink:type="simple"><license-p>This work is licensed under a Creative Commons Attribution 4.0 License.</license-p></license></permissions><self-uri xlink:href="https://vavilov.elpub.ru/jour/article/view/1223">https://vavilov.elpub.ru/jour/article/view/1223</self-uri><abstract><p>Новые технологии определения последовательности нуклеотидов ДНК позволили открыть сотни тысяч мононуклеотидных поли морфных маркеров, часть из которых ассоциирована с племенны ми качествами животных. Разработанная на основе этих достижений геномная селекция произвела революционный сдвиг в птицеводстве. Система полиморфных маркеров  предоставляет уникальную возможность значительно повышать точность расчетных значений селекции, управлять генетической изменчивостью, сокращать интервалы между генерациями и ускорять генетический прогресс. Геномная селекция в птицеводстве имеет ряд отличий от подобной технологии, используемой на сельскохозяйственных видах млекопитающих. Наличие двух категорий хромосом (микро- и макрохромосомы) с разной скоростью рекомбинаций, включение в геномную оценку женских особей, а также быстрая смена поколений вносят свои особенности. Технология интенсивно внедряется в различные отрасли птицеводства, включая бройлерное производство, и используется основными птицеводческими компаниями. Совершенствованию отдельных этапов геномной селекции поможет улучшение регистрации количественных признаков, математической обработки молекулярной базы данных, импутации и оценки генетического неравновесия по сцеплению.</p></abstract><trans-abstract xml:lang="en"><p>New technologies determining the DNA sequence of nucleotides have led to the discovery of hundreds of thousands of mononucleotide polymorphic markers, some of which are associated with breeding quality of animals. Developed on the basis of these achievements, genomic selection has produced a revolutionary shift in the poultry industry. The developed molecular marker system provides a unique opportunity to significantly improve the accuracy of estimated breeding values to manage genetic variability, to reduce the interval between generations, and accelerate genetic progress. Genomic breeding in the poultry industry has a number of differences from similar technology used in agricultural mammalian species. The existence of two categories of chromosomes (macro- and microchromosomes) with different rates of recombination, the preferred genomic females evaluation, rapid change of generations make their own features. Technology is introduced rapidly in various sectors of the poultry industry, including broiler production, and is used by major poultry companies. The individual steps of genomic selection need to be improved, and the continuous improvement of technology can be attained though its use in practical and scientific. The improvement of the separate stages of genome selection will be helped by perfection of registration and mathematical treatment of the phenotypical and molecular database, imputation and estimations of linkage disequilibrium.</p></trans-abstract><kwd-group xml:lang="ru"><kwd>птица</kwd><kwd>секвенирование</kwd><kwd>мононуклеотидный полиморфизм</kwd><kwd>геномная селекция</kwd><kwd>маркеры</kwd><kwd>неравновесие по сцеплению</kwd><kwd>импутация</kwd></kwd-group><kwd-group xml:lang="en"><kwd>bird</kwd><kwd>sequencing</kwd><kwd>SNP</kwd><kwd>genomic selection</kwd><kwd>markers</kwd><kwd>linkage disequilibrium</kwd><kwd>imputation</kwd></kwd-group></article-meta></front><back><ref-list><title>References</title><ref id="cit1"><label>1</label><citation-alternatives><mixed-citation xml:lang="ru">Abdollahi-Arpanahi R., Morota G., Valente B.D., Kranis A., Rosa G., Gianola D. Differential contribution of genomic regions to marked genetic variation and prediction of quantitative traits in broiler chickens. Genet. Sel. Evol. 2016;48:10. DOI 10.1186/s12711-016-0187-z.</mixed-citation><mixed-citation xml:lang="en">Abdollahi-Arpanahi R., Morota G., Valente B.D., Kranis A., Rosa G., Gianola D. Differential contribution of genomic regions to marked genetic variation and prediction of quantitative traits in broiler chickens. Genet. Sel. Evol. 2016;48:10. DOI 10.1186/s12711-016-0187-z.</mixed-citation></citation-alternatives></ref><ref id="cit2"><label>2</label><citation-alternatives><mixed-citation xml:lang="ru">Aerts J., Megens H.J., Veenendaal T., Ovcharenko I., Crooijmans R., Gordon L., Stubbs L., Groenen M. Extent of linkage disequilibrium in chicken. Cytogenet. Genome Res. 2007;117(1-4):338-345. DOI 10.1159/000103196.</mixed-citation><mixed-citation xml:lang="en">Aerts J., Megens H.J., Veenendaal T., Ovcharenko I., Crooijmans R., Gordon L., Stubbs L., Groenen M. Extent of linkage disequilibrium in chicken. Cytogenet. Genome Res. 2007;117(1-4):338-345. DOI 10.1159/000103196.</mixed-citation></citation-alternatives></ref><ref id="cit3"><label>3</label><citation-alternatives><mixed-citation xml:lang="ru">Andreescu C., Avendano S., Brown S.R., Hassen A., Lamont S.J., Dekkers J.C. Linkage disequilibrium in related breeding lines of chickens. Genetics. 2007;177:2161-2169. DOI 10.1534/genetics. 107.082206.</mixed-citation><mixed-citation xml:lang="en">Andreescu C., Avendano S., Brown S.R., Hassen A., Lamont S.J., Dekkers J.C. Linkage disequilibrium in related breeding lines of chickens. Genetics. 2007;177:2161-2169. DOI 10.1534/genetics. 107.082206.</mixed-citation></citation-alternatives></ref><ref id="cit4"><label>4</label><citation-alternatives><mixed-citation xml:lang="ru">Bai Y., Sun G., Kang X., Han R., Tian Y., Li H., Wei Y., Zhu S. Polymorphisms of the pro-opiomelanocortin and agouti-related protein genes and their association with chicken production traits. Mol. Biol. Rep. 2012;39(7):7533-7539. DOI 10.1007/s11033-012-1587-y.</mixed-citation><mixed-citation xml:lang="en">Bai Y., Sun G., Kang X., Han R., Tian Y., Li H., Wei Y., Zhu S. Polymorphisms of the pro-opiomelanocortin and agouti-related protein genes and their association with chicken production traits. Mol. Biol. Rep. 2012;39(7):7533-7539. DOI 10.1007/s11033-012-1587-y.</mixed-citation></citation-alternatives></ref><ref id="cit5"><label>5</label><citation-alternatives><mixed-citation xml:lang="ru">Browning B.L., Browning S.R. A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am. J. Hum. Genet. 2009; 84(2):210-223. DOI 10.1016/j.ajhg.2009.01.005.</mixed-citation><mixed-citation xml:lang="en">Browning B.L., Browning S.R. A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am. J. Hum. Genet. 2009; 84(2):210-223. DOI 10.1016/j.ajhg.2009.01.005.</mixed-citation></citation-alternatives></ref><ref id="cit6"><label>6</label><citation-alternatives><mixed-citation xml:lang="ru">Brzyski D., Peterson Ch.B., Sobczyk P., Candes E.J., Bogdan M., Sa-batti C. Controlling the rate of GWAS false discoveries. Genetics. 2017;205(1):61-75. DOI 10.1534/genetics.116.193987.</mixed-citation><mixed-citation xml:lang="en">Brzyski D., Peterson Ch.B., Sobczyk P., Candes E.J., Bogdan M., Sa-batti C. Controlling the rate of GWAS false discoveries. Genetics. 2017;205(1):61-75. DOI 10.1534/genetics.116.193987.</mixed-citation></citation-alternatives></ref><ref id="cit7"><label>7</label><citation-alternatives><mixed-citation xml:lang="ru">Cosart T., Beja-Pereira A., Luikart G. EXONSAMPLER: a computer program for genome-wide and candidate gene exon sampling for targeted next generation sequencing. Mol. Ecol. Resour. 2014;14(6): 1296-1301. DOI 10.1111/1755-0998.12267.</mixed-citation><mixed-citation xml:lang="en">Cosart T., Beja-Pereira A., Luikart G. EXONSAMPLER: a computer program for genome-wide and candidate gene exon sampling for targeted next generation sequencing. Mol. Ecol. Resour. 2014;14(6): 1296-1301. DOI 10.1111/1755-0998.12267.</mixed-citation></citation-alternatives></ref><ref id="cit8"><label>8</label><citation-alternatives><mixed-citation xml:lang="ru">Daetwyler H.D., Pong-Wong R., Villanueva B. The impact of genetic architecture on genome-wide evaluation methods. Genetics. 2010; 185:1021-1031. DOI 10.1534/genetics.110.116855.</mixed-citation><mixed-citation xml:lang="en">Daetwyler H.D., Pong-Wong R., Villanueva B. The impact of genetic architecture on genome-wide evaluation methods. Genetics. 2010; 185:1021-1031. DOI 10.1534/genetics.110.116855.</mixed-citation></citation-alternatives></ref><ref id="cit9"><label>9</label><citation-alternatives><mixed-citation xml:lang="ru">Daetwyler H.D., Villanueva B., Woolliams J.A. Accuracy of predicting the genetic risk of disease using a genome-wide approach. PLoS ONE. 2008;3(10):e3395. DOI 10.1371/journal.pone.0003395.</mixed-citation><mixed-citation xml:lang="en">Daetwyler H.D., Villanueva B., Woolliams J.A. Accuracy of predicting the genetic risk of disease using a genome-wide approach. PLoS ONE. 2008;3(10):e3395. DOI 10.1371/journal.pone.0003395.</mixed-citation></citation-alternatives></ref><ref id="cit10"><label>10</label><citation-alternatives><mixed-citation xml:lang="ru">Dekkers J.C.M. Commercial application of marker- and gene-assisted selection in livestock: strategies and lessons. J. Anim. Sci. 2004; 82(E-Suppl.):E313-E328.</mixed-citation><mixed-citation xml:lang="en">Dekkers J.C.M. Commercial application of marker- and gene-assisted selection in livestock: strategies and lessons. J. Anim. Sci. 2004; 82(E-Suppl.):E313-E328.</mixed-citation></citation-alternatives></ref><ref id="cit11"><label>11</label><citation-alternatives><mixed-citation xml:lang="ru">de Roos A.P.W., Hayes B.J., Spelman R.J., Goddard M.E. Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle. Genetics. 2008;179(3):1503-1512. DOI 10.1534/ genetics.107.084301.</mixed-citation><mixed-citation xml:lang="en">de Roos A.P.W., Hayes B.J., Spelman R.J., Goddard M.E. Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle. Genetics. 2008;179(3):1503-1512. DOI 10.1534/ genetics.107.084301.</mixed-citation></citation-alternatives></ref><ref id="cit12"><label>12</label><citation-alternatives><mixed-citation xml:lang="ru">Do D.N., Janss L.L., Jensen J., Kadarmideen H.N. SNP annotation-based whole genomic prediction and selection: an application to feed efficiency and its component traits in pigs. J. Anim. Sci. 2015;93:2056-2063. DOI 10.2527/jas.2014-8640.</mixed-citation><mixed-citation xml:lang="en">Do D.N., Janss L.L., Jensen J., Kadarmideen H.N. SNP annotation-based whole genomic prediction and selection: an application to feed efficiency and its component traits in pigs. J. Anim. Sci. 2015;93:2056-2063. DOI 10.2527/jas.2014-8640.</mixed-citation></citation-alternatives></ref><ref id="cit13"><label>13</label><citation-alternatives><mixed-citation xml:lang="ru">Elferink M.G., Megens H.J., Vereijken A., Hu X., Crooijmans R.P., Groenen M.A. Signatures of selection in the genomes of commercial and non-commercial chicken breeds. PloS ONE. 2012;7(2):e32720.</mixed-citation><mixed-citation xml:lang="en">Elferink M.G., Megens H.J., Vereijken A., Hu X., Crooijmans R.P., Groenen M.A. Signatures of selection in the genomes of commercial and non-commercial chicken breeds. PloS ONE. 2012;7(2):e32720.</mixed-citation></citation-alternatives></ref><ref id="cit14"><label>14</label><citation-alternatives><mixed-citation xml:lang="ru">Ennis S. Linkage disequilibrium as a tool for detecting signatures of natural selection. Methods Mol. Biol. 2007;376:59-70. DOI 10.1007/978-1-59745-389-9_5.</mixed-citation><mixed-citation xml:lang="en">Ennis S. Linkage disequilibrium as a tool for detecting signatures of natural selection. Methods Mol. Biol. 2007;376:59-70. DOI 10.1007/978-1-59745-389-9_5.</mixed-citation></citation-alternatives></ref><ref id="cit15"><label>15</label><citation-alternatives><mixed-citation xml:lang="ru">Ewald S.J., Kapczynski D.R., Livant E.J., Suarez D.L., Ralph J., McLeod S., Miller C. Association of Mx1 Asn631 variant alleles with reductions in morbidity, early mortality, viral shedding, and cytokine responses in chickens infected with a highly pathogenic avian influenza virus. Immunogenetics. 2011;63:363-375. DOI 10.1007/ s00251-010-0509-1.</mixed-citation><mixed-citation xml:lang="en">Ewald S.J., Kapczynski D.R., Livant E.J., Suarez D.L., Ralph J., McLeod S., Miller C. Association of Mx1 Asn631 variant alleles with reductions in morbidity, early mortality, viral shedding, and cytokine responses in chickens infected with a highly pathogenic avian influenza virus. Immunogenetics. 2011;63:363-375. DOI 10.1007/ s00251-010-0509-1.</mixed-citation></citation-alternatives></ref><ref id="cit16"><label>16</label><citation-alternatives><mixed-citation xml:lang="ru">Fan W.L., Ng C.S., Chen C.F., Lu M.Y., Chen Y.H., Liu C.J., Wu S.M., Chen C.K., Chen J.J., Mao C.T., Lai Y.T., Lo W.S., Chang W.H., Li W.H. Genome-wide patterns of genetic variation in two domestic chickens. Genome Biol. Evol. 2013;5:1376-1392. DOI 10.1093/gbe/ evt097.</mixed-citation><mixed-citation xml:lang="en">Fan W.L., Ng C.S., Chen C.F., Lu M.Y., Chen Y.H., Liu C.J., Wu S.M., Chen C.K., Chen J.J., Mao C.T., Lai Y.T., Lo W.S., Chang W.H., Li W.H. Genome-wide patterns of genetic variation in two domestic chickens. Genome Biol. Evol. 2013;5:1376-1392. DOI 10.1093/gbe/ evt097.</mixed-citation></citation-alternatives></ref><ref id="cit17"><label>17</label><citation-alternatives><mixed-citation xml:lang="ru">Fariello M.I., Boitard S., Naya H., SanCristobal M., Servin B. Detecting signatures of selection through haplotype differentiation among hierarchically structured populations. Genetics. 2013;193:929-941. DOI 10.1534/genetics.112.147231.</mixed-citation><mixed-citation xml:lang="en">Fariello M.I., Boitard S., Naya H., SanCristobal M., Servin B. Detecting signatures of selection through haplotype differentiation among hierarchically structured populations. Genetics. 2013;193:929-941. DOI 10.1534/genetics.112.147231.</mixed-citation></citation-alternatives></ref><ref id="cit18"><label>18</label><citation-alternatives><mixed-citation xml:lang="ru">Fu W., Dekkers J.C.M., Lee W.R., Abasht B. Linkage disequilibrium in crossbred and pure line chickens. Genet. Sel. Evol. 2015;47(1):11. DOI 10.1186/s12711-015-0098-4.</mixed-citation><mixed-citation xml:lang="en">Fu W., Dekkers J.C.M., Lee W.R., Abasht B. Linkage disequilibrium in crossbred and pure line chickens. Genet. Sel. Evol. 2015;47(1):11. DOI 10.1186/s12711-015-0098-4.</mixed-citation></citation-alternatives></ref><ref id="cit19"><label>19</label><citation-alternatives><mixed-citation xml:lang="ru">Gabriel S.B., Schaffner S.F., Nguyen H., Moore J.M., Roy J., Blu-menstiel B., Higgins J., DeFelice M., Lochner A., Faggart M., Liu-Cordero S.N., Rotimi C., Adeyemo A., Cooper R., Ward R., Lander E.S., Daly M.J., Altshuler D. The structure of haplotype blocks in the human genome. Science. 2002;296(5576):2225-2229. DOI 10.1126/science.1069424.</mixed-citation><mixed-citation xml:lang="en">Gabriel S.B., Schaffner S.F., Nguyen H., Moore J.M., Roy J., Blu-menstiel B., Higgins J., DeFelice M., Lochner A., Faggart M., Liu-Cordero S.N., Rotimi C., Adeyemo A., Cooper R., Ward R., Lander E.S., Daly M.J., Altshuler D. The structure of haplotype blocks in the human genome. Science. 2002;296(5576):2225-2229. DOI 10.1126/science.1069424.</mixed-citation></citation-alternatives></ref><ref id="cit20"><label>20</label><citation-alternatives><mixed-citation xml:lang="ru">Garcia-Gamez E., Sahana G., Gutierrez-Gil B. Linkage disequilibrium and inbreeding estimation in Spanish Churra sheep. BMC Genet. 2012;13:43. DOI 10.1186/1471-2156-13-43.</mixed-citation><mixed-citation xml:lang="en">Garcia-Gamez E., Sahana G., Gutierrez-Gil B. Linkage disequilibrium and inbreeding estimation in Spanish Churra sheep. BMC Genet. 2012;13:43. DOI 10.1186/1471-2156-13-43.</mixed-citation></citation-alternatives></ref><ref id="cit21"><label>21</label><citation-alternatives><mixed-citation xml:lang="ru">Gholami M., Reimer C., Erbe M., Preisinger R., Weigend A., Wei-gend S., Servin B., Simianer H. Genome scan for selection in structured layer chicken populations exploiting linkage disequilibrium information. PLoS ONE. 2015;10(7):e0130497. DOI 10.1371/journal.pone.0130497.</mixed-citation><mixed-citation xml:lang="en">Gholami M., Reimer C., Erbe M., Preisinger R., Weigend A., Wei-gend S., Servin B., Simianer H. Genome scan for selection in structured layer chicken populations exploiting linkage disequilibrium information. PLoS ONE. 2015;10(7):e0130497. DOI 10.1371/journal.pone.0130497.</mixed-citation></citation-alternatives></ref><ref id="cit22"><label>22</label><citation-alternatives><mixed-citation xml:lang="ru">Groenen M., Megens H.J., Zare Y., Warren W.C., Hillier L.W., Crooij-mans R.P., Vereijken A., Okimoto R., Muir W.M., Cheng H.H. The development and characterization of a 60K SNP chip for chicken. BMC Genomics. 2011;12:274. DOI 10.1186/1471-2164-12-274.</mixed-citation><mixed-citation xml:lang="en">Groenen M., Megens H.J., Zare Y., Warren W.C., Hillier L.W., Crooij-mans R.P., Vereijken A., Okimoto R., Muir W.M., Cheng H.H. The development and characterization of a 60K SNP chip for chicken. BMC Genomics. 2011;12:274. DOI 10.1186/1471-2164-12-274.</mixed-citation></citation-alternatives></ref><ref id="cit23"><label>23</label><citation-alternatives><mixed-citation xml:lang="ru">Habier D., Fernando R.L., Dekkers J.C.M. The impact of genetic relationship information on genome-assisted breeding values. Genetics. 2007;177(4):2389-2397. DOI 10.1534/genetics.107.081190.</mixed-citation><mixed-citation xml:lang="en">Habier D., Fernando R.L., Dekkers J.C.M. The impact of genetic relationship information on genome-assisted breeding values. Genetics. 2007;177(4):2389-2397. DOI 10.1534/genetics.107.081190.</mixed-citation></citation-alternatives></ref><ref id="cit24"><label>24</label><citation-alternatives><mixed-citation xml:lang="ru">Habier D., Tetens J., Seefried F.R., Lichtner P., Thaller G. The impact of genetic relationship information on genomic breeding values in German Holstein cattle. Genet. Sel. Evol. 2010;42:5. DOI 10.1186/1297-9686-42-5.</mixed-citation><mixed-citation xml:lang="en">Habier D., Tetens J., Seefried F.R., Lichtner P., Thaller G. The impact of genetic relationship information on genomic breeding values in German Holstein cattle. Genet. Sel. Evol. 2010;42:5. DOI 10.1186/1297-9686-42-5.</mixed-citation></citation-alternatives></ref><ref id="cit25"><label>25</label><citation-alternatives><mixed-citation xml:lang="ru">Hayes B.J., Bowman P.J., Chamberlain A.J., Goddard M.E. Invited review: genomic selection in dairy cattle: progress and challenges. J. Dairy Sci. 2009;92:433-443. DOI 10.3168/jds.2008-1646.</mixed-citation><mixed-citation xml:lang="en">Hayes B.J., Bowman P.J., Chamberlain A.J., Goddard M.E. Invited review: genomic selection in dairy cattle: progress and challenges. J. Dairy Sci. 2009;92:433-443. DOI 10.3168/jds.2008-1646.</mixed-citation></citation-alternatives></ref><ref id="cit26"><label>26</label><citation-alternatives><mixed-citation xml:lang="ru">Heidaritabar M., Calus M., Vereijken A., Groenen M., Bastiaansen J. Accuracy of imputation using the most common sires as reference population in layer chickens. BMC Genetics. 2015;16:101. DOI 10.1186/s12863-015-0253-5.</mixed-citation><mixed-citation xml:lang="en">Heidaritabar M., Calus M., Vereijken A., Groenen M., Bastiaansen J. Accuracy of imputation using the most common sires as reference population in layer chickens. BMC Genetics. 2015;16:101. DOI 10.1186/s12863-015-0253-5.</mixed-citation></citation-alternatives></ref><ref id="cit27"><label>27</label><citation-alternatives><mixed-citation xml:lang="ru">Heidaritabar M., Vereijken A., Muir W.M., Meuwissen T., Cheng H., Megens H.J., Groenen M.A., Bastiaansen J.W. Systematic differences in the response of genetic variation to pedigree and genome-based selection methods. Heredity (Edinb.). 2014;13(6):503-513. DOI 10.1038/hdy.2014.55.</mixed-citation><mixed-citation xml:lang="en">Heidaritabar M., Vereijken A., Muir W.M., Meuwissen T., Cheng H., Megens H.J., Groenen M.A., Bastiaansen J.W. Systematic differences in the response of genetic variation to pedigree and genome-based selection methods. Heredity (Edinb.). 2014;13(6):503-513. DOI 10.1038/hdy.2014.55.</mixed-citation></citation-alternatives></ref><ref id="cit28"><label>28</label><citation-alternatives><mixed-citation xml:lang="ru">Heifetz E.M., Fulton J.E., O'Sullivan N., Zhao H., Dekkers J.C., Soller M. Extent and consistency across generations of linkage disequilibrium in commercial layer chicken breeding populations. Genetics. 2005;171(3):1173-1181. DOI 10.1534/genetics.105. 040782.</mixed-citation><mixed-citation xml:lang="en">Heifetz E.M., Fulton J.E., O'Sullivan N., Zhao H., Dekkers J.C., Soller M. Extent and consistency across generations of linkage disequilibrium in commercial layer chicken breeding populations. Genetics. 2005;171(3):1173-1181. DOI 10.1534/genetics.105. 040782.</mixed-citation></citation-alternatives></ref><ref id="cit29"><label>29</label><citation-alternatives><mixed-citation xml:lang="ru">Hickey J.M., Kinghorn B.P., Tier B., Wilson J.F., Dunstan N., van der Werf J.H. A combined long-range phasing and long haplotype imputation method to impute phase for SNP genotypes. Genet. Sel. Evol. 2011;43:12. DOI 10.1186/1297-9686-44-9.</mixed-citation><mixed-citation xml:lang="en">Hickey J.M., Kinghorn B.P., Tier B., Wilson J.F., Dunstan N., van der Werf J.H. A combined long-range phasing and long haplotype imputation method to impute phase for SNP genotypes. Genet. Sel. Evol. 2011;43:12. DOI 10.1186/1297-9686-44-9.</mixed-citation></citation-alternatives></ref><ref id="cit30"><label>30</label><citation-alternatives><mixed-citation xml:lang="ru">Hillier L.W., Miller W., Birney E., Warren W., Hardison R.C., Ponting C.P., Bork P., Burt D.W., Groenen M.A., Delany M.E., Dodg-son J.B., Chinvalla A.T., Cliften P.F., Clifton S.W., Delehaunty K.D. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004;432:695-716. DOI 10.1038/nature03154.</mixed-citation><mixed-citation xml:lang="en">Hillier L.W., Miller W., Birney E., Warren W., Hardison R.C., Ponting C.P., Bork P., Burt D.W., Groenen M.A., Delany M.E., Dodg-son J.B., Chinvalla A.T., Cliften P.F., Clifton S.W., Delehaunty K.D. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004;432:695-716. DOI 10.1038/nature03154.</mixed-citation></citation-alternatives></ref><ref id="cit31"><label>31</label><citation-alternatives><mixed-citation xml:lang="ru">Hindorff L.A., Sethupathy P., Junkins H.A., Ramos E.M., Mehta J.P., Collins F.S., Manolio T.A. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl. Acad. Sci. USA. 2009;106:9362-9367. DOI 10.1073/pnas.0903103106.</mixed-citation><mixed-citation xml:lang="en">Hindorff L.A., Sethupathy P., Junkins H.A., Ramos E.M., Mehta J.P., Collins F.S., Manolio T.A. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl. Acad. Sci. USA. 2009;106:9362-9367. DOI 10.1073/pnas.0903103106.</mixed-citation></citation-alternatives></ref><ref id="cit32"><label>32</label><citation-alternatives><mixed-citation xml:lang="ru">Hormozdiari F., Kostem E., Kang Y., Pasaniuc B., Eskin E. Identifying causal variants at loci with multiple signals of association. Genetics. 2014;198:497-508. DOI 10.1534/genetics.114.167908.</mixed-citation><mixed-citation xml:lang="en">Hormozdiari F., Kostem E., Kang Y., Pasaniuc B., Eskin E. Identifying causal variants at loci with multiple signals of association. Genetics. 2014;198:497-508. DOI 10.1534/genetics.114.167908.</mixed-citation></citation-alternatives></ref><ref id="cit33"><label>33</label><citation-alternatives><mixed-citation xml:lang="ru">International HapMap Consortium: A haplotype map of the human genome. Nature. 2005;437:1299-1320. DOI 10.1038/nature04226. International HapMap Consortium: A second generation human haplo-type map of over 3.1 million SNPs. Nature. 2007;449:851-861. DOI 10.1038/nature06258.</mixed-citation><mixed-citation xml:lang="en">International HapMap Consortium: A haplotype map of the human genome. Nature. 2005;437:1299-1320. DOI 10.1038/nature04226. International HapMap Consortium: A second generation human haplo-type map of over 3.1 million SNPs. Nature. 2007;449:851-861. DOI 10.1038/nature06258.</mixed-citation></citation-alternatives></ref><ref id="cit34"><label>34</label><citation-alternatives><mixed-citation xml:lang="ru">Johansson A.M., Pettersson M.E., Siegel P.B., Carlborg O. Genomewide effects of long-term divergent selection. PLoS Genet. 2010; 6(11):e1001188. DOI 10.1371/journal.pgen.1001188.</mixed-citation><mixed-citation xml:lang="en">Johansson A.M., Pettersson M.E., Siegel P.B., Carlborg O. Genomewide effects of long-term divergent selection. PLoS Genet. 2010; 6(11):e1001188. DOI 10.1371/journal.pgen.1001188.</mixed-citation></citation-alternatives></ref><ref id="cit35"><label>35</label><citation-alternatives><mixed-citation xml:lang="ru">Kim Y., Nielsen R. Linkage disequilibrium as a signature of selective sweeps. Genetics. 2004;167(3):1513-1524. DOI 10.1534/genetics. 103.025387.</mixed-citation><mixed-citation xml:lang="en">Kim Y., Nielsen R. Linkage disequilibrium as a signature of selective sweeps. Genetics. 2004;167(3):1513-1524. DOI 10.1534/genetics. 103.025387.</mixed-citation></citation-alternatives></ref><ref id="cit36"><label>36</label><citation-alternatives><mixed-citation xml:lang="ru">Kindt A.S., Navarro P., Semple C.A., Haley C.S. The genomic signature of trait-associated variants. BMC Genomics. 2013;14:108. DOI 10.1186/1471-2164-14-108.</mixed-citation><mixed-citation xml:lang="en">Kindt A.S., Navarro P., Semple C.A., Haley C.S. The genomic signature of trait-associated variants. BMC Genomics. 2013;14:108. DOI 10.1186/1471-2164-14-108.</mixed-citation></citation-alternatives></ref><ref id="cit37"><label>37</label><citation-alternatives><mixed-citation xml:lang="ru">Kizilkaya K., Fernando R.L., Garrick D.J. Genomic prediction of simulated multibreed and purebred performance using observed fifty thousand single nucleotide polymorphism genotypes. J. Anim. Sci. 2010;88:544-551. DOI 10.2527/jas.2009-2064.</mixed-citation><mixed-citation xml:lang="en">Kizilkaya K., Fernando R.L., Garrick D.J. Genomic prediction of simulated multibreed and purebred performance using observed fifty thousand single nucleotide polymorphism genotypes. J. Anim. Sci. 2010;88:544-551. DOI 10.2527/jas.2009-2064.</mixed-citation></citation-alternatives></ref><ref id="cit38"><label>38</label><citation-alternatives><mixed-citation xml:lang="ru">Koufariotis L., Chen Y.P., Bolormaa S., Hayes B.J. Regulatory and coding genome regions are enriched for trait associated variants in dairy and beef cattle. BMC Genomics. 2014;15:436. DOI 10.1186/1471-2164-15-436.</mixed-citation><mixed-citation xml:lang="en">Koufariotis L., Chen Y.P., Bolormaa S., Hayes B.J. Regulatory and coding genome regions are enriched for trait associated variants in dairy and beef cattle. BMC Genomics. 2014;15:436. DOI 10.1186/1471-2164-15-436.</mixed-citation></citation-alternatives></ref><ref id="cit39"><label>39</label><citation-alternatives><mixed-citation xml:lang="ru">Kranis A., Gheyas A.A., Boschiero C., Turner F., Yu L., Smith S., Talbot R., Pirani A., Brew F., Kaiser P., Hocking P.M., Fife M., Salmon N., Fulton J., Strom T.M., Haberer G., Weigend S., Preis-inger R., Gholami M., Qanbari S., Simianer H., Watson K.A., Wool-liams J.A., Burt D.W. Development of a high density 600K SNP genotyping array for chicken. BMC Genomics. 2013;14:59. DOI 10.1186/1471-2164-14-59.</mixed-citation><mixed-citation xml:lang="en">Kranis A., Gheyas A.A., Boschiero C., Turner F., Yu L., Smith S., Talbot R., Pirani A., Brew F., Kaiser P., Hocking P.M., Fife M., Salmon N., Fulton J., Strom T.M., Haberer G., Weigend S., Preis-inger R., Gholami M., Qanbari S., Simianer H., Watson K.A., Wool-liams J.A., Burt D.W. Development of a high density 600K SNP genotyping array for chicken. BMC Genomics. 2013;14:59. DOI 10.1186/1471-2164-14-59.</mixed-citation></citation-alternatives></ref><ref id="cit40"><label>40</label><citation-alternatives><mixed-citation xml:lang="ru">Liu R., Lourenco D.A.L., Fragomeni B.O., Tsuruta S. Accuracy of estimated breeding values with genomic information on males, females, or both: an example on broiler chicken. Genet. Sel. Evol. 2015; 47:56. DOI 10.1186/s12711-015-0137-1.</mixed-citation><mixed-citation xml:lang="en">Liu R., Lourenco D.A.L., Fragomeni B.O., Tsuruta S. Accuracy of estimated breeding values with genomic information on males, females, or both: an example on broiler chicken. Genet. Sel. Evol. 2015; 47:56. DOI 10.1186/s12711-015-0137-1.</mixed-citation></citation-alternatives></ref><ref id="cit41"><label>41</label><citation-alternatives><mixed-citation xml:lang="ru">Liu R., Wang Y.C., Sun D.X., Genomics and gene engineering Livant E.J., Avendano S., McLeod S., Ye X., Lamont S.J., Dekkers J.C., Ewald S.J. MX1 exon 13 polymorphisms in broiler breeder chickens and associations with commercial traits. Anim. Genet. 2007;38:177-179. DOI 10.1111/j.1365-2052.2007.01577.x.</mixed-citation><mixed-citation xml:lang="en">Liu R., Wang Y.C., Sun D.X., Genomics and gene engineering Livant E.J., Avendano S., McLeod S., Ye X., Lamont S.J., Dekkers J.C., Ewald S.J. MX1 exon 13 polymorphisms in broiler breeder chickens and associations with commercial traits. Anim. Genet. 2007;38:177-179. DOI 10.1111/j.1365-2052.2007.01577.x.</mixed-citation></citation-alternatives></ref><ref id="cit42"><label>42</label><citation-alternatives><mixed-citation xml:lang="ru">Lourenco D.A.L., Misztal I., Tsuruta S., Aguilar I., Lawlor T.J., For-ni S., Weller J.I. Are evaluations on young genotyped animals benefiting from the past generations? J. Dairy Sci. 2014;97:3930-3942. DOI 10.3168/jds.2013-7769.</mixed-citation><mixed-citation xml:lang="en">Lourenco D.A.L., Misztal I., Tsuruta S., Aguilar I., Lawlor T.J., For-ni S., Weller J.I. Are evaluations on young genotyped animals benefiting from the past generations? J. Dairy Sci. 2014;97:3930-3942. DOI 10.3168/jds.2013-7769.</mixed-citation></citation-alternatives></ref><ref id="cit43"><label>43</label><citation-alternatives><mixed-citation xml:lang="ru">Lu D., Sargolzaei M., Kelly M., Li C., Vander Voort G., Wang Z., Plastow G., Moore S., Miller S.P. Linkage disequilibrium in Angus, Charolais, and Crossbred beef cattle. Front. Genet. 2012;3:152. DOI 10.3389/fgene.2012.00152.</mixed-citation><mixed-citation xml:lang="en">Lu D., Sargolzaei M., Kelly M., Li C., Vander Voort G., Wang Z., Plastow G., Moore S., Miller S.P. Linkage disequilibrium in Angus, Charolais, and Crossbred beef cattle. Front. Genet. 2012;3:152. DOI 10.3389/fgene.2012.00152.</mixed-citation></citation-alternatives></ref><ref id="cit44"><label>44</label><citation-alternatives><mixed-citation xml:lang="ru">Megens H.J., Crooijmans R.P., Bastiaansen J.W., Kerstens H.H., Coster A., Jalving R., Vereijken A., Silva P., Muir W.M., Cheng H.H., Hanotte O., Groenen M.A. Comparison of linkage disequilibrium and haplotype diversity on macro- and microchromosomes in chicken. BMC Genet. 2009;10:86. DOI 10.1186/1471-2156-10-86.</mixed-citation><mixed-citation xml:lang="en">Megens H.J., Crooijmans R.P., Bastiaansen J.W., Kerstens H.H., Coster A., Jalving R., Vereijken A., Silva P., Muir W.M., Cheng H.H., Hanotte O., Groenen M.A. Comparison of linkage disequilibrium and haplotype diversity on macro- and microchromosomes in chicken. BMC Genet. 2009;10:86. DOI 10.1186/1471-2156-10-86.</mixed-citation></citation-alternatives></ref><ref id="cit45"><label>45</label><citation-alternatives><mixed-citation xml:lang="ru">Meuwissen T.H., Hayes B.J., Goddard M.E. Prediction of total genetic value using genome-wide dense marker maps. Genetics. 2001; 157(4):1819-1829.</mixed-citation><mixed-citation xml:lang="en">Meuwissen T.H., Hayes B.J., Goddard M.E. Prediction of total genetic value using genome-wide dense marker maps. Genetics. 2001; 157(4):1819-1829.</mixed-citation></citation-alternatives></ref><ref id="cit46"><label>46</label><citation-alternatives><mixed-citation xml:lang="ru">Morota G., Abdollahi-Arpanahi R., Kranis A. Genome-enabled prediction of quantitative traits in chickens using genomic annotation. BMC Genomics. 2014;15:109. DOI 10.1186/1471-2164-15-109.</mixed-citation><mixed-citation xml:lang="en">Morota G., Abdollahi-Arpanahi R., Kranis A. Genome-enabled prediction of quantitative traits in chickens using genomic annotation. BMC Genomics. 2014;15:109. DOI 10.1186/1471-2164-15-109.</mixed-citation></citation-alternatives></ref><ref id="cit47"><label>47</label><citation-alternatives><mixed-citation xml:lang="ru">Mugal C.F., Nabholz B., Ellegren H. Genome-wide analysis in chicken reveals that local levels of genetic diversity are mainly governed by the rate of recombination. BMC Genomics. 2013;14:86. DOI 10.1186/1471-2164-14-86.</mixed-citation><mixed-citation xml:lang="en">Mugal C.F., Nabholz B., Ellegren H. Genome-wide analysis in chicken reveals that local levels of genetic diversity are mainly governed by the rate of recombination. BMC Genomics. 2013;14:86. DOI 10.1186/1471-2164-14-86.</mixed-citation></citation-alternatives></ref><ref id="cit48"><label>48</label><citation-alternatives><mixed-citation xml:lang="ru">Pertille F., Guerrero-Bosagna C., Henrique da Silva V., Boschiero C., da Silva Nunes J.R., Ledur M.C., Jensen P., Coutinho L.L. High-throughput and cost-effective chicken genotyping using next-generation sequencing. Sci. Rep. 2016;6:26929. DOI 10.1038/srep26929.</mixed-citation><mixed-citation xml:lang="en">Pertille F., Guerrero-Bosagna C., Henrique da Silva V., Boschiero C., da Silva Nunes J.R., Ledur M.C., Jensen P., Coutinho L.L. High-throughput and cost-effective chicken genotyping using next-generation sequencing. Sci. Rep. 2016;6:26929. DOI 10.1038/srep26929.</mixed-citation></citation-alternatives></ref><ref id="cit49"><label>49</label><citation-alternatives><mixed-citation xml:lang="ru">Peterson C.B., Bogomolov M., Benjamini Y. Many phenotypes without many false discoveries: error controlling strategies for vulti-trait association studies. Genet. Epidemiol. 2016;40(1):45-56. DOI 10.1002/gepi.21942.</mixed-citation><mixed-citation xml:lang="en">Peterson C.B., Bogomolov M., Benjamini Y. Many phenotypes without many false discoveries: error controlling strategies for vulti-trait association studies. Genet. Epidemiol. 2016;40(1):45-56. DOI 10.1002/gepi.21942.</mixed-citation></citation-alternatives></ref><ref id="cit50"><label>50</label><citation-alternatives><mixed-citation xml:lang="ru">Porto-Neto L.R., Kijas J.W., Reverter A. The extent of linkage disequilibrium in beef cattle breeds using high-density SNP genotypes. Genet. Sel. Evol. 2014;46:22. DOI 10.1186/1297-9686-46-22.</mixed-citation><mixed-citation xml:lang="en">Porto-Neto L.R., Kijas J.W., Reverter A. The extent of linkage disequilibrium in beef cattle breeds using high-density SNP genotypes. Genet. Sel. Evol. 2014;46:22. DOI 10.1186/1297-9686-46-22.</mixed-citation></citation-alternatives></ref><ref id="cit51"><label>51</label><citation-alternatives><mixed-citation xml:lang="ru">Qanbari S., Hansen M., Weigend S., Preisinger R., Simianer H. Linkage disequilibrium reveals different demographic history in egg laying chickens.BMCGenet.2010;11:103.DOI10.1186/1471-2156-11-103.</mixed-citation><mixed-citation xml:lang="en">Qanbari S., Hansen M., Weigend S., Preisinger R., Simianer H. Linkage disequilibrium reveals different demographic history in egg laying chickens.BMCGenet.2010;11:103.DOI10.1186/1471-2156-11-103.</mixed-citation></citation-alternatives></ref><ref id="cit52"><label>52</label><citation-alternatives><mixed-citation xml:lang="ru">Rao Y., Sun L., Nie Q. The influence of recombination on SNP diversity in chickens. Hereditas. 2011;148(2):63-69. DOI 10.1111/j.1601-5223.2010.02210.x.</mixed-citation><mixed-citation xml:lang="en">Rao Y., Sun L., Nie Q. The influence of recombination on SNP diversity in chickens. Hereditas. 2011;148(2):63-69. DOI 10.1111/j.1601-5223.2010.02210.x.</mixed-citation></citation-alternatives></ref><ref id="cit53"><label>53</label><citation-alternatives><mixed-citation xml:lang="ru">Resnyk C., Carre W., Wang X., Porter T.E., Simon J., Le Bihan-Duval E., Duclos M.J., Aggrey S.E., Cogburn L.A. Transcriptional analysis of abdominal fat in genetically fat and lean chickens reveals adipo-kines, lipogenic genes and a link between hemostasis and leanness. BMC Genomics. 2013;14:557. DOI 10.1186/1471-2164-14-557.</mixed-citation><mixed-citation xml:lang="en">Resnyk C., Carre W., Wang X., Porter T.E., Simon J., Le Bihan-Duval E., Duclos M.J., Aggrey S.E., Cogburn L.A. Transcriptional analysis of abdominal fat in genetically fat and lean chickens reveals adipo-kines, lipogenic genes and a link between hemostasis and leanness. BMC Genomics. 2013;14:557. DOI 10.1186/1471-2164-14-557.</mixed-citation></citation-alternatives></ref><ref id="cit54"><label>54</label><citation-alternatives><mixed-citation xml:lang="ru">Sabeti P.C., Reich D.E., Higgins J.M., Levine H.Z., Richter D.J., Schaffner S.F., Gabriel S.B., Platko J.V., Patterson N.J., McDonald G.J., Ackerman H.C., Campbell S.J., Altshuler D., Cooper R., Kwiatkowski D., Ward R., Lander E.S. Detecting recent positive selection in the human genome from haplotype structure. Nature. 2002;419:832-837. DOI 10.1038/nature01140.</mixed-citation><mixed-citation xml:lang="en">Sabeti P.C., Reich D.E., Higgins J.M., Levine H.Z., Richter D.J., Schaffner S.F., Gabriel S.B., Platko J.V., Patterson N.J., McDonald G.J., Ackerman H.C., Campbell S.J., Altshuler D., Cooper R., Kwiatkowski D., Ward R., Lander E.S. Detecting recent positive selection in the human genome from haplotype structure. Nature. 2002;419:832-837. DOI 10.1038/nature01140.</mixed-citation></citation-alternatives></ref><ref id="cit55"><label>55</label><citation-alternatives><mixed-citation xml:lang="ru">Sharma P., Bottje W., Okimoto R. Polymorphisms in uncoupling protein, melanocortin 3 receptor, melanocortin 4 receptor, and pro-opio-melanocortin genes and association with production traits in a commercial broiler line. Poult Sci. 2008;87:2073-2086. DOI 10.3382/ps.2008-00060.</mixed-citation><mixed-citation xml:lang="en">Sharma P., Bottje W., Okimoto R. Polymorphisms in uncoupling protein, melanocortin 3 receptor, melanocortin 4 receptor, and pro-opio-melanocortin genes and association with production traits in a commercial broiler line. Poult Sci. 2008;87:2073-2086. DOI 10.3382/ps.2008-00060.</mixed-citation></citation-alternatives></ref><ref id="cit56"><label>56</label><citation-alternatives><mixed-citation xml:lang="ru">Smaragdov M.G. Genomic selection as a possible accelerator of traditional selection. Russ. J. Genet. 2009;45(6):633-636. DOI 10.1134/S1022795409060015.</mixed-citation><mixed-citation xml:lang="en">Smaragdov M.G. Genomic selection as a possible accelerator of traditional selection. Russ. J. Genet. 2009;45(6):633-636. DOI 10.1134/S1022795409060015.</mixed-citation></citation-alternatives></ref><ref id="cit57"><label>57</label><citation-alternatives><mixed-citation xml:lang="ru">Smith J.M., Haigh J. The hitch-hiking effect of a favourable gene. Genet. Res. 1974;23(1):23-35. DOI 10.1017/S0016672308009579.</mixed-citation><mixed-citation xml:lang="en">Smith J.M., Haigh J. The hitch-hiking effect of a favourable gene. Genet. Res. 1974;23(1):23-35. DOI 10.1017/S0016672308009579.</mixed-citation></citation-alternatives></ref><ref id="cit58"><label>58</label><citation-alternatives><mixed-citation xml:lang="ru">Solberg T.R., Sonesson A.K., Woolliams J.A., Odegard J., Meuwis-sen T.H. Persistence of accuracy of genome-wide breeding values over generations when including a polygenic effect. Genet. Sel. Evol. 2009;41:53. DOI 10.1186/1297-9686-41-53.</mixed-citation><mixed-citation xml:lang="en">Solberg T.R., Sonesson A.K., Woolliams J.A., Odegard J., Meuwis-sen T.H. Persistence of accuracy of genome-wide breeding values over generations when including a polygenic effect. Genet. Sel. Evol. 2009;41:53. DOI 10.1186/1297-9686-41-53.</mixed-citation></citation-alternatives></ref><ref id="cit59"><label>59</label><citation-alternatives><mixed-citation xml:lang="ru">Stainton J.J., Charlesworth B., Haley C.S., Kranis A., Watson K., Wiener P. Use of high-density SNP data to identify patterns of diversity and signatures of selection in broiler chickens. J. Anim. Breed. Genet. 2016;46(1):37-49. DOI 10.1111/jbg.12228.</mixed-citation><mixed-citation xml:lang="en">Stainton J.J., Charlesworth B., Haley C.S., Kranis A., Watson K., Wiener P. Use of high-density SNP data to identify patterns of diversity and signatures of selection in broiler chickens. J. Anim. Breed. Genet. 2016;46(1):37-49. DOI 10.1111/jbg.12228.</mixed-citation></citation-alternatives></ref><ref id="cit60"><label>60</label><citation-alternatives><mixed-citation xml:lang="ru">The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57-74. DOI 10.1038/nature11247.</mixed-citation><mixed-citation xml:lang="en">The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57-74. DOI 10.1038/nature11247.</mixed-citation></citation-alternatives></ref><ref id="cit61"><label>61</label><citation-alternatives><mixed-citation xml:lang="ru">Wang C.L., Ding X.D., Wang J.Y., Liu J.F., Fu W.X., Zhang Z., Yin Z.J., Zhang Q. Bayesian methods for estimating GEBVs of threshold traits. Heredity. 2013a;110(3):213-219. DOI 10.1038/hdy.2012.65.</mixed-citation><mixed-citation xml:lang="en">Wang C.L., Ding X.D., Wang J.Y., Liu J.F., Fu W.X., Zhang Z., Yin Z.J., Zhang Q. Bayesian methods for estimating GEBVs of threshold traits. Heredity. 2013a;110(3):213-219. DOI 10.1038/hdy.2012.65.</mixed-citation></citation-alternatives></ref><ref id="cit62"><label>62</label><citation-alternatives><mixed-citation xml:lang="ru">Wang C., Habier D., Peiris B.L., Wolc A., Kranis A., Watson K.A., Avendano S., Garrick D.J., Fernando R.L., Lamont S.J., Dekkers J.C. Accuracy of genomic prediction using an evenly spaced, low-density single nucleotide polymorphism panel in broiler chickens. Poultry Science. 2013b;92(7):1712-1723. DOI 10.3382/ps.2012-02941.</mixed-citation><mixed-citation xml:lang="en">Wang C., Habier D., Peiris B.L., Wolc A., Kranis A., Watson K.A., Avendano S., Garrick D.J., Fernando R.L., Lamont S.J., Dekkers J.C. Accuracy of genomic prediction using an evenly spaced, low-density single nucleotide polymorphism panel in broiler chickens. Poultry Science. 2013b;92(7):1712-1723. DOI 10.3382/ps.2012-02941.</mixed-citation></citation-alternatives></ref><ref id="cit63"><label>63</label><citation-alternatives><mixed-citation xml:lang="ru">Wang J., Lin M., Crenshaw A., Hutchinson A., Hicks B., Yeager M., Berndt S., Huang W.Y., Hayes R.B., Chanock S.J., Jones R.C., Ra-makrishnan R. High-throughput single nucleotide polymorphism ge-notyping using nanofluidic Dynamic Arrays. BMC Genomics. 2009; 10:561. DOI 10.1186/1471-2164-10-561.</mixed-citation><mixed-citation xml:lang="en">Wang J., Lin M., Crenshaw A., Hutchinson A., Hicks B., Yeager M., Berndt S., Huang W.Y., Hayes R.B., Chanock S.J., Jones R.C., Ra-makrishnan R. High-throughput single nucleotide polymorphism ge-notyping using nanofluidic Dynamic Arrays. BMC Genomics. 2009; 10:561. DOI 10.1186/1471-2164-10-561.</mixed-citation></citation-alternatives></ref><ref id="cit64"><label>64</label><citation-alternatives><mixed-citation xml:lang="ru">Weng Z., Wolc A., Shen X., Fernando R.L., Dekkers J.C., Arango J., Settar P., Fulton J.E., O'Sullivan N.P., Garrick D.J. Effects of number of training generations on genomic prediction for various traits in a layer chicken population. Genet. Sel. Evol. 2016;48:22. DOI 10.1186/s12711-016-0198-9.</mixed-citation><mixed-citation xml:lang="en">Weng Z., Wolc A., Shen X., Fernando R.L., Dekkers J.C., Arango J., Settar P., Fulton J.E., O'Sullivan N.P., Garrick D.J. Effects of number of training generations on genomic prediction for various traits in a layer chicken population. Genet. Sel. Evol. 2016;48:22. DOI 10.1186/s12711-016-0198-9.</mixed-citation></citation-alternatives></ref><ref id="cit65"><label>65</label><citation-alternatives><mixed-citation xml:lang="ru">Wolc A., Arango J., Settar P., Fulton J.E., O'Sullivan N.P., Preising-er R., Habier D., Fernando R., Garrick D.J., Dekkers J.C. Persistence of accuracy of genomic estimated breeding values over generations in layer chickens. Genet. Sel. Evol. 2011;43:23. DOI 10.1186/1297-9686-43-23.</mixed-citation><mixed-citation xml:lang="en">Wolc A., Arango J., Settar P., Fulton J.E., O'Sullivan N.P., Preising-er R., Habier D., Fernando R., Garrick D.J., Dekkers J.C. Persistence of accuracy of genomic estimated breeding values over generations in layer chickens. Genet. Sel. Evol. 2011;43:23. DOI 10.1186/1297-9686-43-23.</mixed-citation></citation-alternatives></ref><ref id="cit66"><label>66</label><citation-alternatives><mixed-citation xml:lang="ru">Wragg D., Mwacharo J., Alcalde J., Hocking P.M., Hanotte O. Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens. Heredity. 2012;109:6-18. DOI 10.1038/hdy.2012.9.</mixed-citation><mixed-citation xml:lang="en">Wragg D., Mwacharo J., Alcalde J., Hocking P.M., Hanotte O. Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens. Heredity. 2012;109:6-18. DOI 10.1038/hdy.2012.9.</mixed-citation></citation-alternatives></ref><ref id="cit67"><label>67</label><citation-alternatives><mixed-citation xml:lang="ru">Yakovlev A.F., Smaragdov M.G. A significant increase in the accuracy of estimation of the breeding value of animals in dairy cattle. Zoo-techniya = Zootechnics. 2011;5:2-4. (in Russian)</mixed-citation><mixed-citation xml:lang="en">Yakovlev A.F., Smaragdov M.G. A significant increase in the accuracy of estimation of the breeding value of animals in dairy cattle. Zoo-techniya = Zootechnics. 2011;5:2-4. (in Russian)</mixed-citation></citation-alternatives></ref><ref id="cit68"><label>68</label><citation-alternatives><mixed-citation xml:lang="ru">Yang J., Manolio T.A., Pasquale L.R., Boerwinkle E., Caporaso N., Cunningham J.M., de Andrade M., Feenstra B., Feingold E., Hayes M.G., Hill W.G., Landi M.T., Alonso A., Lettre G., Lin P., Ling H., Lowe W., Mathias R.A., Melbye M., Pugh E., Corne-lis M.C., Weir B.S., Goddard M.E., Visscher P.M. Genome partitioning of genetic variation for complex traits using common SNPs. Nat. Genet. 2011;43:519-525. DOI 10.1038/ng.823.</mixed-citation><mixed-citation xml:lang="en">Yang J., Manolio T.A., Pasquale L.R., Boerwinkle E., Caporaso N., Cunningham J.M., de Andrade M., Feenstra B., Feingold E., Hayes M.G., Hill W.G., Landi M.T., Alonso A., Lettre G., Lin P., Ling H., Lowe W., Mathias R.A., Melbye M., Pugh E., Corne-lis M.C., Weir B.S., Goddard M.E., Visscher P.M. Genome partitioning of genetic variation for complex traits using common SNPs. Nat. Genet. 2011;43:519-525. DOI 10.1038/ng.823.</mixed-citation></citation-alternatives></ref><ref id="cit69"><label>69</label><citation-alternatives><mixed-citation xml:lang="ru">Zhang H., Hu X., Wang Z., Zhang Y., Wang S., Wang N., Ma L., Leng L., Wang S., Wang Q., Wang Y., Tang Z., Li N., Da Y., Li H. Selection signature analysis implicates the PC1/PCSK1 region for chicken abdominal fat content. PLoS ONE. 2012;7(7):e40736. DOI 10.1371/journal.pone.0040736.</mixed-citation><mixed-citation xml:lang="en">Zhang H., Hu X., Wang Z., Zhang Y., Wang S., Wang N., Ma L., Leng L., Wang S., Wang Q., Wang Y., Tang Z., Li N., Da Y., Li H. Selection signature analysis implicates the PC1/PCSK1 region for chicken abdominal fat content. PLoS ONE. 2012;7(7):e40736. DOI 10.1371/journal.pone.0040736.</mixed-citation></citation-alternatives></ref><ref id="cit70"><label>70</label><citation-alternatives><mixed-citation xml:lang="ru">Zhang Z., Druet T. Marker imputation with low-density marker panels in Dutch Holstein cattle. J. Dairy Sci. 2010;93:5487-5494. DOI 10.3168/jds.2010-3501.</mixed-citation><mixed-citation xml:lang="en">Zhang Z., Druet T. Marker imputation with low-density marker panels in Dutch Holstein cattle. J. Dairy Sci. 2010;93:5487-5494. DOI 10.3168/jds.2010-3501.</mixed-citation></citation-alternatives></ref><ref id="cit71"><label>71</label><citation-alternatives><mixed-citation xml:lang="ru">Zhao H., Nettleton D., Dekkers J.C.M. Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between single nucleotide polymorphisms. Genet. Res. 2007;89:91-96. DOI 10.1017/S0016672307008634.</mixed-citation><mixed-citation xml:lang="en">Zhao H., Nettleton D., Dekkers J.C.M. Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between single nucleotide polymorphisms. Genet. Res. 2007;89:91-96. DOI 10.1017/S0016672307008634.</mixed-citation></citation-alternatives></ref><ref id="cit72"><label>72</label><citation-alternatives><mixed-citation xml:lang="ru">Zhou H., Mitchell A.D., McMurtry J.P., Ashwell C.M., Lamont S.J. Insulin-like growth factor-I gene polymorphism associations with growth, body composition, skeleton integrity, and metabolic traits in chickens. Poult. Sci. 2005;84(2):212-219. DOI 10.1093/ps/84.2.212.</mixed-citation><mixed-citation xml:lang="en">Zhou H., Mitchell A.D., McMurtry J.P., Ashwell C.M., Lamont S.J. Insulin-like growth factor-I gene polymorphism associations with growth, body composition, skeleton integrity, and metabolic traits in chickens. Poult. Sci. 2005;84(2):212-219. DOI 10.1093/ps/84.2.212.</mixed-citation></citation-alternatives></ref></ref-list><fn-group><fn fn-type="conflict"><p>The authors declare that there are no conflicts of interest present.</p></fn></fn-group></back></article>
