• Traditional marker-assisted selection (MAS) did not result in a widespread use of DNA information in animal breeding. The main reason was that the traits of interest in livestock production were much more complex than expected: they were determined by thousands of genes with small effects on phenotype. These effects were usually too small to be statistically significant and so were ignored. • Genomic selection (GS) assumes that all markers might be linked to a gene affecting the trait and concentrates on estimating their effect rather than testing its significance. Three technological breakthroughs resulted in the current wide-spread use of DNA information in animal breeding: the development of the genomic selection technology, the discovery of massive numbers of genetic markers (single nucleotide polymorphisms; SNPs), and high-throughput technology to genotype animals for (hundreds of) thousands of SNPs in a cost-effective manner. • Here we review current methods for GS, including how they deal with practical data, where genotypes are missing on a large scale. The use of whole-genome sequence data is anticipated, and its advantages and disadvantages are depicted. Current and predicted future impacts of GS on dairy and beef cattle, pigs, and poultry breeding are described. Finally, future directions for GS are discussed. • It is anticipated that future GS applications will either be: within breed (wbGS), where accuracy is obtained by maintaining huge withinbreed reference populations; or across breed (abGS) where accuracy is obtained from across-breed reference populations and high-density GS methods that focus on causative genomic regions. We argue that future GS applications will increasingly turn toward abGS.
{"title":"Genomic selection: A paradigm shift in animal breeding","authors":"T. Meuwissen, B. Hayes, M. Goddard","doi":"10.2527/AF.2016-0002","DOIUrl":"https://doi.org/10.2527/AF.2016-0002","url":null,"abstract":"• Traditional marker-assisted selection (MAS) did not result in a widespread use of DNA information in animal breeding. The main reason was that the traits of interest in livestock production were much more complex than expected: they were determined by thousands of genes with small effects on phenotype. These effects were usually too small to be statistically significant and so were ignored. • Genomic selection (GS) assumes that all markers might be linked to a gene affecting the trait and concentrates on estimating their effect rather than testing its significance. Three technological breakthroughs resulted in the current wide-spread use of DNA information in animal breeding: the development of the genomic selection technology, the discovery of massive numbers of genetic markers (single nucleotide polymorphisms; SNPs), and high-throughput technology to genotype animals for (hundreds of) thousands of SNPs in a cost-effective manner. • Here we review current methods for GS, including how they deal with practical data, where genotypes are missing on a large scale. The use of whole-genome sequence data is anticipated, and its advantages and disadvantages are depicted. Current and predicted future impacts of GS on dairy and beef cattle, pigs, and poultry breeding are described. Finally, future directions for GS are discussed. • It is anticipated that future GS applications will either be: within breed (wbGS), where accuracy is obtained by maintaining huge withinbreed reference populations; or across breed (abGS) where accuracy is obtained from across-breed reference populations and high-density GS methods that focus on causative genomic regions. We argue that future GS applications will increasingly turn toward abGS.","PeriodicalId":48645,"journal":{"name":"Animal Frontiers","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2527/AF.2016-0002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68975429","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
R. Rupp, S. Mucha, H. Larroque, J. McEwan, J. Conington
Sheep and goat breeds are selected worldwide for meat, wool, and dairy production, and breeding objectives also include other functional traits such as reproductive performance and disease resistance. In early 2007, the development of next-generation sequencing (NGS) allowed de novo sequencing of sheep (Jiang et al., 2014) and goat genomes (Dong et al., 2013). In turn, it offered an opportunity to create high-density SNP chips. The Illumina OvineSNP50 BeadChip (www.illumina.com) is a 54K SNP microarray that was developed as part of the International Sheep Genomics Consortium (ISGC; www.sheephapmap.org; Kijas et al., 2009). Similarly, the International Goat Genome Consortium (IGGC; www.goatgenome.org) was created in 2010 and promoted international effort toward the development of a 52K SNP chip for goats (Tosser-Klopp et al., 2014) commercialized by Illumina (SNP50 BeadChip; www.illumina.com). The availability of such high throughput DNA methods and tools in recent years has opened up the use of genome-wide information for sheep and goat breeding.
绵羊和山羊品种在世界范围内被选择用于肉类、羊毛和乳制品生产，育种目标还包括其他功能性状，如繁殖性能和抗病能力。2007年初，新一代测序技术(NGS)的发展使绵羊(Jiang et al.， 2014)和山羊基因组(Dong et al.， 2013)得以重新测序。反过来，它提供了一个创造高密度SNP芯片的机会。Illumina OvineSNP50 BeadChip (www.illumina.com)是一种54K SNP微阵列，是国际绵羊基因组学联盟(ISGC;www.sheephapmap.org;Kijas et al.， 2009)。同样，国际山羊基因组联盟(IGGC;www.goatgenome.org)成立于2010年，促进了国际上对山羊52K SNP芯片开发的努力(Tosser-Klopp et al.， 2014)，由Illumina (SNP50 BeadChip;www.illumina.com)。近年来，这种高通量DNA方法和工具的可用性为绵羊和山羊育种开辟了全基因组信息的使用。
{"title":"Genomic application in sheep and goat breeding","authors":"R. Rupp, S. Mucha, H. Larroque, J. McEwan, J. Conington","doi":"10.2527/AF.2016-0006","DOIUrl":"https://doi.org/10.2527/AF.2016-0006","url":null,"abstract":"Sheep and goat breeds are selected worldwide for meat, wool, and dairy production, and breeding objectives also include other functional traits such as reproductive performance and disease resistance. In early 2007, the development of next-generation sequencing (NGS) allowed de novo sequencing of sheep (Jiang et al., 2014) and goat genomes (Dong et al., 2013). In turn, it offered an opportunity to create high-density SNP chips. The Illumina OvineSNP50 BeadChip (www.illumina.com) is a 54K SNP microarray that was developed as part of the International Sheep Genomics Consortium (ISGC; www.sheephapmap.org; Kijas et al., 2009). Similarly, the International Goat Genome Consortium (IGGC; www.goatgenome.org) was created in 2010 and promoted international effort toward the development of a 52K SNP chip for goats (Tosser-Klopp et al., 2014) commercialized by Illumina (SNP50 BeadChip; www.illumina.com). The availability of such high throughput DNA methods and tools in recent years has opened up the use of genome-wide information for sheep and goat breeding.","PeriodicalId":48645,"journal":{"name":"Animal Frontiers","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2527/AF.2016-0006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68976313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Does biotechnological innovation require organizational innovation? Learning from the cattle breeding industry in France","authors":"M. Hannachi, M. Tichit","doi":"10.2527/AF.2016-0012","DOIUrl":"https://doi.org/10.2527/AF.2016-0012","url":null,"abstract":"","PeriodicalId":48645,"journal":{"name":"Animal Frontiers","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2527/AF.2016-0012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68978111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Development and implementation of genomic predictions in beef cattle","authors":"D. Berry, José Fernando Garcia, D. Garrick","doi":"10.2527/AF.2016-0005","DOIUrl":"https://doi.org/10.2527/AF.2016-0005","url":null,"abstract":"","PeriodicalId":48645,"journal":{"name":"Animal Frontiers","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2527/AF.2016-0005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68976226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. Wolc, A. Kranis, J. Arango, P. Settar, J. Fulton, N. O'sullivan, A. Avendano, K. Watson, J. Hickey, G. Campos, R. Fernando, D. Garrick, J. Dekkers
Genomic selection using high-density SNP panels was first implemented in dairy cattle breeding programs. It provided benefits in terms of reduced generation intervals, improved accuracies of selecting young animals, and reductions in costs associated with the requirement of progeny testing bulls in traditional breeding programs (Hayes et al., 2009). Several distinct features of the poultry breeding industry differ markedly from dairy cattle breeding and influence the manner in which genomic selection can be used for genetic improvement in poultry breeding: · Traditional genetic improvement programs in poultry already have short generation intervals (multiple overlapping generations per year with selection every 6 wk in broilers, non-overlapping annual generations in layers). There is some scope for shortening the generation interval in layers but not as much as was the case for dairy cattle breeding where bull pathways could be reduced in length from greater than 6 yr to less than 3 yr (Schaeffer, 2006, Schefers and Weigel, 2012).
{"title":"Implementation of genomic selection in the poultry industry","authors":"A. Wolc, A. Kranis, J. Arango, P. Settar, J. Fulton, N. O'sullivan, A. Avendano, K. Watson, J. Hickey, G. Campos, R. Fernando, D. Garrick, J. Dekkers","doi":"10.2527/AF.2016-0004","DOIUrl":"https://doi.org/10.2527/AF.2016-0004","url":null,"abstract":"Genomic selection using high-density SNP panels was first implemented in dairy cattle breeding programs. It provided benefits in terms of reduced generation intervals, improved accuracies of selecting young animals, and reductions in costs associated with the requirement of progeny testing bulls in traditional breeding programs (Hayes et al., 2009). Several distinct features of the poultry breeding industry differ markedly from dairy cattle breeding and influence the manner in which genomic selection can be used for genetic improvement in poultry breeding: · Traditional genetic improvement programs in poultry already have short generation intervals (multiple overlapping generations per year with selection every 6 wk in broilers, non-overlapping annual generations in layers). There is some scope for shortening the generation interval in layers but not as much as was the case for dairy cattle breeding where bull pathways could be reduced in length from greater than 6 yr to less than 3 yr (Schaeffer, 2006, Schefers and Weigel, 2012).","PeriodicalId":48645,"journal":{"name":"Animal Frontiers","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2527/AF.2016-0004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68976348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Genomic and other revolutions—why some technologies are quickly adopted and others are not","authors":"H. Simianer","doi":"10.2527/AF.2016-0008","DOIUrl":"https://doi.org/10.2527/AF.2016-0008","url":null,"abstract":"","PeriodicalId":48645,"journal":{"name":"Animal Frontiers","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2527/AF.2016-0008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68976761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
J. Fernández, Toro, F. Gómez-Romano, B. Villanueva
{"title":"The use of genomic information can enhance the efficiency of conservation programs","authors":"J. Fernández, Toro, F. Gómez-Romano, B. Villanueva","doi":"10.2527/AF.2016-0009","DOIUrl":"https://doi.org/10.2527/AF.2016-0009","url":null,"abstract":"","PeriodicalId":48645,"journal":{"name":"Animal Frontiers","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2527/AF.2016-0009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68976822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
• The western United States (US) has been a food-security resource to generate a consistent supply of nutritious, high-protein foods from grazing livestock. • Much of the lands in the western US are “public lands” that are administered by US federal land management agencies. Public lands have been historically used to provide multiple ecosystem services that benefit humans, which include food production from grazing livestock. • Recent US public land management policies that have been focused specifically on wildlife species-of-interest have resulted in permanent withdrawal of federal public lands from livestock grazing and food production. • Decisions to reduce or eliminate grazing on federal public lands reflect a shift from long-standing federal policies designed to ensure a ready supply of domestic food and fiber. • Approximately 23% of the US sheep industry is facing imminent loss of grazing access to public lands, which will irretrievably alter the many small-business and family-owned livestock operations and the rural communities that rely on the public lands that surround them. • Elimination of livestock grazing removes an effective tool for land managers to maintain range and forest health, enhancing wildlife habitat, controlling invasive weeds, and mitigating wildfire risk.
{"title":"A paradigm shift in use and management of United States public lands for livestock grazing","authors":"A. Hendrickson","doi":"10.2527/AF.2015-0045","DOIUrl":"https://doi.org/10.2527/AF.2015-0045","url":null,"abstract":"• The western United States (US) has been a food-security resource to generate a consistent supply of nutritious, high-protein foods from grazing livestock. • Much of the lands in the western US are “public lands” that are administered by US federal land management agencies. Public lands have been historically used to provide multiple ecosystem services that benefit humans, which include food production from grazing livestock. • Recent US public land management policies that have been focused specifically on wildlife species-of-interest have resulted in permanent withdrawal of federal public lands from livestock grazing and food production. • Decisions to reduce or eliminate grazing on federal public lands reflect a shift from long-standing federal policies designed to ensure a ready supply of domestic food and fiber. • Approximately 23% of the US sheep industry is facing imminent loss of grazing access to public lands, which will irretrievably alter the many small-business and family-owned livestock operations and the rural communities that rely on the public lands that surround them. • Elimination of livestock grazing removes an effective tool for land managers to maintain range and forest health, enhancing wildlife habitat, controlling invasive weeds, and mitigating wildfire risk.","PeriodicalId":48645,"journal":{"name":"Animal Frontiers","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2015-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68975288","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Economic considerations of livestock grazing on public lands in the United States of America","authors":"N. Rimbey, J. Tanaka, L. A. Torell","doi":"10.2527/AF.2015-0044","DOIUrl":"https://doi.org/10.2527/AF.2015-0044","url":null,"abstract":"","PeriodicalId":48645,"journal":{"name":"Animal Frontiers","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2015-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68975283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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