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https://hdl.handle.net/1959.11/14745
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DC Field | Value | Language |
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dc.contributor.author | Huang, Yijian | en |
dc.contributor.author | Hickey, John | en |
dc.contributor.author | Cleveland, Matthew A | en |
dc.contributor.author | Maltecca, Christian | en |
dc.date.accessioned | 2014-04-17T15:59:00Z | - |
dc.date.issued | 2012 | - |
dc.identifier.citation | Genetics Selection Evolution, v.44, p. 1-8 | en |
dc.identifier.issn | 1297-9686 | en |
dc.identifier.issn | 0999-193X | en |
dc.identifier.uri | https://hdl.handle.net/1959.11/14745 | - |
dc.description.abstract | Background: Commercial breeding programs seek to maximise the rate of genetic gain while minimizing the costs of attaining that gain. Genomic information offers great potential to increase rates of genetic gain but it is expensive to generate. Low-cost genotyping strategies combined with genotype imputation offer dramatically reduced costs. However, both the costs and accuracy of imputation of these strategies are highly sensitive to several factors. The objective of this paper was to explore the cost and imputation accuracy of several alternative genotyping strategies in pedigreed populations. Methods: Pedigree and genotype data from a commercial pig population were used. Several alternative genotyping strategies were explored. The strategies differed in the density of genotypes used for the ancestors and the individuals to be imputed. Parents, grandparents, and other relatives that were not descendants, were genotyped at high-density, low-density, or extremely low-density, and associated costs and imputation accuracies were evaluated. Results: Imputation accuracy and cost were influenced by the alternative genotyping strategies. Given the mating ratios and the numbers of offspring produced by males and females, an optimized low-cost genotyping strategy for a commercial pig population could involve genotyping male parents at high-density, female parents at low-density (e.g. 3000 SNP), and selection candidates at very low-density (384 SNP). Conclusions: Among the selection candidates, 95.5 % and 93.5 % of the genotype variation contained in the high-density SNP panels were recovered using a genotyping strategy that costs respectively, $24.74 and $20.58 per candidate. | en |
dc.language | en | en |
dc.publisher | BioMed Central Ltd | en |
dc.relation.ispartof | Genetics Selection Evolution | en |
dc.title | Assessment of alternative genotyping strategies to maximize imputation accuracy at minimal cost | en |
dc.type | Journal Article | en |
dc.identifier.doi | 10.1186/1297-9686-44-25 | en |
dcterms.accessRights | Gold | en |
dc.subject.keywords | Animal Breeding | en |
dc.subject.keywords | Quantitative Genetics (incl Disease and Trait Mapping Genetics) | en |
local.contributor.firstname | Yijian | en |
local.contributor.firstname | John | en |
local.contributor.firstname | Matthew A | en |
local.contributor.firstname | Christian | en |
local.subject.for2008 | 060412 Quantitative Genetics (incl Disease and Trait Mapping Genetics) | en |
local.subject.for2008 | 070201 Animal Breeding | en |
local.subject.seo2008 | 970107 Expanding Knowledge in the Agricultural and Veterinary Sciences | en |
local.profile.email | jhickey5@une.edu.au | en |
local.output.category | C1 | en |
local.record.place | au | en |
local.record.institution | University of New England | en |
local.identifier.epublicationsrecord | une-20130621-00224 | en |
local.publisher.place | United Kingdom | en |
local.identifier.runningnumber | 25 | en |
local.format.startpage | 1 | en |
local.format.endpage | 8 | en |
local.peerreviewed | Yes | en |
local.identifier.volume | 44 | en |
local.access.fulltext | Yes | en |
local.contributor.lastname | Huang | en |
local.contributor.lastname | Hickey | en |
local.contributor.lastname | Cleveland | en |
local.contributor.lastname | Maltecca | en |
dc.identifier.staff | une-id:jhickey5 | en |
local.profile.role | author | en |
local.profile.role | author | en |
local.profile.role | author | en |
local.profile.role | author | en |
local.identifier.unepublicationid | une:14960 | en |
local.identifier.handle | https://hdl.handle.net/1959.11/14745 | en |
dc.identifier.academiclevel | Academic | en |
local.title.maintitle | Assessment of alternative genotyping strategies to maximize imputation accuracy at minimal cost | en |
local.output.categorydescription | C1 Refereed Article in a Scholarly Journal | en |
local.search.author | Huang, Yijian | en |
local.search.author | Hickey, John | en |
local.search.author | Cleveland, Matthew A | en |
local.search.author | Maltecca, Christian | en |
local.uneassociation | Unknown | en |
local.identifier.wosid | 000308541800001 | en |
local.year.published | 2012 | en |
local.subject.for2020 | 310506 Gene mapping | en |
local.subject.for2020 | 300305 Animal reproduction and breeding | en |
local.subject.seo2020 | 280101 Expanding knowledge in the agricultural, food and veterinary sciences | en |
Appears in Collections: | Journal Article |
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