Single nucleotide polymorphisms and haplotypes associated with feed efficiency in beef cattle

Persistent Link:
http://hdl.handle.net/10150/610391
Title:
Single nucleotide polymorphisms and haplotypes associated with feed efficiency in beef cattle
Author:
Serao, Nick; Gonzalez-Pena, Dianelys; Beever, Jonathan; Faulkner, Dan; Southey, Bruce; Rodriguez-Zas, Sandra
Affiliation:
Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Animal Sciences Department, University of Arizona, Tucson, AZ, USA; Department of Statistics, University of Illinois at Urbana-Champaign, Champaign, IL, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
Issue Date:
2013
Publisher:
BioMed Central
Citation:
Serão et al. BMC Genetics 2013, 14:94 http://www.biomedcentral.com/1471-2156/14/94
Journal:
BMC Genetics
Rights:
© 2013 Serão et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
BACKGROUND:General, breed- and diet-dependent associations between feed efficiency in beef cattle and single nucleotide polymorphisms (SNPs) or haplotypes were identified on a population of 1321 steers using a 50K SNP panel. Genomic associations with traditional two-step indicators of feed efficiency - residual feed intake (RFI), residual average daily gain (RADG), and residual intake gain (RIG) - were compared to associations with two complementary one-step indicators of feed efficiency: efficiency of intake (EI) and efficiency of gain (EG). Associations uncovered in a training data set were evaluated on independent validation data set. A multi-SNP model was developed to predict feed efficiency. Functional analysis of genes harboring SNPs significantly associated with feed efficiency and network visualization aided in the interpretation of the results.RESULTS:For the five feed efficiency indicators, the numbers of general, breed-dependent, and diet-dependent associations with SNPs (P-value<0.0001) were 31, 40, and 25, and with haplotypes were six, ten, and nine, respectively. Of these, 20 SNP and six haplotype associations overlapped between RFI and EI, and five SNP and one haplotype associations overlapped between RADG and EG. This result confirms the complementary value of the one and two-step indicators. The multi-SNP models included 89 SNPs and offered a precise prediction of the five feed efficiency indicators. The associations of 17 SNPs and 7 haplotypes with feed efficiency were confirmed on the validation data set. Nine clusters of Gene Ontology and KEGG pathway categories (mean P-value<0.001) including, 9nucleotide binding; ion transport, phosphorous metabolic process, and the MAPK signaling pathway were overrepresented among the genes harboring the SNPs associated with feed efficiency.CONCLUSIONS:The general SNP associations suggest that a single panel of genomic variants can be used regardless of breed and diet. The breed- and diet-dependent associations between SNPs and feed efficiency suggest that further refinement of variant panels require the consideration of the breed and management practices. The unique genomic variants associated with the one- and two-step indicators suggest that both types of indicators offer complementary description of feed efficiency that can be exploited for genome-enabled selection purposes.
EISSN:
1471-2156
DOI:
10.1186/1471-2156-14-94
Keywords:
Feed efficiency; Beef cattle; Single nucleotide polymorphism; Haplotype; Functional analysis; MAPK pathway; Serine/Threonine kinase activity
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2156/14/94

Full metadata record

DC FieldValue Language
dc.contributor.authorSerao, Nicken
dc.contributor.authorGonzalez-Pena, Dianelysen
dc.contributor.authorBeever, Jonathanen
dc.contributor.authorFaulkner, Danen
dc.contributor.authorSouthey, Bruceen
dc.contributor.authorRodriguez-Zas, Sandraen
dc.date.accessioned2016-05-20T09:05:46Z-
dc.date.available2016-05-20T09:05:46Z-
dc.date.issued2013en
dc.identifier.citationSerão et al. BMC Genetics 2013, 14:94 http://www.biomedcentral.com/1471-2156/14/94en
dc.identifier.doi10.1186/1471-2156-14-94en
dc.identifier.urihttp://hdl.handle.net/10150/610391-
dc.description.abstractBACKGROUND:General, breed- and diet-dependent associations between feed efficiency in beef cattle and single nucleotide polymorphisms (SNPs) or haplotypes were identified on a population of 1321 steers using a 50K SNP panel. Genomic associations with traditional two-step indicators of feed efficiency - residual feed intake (RFI), residual average daily gain (RADG), and residual intake gain (RIG) - were compared to associations with two complementary one-step indicators of feed efficiency: efficiency of intake (EI) and efficiency of gain (EG). Associations uncovered in a training data set were evaluated on independent validation data set. A multi-SNP model was developed to predict feed efficiency. Functional analysis of genes harboring SNPs significantly associated with feed efficiency and network visualization aided in the interpretation of the results.RESULTS:For the five feed efficiency indicators, the numbers of general, breed-dependent, and diet-dependent associations with SNPs (P-value<0.0001) were 31, 40, and 25, and with haplotypes were six, ten, and nine, respectively. Of these, 20 SNP and six haplotype associations overlapped between RFI and EI, and five SNP and one haplotype associations overlapped between RADG and EG. This result confirms the complementary value of the one and two-step indicators. The multi-SNP models included 89 SNPs and offered a precise prediction of the five feed efficiency indicators. The associations of 17 SNPs and 7 haplotypes with feed efficiency were confirmed on the validation data set. Nine clusters of Gene Ontology and KEGG pathway categories (mean P-value<0.001) including, 9nucleotide bindingen
dc.description.abstraction transport, phosphorous metabolic process, and the MAPK signaling pathway were overrepresented among the genes harboring the SNPs associated with feed efficiency.CONCLUSIONS:The general SNP associations suggest that a single panel of genomic variants can be used regardless of breed and diet. The breed- and diet-dependent associations between SNPs and feed efficiency suggest that further refinement of variant panels require the consideration of the breed and management practices. The unique genomic variants associated with the one- and two-step indicators suggest that both types of indicators offer complementary description of feed efficiency that can be exploited for genome-enabled selection purposes.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2156/14/94en
dc.rights© 2013 Serão et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)en
dc.subjectFeed efficiencyen
dc.subjectBeef cattleen
dc.subjectSingle nucleotide polymorphismen
dc.subjectHaplotypeen
dc.subjectFunctional analysisen
dc.subjectMAPK pathwayen
dc.subjectSerine/Threonine kinase activityen
dc.titleSingle nucleotide polymorphisms and haplotypes associated with feed efficiency in beef cattleen
dc.typeArticleen
dc.identifier.eissn1471-2156en
dc.contributor.departmentDepartment of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USAen
dc.contributor.departmentAnimal Sciences Department, University of Arizona, Tucson, AZ, USAen
dc.contributor.departmentDepartment of Statistics, University of Illinois at Urbana-Champaign, Champaign, IL, USAen
dc.contributor.departmentInstitute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USAen
dc.identifier.journalBMC Geneticsen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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