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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Genotype imputation in a tropical crossbred dairy cattle population

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Author(s):
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Oliveira Junior, Gerson A. [1] ; Chud, Tatiane C. S. [2] ; Ventura, Ricardo V. [3, 4] ; Garrick, Dorian J. [5] ; Cole, John B. [6] ; Munari, Danisio P. [2] ; Ferraz, Jose B. S. [1] ; Mullart, Erik [7] ; DeNise, Sue [8] ; Smith, Shannon [8] ; da Silva, Marcos Vinicius G. B. [9]
Total Authors: 11
Affiliation:
[1] Univ Sao Paulo, Dept Med Vet, Fac Zootecnia & Engn Alimentos, BR-13635900 Pirassununga, SP - Brazil
[2] Univ Estadual Paulista Unesp, Dept Ciencias Exatas, Fac Ciencias Agr & Vet, BR-14884900 Jaboticabal, SP - Brazil
[3] Univ Guelph, Ctr Genet Improvement Livestock, Guelph, ON N1G 2W1 - Canada
[4] Beef Improvement Opportun, Guelph, ON N1K 1E5 - Canada
[5] Iowa State Univ, Dept Anim Sci, Ames, IA 50011 - USA
[6] ARS, Anim Genom & Improvement Lab, USDA, Beltsville, MD 20705 - USA
[7] CRV Holding BV, Arnhem 454 - Netherlands
[8] Zoetis, Kalamazoo, MI 49007 - USA
[9] Brazilian Corp Agr Res, Embrapa Dairy Cattle, BR-36038330 Juiz De Fora, MG - Brazil
Total Affiliations: 9
Document type: Journal article
Source: JOURNAL OF DAIRY SCIENCE; v. 100, n. 12, p. 9623-9634, DEC 2017.
Web of Science Citations: 1
Abstract

The objective of this study was to investigate different strategies for genotype imputation in a population of crossbred Girolando (Gyr x Holstein) dairy cattle. The data set consisted of 478 Girolando, 583 Gyr, and 1,198 Holstein sires genotyped at high density with the Illumina BovineHD (Illumina, San Diego, CA) panel, which includes similar to 777K markers. The accuracy of imputation from low (20K) and medium densities (50K and 70K) to the HD panel density and from low to 50K density were investigated. Seven scenarios using different reference populations (RPop) considering Girolando, Gyr, and Holstein breeds separately or combinations of animals of these breeds were tested for imputing genotypes of 166 randomly chosen Girolando animals. The population genotype imputation were performed using FImpute. Imputation accuracy was measured as the correlation between observed and imputed genotypes (CORR) and also as the proportion of genotypes that were imputed correctly (CR). This is the first paper on imputation accuracy in a Girolando population. The sample-specific imputation accuracies ranged from 0.38 to 0.97 (CORR) and from 0.49 to 0.96 (CR) imputing from low and medium densities to HD, and 0.41 to 0.95 (CORR) and from 0.50 to 0.94 (CR) for imputation from 20K to 50K. The CORRanim exceeded 0.96 (for 50K and 70K panels) when only Girolando animals were included in RPop (S1). We found smaller CORRanim when Gyr (S2) was used instead of Holstein (S3) as RPop. The same behavior was observed between S4 (Gyr + Girolando) and S5 (Holstein + Girolando) because the target animals were more related to the Holstein population than to the Gyr population. The highest imputation accuracies were observed for scenarios including Girolando animals in the reference population, whereas using only Gyr animals resulted in low imputation accuracies, suggesting that the haplotypes segregating in the Girolando population had a greater effect on accuracy than the purebred haplotypes. All chromosomes had similar imputation accuracies (CORRsnp) within each scenario. Crossbred animals (Girolando) must be included in the reference population to provide the best imputation accuracies. (AU)

FAPESP's process: 15/08939-0 - Identification of copy number variations in Girolando cattle
Grantee:Tatiane Cristina Seleguim Chud
Support type: Scholarships in Brazil - Doctorate
FAPESP's process: 13/12097-9 - Genome-wide association studies (GWAS) applied to reproductive traits in Nellore heifers
Grantee:Gerson Antônio de Oliveira Júnior
Support type: Scholarships in Brazil - Doctorate