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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.)

Strategies for genotype imputation in composite beef cattle

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Author(s):
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Chud, Tatiane C. S. [1] ; Ventura, Ricardo V. [2, 3] ; Schenkel, Flavio S. [3] ; Carvalheiro, Roberto [4] ; Buzanskas, Marcos E. [1] ; Rosa, Jaqueline O. [1] ; Mudadu, Mauricio de Alvarenga [5] ; da Silva, Marcos Vinicius G. B. [6] ; Mokry, Fabiana B. [7] ; Marcondes, Cintia R. [5] ; Regitano, Luciana C. A. [5] ; Munari, Danisio P. [1]
Total Authors: 12
Affiliation:
[1] UNESP Univ Estadual Paulista Julio de Mesquita Fi, Dept Ciencias Exatas, Jaboticabal, SP - Brazil
[2] Beef Improvement Opportun, Guelph, ON - Canada
[3] Univ Guelph, Guelph, ON N1G 2W1 - Canada
[4] UNESP Univ Estadual Paulista Julio de Mesquita Fi, Dept Zootecnia, Jaboticabal, SP - Brazil
[5] Brazilian Corp Agr Res, Embrapa Southeast Livestock, Sao Carlos, SP - Brazil
[6] Brazilian Corp Agr Res, Embrapa Dairy Cattle, Juiz De Fora, MG - Brazil
[7] Univ Fed Sao Carlos, Dept Genet & Evolut, BR-13560 Sao Carlos, SP - Brazil
Total Affiliations: 7
Document type: Journal article
Source: BMC GENETICS; v. 16, AUG 7 2015.
Web of Science Citations: 7
Abstract

Background: Genotype imputation has been used to increase genomic information, allow more animals in genome-wide analyses, and reduce genotyping costs. In Brazilian beef cattle production, many animals are resulting from crossbreeding and such an event may alter linkage disequilibrium patterns. Thus, the challenge is to obtain accurately imputed genotypes in crossbred animals. The objective of this study was to evaluate the best fitting and most accurate imputation strategy on the MA genetic group (the progeny of a Charolais sire mated with crossbred Canchim X Zebu cows) and Canchim cattle. The data set contained 400 animals (born between 1999 and 2005) genotyped with the Illumina BovineHD panel. Imputation accuracy of genotypes from the Illumina-Bovine3K (3K), Illumina-BovineLD (6K), GeneSeek-Genomic-Profiler (GGP) BeefLD (GGP9K), GGP-IndicusLD (GGP20Ki), Illumina-BovineSNP50 (50K), GGP-IndicusHD (GGP75Ki), and GGP-BeefHD (GGP80K) to Illumina-BovineHD (HD) SNP panels were investigated. Seven scenarios for reference and target populations were tested; the animals were grouped according with birth year (S1), genetic groups (S2 and S3), genetic groups and birth year (S4 and S5), gender (S6), and gender and birth year (S7). Analyses were performed using FImpute and BEAGLE software and computation run-time was recorded. Genotype imputation accuracy was measured by concordance rate (CR) and allelic R square (R-2). Results: The highest imputation accuracy scenario consisted of a reference population with males and females and a target population with young females. Among the SNP panels in the tested scenarios, from the 50K, GGP75Ki and GGP80K were the most adequate to impute to HD in Canchim cattle. FImpute reduced computation run-time to impute genotypes from 20 to 100 times when compared to BEAGLE. Conclusion: The genotyping panels possessing at least 50 thousands markers are suitable for genotype imputation to HD with acceptable accuracy. The FImpute algorithm demonstrated a higher efficiency of imputed markers, especially in lower density panels. These considerations may assist to increase genotypic information, reduce genotyping costs, and aid in genomic selection evaluations in crossbred animals. (AU)

FAPESP's process: 13/19335-2 - Study of admixture level in Canchim breed and ma genetic group animals using high density single nucleotide polymorphism markers
Grantee:Marcos Eli Buzanskas
Support type: Scholarships in Brazil - Post-Doctorate
FAPESP's process: 12/21891-8 - Imputation of molecular markers in Canchim Cattle
Grantee:Tatiane Cristina Seleguim Chud
Support type: Scholarships in Brazil - Master