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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.)

Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle

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Author(s):
Bernardes, Priscila Arrigucci [1] ; do Nascimento, Guilherme Batista [2] ; Savegnago, Rodrigo Pelicioni [3] ; Buzanskas, Marcos Eli [4] ; Watanabe, Rafael Nakamura [1] ; de Almeida Regitano, Luciana Correia [5] ; Coutinho, Luiz Lehmann [6] ; Gondro, Cedric [7] ; Munari, Danisio Prado [1]
Total Authors: 9
Affiliation:
[1] Univ Estadual Paulista, Dept Ciencias Exatas, Fac Ciencias Agr & Vet, Sao Paulo, SP - Brazil
[2] Ctr Univ Adamantina, Sao Paulo, SP - Brazil
[3] Inst Zootecnia, Sao Paulo, SP - Brazil
[4] Univ Fed Paraiba, Ctr Ciencias Agr, Areia, PB - Brazil
[5] Embrapa Pecuaria Sudeste, Sao Paulo, SP - Brazil
[6] Univ Sao Paulo, Dept Zootecnia, Escola Super Agr Luiz de Queiroz, Sao Paulo, SP - Brazil
[7] Michigan State Univ, Dept Anim Sci, Coll Agr & Nat Resources, E Lansing, MI 48824 - USA
Total Affiliations: 7
Document type: Journal article
Source: SCIENTIFIC REPORTS; v. 9, NOV 29 2019.
Web of Science Citations: 0
Abstract

This study compared imputation from lower-density commercial and customized panels to high-density panels and a combined panel (Illumina and Affymetrix) in Nelore beef cattle. Additionally, linkage disequilibrium and haplotype block conformation were estimated in individual high-density panels and compared with corresponding values in the combined panel after imputation. Overall, 814 animals were genotyped using BovineHD BeadChip (IllumHD), and 93 of these animals were also genotyped using the Axion Genome-Wide BOS 1 Array Plate (AffyHD). In general, customization considering linkage disequilibrium and minor allele frequency had the highest accuracies. The IllumHD panel had higher values of linkage disequilibrium for short distances between SNPs than AffyHD and the combined panel. The combined panel had an increased number of small haplotype blocks. The use of a combined panel is recommended due to its increased density and number of haplotype blocks, which in turn increase the probability of a marker being close to a quantitative trait locus of interest. Considering common SNPs between IllumHD and AffyHD for the customization of a low-density panel increases the imputation accuracy for IllumHD, AffyHD and the combined panel. (AU)

FAPESP's process: 13/20091-0 - Prediction of breeding values in a experimental mice population using selective genotyping
Grantee:Rodrigo Pelicioni Savegnago
Support Opportunities: Scholarships in Brazil - Post-Doctoral
FAPESP's process: 12/23638-8 - Molecular basis of meat quality in Nelore beef cattle
Grantee:Luciana Correia de Almeida Regitano
Support Opportunities: Research Projects - Thematic Grants
FAPESP's process: 16/22940-3 - Imputation, linkage desequilibrium, haplotype blocks and inbreeding in Nelore cattle
Grantee:Priscila Arrigucci Bernardes
Support Opportunities: Scholarships abroad - Research Internship - Doctorate
FAPESP's process: 15/25096-6 - Imputation, linkage desequilibrium, haplotype blocks and inbreeding in Nelore cattle
Grantee:Priscila Arrigucci Bernardes
Support Opportunities: Scholarships in Brazil - Doctorate
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 Opportunities: Scholarships in Brazil - Post-Doctoral