Open AccessAssessing the accuracy of imputation in the Gyr breed using different SNP panels
Author(s) -
Alejandra Maria Toro Ospina,
Ignácio Aguilar,
Matheus Henrique Vargas de Oliveira,
Luiz Eduardo Cruz dos Santos Correia,
Aníbal Eugênio Vercesi Filho,
Lúcia Galvão de Albuquerque,
Josineudson Augusto Ii Vasconcelos Silva
Publication year - 2021
Publication title -
genome
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.642
H-Index - 99
eISSN - 1480-3321
pISSN - 0831-2796
DOI - 10.1139/gen-2020-0081
Subject(s) - imputation (statistics) , biology , breed , single nucleotide polymorphism , principal component analysis , subspecies , snp , genetics , population , repeatability , statistics , genomic selection , concordance , genotype , zoology , mathematics , missing data , gene , demography , sociology
The aim of this study was to evaluate the accuracy of imputation in a Gyr population using two medium-density panels (Bos taurus - Bos indicus) and to test whether the inclusion of the Nellore breed increases the imputation accuracy in the Gyr population. The database consisted of 289 Gyr females from Brazil genotyped with the GGP Bovine LDv4 chip containing 30 000 SNPs and 158 Gyr females from Colombia genotyped with the GGP indicus chip containing 35 000 SNPs. A customized chip was created that contained the information of 9109 SNPs (9K) to test the imputation accuracy in Gyr populations; 604 Nellore animals with information of LD SNPs tested in the scenarios were included in the reference population. Four scenarios were tested: LD9K_30KGIR, LD9K_35INDGIR, LD9K_30KGIR_NEL, and LD9K_35INDGIR_NEL. Principal component analysis (PCA) was computed for the genomic matrix and sample-specific imputation accuracies were calculated using Pearson’s correlation (CS) and the concordance rate (CR) for imputed genotypes. The results of PCA of the Colombian and Brazilian Gyr populations demonstrated the genomic relationship between the two populations. The CS and CR ranged from 0.88 to 0.94 and from 0.93 to 0.96, respectively. Among the scenarios tested, the highest CS (0.94) was observed for the LD9K_30KGIR scenario. The present results highlight the importance of the choice of chip for imputation in the Gyr breed. However, the variation in SNPs may reduce the imputation accuracy even when the chip of the Bos indicus subspecies is used.