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Increasing imputation and prediction accuracy for C hinese H olsteins using joint C hinese– N ordic reference population
Author(s) -
Ma P.,
Lund M.S.,
Ding X.,
Zhang Q.,
Su G.
Publication year - 2014
Publication title -
journal of animal breeding and genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.689
H-Index - 51
eISSN - 1439-0388
pISSN - 0931-2668
DOI - 10.1111/jbg.12111
Subject(s) - imputation (statistics) , biology , population , genotype , genomic selection , chinese population , allele , genetics , statistics , single nucleotide polymorphism , gene , mathematics , missing data , medicine , environmental health
Summary This study investigated the effect of including N ordic H olsteins in the reference population on the imputation accuracy and prediction accuracy for C hinese H olsteins. The data used in this study include 85 C hinese H olstein bulls genotyped with both 54K chip and 777K ( HD ) chip, 2862 C hinese cows genotyped with 54K chip, 510 N ordic H olstein bulls genotyped with HD chip, and 4398 N ordic H olstein bulls genotyped with 54K chip and with deregressed proofs for five milk production traits. Based on these data, the accuracy of imputation from 54K to HD marker data and the accuracy of genomic predictions in C hinese H olstein were assessed. The allele correct rate increased around 2.7 and 1.7% in imputation from the 54K to the HD marker data for C hinese H olstein bulls and cows, respectively, when the N ordic HD ‐genotyped bulls were included in the reference data for imputation. However, the prediction accuracy was improved slightly when using the marker data imputed based on the combined HD reference data, compared with using the marker data imputed based on the C hinese HD reference data only. On the other hand, when using the combined reference population including 4398 N ordic H olstein bulls, the accuracy of genomic predictions increased 6.5 percentage points together with a reduction of prediction bias. The HD markers did not outperform the 54K markers in genomic prediction based on the present data. The results indicate that for C hinese H olsteins, it is necessary to genotype more individuals with 54K chip to increase reference population rather than increasing marker density.