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Use of partial least squares regression to impute SNP genotypes in Italian Cattle breeds

Dimauro, Corrado and Cellesi, Massimo and Gaspa, Giustino and Ajmone-Marsan, Paolo and Steri, Roberto and Marras, Gabriele and Macciotta, Nicolò Pietro Paolo (2013) Use of partial least squares regression to impute SNP genotypes in Italian Cattle breeds. Genetics Selection Evolution, Vol. 45 (15), p. 1-8. eISSN 0999-193X. Article.

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DOI: 10.1186/1297-9686-45-15

Abstract

Background
The objective of the present study was to test the ability of the partial least squares regression technique to impute genotypes from low density single nucleotide polymorphisms (SNP) panels i.e. 3K or 7K to a high density panel with 50K SNP. No pedigree information was used.
Methods
Data consisted of 2093 Holstein, 749 Brown Swiss and 479 Simmental bulls genotyped with the Illumina 50K Beadchip. First, a single-breed approach was applied by using only data from Holstein animals. Then, to enlarge the training population, data from the three breeds were combined and a multi-breed analysis was performed. Accuracies of genotypes imputed using the partial least squares regression method were compared with those obtained by using the Beagle software. The impact of genotype imputation on breeding value prediction was evaluated for milk yield, fat content and protein content.
Results
In the single-breed approach, the accuracy of imputation using partial least squares regression was around 90 and 94% for the 3K and 7K platforms, respectively; corresponding accuracies obtained with Beagle were around 85% and 90%. Moreover, computing time required by the partial least squares regression method was on average around 10 times lower than computing time required by Beagle. Using the partial least squares regression method in the multi-breed resulted in lower imputation accuracies than using single-breed data. The impact of the SNP-genotype imputation on the accuracy of direct genomic breeding values was small. The correlation between estimates of genetic merit obtained by using imputed versus actual genotypes was around 0.96 for the 7K chip.
Conclusions
Results of the present work suggested that the partial least squares regression imputation method could be useful to impute SNP genotypes when pedigree information is not available.

Item Type:Article
ID Code:9161
Status:Published
Refereed:Yes
Uncontrolled Keywords:Inputation, partial least squares regression, SNP
Subjects:Area 07 - Scienze agrarie e veterinarie > AGR/17 Zootecnica generale e miglioramento genetico
Divisions:001 Università di Sassari > 01-a Nuovi Dipartimenti dal 2012 > Agraria
Publisher:BioMed Central
eISSN:0999-193X
Copyright Holders:© 2013 Dimauro et al.; licensee BioMed Central Ltd.
Publisher Policy:Depositato in conformità con la politica di copyright dell'Editore
Deposited On:26 Jul 2013 08:40

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