Combined use of principal component analysis and random forests identify population-informative single nucleotide polymorphisms: application in cattle breeds

Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie
F BertoliniL Fontanesi

Abstract

The genetic identification of the population of origin of individuals, including animals, has several practical applications in forensics, evolution, conservation genetics, breeding and authentication of animal products. Commercial high-density single nucleotide polymorphism (SNP) genotyping tools that have been recently developed in many species provide information from a large number of polymorphic sites that can be used to identify population-/breed-informative markers. In this study, starting from Illumina BovineSNP50 v1 BeadChip array genotyping data available from 3711 cattle of four breeds (2091 Italian Holstein, 738 Italian Brown, 475 Italian Simmental and 407 Marchigiana), principal component analysis (PCA) and random forests (RFs) were combined to identify informative SNP panels useful for cattle breed identification. From a PCA preselected list of 580 SNPs, RFs were computed using ranking methods (Mean Decrease in the Gini Index and Mean Accuracy Decrease) to identify the most informative 48 and 96 SNPs for breed assignment. The out-of-bag (OOB) error rate for both ranking methods and SNP densities ranged from 0.0 to 0.1% in the reference population. Application of this approach in a test population (10% of individua...Continue Reading

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Citations

Oct 25, 2017·Animal : an International Journal of Animal Bioscience·G SottileB Portolano
Aug 2, 2017·PloS One·Parthan KasarapuAntonio Reverter
Jan 4, 2019·Horticulture Research·Tetyana ZhebentyayevaChris Dardick
Apr 3, 2020·Animals : an Open Access Journal From MDPI·Elisa SomenziMario Barbato
Mar 24, 2016·Biological Reviews of the Cambridge Philosophical Society·Mohammed YaroDavid M Groth
Sep 6, 2020·Genetics, Selection, Evolution : GSE·Seyed Mohammad GhoreishifarArash Javanmard
Jan 23, 2021·Animals : an Open Access Journal From MDPI·Dongwon SeoJun Heon Lee
Aug 25, 2021·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Hélène WilmotNicolas Gengler

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