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Preselection statistics and Random Forest classification identify population informative single nucleotide polymorphisms in cosmopolitan and autochthonous cattle breeds
- Source :
- Animal, Vol 12, Iss 1, Pp 12-19 (2018)
- Publication Year :
- 2018
- Publisher :
- Elsevier, 2018.
-
Abstract
- Commercial single nucleotide polymorphism (SNP) arrays have been recently developed for several species and can be used to identify informative markers to differentiate breeds or populations for several downstream applications. To identify the most discriminating genetic markers among thousands of genotyped SNPs, a few statistical approaches have been proposed. In this work, we compared several methods of SNPs preselection (Delta, F st and principal component analyses (PCA)) in addition to Random Forest classifications to analyse SNP data from six dairy cattle breeds, including cosmopolitan (Holstein, Brown and Simmental) and autochthonous Italian breeds raised in two different regions and subjected to limited or no breeding programmes (Cinisara, Modicana, raised only in Sicily and Reggiana, raised only in Emilia Romagna). From these classifications, two panels of 96 and 48 SNPs that contain the most discriminant SNPs were created for each preselection method. These panels were evaluated in terms of the ability to discriminate as a whole and breed-by-breed, as well as linkage disequilibrium within each panel. The obtained results showed that for the 48-SNP panel, the error rate increased mainly for autochthonous breeds, probably as a consequence of their admixed origin lower selection pressure and by ascertaining bias in the construction of the SNP chip. The 96-SNP panels were generally more able to discriminate all breeds. The panel derived by PCA-chrom (obtained by a preselection chromosome by chromosome) could identify informative SNPs that were particularly useful for the assignment of minor breeds that reached the lowest value of Out Of Bag error even in the Cinisara, whose value was quite high in all other panels. Moreover, this panel contained also the lowest number of SNPs in linkage disequilibrium. Several selected SNPs are located nearby genes affecting breed-specific phenotypic traits (coat colour and stature) or associated with production traits. In general, our results demonstrated the usefulness of Random Forest in combination to other reduction techniques to identify population informative SNPs.
- Subjects :
- 0301 basic medicine
Genetic Markers
Linkage disequilibrium
Genotype
Population
Animal Identification Systems
SNP
Single-nucleotide polymorphism
Biology
Breeding
Polymorphism, Single Nucleotide
SF1-1100
Linkage Disequilibrium
03 medical and health sciences
Settore AGR/17 - Zootecnica Generale E Miglioramento Genetico
Animals
Bos tauru
Selection, Genetic
education
Selection (genetic algorithm)
Genetics
education.field_of_study
Principal Component Analysis
Random Forest
Bos taurus
breed assignment
Animal Science and Zoology
0402 animal and dairy science
04 agricultural and veterinary sciences
Phenotypic trait
040201 dairy & animal science
SNP genotyping
Animal culture
030104 developmental biology
Phenotype
Italy
Genetic marker
SNP, breed assignment, Random Forest, Bos taurus
Cattle
Subjects
Details
- Language :
- English
- ISSN :
- 17517311
- Volume :
- 12
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- Animal
- Accession number :
- edsair.doi.dedup.....520ddf12dd3fb29bca3e82285466848a