6533b83afe1ef96bd12a7acf
RESEARCH PRODUCT
Penalized classification for optimal statistical selection of markers from high-throughput genotyping: application in sheep breeds
Marcello ChiodiSalvatore MastrangeloMaria Teresa SardinaBaldassare PortolanoMarco ToloneGianluca SottileR. Di Gerlandosubject
0301 basic medicinepenalized multinomial regression stability selection sheep breeds livestock genetic resources single nucleotide polymorphism markersGenotypePopulationSingle-nucleotide polymorphismComputational biologyBreedingBiologySF1-1100Polymorphism Single Nucleotidesheep breeds03 medical and health sciencesSettore AGR/17 - Zootecnica Generale E Miglioramento Geneticolivestock genetic resourcessingle nucleotide polymorphism markersAnimalseducationGenotypingSelection (genetic algorithm)Multinomial logistic regressionGeneticsPrincipal Component Analysiseducation.field_of_studySheeppenalized multinomial regressionHigh-Throughput Nucleotide SequencingBreedstability selectionAnimal cultureRandom forest030104 developmental biologyPrincipal component analysisAnimal Science and ZoologySettore SECS-S/01 - StatisticaBiomarkersdescription
The identification of individuals’ breed of origin has several practical applications in livestock and is useful in different biological contexts such as conservation genetics, breeding and authentication of animal products. In this paper, penalized multinomial regression was applied to identify the minimum number of single nucleotide polymorphisms (SNPs) from high-throughput genotyping data for individual assignment to dairy sheep breeds reared in Sicily. The combined use of penalized multinomial regression and stability selection reduced the number of SNPs required to 48. A final validation step on an independent population was carried out obtaining 100% correctly classified individuals. The results using independent analysis, such as admixture, F st, principal component analysis and random forest, confirmed the ability of these methods in selecting distinctive markers. The identified SNPs may constitute a starting point for the development of a SNP based identification test as a tool for breed assignment and traceability of animal products.
| year | journal | country | edition | language |
|---|---|---|---|---|
| 2018-01-01 |