Evidence map›Paper›PMID 41318401›Full record

ArticleBMC genomics2025

Comparison between SNP array and imputed data to estimate population structure and ROH hotspots in horse breeds.

Giorgio Chessari, Paula Reich, Andrea Criscione, Clemens Falker-Gieske, Salvatore Mastrangelo, Serena Tumino, Salvatore Bordonaro, Donata Marletta, Jens Tetens

Abstract readComparative Study
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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2 · The registry

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4 · The record

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5 · Who and what money

Authors and funding

9 authors.

Giorgio Chessari *Department of Agriculture, Food and Environment, University of Catania, Catania, 95131, Italy. giorgio.chessari@unict.it.
Paula Reich *Department of Animal Sciences, Georg-August-University Göttingen, Göttingen, 37077, Germany.
Andrea CriscioneDepartment of Agriculture, Food and Environment, University of Catania, Catania, 95131, Italy.
Clemens Falker-GieskeDepartment of Animal Sciences, Georg-August-University Göttingen, Göttingen, 37077, Germany.
Salvatore MastrangeloDepartment of Agricultural, Food and Forestry Sciences, University of Palermo, Palermo, 90128, Italy.
Serena TuminoDepartment of Agriculture, Food and Environment, University of Catania, Catania, 95131, Italy.
Salvatore BordonaroDepartment of Agriculture, Food and Environment, University of Catania, Catania, 95131, Italy.
Donata MarlettaDepartment of Agriculture, Food and Environment, University of Catania, Catania, 95131, Italy.
Jens TetensDepartment of Animal Sciences, Georg-August-University Göttingen, Göttingen, 37077, Germany.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundSingle nucleotide polymorphism (SNP) arrays are commonly used for studying the genomic structure and diversity of livestock breeds, but whole-genome sequencing (WGS) provides higher-resolution genomic data. Genotype imputation has become a standard practice for increasing the genomic resolution of association studies. This work aimed to extend imputation to biodiversity analyses, comparing SNP array data before and after imputation. A 40 k SNP dataset of 281 horses from 12 breeds (DS

resultsGenetic indices and relationships showed similar trends for both datasets, with high Pearson correlations and Mantel test values (> 0.8) indicating that the imputed data are a reliable alternative to SNP array data for genetic studies. Multidimensional scaling and admixture analyses highlighted how the genetic proximity between breeds observed for the DS

conclusionsHigh correlations between SNP array and imputed data indicate that imputed genotypes provide a reliable alternative for assessing population structure and genetic diversity in horse breeds. Specifically, imputation can enhance the detection of ROH and the annotation of genes within ROH islands, with the reliability of these results depending on the quality of the reference panel and its representation of the studied breeds, among others.

Indexed as

Genetics, PopulationPolymorphism, Single NucleotideAnimalsBreedingGenomicsGenotypeHomozygoteHorsesWhole Genome SequencingGenome diversityHorse speciesImputationRuns of homozygositySNPWhole-genome sequencing

Identifiers

PMID41318401
PMCPMC12670763

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