ArticlePloS one2015
Genome-wide estimates of coancestry, inbreeding and effective population size in the Spanish Holstein population.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Genomic Analysis of Inbreeding Depression on Productive Traits in Rubia Galega Beef Cattle Breed.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2026Article
- Estimating Linkage Disequilibrium and Effective Population Size Across Generations in Holstein Cattle.Veterinary medicine and science · 2025Article
- Reproductive Performance, Inbreeding, and Genetic Diversity in Montbeliarde Dairy Cattle Obtained by Absorption Crossing.Animals : an open access journal from MDPI · 2025Article
- Genomic diversity and population structure analysis of four geographically distinct Holstein cattle populations using genome-wide DNA profiling.Archives animal breeding · 2025Article
- Analyses of whole-genome sequences from 185 North American Thoroughbred horses, spanning 5 generations.Scientific reports · 2024Article
- Genetic insights into crossbred dairy cattle of Pakistan: exploring allele frequency, linkage disequilibrium, and effective population size at a genome-wide scale.Mammalian genome : official journal of the International Mammalian Genome Society · 2023Article
- Genomic variability and population structure of six Colombian cattle breeds.Tropical animal health and production · 2023Article
- The role of inbreeding depression on productive performance in the Italian Holstein breed.Journal of animal science · 2023Article
- Evaluating the use of statistical and machine learning methods for estimating breed composition of purebred and crossbred animals in thirteen cattle breeds using genomic information.Frontiers in genetics · 2023Article
- Runs of homocigosity and its association with productive traits in Mexican Holstein cattle.PloS one · 2022Article
- Development of a High-Density 665 K SNP Array for Rainbow Trout Genome-Wide Genotyping.Frontiers in genetics · 2022Article
- Challenges in quantifying genome erosion for conservation.Frontiers in genetics · 2022Review
- Correlation of Genomic and Pedigree Inbreeding Coefficients in Small Cattle Populations.Animals : an open access journal from MDPI · 2021Article
- Article
- Genetic Diversity in the Italian Holstein Dairy Cattle Based on Pedigree and SNP Data Prior and After Genomic Selection.Frontiers in veterinary science · 2021Article
- How to study runs of homozygosity using PLINK? A guide for analyzing medium density SNP data in livestock and pet species.BMC genomics · 2020Article
- Linkage Disequilibrium, Effective Population Size and Genomic Inbreeding Rates in American Mink Using Genotyping-by-Sequencing Data.Frontiers in genetics · 2020Article
- Management of Genetic Diversity in the Era of Genomics.Frontiers in genetics · 2020Article
- Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding.Genetics, selection, evolution : GSE · 2019Article
- A Strategy To Exploit Surrogate Sire Technology in Livestock Breeding Programs.G3 (Bethesda, Md.) · 2019Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Estimates of effective population size in the Holstein cattle breed have usually been low despite the large number of animals that constitute this breed. Effective population size is inversely related to the rates at which coancestry and inbreeding increase and these rates have been high as a consequence of intense and accurate selection. Traditionally, coancestry and inbreeding coefficients have been calculated from pedigree data. However, the development of genome-wide single nucleotide polymorphisms has increased the interest of calculating these coefficients from molecular data in order to improve their accuracy. In this study, genomic estimates of coancestry, inbreeding and effective population size were obtained in the Spanish Holstein population and then compared with pedigree-based estimates. A total of 11,135 animals genotyped with the Illumina BovineSNP50 BeadChip were available for the study. After applying filtering criteria, the final genomic dataset included 36,693 autosomal SNPs and 10,569 animals. Pedigree data from those genotyped animals included 31,203 animals. These individuals represented only the last five generations in order to homogenise the amount of pedigree information across animals. Genomic estimates of coancestry and inbreeding were obtained from identity by descent segments (coancestry) or runs of homozygosity (inbreeding). The results indicate that the percentage of variance of pedigree-based coancestry estimates explained by genomic coancestry estimates was higher than that for inbreeding. Estimates of effective population size obtained from genome-wide and pedigree information were consistent and ranged from about 66 to 79. These low values emphasize the need of controlling the rate of increase of coancestry and inbreeding in Holstein selection programmes.
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