ArticleBMC genetics2013
Improved estimation of inbreeding and kinship in pigs using optimized SNP panels.
Article in BMC genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 50 citations in OpenAlex.
- Genomic diversity, inbreeding, and selection signatures in duroc, landrace, and yorkshire pigs from a long-term closed breeding system.Journal of applied genetics · 2026Article
- Assessing kinship detection: single nucleotide polymorphism array density and estimator comparison in white-tailed deer.G3 (Bethesda, Md.) · 2026Article
- Impact of reducing metagenomic sequencing depth on phenotypic prediction accuracy of feed intake and average daily gain in beef cattle.Journal of animal science · 2026Article
- Development and evaluation of a novel single nucleotide polymorphism panel for North American bison.Evolutionary applications · 2024Article
- Construction of a strawberry breeding core collection to capture and exploit genetic variation.BMC genomics · 2023Article
- The coefficients of inbreeding revealed by ROH study among inbred individuals belonging to each type of the first cousin marriage: A preliminary report from North India.Genes & genomics · 2023Article
- Genome-Wide Assessment of a Korean Composite Pig Breed, Woori-Heukdon.Frontiers in genetics · 2022Article
- Estimation of inbreeding and identification of regions under heavy selection based on runs of homozygosity in a Large White pig population.Journal of animal science and biotechnology · 2020Article
- Article
- Genomic Analysis Reveals Specific Patterns of Homozygosity and Heterozygosity in Inbred Pigs.Animals : an open access journal from MDPI · 2019Article
- Effects of heterozygosity on performance of purebred and crossbred pigs.Genetics, selection, evolution : GSE · 2019Article
- Multi-strategy genome-wide association studies identify the DCAF16-NCAPG region as a susceptibility locus for average daily gain in cattle.Scientific reports · 2016Article
- Characterization and management of long runs of homozygosity in parental nucleus lines and their associated crossbred progeny.Genetics, selection, evolution : GSE · 2016Article
- Strategies for determining kinship in wild populations using genetic data.Ecology and evolution · 2016Review
- Genetic diversity analysis of two commercial breeds of pigs using genomic and pedigree data.Genetics, selection, evolution : GSE · 2016Article
- Relatedness in the post-genomic era: is it still useful?Nature reviews. Genetics · 2015Review
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTraditional breeding programs consider an average pairwise kinship between sibs. Based on pedigree information, the relationship matrix is used for genetic evaluations disregarding variation due to Mendelian sampling. Therefore, inbreeding and kinship coefficients are either over or underestimated resulting in reduction of accuracy of genetic evaluations and genetic progress. Single nucleotide polymorphism (SNPs) can be used to estimate pairwise kinship and individual inbreeding more accurately. The aim of this study was to optimize the selection of markers and determine the required number of SNPs for estimation of kinship and inbreeding.
resultsA total of 1,565 animals from three commercial pig populations were analyzed for 28,740 SNPs from the PorcineSNP60 Beadchip. Mean genomic inbreeding was higher than pedigree-based estimates in lines 2 and 3, but lower in line 1. As expected, a larger variation of genomic kinship estimates was observed for half and full sibs than for pedigree-based kinship reflecting Mendelian sampling. Genomic kinship between father-offspring pairs was lower (0.23) than the estimate based on pedigree (0.26). Bootstrap analyses using six reduced SNP panels (n = 500, 1000, 1500, 2000, 2500 and 3000) showed that 2,000 SNPs were able to reproduce the results very close to those obtained using the full set of unlinked markers (n = 7,984-10,235) with high correlations (inbreeding r > 0.82 and kinship r > 0.96) and low variation between different sets with the same number of SNPs.
conclusionsVariation of kinship between sibs due to Mendelian sampling is better captured using genomic information than the pedigree-based method. Therefore, the reduced sets of SNPs could generate more accurate kinship coefficients between sibs than the pedigree-based method. Variation of genomic kinship of father-offspring pairs is recommended as a parameter to determine accuracy of the method rather than correlation with pedigree-based estimates. Inbreeding and kinship coefficients can be estimated with high accuracy using ≥2,000 unlinked SNPs within all three commercial pig lines evaluated. However, a larger number of SNPs might be necessary in other populations or across lines.
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