ArticleG3 (Bethesda, Md.)2022
Estimate of inbreeding depression on growth and reproductive traits in a Large White pig population.
Article in G3 (Bethesda, Md.), 2022. 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, 26 citations in OpenAlex.
- Updating the RZooRoH Package for the Analysis of Inbreeding, Identity-By-Descent and Relatedness From Genomic Data.Molecular ecology resources · 2026Article
- Evaluation of pedigree structure, inbreeding levels, and inbreeding depression in reproduction traits in two Polish Złotnicka native pig breeds.Journal of applied genetics · 2026Article
- Genome-Wide Homozygosity Predicts Inbreeding Depression in the Hihi/Stitchbird (Evolutionary applications · 2026Article
- Review
- The hybridization analysis of pedigree: whole-genome re-sequencing reveals genomics characterization and genetic basis of growth trait of Qinchuan black pigs.BMC genomics · 2026Article
- Mutual information stacking method for prediction of the growth traits in pigs.Briefings in bioinformatics · 2025Article
- Mining of candidate genes related to body size in Chinese native pig breeds based on public data.Scientific reports · 2025Article
- Genomic selection in pig breeding: comparative analysis of machine learning algorithms.Genetics, selection, evolution : GSE · 2025Article
- The effects of runs-of-homozygosity on pig domestication and breeding.BMC genomics · 2025Article
- Genomic analysis reveals genetic diversity and selection signatures of the Yantai Black pig during domestication and breeding.Frontiers in genetics · 2025Article
- Population dynamics of potentially harmful haplotypes: a pedigree analysis.BMC genomics · 2024Article
- Detection of Runs of Homozygosity and Identification of Candidate Genes in the Whole Genome of Tunchang Pigs.Animals : an open access journal from MDPI · 2024Article
- Article
- Identification of ROH Islands Conserved through Generations in Pigs Belonging to the Nero Lucano Breed.Genes · 2023Article
- Comparing pedigree and genomic inbreeding coefficients, and inbreeding depression of reproductive traits in Japanese Black cattle.BMC genomics · 2023Article
- An empirical evaluation of the estimation of inbreeding depression from molecular markers under suboptimal conditions.Evolutionary applications · 2023Article
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With the broad application of genomic information, SNP-based measures of estimating inbreeding have been widely used in animal breeding, especially based on runs of homozygosity. Inbreeding depression is better estimated by SNP-based inbreeding coefficients than pedigree-based inbreeding in general. However, there are few comprehensive comparisons of multiple methods in pigs so far, to some extent limiting their application. In this study, to explore an appropriate strategy for estimating inbreeding depression on both growth traits and reproductive traits in a Large White pig population, we compared multiple methods for the inbreeding coefficient estimation based on both pedigree and genomic information. This pig population for analyzing the influence of inbreeding was from a pig breeding farm in the Inner Mongolia of China. There were 26,204 pigs with records of age at 100 kg (AGE) and back-fat thickness at 100 kg (BF), and 6,656 sows with reproductive records of the total number of piglets at birth (TNB), and the number of alive piglets at birth (NBA), and litter weight at birth. Inbreeding depression affected growth and reproductive traits. The results indicated that pedigree-based and SNP-based inbreeding coefficients had significant effects on AGE, TNB, and NBA, except for BF. However, only SNP-based inbreeding coefficients revealed a strong association with inbreeding depression on litter weight at birth. Runs of homozygosity-based methods showed a slight advantage over other methods in the correlation analysis of inbreeding coefficients and estimation of inbreeding depression. Furthermore, our results demonstrated that the model-based approach (RZooRoH) could avoid miscalculations of inbreeding and inbreeding depression caused by inappropriate parameters, which had a good performance on both AGE and reproductive traits. These findings might improve the extensive application of runs of homozygosity analysis in pig breeding and breed conservation.
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