ArticleGenome research2015
Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Genome-Wide Characterisation of the Ashanti Dwarf Pig Within a Global Context: Insights into Diversity, Inbreeding, and Adaptive Signatures.Life (Basel, Switzerland) · 2026Article
- Review
- Genomic insights into the demographic history and local adaptation of wild boars across Eurasia.Cell genomics · 2025Article
- Positive selection on rare variants of IGF1R and BRD4 underlying the cold adaptation of wild boar.Genetics, selection, evolution : GSE · 2025Article
- Genetic Diversity Analysis and Identification of Candidate Genes for Growth Traits in Chengkou Mountain Chicken.International journal of molecular sciences · 2024Article
- Swine global genomic resources: insights into wild and domesticated populations.Mammalian genome : official journal of the International Mammalian Genome Society · 2023Article
- Genome-Wide Genetic Structure of Henan Indigenous Chicken Breeds.Animals : an open access journal from MDPI · 2023Article
- The de novo assembly of a European wild boar genome revealed unique patterns of chromosomal structural variations and segmental duplications.Animal genetics · 2022Article
- Challenges in quantifying genome erosion for conservation.Frontiers in genetics · 2022Review
- Association Studies and Genomic Prediction for Genetic Improvements in Agriculture.Frontiers in plant science · 2022Review
- Genome-Wide Patterns of Homozygosity Reveal the Conservation Status in Five Italian Goat Populations.Animals : an open access journal from MDPI · 2021Article
- Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes.Genetics, selection, evolution : GSE · 2021Article
- Analysis of Autozygosity Using Whole-Genome Sequence Data of Full-Sib Families in Pikeperch (Frontiers in genetics · 2021Article
- Article
- Examination of the efficacy of small genetic panels in genomic conservation of companion animal populations.Evolutionary applications · 2020Article
- Genome-Wide Assessment of Runs of Homozygosity in Chinese Wagyu Beef Cattle.Animals : an open access journal from MDPI · 2020Article
- Population Genetic Analysis of Ten Geographically Isolated Tibetan Pig Populations.Animals : an open access journal from MDPI · 2020Article
- Long-Term Evaluation of Breeding Scheme Alternatives for Endangered Honeybee Subspecies.Insects · 2020Article
- Assessing breed integrity of Göttingen Minipigs.BMC genomics · 2020Article
- A double-labeling marker-based method for estimating inbreeding and parental genomic components in a population under conservation.Asian-Australasian journal of animal sciences · 2020Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Conservation and breeding programs aim at maintaining the most diversity, thereby avoiding deleterious effects of inbreeding while maintaining enough variation from which traits of interest can be selected. Theoretically, the most diversity is maintained using optimal contributions based on many markers to calculate coancestries, but this can decrease fitness by maintaining linked deleterious variants. The heterogeneous patterns of coancestry displayed in pigs make them an excellent model to test these predictions. We propose methods to measure coancestry and fitness from resequencing data and use them in population management. We analyzed the resequencing data of Sus cebifrons, a highly endangered porcine species from the Philippines, and genotype data from the Pietrain domestic breed. By analyzing the demographic history of Sus cebifrons, we inferred two past bottlenecks that resulted in some inbreeding load. In Pietrain, we analyzed signatures of selection possibly associated with commercial traits. We also simulated the management of each population to assess the performance of different optimal contribution methods to maintain diversity, fitness, and selection signatures. Maximum genetic diversity was maintained using marker-by-marker coancestry, and least using genealogical coancestry. Using a measure of coancestry based on shared segments of the genome achieved the best results in terms of diversity and fitness. However, this segment-based management eliminated signatures of selection. We demonstrate that maintaining both diversity and fitness depends on the genomic distribution of deleterious variants, which is shaped by demographic and selection histories. Our findings show the importance of genomic and next-generation sequencing information in the optimal design of breeding or conservation programs.
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