{"doi":"10.1073/pnas.0810388105","title":"Genetic architecture of complex traits: Large phenotypic effects and pervasive epistasis","abstract":"<jats:p>The genetic architecture of complex traits underlying physiology and disease in most organisms remains elusive. We still know little about the number of genes that underlie these traits, the magnitude of their effects, or the extent to which they interact. Chromosome substitution strains (CSSs) enable statistically powerful studies based on testing engineered inbred strains that have single, unique, and nonoverlapping genetic differences, thereby providing measures of phenotypic effects that are attributable to individual chromosomes. Here, we report a study of phenotypic effects and gene interactions for 90 blood, bone, and metabolic traits in a mouse CSS panel and 54 traits in a rat CSS panel. Two key observations emerge about the genetic architecture of these traits. First, the traits tend to be highly polygenic: across the genome, many individual chromosome substitutions each had significant phenotypic effects and, within each of the chromosomes studied, multiple distinct loci were found. Second, strong epistasis was found among the individual chromosomes. Specifically, individual chromosome substitutions often conferred surprisingly large effects (often a substantial fraction of the entire phenotypic difference between the parental strains), with the result that the sum of these individual effects often dramatically exceeded the difference between the parental strains. We suggest that strong, pervasive epistasis may reflect the presence of several phenotypically-buffered physiological states. These results have implications for identification of complex trait genes, developmental and physiological studies of phenotypic variation, and opportunities to engineer phenotypic outcomes in complex biological systems.</jats:p>","journal":"Proceedings of the National Academy of Sciences","year":2008,"id":31692,"datarank":9.478203439874811,"base_score":5.594711379601839,"endowment":5.594711379601839,"self_citation_contribution":0.839206706940276,"citation_network_contribution":8.638996732934535,"self_endowment_contribution":0.839206706940276,"citer_contribution":8.638996732934535,"corpus_percentile":null,"corpus_rank":null,"citation_count":268,"citer_count":200,"citers_with_citation_signal":200,"citers_with_endowment":200,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":169275,"name":"Lindsay C. 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Nadeau","orcid":null,"position":13,"is_corresponding":false},{"id":169274,"name":"Haifeng Shao","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":5.594711379601839,"endowment":5.594711379601839,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"19066216","pmcid":"PMC2604967","openalex_id":"https://openalex.org/W2140140747","authors":[],"funders":[{"funder_name":"NCRR NIH HHS","grant_id":"RR12305","title":null},{"funder_name":"NIAMS NIH HHS","grant_id":"R01 AR044927","title":null},{"funder_name":"NIAMS NIH HHS","grant_id":"AR44927","title":null},{"funder_name":"NCRR NIH HHS","grant_id":"P40 RR012305","title":null},{"funder_name":"NIAMS NIH HHS","grant_id":"R29 AR044927","title":null},{"funder_name":"NIAMS NIH HHS","grant_id":"R56 AR044927","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"T32 GM007250","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"T32 GM07250","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"GM08613","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"T32 GM008613","title":null}],"total_grants":10,"fwci":16.5529,"citation_percentile":0.99332751,"influential_citations":5,"citation_trend":[{"year":2012,"count":22},{"year":2013,"count":18},{"year":2014,"count":19},{"year":2015,"count":18},{"year":2016,"count":16},{"year":2017,"count":19},{"year":2018,"count":12},{"year":2019,"count":18},{"year":2020,"count":14},{"year":2021,"count":7},{"year":2022,"count":8},{"year":2023,"count":5},{"year":2024,"count":4},{"year":2025,"count":2},{"year":2026,"count":2}],"oa_status":"green","license":null,"oa_locations":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2604967","host_type":"repository"},{"url":"https://doi.org/10.1073/pnas.0810388105","host_type":"GREEN"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2604967","host_type":"repository"},{"url":"https://pnas.org/doi/pdf/10.1073/pnas.0810388105","host_type":"publisher"},{"url":"https://pubmed.ncbi.nlm.nih.gov/19066216","host_type":"repository"}],"fields_of_study":["Genetic Mapping and Diversity in Plants and Animals","Genetic and phenotypic traits in livestock","Genetics and Plant Breeding","Biology","Medicine","Animals","Body Weight","Disease","Epistasis, Genetic","Mice","Mice, Congenic","Mice, Inbred C57BL","Phenotype","Quantitative Trait Loci","Rats"],"mesh_terms":["Animals","Body Weight","Disease","Epistasis, Genetic","Mice, Inbred C57BL","Phenotype","Mice, Congenic","Quantitative Trait Loci","Mice","Rats"],"keywords":["Epistasis","Genetic architecture","Biology","Phenotype","Genetics","Quantitative trait locus","Gene","Phenotypic trait","Evolutionary biology","Chromosome","Trait"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Life in Land"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-06-09T08:12:15.954519Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}