{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,15]],"date-time":"2025-07-15T03:27:34Z","timestamp":1752550054724,"version":"3.37.3"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2019,11,25]],"date-time":"2019-11-25T00:00:00Z","timestamp":1574640000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100004543","name":"China Scholarship Council","doi-asserted-by":"publisher","award":["No.201508360093"],"award-info":[{"award-number":["No.201508360093"]}],"id":[{"id":"10.13039\/501100004543","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Prof. Richard Mott's BBSRC equipment grant","award":["BB\/R01356X\/1"],"award-info":[{"award-number":["BB\/R01356X\/1"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>During the past decade, genome-wide association studies (GWAS) have been used to map quantitative trait loci (QTLs) underlying complex traits. However, most GWAS focus on additive genetic effects while ignoring non-additive effects, on the assumption that most QTL act additively. Consequently, QTLs driven by dominance and other non-additive effects could be overlooked.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed ADDO, a highly efficient tool to detect, classify and visualize QTLs with additive and non-additive effects. ADDO implements a mixed-model transformation to control for population structure and unequal relatedness that accounts for both additive and dominant genetic covariance among individuals, and decomposes single-nucleotide polymorphism effects as either additive, partial dominant, dominant or over-dominant. A matrix multiplication approach is used to accelerate the computation: a genome scan on 13 million markers from 900 individuals takes about 5\u2009h with 10 CPUs. Analysis of simulated data confirms ADDO\u2019s performance on traits with different additive and dominance genetic variance components. We showed two real examples in outbred rat where ADDO identified significant dominant QTL that were not detectable by an additive model. ADDO provides a systematic pipeline to characterize additive and non-additive QTL in whole genome sequence data, which complements current mainstream GWAS software for additive genetic effects.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>ADDO is customizable and convenient to install and provides extensive analytics and visualizations. The package is freely available online at https:\/\/github.com\/LeileiCui\/ADDO.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz786","type":"journal-article","created":{"date-parts":[[2019,11,22]],"date-time":"2019-11-22T20:10:46Z","timestamp":1574453446000},"page":"1517-1521","source":"Crossref","is-referenced-by-count":5,"title":["ADDO: a comprehensive toolkit to detect, classify and visualize additive and non-additive quantitative trait loci"],"prefix":"10.1093","volume":"36","author":[{"given":"Leilei","family":"Cui","sequence":"first","affiliation":[{"name":"State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University , Nanchang 330045, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bin","family":"Yang","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University , Nanchang 330045, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1782-4711","authenticated-orcid":false,"given":"Nikolas","family":"Pontikos","sequence":"additional","affiliation":[{"name":"UCL Genetics Institute"},{"name":"UCL Institute of Ophthalmology, University College London , London WC1E 6BT"},{"name":"Department of Genetics , Moorfields Eye Hospital, London EC1V 2PD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard","family":"Mott","sequence":"additional","affiliation":[{"name":"UCL Genetics Institute"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lusheng","family":"Huang","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University , Nanchang 330045, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,11,25]]},"reference":[{"key":"2023060910275228300_btz786-B1","doi-asserted-by":"crossref","DOI":"10.1186\/s12711-018-0405-y","article-title":"Genome-wide association scan for heterotic quantitative trait loci in multi-breed and crossbred beef cattle","volume":"50","author":"Akanno","year":"2018","journal-title":"Genet. 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