{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T16:22:06Z","timestamp":1780417326481,"version":"3.54.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1009923","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,3,23]],"date-time":"2022-03-23T00:00:00Z","timestamp":1647993600000}}],"reference-count":61,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2022,3,11]],"date-time":"2022-03-11T00:00:00Z","timestamp":1646956800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Hatch Project","award":["CA-R-BPS-5028-H"],"award-info":[{"award-number":["CA-R-BPS-5028-H"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Detecting quantitative trait loci (QTL) and estimating QTL variances (represented by the squared QTL effects) are two main goals of QTL mapping and genome-wide association studies (GWAS). However, there are issues associated with estimated QTL variances and such issues have not attracted much attention from the QTL mapping community. Estimated QTL variances are usually biased upwards due to estimation being associated with significance tests. The phenomenon is called the Beavis effect. However, estimated variances of QTL without significance tests can also be biased upwards, which cannot be explained by the Beavis effect; rather, this bias is due to the fact that QTL variances are often estimated as the squares of the estimated QTL effects. The parameters are the QTL effects and the estimated QTL variances are obtained by squaring the estimated QTL effects. This square transformation failed to incorporate the errors of estimated QTL effects into the transformation. The consequence is biases in estimated QTL variances. To correct the biases, we can either reformulate the QTL model by treating the QTL effect as random and directly estimate the QTL variance (as a variance component) or adjust the bias by taking into account the error of the estimated QTL effect. A moment method of estimation has been proposed to correct the bias. The method has been validated via Monte Carlo simulation studies. The method has been applied to QTL mapping for the 10-week-body-weight trait from an F<jats:sub>2<\/jats:sub> mouse population.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1009923","type":"journal-article","created":{"date-parts":[[2022,3,11]],"date-time":"2022-03-11T18:41:32Z","timestamp":1647024092000},"page":"e1009923","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":8,"title":["Estimating genetic variance contributed by a quantitative trait locus: A random model approach"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5937-4718","authenticated-orcid":true,"given":"Shibo","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fangjie","family":"Xie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6789-6655","authenticated-orcid":true,"given":"Shizhong","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,3,11]]},"reference":[{"issue":"1","key":"pcbi.1009923.ref001","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1093\/genetics\/121.1.185","article-title":"Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps","volume":"121","author":"ES Lander","year":"1989","journal-title":"Genetics"},{"key":"pcbi.1009923.ref002","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1038\/ng1702","article-title":"A unified mixed-model method for association mapping that accounts for multiple levels of relatedness","volume":"38","author":"J Yu","year":"2006","journal-title":"Nature Genetics"},{"issue":"3","key":"pcbi.1009923.ref003","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1093\/genetics\/124.3.743","article-title":"Efficiency of marker-assisted selection in the improvement of quantitative traits","volume":"124","author":"R Lande","year":"1990","journal-title":"Genetics"},{"issue":"6","key":"pcbi.1009923.ref004","doi-asserted-by":"crossref","first-page":"1357","DOI":"10.1086\/324471","article-title":"Large upward bias in estimation of locus-specific effects from genomewide scans","volume":"69","author":"HH Goring","year":"2001","journal-title":"Am J Hum Genet"},{"issue":"6","key":"pcbi.1009923.ref005","doi-asserted-by":"crossref","first-page":"978","DOI":"10.1093\/bioinformatics\/btx703","article-title":"Estimation of QTL heritability based on pooled sequencing data","volume":"34","author":"W Tang","year":"2018","journal-title":"Bioinformatics"},{"issue":"2","key":"pcbi.1009923.ref006","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1023\/A:1026028928003","article-title":"Correcting the bias in estimation of genetic variances contributed by individual QTL","volume":"119","author":"L Luo","year":"2003","journal-title":"Genetica"},{"issue":"4","key":"pcbi.1009923.ref007","doi-asserted-by":"crossref","first-page":"1447","DOI":"10.1093\/genetics\/136.4.1447","article-title":"High resolution of quantitative traits into multiple loci via interval mapping","volume":"136","author":"RC Jansen","year":"1994","journal-title":"Genetics"},{"issue":"4","key":"pcbi.1009923.ref008","doi-asserted-by":"crossref","first-page":"1457","DOI":"10.1093\/genetics\/136.4.1457","article-title":"Precision mapping of quantitative trait loci","volume":"136","author":"Z-B Zeng","year":"1994","journal-title":"Genetics"},{"key":"pcbi.1009923.ref009","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1038\/hdy.1992.131","article-title":"A simple regression method for mapping quantitative trait loci in line crosses using flanking markers","volume":"69","author":"CS Haley","year":"1992","journal-title":"Heredity"},{"key":"pcbi.1009923.ref010","unstructured":"Beavis WD. 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