{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T23:34:41Z","timestamp":1775000081290,"version":"3.50.1"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"23","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Of many statistical methods developed to date for quantitative trait locus (QTL) analysis, only a limited subset are available in public software allowing their exploration, comparison and practical application by researchers. We have developed QGene 4.0, a plug-in platform that allows execution and comparison of a variety of modern QTL-mapping methods and supports third-party addition of new ones. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable.<\/jats:p>\n               <jats:p>Availability: Software and documentation are available at http:\/\/coding.plantpath.ksu.edu\/qgene. Source code is available on request.<\/jats:p>\n               <jats:p>Contact: \u00a0jcn@ksu.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn523","type":"journal-article","created":{"date-parts":[[2008,10,22]],"date-time":"2008-10-22T00:23:54Z","timestamp":1224635034000},"page":"2788-2789","source":"Crossref","is-referenced-by-count":333,"title":["QGene 4.0, an extensible Java QTL-analysis platform"],"prefix":"10.1093","volume":"24","author":[{"given":"Roby","family":"Joehanes","sequence":"first","affiliation":[{"name":"Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA"}]},{"given":"James C.","family":"Nelson","sequence":"additional","affiliation":[{"name":"Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA"}]}],"member":"286","published-online":{"date-parts":[[2008,10,21]]},"reference":[{"key":"2023020212234050100_B1","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1093\/bioinformatics\/btg112","article-title":"R\/qtl: QTL mapping in experimental crosses","volume":"19","author":"Broman","year":"2003","journal-title":"Bioinformatics"},{"key":"2023020212234050100_B2","doi-asserted-by":"crossref","first-page":"963","DOI":"10.1093\/genetics\/138.3.963","article-title":"Empirical threshold values for quantitative trait mapping","volume":"138","author":"Churchill","year":"1994","journal-title":"Genetics"},{"key":"2023020212234050100_B3","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":"Haley","year":"1992","journal-title":"Heredity"},{"key":"2023020212234050100_B4","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1093\/genetics\/135.1.205","article-title":"Interval mapping of multiple quantitative trait loci","volume":"135","author":"Jansen","year":"1993","journal-title":"Genetics"},{"key":"2023020212234050100_B5","doi-asserted-by":"crossref","first-page":"1111","DOI":"10.1093\/genetics\/140.3.1111","article-title":"Multiple trait analysis of genetic mapping for quantitative trait loci","volume":"140","author":"Jiang","year":"1995","journal-title":"Genetics"},{"key":"2023020212234050100_B6","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1023\/A:1018394410659","article-title":"Mapping quantitative trait loci with dominant and missing markers in various crosses from two inbred lines","volume":"101","author":"Jiang","year":"1997","journal-title":"Genetica"},{"key":"2023020212234050100_B7","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1093\/bioinformatics\/bth481","article-title":"MCQTL: multi-allelic QTL mapping in multi-cross design","volume":"21","author":"Jourjon","year":"2004","journal-title":"Bioinformatics"},{"key":"2023020212234050100_B8","doi-asserted-by":"crossref","first-page":"1203","DOI":"10.1093\/genetics\/152.3.1203","article-title":"Multiple interval mapping for quantitative trait loci","volume":"152","author":"Kao","year":"1999","journal-title":"Genetics"},{"key":"2023020212234050100_B9","doi-asserted-by":"crossref","first-page":"1137","DOI":"10.1093\/genetics\/140.3.1137","article-title":"Interval mapping of quantitative trait loci employing correlated trait complexes","volume":"140","author":"Korol","year":"1995","journal-title":"Genetics"},{"key":"2023020212234050100_B10","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1093\/bib\/bbn017","article-title":"MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences","volume":"9","author":"Kumar","year":"2008","journal-title":"Brief. 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