{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T19:52:52Z","timestamp":1772826772519,"version":"3.50.1"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2017,11,2]],"date-time":"2017-11-02T00:00:00Z","timestamp":1509580800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Bulked segregant analysis combined with next generation sequencing has proven to be a simple and efficient approach for fast mapping of quantitative trait loci (QTLs). However, how to estimate the proportion of phenotypic variance explained by a QTL (or termed QTL heritability) in such pooled QTL mapping is an unsolved problem.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>In this paper, we propose a method called PQHE to estimate QTL heritability using pooled sequencing data obtained under different experimental designs. Simulation studies indicated that our method is correct and feasible. Four practical examples from rice and yeast are demonstrated, each representing a different situation.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The R scripts of our method are open source under GPLv3 license at http:\/\/genetics.fafu.edu.cn\/PQHE or https:\/\/github.com\/biotangweiqi\/PQHE. The R scripts require the R package rootSolve.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx703","type":"journal-article","created":{"date-parts":[[2017,11,1]],"date-time":"2017-11-01T21:35:18Z","timestamp":1509572118000},"page":"978-984","source":"Crossref","is-referenced-by-count":13,"title":["Estimation of QTL heritability based on pooled sequencing data"],"prefix":"10.1093","volume":"34","author":[{"given":"Weiqi","family":"Tang","sequence":"first","affiliation":[{"name":"Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China"},{"name":"Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China"}]},{"given":"Likun","family":"Huang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China"},{"name":"Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China"}]},{"given":"Suhong","family":"Bu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China"},{"name":"Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China"}]},{"given":"Xuzhang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China"},{"name":"Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China"}]},{"given":"Weiren","family":"Wu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China"},{"name":"Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China"}]}],"member":"286","published-online":{"date-parts":[[2017,11,2]]},"reference":[{"key":"2023012712572417300_btx703-B1","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1007\/s00122-014-2452-2","article-title":"Genetic mapping of the nulliplex-branch gene (gb_nb1) in cotton using next-generation sequencing, TAG","volume":"128","author":"Chen","year":"2015","journal-title":"Theor. Appl. Genet. Theor. Angew. Genet"},{"key":"2023012712572417300_btx703-B2","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1515\/sagmb-2014-0007","article-title":"A hidden Markov-model for gene mapping based on whole-genome next generation sequencing data","volume":"14","author":"Claesen","year":"2015","journal-title":"Stat. Appl. Genet. Mol. Biol"},{"key":"2023012712572417300_btx703-B3","doi-asserted-by":"crossref","first-page":"e55133.","DOI":"10.1371\/journal.pone.0055133","article-title":"Simultaneous mapping of multiple gene loci with pooled segregants","volume":"8","author":"Claesen","year":"2013","journal-title":"PLoS One"},{"key":"2023012712572417300_btx703-B4","doi-asserted-by":"crossref","first-page":"2317","DOI":"10.1093\/molbev\/msv112","article-title":"Ecological and genetic barriers differentiate natural populations of Saccharomyces cerevisiae","volume":"32","author":"Clowers","year":"2015","journal-title":"Mol. Biol. Evol"},{"key":"2023012712572417300_btx703-B5","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1093\/dnares\/dsv004","article-title":"Deploying QTL-seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea","volume":"22","author":"Das","year":"2015","journal-title":"DNA Res"},{"key":"2023012712572417300_btx703-B6","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1186\/1471-2164-15-207","article-title":"Improved linkage analysis of Quantitative Trait Loci using bulk segregants unveils a novel determinant of high ethanol tolerance in yeast","volume":"15","author":"Duitama","year":"2014","journal-title":"BMC Genomics"},{"key":"2023012712572417300_btx703-B7","doi-asserted-by":"crossref","first-page":"S8","DOI":"10.1186\/1471-2105-13-S6-S8","article-title":"High-resolution genetic mapping with pooled sequencing","volume":"13","author":"Edwards","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2023012712572417300_btx703-B8","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1038\/nature08923","article-title":"Dissection of genetically complex traits with extremely large pools of yeast segregants","volume":"464","author":"Ehrenreich","year":"2010","journal-title":"Nature"},{"key":"2023012712572417300_btx703-B9","doi-asserted-by":"crossref","first-page":"e1002570.","DOI":"10.1371\/journal.pgen.1002570","article-title":"Genetic architecture of highly complex chemical resistance traits across four yeast strains","volume":"8","author":"Ehrenreich","year":"2012","journal-title":"PLoS Genet"},{"key":"2023012712572417300_btx703-B10","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1093\/aob\/mcv080","article-title":"Leaf shape evolution has a similar genetic architecture in three edaphic specialists within the Mimulus guttatus species complex","volume":"116","author":"Ferris","year":"2015","journal-title":"Ann. Bot"},{"key":"2023012712572417300_btx703-B11","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1111\/mec.13004","article-title":"The extent and genetic basis of phenotypic divergence in life history traits in Mimulus guttatus","volume":"24","author":"Friedman","year":"2015","journal-title":"Mol. Ecol"},{"key":"2023012712572417300_btx703-B12","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1089\/cmb.2014.0258","article-title":"A nonhomogeneous hidden markov model for gene mapping based on next-generation sequencing data","volume":"22","author":"Ghavidel","year":"2015","journal-title":"J. Comput. Biol"},{"key":"2023012712572417300_btx703-B13","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1534\/genetics.112.142067","article-title":"The genetic architecture of biofilm formation in a clinical isolate of Saccharomyces cerevisiae","volume":"193","author":"Granek","year":"2013","journal-title":"Genetics"},{"key":"2023012712572417300_btx703-B14","doi-asserted-by":"crossref","first-page":"1593","DOI":"10.1534\/g3.115.017665","article-title":"Shared genomic regions between derivatives of a large segregating population of maize identified using bulked segregant analysis sequencing and traditional linkage analysis","volume":"5","author":"Haase","year":"2015","journal-title":"G3 Genes Genomes Genet"},{"key":"2023012712572417300_btx703-B15","doi-asserted-by":"crossref","first-page":"3496","DOI":"10.1093\/gbe\/evv238","article-title":"Bulk segregant analysis reveals the genetic basis of a natural trait variation in fission yeast","volume":"7","author":"Hu","year":"2015","journal-title":"Genome Biol. Evol"},{"key":"2023012712572417300_btx703-B16","doi-asserted-by":"crossref","first-page":"1329","DOI":"10.1007\/s00122-015-2509-x","article-title":"Rapid and reliable identification of tomato fruit weight and locule number loci by QTL-seq, TAG","volume":"128","author":"Illa-Berenguer","year":"2015","journal-title":"Theor. Appl. Genet. Theor. Angew. Genet"},{"key":"2023012712572417300_btx703-B17","doi-asserted-by":"crossref","first-page":"2143","DOI":"10.1007\/s00122-015-2573-2","article-title":"Cytosolic glutamine synthetase is important for photosynthetic efficiency and water use efficiency in potato as revealed by high-throughput sequencing QTL analysis","volume":"128","author":"Kaminski","year":"2015","journal-title":"Theor. Appl. Genet"},{"key":"2023012712572417300_btx703-B18","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1007\/s11540-015-9314-4","article-title":"Next generation sequencing bulk segregant analysis of potato support that differential flux into the cholesterol and stigmasterol metabolite pools is important for steroidal glycoalkaloid content","volume":"59","author":"Kaminski","year":"2016","journal-title":"Potato Res"},{"key":"2023012712572417300_btx703-B19","doi-asserted-by":"crossref","first-page":"1491","DOI":"10.1007\/s00122-014-2313-z","article-title":"QTL-seq identifies an early flowering QTL located near flowering locus T in cucumber","volume":"127","author":"Lu","year":"2014","journal-title":"TAG Theor. Appl. Genet. Theor. Angew. Genet"},{"key":"2023012712572417300_btx703-B20","doi-asserted-by":"crossref","first-page":"e1002255.","DOI":"10.1371\/journal.pcbi.1002255","article-title":"The statistics of bulk segregant analysis using next generation sequencing","volume":"7","author":"Magwene","year":"2011","journal-title":"PLoS Comput. Biol"},{"key":"2023012712572417300_btx703-B21","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1146\/annurev.genom.9.081307.164359","article-title":"Next-generation DNA sequencing methods","volume":"9","author":"Mardis","year":"2008","journal-title":"Annu. Rev. Genomics Hum. Genet"},{"key":"2023012712572417300_btx703-B22","doi-asserted-by":"crossref","first-page":"5.","DOI":"10.1186\/s13068-015-0421-x","article-title":"Polygenic analysis and targeted improvement of the complex trait of high acetic acid tolerance in the yeast Saccharomyces cerevisiae","volume":"9","author":"Meijnen","year":"2016","journal-title":"Biotechnol. Biofuels"},{"key":"2023012712572417300_btx703-B23","doi-asserted-by":"crossref","first-page":"9828","DOI":"10.1073\/pnas.88.21.9828","article-title":"Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations","volume":"88","author":"Michelmore","year":"1991","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023012712572417300_btx703-B24","doi-asserted-by":"crossref","first-page":"927","DOI":"10.1111\/pbi.12686","article-title":"QTL-seq approach identified genomic regions and diagnostic markers for rust and late leaf spot resistance in groundnut (Arachis hypogaea L.)","volume":"15","author":"Pandey","year":"2016","journal-title":"Plant Biotechnol. J"},{"key":"2023012712572417300_btx703-B25","doi-asserted-by":"crossref","first-page":"e1003548","DOI":"10.1371\/journal.pgen.1003548","article-title":"Comparative polygenic analysis of maximal ethanol accumulation capacity and tolerance to high ethanol levels of cell proliferation in yeast","volume":"9","author":"Pais","year":"2013","journal-title":"PLoS Genet"},{"key":"2023012712572417300_btx703-B26","doi-asserted-by":"crossref","first-page":"e1005806.","DOI":"10.1371\/journal.pgen.1005806","article-title":"Quantitative genetics identifies cryptic genetic variation involved in the paternal regulation of seed development","volume":"12","author":"Pires","year":"2016","journal-title":"PLoS Genet"},{"key":"2023012712572417300_btx703-B27","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1534\/genetics.112.140053","article-title":"APJ1 and GRE3 homologs work in concert to allow growth in xylose in a natural Saccharomyces sensu stricto hybrid yeast","volume":"191","author":"Schwartz","year":"2012","journal-title":"Genetics"},{"key":"2023012712572417300_btx703-B28","doi-asserted-by":"crossref","first-page":"1183","DOI":"10.1111\/pbi.12470","article-title":"Next-generation sequencing for identification of candidate genes for Fusarium wilt and sterility mosaic disease in pigeonpea (Cajanus cajan)","volume":"14","author":"Singh","year":"2016","journal-title":"Plant Biotechnol. J"},{"key":"2023012712572417300_btx703-B29","doi-asserted-by":"crossref","first-page":"2110","DOI":"10.1111\/pbi.12567","article-title":"QTL-seq for rapid identification of candidate genes for 100-seed weight and root\/total plant dry weight ratio under rainfed conditions in chickpea","volume":"14","author":"Singh","year":"2016","journal-title":"Plant Biotechnol. J"},{"key":"2023012712572417300_btx703-B30","doi-asserted-by":"crossref","first-page":"975","DOI":"10.1101\/gr.131698.111","article-title":"Identification of novel causative genes determining the complex trait of high ethanol tolerance in yeast using pooled-segregant whole-genome sequence analysis","volume":"22","author":"Swinnen","year":"2012","journal-title":"Genome Res"},{"key":"2023012712572417300_btx703-B31","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1111\/tpj.12105","article-title":"QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations","volume":"74","author":"Takagi","year":"2013","journal-title":"Plant J"},{"key":"2023012712572417300_btx703-B32","doi-asserted-by":"crossref","first-page":"e1004913","DOI":"10.1371\/journal.pgen.1004913","article-title":"Genetic mapping of MAPK-mediated complex traits across S. cerevisiae","volume":"11","author":"Treusch","year":"2015","journal-title":"PLoS Genet"},{"key":"2023012712572417300_btx703-B33","doi-asserted-by":"crossref","first-page":"e1003693","DOI":"10.1371\/journal.pgen.1003693","article-title":"QTL analysis of high thermotolerance with superior and downgraded parental yeast strains reveals new minor QTLs and converges on novel causative alleles involved in RNA processing","volume":"9","author":"Yang","year":"2013","journal-title":"PLoS Genet"},{"key":"2023012712572417300_btx703-B34","doi-asserted-by":"crossref","first-page":"e68433","DOI":"10.1371\/journal.pone.0068433","article-title":"Mapping of quantitative trait loci underlying cold tolerance in rice seedlings via high-throughput sequencing of pooled extremes","volume":"8","author":"Yang","year":"2013","journal-title":"PLoS One"},{"key":"2023012712572417300_btx703-B35","doi-asserted-by":"crossref","first-page":"4177","DOI":"10.1111\/mec.13768","article-title":"Extreme QTL mapping of germination speed in Arabidopsis thaliana","volume":"25","author":"Yuan","year":"2016","journal-title":"Mol. Ecol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/6\/978\/48914545\/bioinformatics_34_6_978.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/6\/978\/48914545\/bioinformatics_34_6_978.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,27]],"date-time":"2023-08-27T21:26:30Z","timestamp":1693171590000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/6\/978\/4587583"}},"subtitle":[],"editor":[{"given":"Oliver","family":"Stegle","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,11,2]]},"references-count":35,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2018,3,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx703","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,3,15]]},"published":{"date-parts":[[2017,11,2]]}}}