{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:49Z","timestamp":1772138089669,"version":"3.50.1"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2018,5,2]],"date-time":"2018-05-02T00:00:00Z","timestamp":1525219200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"TKI projects","award":["BO-26.03-002-001"],"award-info":[{"award-number":["BO-26.03-002-001"]}]},{"name":"Novel genetic and genomic tools for polyploid crops","award":["BO-26.03-009-004"],"award-info":[{"award-number":["BO-26.03-009-004"]}]},{"name":"Novel genetic and genomic tools for polyploid crops","award":["BO-50-002-022"],"award-info":[{"award-number":["BO-50-002-022"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Polyploid species carry more than two copies of each chromosome, a condition found in many of the world\u2019s most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realize all the opportunities offered by modern genotyping platforms for genetic research and breeding in polyploid crops.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>polymapR is an R package for genetic linkage analysis and integrated genetic map construction from bi-parental populations of outcrossing autopolyploids. It can currently analyse triploid, tetraploid and hexaploid marker datasets and is applicable to various crops including potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato or kiwifruit. It can detect, estimate and correct for preferential chromosome pairing, and has been tested on high-density marker datasets from potato, rose and chrysanthemum, generating high-density integrated linkage maps in all of these crops.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>polymapR is freely available under the general public license from the Comprehensive R Archive Network (CRAN) at http:\/\/cran.r-project.org\/package=polymapR.<\/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\/bty371","type":"journal-article","created":{"date-parts":[[2018,5,1]],"date-time":"2018-05-01T15:09:42Z","timestamp":1525187382000},"page":"3496-3502","source":"Crossref","is-referenced-by-count":92,"title":["polymapR\u2014linkage analysis and genetic map construction from F1 populations of outcrossing polyploids"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0665-6508","authenticated-orcid":false,"given":"Peter M","family":"Bourke","sequence":"first","affiliation":[{"name":"Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands"}]},{"given":"Geert","family":"van Geest","sequence":"additional","affiliation":[{"name":"Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands"},{"name":"Deliflor Chrysanten B.V, Maasdijk, BS, The Netherlands"}]},{"given":"Roeland E","family":"Voorrips","sequence":"additional","affiliation":[{"name":"Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands"}]},{"given":"Johannes","family":"Jansen","sequence":"additional","affiliation":[{"name":"Biometris, Wageningen University & Research, Wageningen, PB, The Netherlands"}]},{"given":"Twan","family":"Kranenburg","sequence":"additional","affiliation":[{"name":"Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands"}]},{"given":"Arwa","family":"Shahin","sequence":"additional","affiliation":[{"name":"Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands"},{"name":"Van Zanten Breeding B. V, Rijsenhout, EW, The Netherlands"}]},{"given":"Richard G F","family":"Visser","sequence":"additional","affiliation":[{"name":"Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands"}]},{"given":"Paul","family":"Arens","sequence":"additional","affiliation":[{"name":"Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands"}]},{"given":"Marinus J M","family":"Smulders","sequence":"additional","affiliation":[{"name":"Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands"}]},{"given":"Chris","family":"Maliepaard","sequence":"additional","affiliation":[{"name":"Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands"}]}],"member":"286","published-online":{"date-parts":[[2018,5,2]]},"reference":[{"key":"2023012712415868300_bty371-B1","doi-asserted-by":"crossref","DOI":"10.1002\/9781118313718","volume-title":"Principles of Plant Genetics and Breeding","author":"Acquaah","year":"2012"},{"key":"2023012712415868300_bty371-B2","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1007\/s00412-015-0571-4","article-title":"The challenge of evolving stable polyploidy: could an increase in \u201ccrossover interference distance\u201d play a central role?","volume":"125","author":"Bomblies","year":"2016","journal-title":"Chromosoma"},{"key":"2023012712415868300_bty371-B3","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1111\/tpj.13496","article-title":"Partial preferential chromosome pairing is genotype dependent in tetraploid rose","volume":"90","author":"Bourke","year":"2017","journal-title":"Plant J"},{"key":"2023012712415868300_bty371-B4","doi-asserted-by":"crossref","first-page":"2211","DOI":"10.1007\/s00122-016-2768-1","article-title":"Integrating haplotype-specific linkage maps in tetraploid species using SNP markers","volume":"129","author":"Bourke","year":"2016","journal-title":"Theor. Appl. Genet"},{"key":"2023012712415868300_bty371-B5","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1534\/genetics.115.181008","article-title":"The double reduction landscape in tetraploid potato as revealed by a high-density linkage map","volume":"201","author":"Bourke","year":"2015","journal-title":"Genetics"},{"key":"2023012712415868300_bty371-B6","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1007\/s00122-007-0659-1","article-title":"QTL mapping of yield, agronomic and quality traits in tetraploid potato (Solanum tuberosum subsp. tuberosum)","volume":"116","author":"Bradshaw","year":"2008","journal-title":"Theor. Appl. Genet"},{"key":"2023012712415868300_bty371-B7","volume-title":"Algorithms for Minimizing Without Derivatives","author":"Brent","year":"1973"},{"key":"2023012712415868300_bty371-B8","first-page":"1","article-title":"The igraph software package for complex network research","volume":"1695","author":"Csardi","year":"2006","journal-title":"InterJ. Complex Syst"},{"key":"2023012712415868300_bty371-B9","doi-asserted-by":"crossref","first-page":"e36347","DOI":"10.1371\/journal.pone.0036347","article-title":"Integration of two diploid potato linkage maps with the potato genome sequence","volume":"7","author":"Felcher","year":"2012","journal-title":"PLoS One"},{"key":"2023012712415868300_bty371-B10","doi-asserted-by":"crossref","first-page":"e20463","DOI":"10.1371\/journal.pone.0020463","article-title":"An autotetraploid linkage map of rose (Rosa hybrida) validated using the strawberry (Fragaria vesca) genome sequence","volume":"6","author":"Gar","year":"2011","journal-title":"PLoS One"},{"key":"2023012712415868300_bty371-B11","doi-asserted-by":"crossref","first-page":"12.","DOI":"10.1186\/s12859-016-1416-8","article-title":"PERGOLA: fast and deterministic linkage mapping of polyploids","volume":"18","author":"Grandke","year":"2017","journal-title":"BMC Bioinformatics"},{"key":"2023012712415868300_bty371-B12","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1093\/jhered\/esg066","article-title":"TetraploidMap: construction of a linkage map in autotetraploid species","volume":"94","author":"Hackett","year":"2003","journal-title":"J. Hered"},{"key":"2023012712415868300_bty371-B13","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1093\/jhered\/esx022","article-title":"TetraploidSNPMap: software for linkage analysis and QTL mapping in autotetraploid populations using SNP dosage data","volume":"108","author":"Hackett","year":"2017","journal-title":"J. Hered"},{"key":"2023012712415868300_bty371-B14","doi-asserted-by":"crossref","first-page":"e63939.","DOI":"10.1371\/journal.pone.0063939","article-title":"Linkage analysis and QTL mapping using SNP dosage data in a tetraploid potato mapping population","volume":"8","author":"Hackett","year":"2013","journal-title":"PLoS One"},{"key":"2023012712415868300_bty371-B15","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1093\/jhered\/esm086","article-title":"TetraploidMap for Windows: linkage map construction and QTL mapping in autotetraploid species","volume":"98","author":"Hackett","year":"2007","journal-title":"J. Hered"},{"key":"2023012712415868300_bty371-B16","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1007\/BF02984197","article-title":"Theoretical genetics of autopolyploids","volume":"22","author":"Haldane","year":"1930","journal-title":"J. Genet"},{"key":"2023012712415868300_bty371-B17","doi-asserted-by":"crossref","first-page":"249","DOI":"10.3389\/fpls.2015.00249","article-title":"Using RNA-Seq to assemble a rose transcriptome with more than 13, 000 full-length expressed genes and to develop the WagRhSNP 68k Axiom SNP array for rose (Rosa L.)","volume":"6","author":"Koning-Boucoiran","year":"2015","journal-title":"Front. Plant. Sci"},{"key":"2023012712415868300_bty371-B18","doi-asserted-by":"crossref","first-page":"e84329.","DOI":"10.1371\/journal.pone.0084329","article-title":"Development of an alfalfa SNP array and its use to evaluate patterns of population structure and linkage disequilibrium","volume":"9","author":"Li","year":"2014","journal-title":"PLoS One"},{"key":"2023012712415868300_bty371-B19","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1007\/s11032-016-0443-5","article-title":"Construction of a SNP and SSR linkage map in autotetraploid blueberry using genotyping by sequencing","volume":"36","author":"Mccallum","year":"2016","journal-title":"Mol. Breeding"},{"key":"2023012712415868300_bty371-B20","author":"Microsoft Corporation","year":"2017"},{"key":"2023012712415868300_bty371-B21","doi-asserted-by":"crossref","first-page":"2117","DOI":"10.1007\/s00122-016-2761-8","article-title":"A rapid marker ordering approach for high-density genetic linkage maps in experimental autotetraploid populations using multidimensional scaling","volume":"129","author":"Preedy","year":"2016","journal-title":"Theor. Appl. Genet"},{"key":"2023012712415868300_bty371-B22","author":"R Core Team","year":"2016"},{"key":"2023012712415868300_bty371-B23","doi-asserted-by":"crossref","first-page":"1780","DOI":"10.2135\/cropsci2008.02.0101","article-title":"Genetic mapping of persistence in tetraploid alfalfa","volume":"48","author":"Robins","year":"2008","journal-title":"Crop Sci"},{"key":"2023012712415868300_bty371-B24","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1093\/genetics\/165.3.1533","article-title":"Partial diploidization of meiosis in autotetraploid Arabidopsis thaliana","volume":"165","author":"Santos","year":"2003","journal-title":"Genetics"},{"key":"2023012712415868300_bty371-B25","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1007\/s00122-016-2845-5","article-title":"Automated tetraploid genotype calling by hierarchical clustering","volume":"130","author":"Schmitz Carley","year":"2017","journal-title":"Theor. Appl. Genet"},{"key":"2023012712415868300_bty371-B26","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1111\/j.1365-313X.1993.00739.x","article-title":"Construction of integrated genetic linkage maps by means of a new computer package: join Map","volume":"3","author":"Stam","year":"1993","journal-title":"Plant J"},{"key":"2023012712415868300_bty371-B27","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0065-2660(08)60490-3","article-title":"Types of polyploids: their classification and significance","volume":"1","author":"Stebbins","year":"1947","journal-title":"Adv. Genet"},{"key":"2023012712415868300_bty371-B28","doi-asserted-by":"crossref","first-page":"2527","DOI":"10.1007\/s00122-017-2974-5","article-title":"An ultra-dense integrated linkage map for hexaploid chrysanthemum enables multi-allelic QTL analysis","volume":"130","author":"Van Geest","year":"2017","journal-title":"Theor. Appl. Genet"},{"key":"2023012712415868300_bty371-B29","doi-asserted-by":"crossref","first-page":"585.","DOI":"10.1186\/s12864-017-4003-0","article-title":"Conclusive evidence for hexasomic inheritance in chrysanthemum based on analysis of a 183 k SNP array","volume":"18","author":"Van Geest","year":"2017","journal-title":"BMC Genomics"},{"key":"2023012712415868300_bty371-B30","author":"Van Ooijen","year":"2006"},{"key":"2023012712415868300_bty371-B31","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9781139003889","volume-title":"Genetic Mapping in Experimental Populations","author":"Van Ooijen","year":"2013"},{"key":"2023012712415868300_bty371-B32","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1186\/1471-2105-12-172","article-title":"Genotype calling in tetraploid species from bi-allelic marker data using mixture models","volume":"12","author":"Voorrips","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2023012712415868300_bty371-B33","doi-asserted-by":"crossref","first-page":"248.","DOI":"10.1186\/1471-2105-13-248","article-title":"The simulation of meiosis in diploid and tetraploid organisms using various genetic models","volume":"13","author":"Voorrips","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2023012712415868300_bty371-B34","doi-asserted-by":"crossref","first-page":"2387","DOI":"10.1007\/s00122-015-2593-y","article-title":"Development and analysis of a 20K SNP array for potato (Solanum tuberosum): an insight into the breeding history","volume":"128","author":"Vos","year":"2015","journal-title":"Theor. Appl. Genet"},{"key":"2023012712415868300_bty371-B35","doi-asserted-by":"crossref","first-page":"16052","DOI":"10.1038\/hortres.2016.52","article-title":"High-density SNP-based genetic maps for the parents of an outcrossed and a selfed tetraploid garden rose cross, inferred from admixed progeny using the 68k rose SNP array","volume":"3","author":"Vukosavljev","year":"2016","journal-title":"Hortic Res"},{"key":"2023012712415868300_bty371-B36","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1006\/tpbi.2002.1608","article-title":"A bivalent polyploid model for linkage analysis in outcrossing tetraploids","volume":"62","author":"Wu","year":"2002","journal-title":"Theor. Popul. Biol"},{"key":"2023012712415868300_bty371-B37","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1534\/genetics.115.185579","article-title":"Probabilistic multilocus haplotype reconstruction in outcrossing tetraploids","volume":"203","author":"Zheng","year":"2016","journal-title":"Genetics"},{"key":"2023012712415868300_bty371-B38","first-page":"919","article-title":"AlloMap6: an R package for genetic linkage analysis in allohexaploids","volume":"18","author":"Zhu","year":"2016","journal-title":"Brief Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/20\/3496\/48918976\/bioinformatics_34_20_3496.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/20\/3496\/48918976\/bioinformatics_34_20_3496.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T08:34:53Z","timestamp":1674808493000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/20\/3496\/4990829"}},"subtitle":[],"editor":[{"given":"Oliver","family":"Stegle","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,5,2]]},"references-count":38,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2018,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty371","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/228817","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,10,15]]},"published":{"date-parts":[[2018,5,2]]}}}