{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,8]],"date-time":"2025-10-08T16:25:58Z","timestamp":1759940758063,"version":"3.37.3"},"reference-count":31,"publisher":"Springer Science and Business Media LLC","issue":"1","funder":[{"DOI":"10.13039\/501100004963","name":"Seventh Framework Programme","doi-asserted-by":"publisher","award":["289974"],"award-info":[{"award-number":["289974"]}],"id":[{"id":"10.13039\/501100004963","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004963","name":"Seventh Framework Programme","doi-asserted-by":"publisher","award":["289974"],"award-info":[{"award-number":["289974"]}],"id":[{"id":"10.13039\/501100004963","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2017,12]]},"DOI":"10.1186\/s12859-016-1416-8","type":"journal-article","created":{"date-parts":[[2017,1,4]],"date-time":"2017-01-04T01:22:57Z","timestamp":1483492977000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":23,"title":["PERGOLA: fast and deterministic linkage mapping of polyploids"],"prefix":"10.1186","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2065-6202","authenticated-orcid":false,"given":"Fabian","family":"Grandke","sequence":"first","affiliation":[]},{"given":"Soumya","family":"Ranganathan","sequence":"additional","affiliation":[]},{"given":"Nikkie","family":"van Bers","sequence":"additional","affiliation":[]},{"given":"Jorn R.","family":"de Haan","sequence":"additional","affiliation":[]},{"given":"Dirk","family":"Metzler","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2017,1,4]]},"reference":[{"key":"1416_CR1","unstructured":"FAOSTAT: Food and Agriculture Organization of the United Nations. 2012. http:\/\/www.fao.org\/faostat\/en\/%23home . Accessed 2 Feb 2015."},{"issue":"1","key":"1416_CR2","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1002\/jez.1400140104","volume":"14","author":"AH Sturtevant","year":"1913","unstructured":"Sturtevant AH. The linear arrangement of six sex-linked factors in drosophila, as shown by their mode of association. J Exp Zool. 1913; 14(1):43\u201359.","journal-title":"J Exp Zool"},{"key":"1416_CR3","doi-asserted-by":"crossref","unstructured":"Hackett CA, Luo ZW. TetraploidMap: Construction of a linkage map in autotetraploid species; 94(4):358\u201359. doi:10.1093\/jhered\/esg066. Accessed 21 Jan 2013.","DOI":"10.1093\/jhered\/esg066"},{"issue":"7","key":"1416_CR4","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1093\/jhered\/esm086","volume":"98","author":"CA Hackett","year":"2007","unstructured":"Hackett CA, Milne I, Bradshaw JE, Luo Z. TetraploidMap for Windows: linkage map construction and QTL mapping in autotetraploid species. J Hered. 2007; 98(7):727\u20139.","journal-title":"J Hered"},{"issue":"8","key":"1416_CR5","doi-asserted-by":"crossref","first-page":"740","DOI":"10.1093\/bioinformatics\/17.8.740","volume":"17","author":"Y He","year":"2001","unstructured":"He Y, Xu X, Tobutt KR, Ridout MS. Polylink: to support two-point linkage analysis in autotetraploids. Bioinformatics. 2001; 17(8):740\u20131.","journal-title":"Bioinformatics"},{"key":"1416_CR6","unstructured":"R Core Team. R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing; 2015. https:\/\/www.R-project.org\/ ."},{"issue":"1","key":"1416_CR7","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1186\/1471-2105-13-248","volume":"13","author":"RE Voorrips","year":"2012","unstructured":"Voorrips RE, Maliepaard CA. The simulation of meiosis in diploid and tetraploid organisms using various genetic models. BMC Bioinformatics. 2012; 13(1):248.","journal-title":"BMC Bioinformatics"},{"issue":"5","key":"1416_CR8","doi-asserted-by":"crossref","first-page":"20463","DOI":"10.1371\/journal.pone.0020463","volume":"6","author":"O Gar","year":"2011","unstructured":"Gar O, Sargent DJ, Tsai CJ, Pleban T, Shalev G, Byrne DH, Zamir D. An autotetraploid linkage map of Rose (Rosa hybrida) validated using the strawberry (Fragaria vesca) genome sequence. PLoS ONE. 2011; 6(5):20463.","journal-title":"PLoS ONE"},{"issue":"1","key":"1416_CR9","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1534\/g3.113.007617","volume":"4","author":"DJ Bertioli","year":"2013","unstructured":"Bertioli DJ, Ozias-Akins P, Chu Y, Dantas KM, Santos SP, Gouvea E, Guimaraes PM, Leal-Bertioli SCM, Knapp SJ, Moretzsohn MC. The use of SNP markers for linkage mapping in diploid and tetraploid peanuts. G3: Genes-Genomes-Genet. 2013; 4(1):89\u201396.","journal-title":"G3: Genes-Genomes-Genet"},{"issue":"11","key":"1416_CR10","doi-asserted-by":"crossref","first-page":"2357","DOI":"10.1534\/g3.115.019646","volume":"5","author":"AN Massa","year":"2015","unstructured":"Massa AN, Manrique-Carpintero NC, Coombs JJ, Zarka DG, Boone AE, Kirk WW, Hackett CA, Bryan GJ, Douches DS. Genetic linkage mapping of economically important traits in cultivated tetraploid potato (solanum tuberosum l.)G3: Genes-Genomes-Genet. 2015; 5(11):2357\u201364.","journal-title":"G3: Genes-Genomes-Genet"},{"issue":"594","key":"1416_CR11","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1098\/rstb.1947.0006","volume":"233","author":"RA Fisher","year":"1947","unstructured":"Fisher RA. The theory of linkage in polysomic inheritance. Philos Trans R Soc.Lond Ser B Biol Sci. 1947; 233(594):55\u201387.","journal-title":"Philos Trans R Soc.Lond Ser B Biol Sci"},{"issue":"4","key":"1416_CR12","doi-asserted-by":"crossref","first-page":"1083","DOI":"10.1534\/genetics.112.145581","volume":"193","author":"M Rehmsmeier","year":"2013","unstructured":"Rehmsmeier M. A computational approach to developing mathematical models of polyploid meiosis. Genetics. 2013; 193(4):1083\u201394.","journal-title":"Genetics"},{"issue":"3","key":"1416_CR13","doi-asserted-by":"crossref","first-page":"1339","DOI":"10.1093\/genetics\/159.3.1339","volume":"159","author":"SS Wu","year":"2001","unstructured":"Wu SS, Wu R, Ma CX, Zeng ZB, Yang MCK, Casella G. A multivalent pairing model of linkage analysis in autotetraploids. Genetics. 2001; 159(3):1339\u201350.","journal-title":"Genetics"},{"issue":"18","key":"1416_CR14","doi-asserted-by":"crossref","first-page":"7040","DOI":"10.1073\/pnas.0304482101","volume":"101","author":"ZW Luo","year":"2004","unstructured":"Luo ZW, Zhang RM, Kearsey MJ. Theoretical basis for genetic linkage analysis in autotetraploid species. Proc Natl Acad Sci U S A. 2004; 101(18):7040\u20135.","journal-title":"Proc Natl Acad Sci U S A."},{"key":"1416_CR15","volume-title":"Modern Genetic Analysis","author":"AJ Griffiths","year":"1999","unstructured":"Griffiths AJ, Gelbart WM, Miller JH, Lewontin RC, Griffiths AJ, Gelbart WM, Miller JH, Lewontin RC. Modern Genetic Analysis. New York: W. H. Freeman; 1999."},{"issue":"2","key":"1416_CR16","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1007\/BF02982683","volume":"32","author":"K Mather","year":"1936","unstructured":"Mather K. Segregation and linkage in autotetraploids. J Genet. 1936; 32(2):287\u2013314.","journal-title":"J Genet"},{"issue":"1-4","key":"1416_CR17","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.aquaculture.2005.11.031","volume":"255","author":"DA Chistiakov","year":"2006","unstructured":"Chistiakov DA, Hellemans B, Volckaert FAM. Microsatellites and their genomic distribution, evolution, function and applications: a review with special reference to fish genetics. Aquaculture. 2006; 255(1-4):1\u201329.","journal-title":"Aquaculture"},{"issue":"6","key":"1416_CR18","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1093\/bib\/bbp045","volume":"10","author":"J Cheema","year":"2009","unstructured":"Cheema J, Dicks J. Computational approaches and software tools for genetic linkage map estimation in plants. Brief Bioinform. 2009; 10(6):595\u2013608.","journal-title":"Brief Bioinform"},{"key":"1416_CR19","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1093\/bioinformatics\/17.suppl_1.S22","volume":"17 Suppl 1","author":"Z Bar-Joseph","year":"2001","unstructured":"Bar-Joseph Z, Gifford DK, Jaakkola TS. Fast optimal leaf ordering for hierarchical clustering. Bioinformatics (Oxford, England). 2001; 17 Suppl 1:22\u20139.","journal-title":"Bioinformatics (Oxford, England)"},{"key":"1416_CR20","volume-title":"Statistical Genomics: Linkage, Mapping, and QTL Analysis","author":"BH Liu","year":"1998","unstructured":"Liu BH. Statistical Genomics: Linkage, Mapping, and QTL Analysis. Boca Raton: CRC Press LLC; 1998, p. 611."},{"key":"1416_CR21","volume-title":"Statistical Methods for QTL Mapping","author":"Z Chen","year":"2013","unstructured":"Chen Z. Statistical Methods for QTL Mapping. Boca Raton: CRC Press; 2013."},{"key":"1416_CR22","first-page":"10","volume":"33","author":"J Van Ooijen","year":"2006","unstructured":"Van Ooijen J. Joinmap\u00ae; 4, software for the calculation of genetic linkage maps in experimental populations. Kyazma BV Wageningen. 2006; 33:10\u20131371.","journal-title":"Kyazma BV Wageningen"},{"issue":"2","key":"1416_CR23","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1016\/0888-7543(87)90010-3","volume":"1","author":"ES Lander","year":"1987","unstructured":"Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L. MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics. 1987; 1(2):174\u201381.","journal-title":"Genomics"},{"issue":"7","key":"1416_CR24","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1093\/bioinformatics\/btg112","volume":"19","author":"KW Broman","year":"2003","unstructured":"Broman KW, Wu H, Sen S, Churchill GA. R\/qtl: QTL mapping in experimental crosses. Bioinformatics (Oxford, England). 2003; 19(7):889\u201390.","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"346","key":"1416_CR25","first-page":"440","volume":"69","author":"FB Baker","year":"1974","unstructured":"Baker FB. Stability of two hierarchical grouping techniques case i: sensitivity to data errors. J Am Stat Assoc. 1974; 69(346):440\u20135.","journal-title":"J Am Stat Assoc"},{"issue":"2","key":"1416_CR26","doi-asserted-by":"crossref","first-page":"33","DOI":"10.2307\/1217208","volume":"11","author":"RR Sokal","year":"1962","unstructured":"Sokal RR, Rohlf FJ. The comparison of dendrograms by objective methods. Taxon. 1962; 11(2):33\u201340.","journal-title":"Taxon"},{"issue":"2","key":"1416_CR27","doi-asserted-by":"crossref","first-page":"899","DOI":"10.1534\/genetics.104.035816","volume":"170","author":"R Wu","year":"2005","unstructured":"Wu R, Ma CX. A general framework for statistical linkage analysis in multivalent tetraploids. Genetics. 2005; 170(2):899\u2013907.","journal-title":"Genetics"},{"issue":"4","key":"1416_CR28","doi-asserted-by":"crossref","first-page":"2149","DOI":"10.1534\/genetics.105.047316","volume":"171","author":"ZW Luo","year":"2005","unstructured":"Luo ZW. Commentary on Wu and Ma. Genetics. 2005; 171(4):2149\u201350.","journal-title":"Genetics"},{"issue":"3-4","key":"1416_CR29","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1080\/00087114.2000.10589206","volume":"53","author":"GI Lavia","year":"2000","unstructured":"Lavia GI. Chromosome studies in wild Arachis(Leguminosae). Caryologia. 2000; 53(3-4):277\u201381.","journal-title":"Caryologia"},{"issue":"22","key":"1416_CR30","doi-asserted-by":"crossref","first-page":"3718","DOI":"10.1093\/bioinformatics\/btv428","volume":"31","author":"T Galili","year":"2015","unstructured":"Galili T. dendextend: an r package for visualizing, adjusting and comparing trees of hierarchical clustering. Bioinformatics. 2015; 31(22):3718\u201320.","journal-title":"Bioinformatics"},{"issue":"5","key":"1416_CR31","doi-asserted-by":"crossref","first-page":"63939","DOI":"10.1371\/journal.pone.0063939","volume":"8","author":"CA Hackett","year":"2013","unstructured":"Hackett CA, McLean K, Bryan GJ. Linkage analysis and QTL mapping using SNP dosage data in a tetraploid potato mapping population. PLoS ONE. 2013; 8(5):63939.","journal-title":"PLoS ONE"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1416-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,7,20]],"date-time":"2022-07-20T14:43:44Z","timestamp":1658328224000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-016-1416-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,1,4]]},"references-count":31,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["1416"],"URL":"https:\/\/doi.org\/10.1186\/s12859-016-1416-8","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2017,1,4]]},"article-number":"12"}}