{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T09:30:05Z","timestamp":1775727005712,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1012483","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,10,4]],"date-time":"2024-10-04T00:00:00Z","timestamp":1728000000000}}],"reference-count":39,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2024,9,24]],"date-time":"2024-09-24T00:00:00Z","timestamp":1727136000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Maritime and Fisheries Fund (EMFF) and the French Government","award":["FEA470019FA1000016"],"award-info":[{"award-number":["FEA470019FA1000016"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Triploidy is very useful in both aquaculture and some cultivated plants as the induced sterility helps to enhance growth and product quality, as well as acting as a barrier against the contamination of wild populations by escapees. To use genetic information from triploids for academic or breeding purposes, an efficient and robust method to genotype triploids is needed. We developed such a method for genotype calling from SNP arrays, and we implemented it in the R package named GenoTriplo. Our method requires no prior information on cluster positions and remains unaffected by shifted luminescence signals. The method relies on starting the clustering algorithm with an initial higher number of groups than expected from the ploidy level of the samples, followed by merging groups that are too close to each other to be considered as distinct genotypes. Accurate classification of SNPs is achieved through multiple thresholds of quality controls. We compared the performance of GenoTriplo with that of fitPoly, the only published method for triploid SNP genotyping with a free software access. This was assessed by comparing the genotypes generated by both methods for a dataset of 1232 triploid rainbow trout genotyped for 38,033 SNPs. The two methods were consistent for 89% of the genotypes, but for 26% of the SNPs, they exhibited a discrepancy in the number of different genotypes identified. For these SNPs, GenoTriplo had &gt;95% concordance with fitPoly when fitPoly genotyped better. On the contrary, when GenoTriplo genotyped better, fitPoly had less than 50% concordance with GenoTriplo. GenoTriplo was more robust with less genotyping errors. It is also efficient at identifying low-frequency genotypes in the sample set. Finally, we assessed parentage assignment based on GenoTriplo genotyping and observed significant differences in mismatch rates between the best and second-best couples, indicating high confidence in the results. GenoTriplo could also be used to genotype diploids as well as individuals with higher ploidy level by adjusting a few input parameters.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1012483","type":"journal-article","created":{"date-parts":[[2024,9,24]],"date-time":"2024-09-24T17:30:34Z","timestamp":1727199034000},"page":"e1012483","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":2,"title":["GenoTriplo: A SNP genotype calling method for triploids"],"prefix":"10.1371","volume":"20","author":[{"given":"Julien","family":"Roche","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mathieu","family":"Besson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fran\u00e7ois","family":"Allal","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pierrick","family":"Haffray","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pierre","family":"Patrice","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marc","family":"Vandeputte","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1161-3665","authenticated-orcid":true,"given":"Florence","family":"Phocas","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2024,9,24]]},"reference":[{"issue":"2","key":"pcbi.1012483.ref001","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1016\/j.pbi.2005.01.001","article-title":"Polyploidy and genome evolution in plants","volume":"8","author":"KL Adams","year":"2005","journal-title":"Current Opinion in Plant Biology"},{"issue":"1","key":"pcbi.1012483.ref002","doi-asserted-by":"crossref","first-page":"154","DOI":"10.3732\/ajb.1000258","article-title":"Discovery of natural Miscanthus (Poaceae) triploid plants in sympatric populations of Miscanthus sacchariflorus and Miscanthus sinensis in southern Japan.","volume":"98","author":"A Nishiwaki","year":"2011","journal-title":"American Journal of Botany"},{"key":"pcbi.1012483.ref003","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/j.gde.2015.11.003","article-title":"Polyploidy and genome evolution in plants","volume":"35","author":"PS Soltis","year":"2015","journal-title":"Current Opinion in Genetics & Development"},{"key":"pcbi.1012483.ref004","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1016\/B978-012301463-4\/50010-3","volume-title":"In: The Evolution of the Genome","author":"TR Gregory","year":"2005"},{"issue":"6","key":"pcbi.1012483.ref005","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1007\/BF00224192","article-title":"Induction of triploid Citrus plants from endosperm calli in vitro","volume":"80","author":"FG Gmitter","year":"1990","journal-title":"Theoret Appl Genetics"},{"issue":"2","key":"pcbi.1012483.ref006","doi-asserted-by":"crossref","first-page":"41","DOI":"10.17221\/151\/2015-CJGPB","article-title":"Breeding triploid plants: a review.t","volume":"52","author":"X Wang","year":"2016","journal-title":"Czech J GenePlant Breed"},{"issue":"3","key":"pcbi.1012483.ref007","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1577\/1548-8659(1999)128<0491:BGIAFD>2.0.CO;2","article-title":"Better Growth in All-Female Diploid and Triploid Rainbow Trout.","volume":"128","author":"RJ Sheehan","year":"1999","journal-title":"Transactions of the American Fisheries Society."},{"issue":"1","key":"pcbi.1012483.ref008","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1016\/S0044-8486(01)00861-4","article-title":"Farming triploid oysters","volume":"210","author":"JA Nell","year":"2002","journal-title":"Aquaculture"},{"issue":"3\u20134","key":"pcbi.1012483.ref009","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1016\/j.aquaculture.2009.04.036","article-title":"Polyploid fish and shellfish: Production, biology and applications to aquaculture for performance improvement and genetic containment","volume":"293","author":"F Piferrer","year":"2009","journal-title":"Aquaculture"},{"issue":"3","key":"pcbi.1012483.ref010","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1111\/raq.12092","article-title":"Effectiveness of triploidy as a management tool for reproductive containment of farmed fish: Atlantic salmon (Salmo salar) as a case study.","volume":"8","author":"TJ Benfey","year":"2016","journal-title":"Rev Aquacult."},{"issue":"1","key":"pcbi.1012483.ref011","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s11240-008-9336-6","article-title":"Endosperm culture: a novel method for triploid plant production","volume":"93","author":"TD Thomas","year":"2008","journal-title":"Plant Cell Tiss Organ Cult"},{"issue":"4","key":"pcbi.1012483.ref012","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1007\/s002990050746","article-title":"Production of triploid plants of mulberry (Morus alba L) by endosperm culture.","volume":"19","author":"TD Thomas","year":"2000","journal-title":"Plant Cell Reports"},{"issue":"1\u20134","key":"pcbi.1012483.ref013","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/0044-8486(81)90002-8","article-title":"Polyploidy induced in the American oyster, Crassostrea virginica, with cytochalasin B.","volume":"23","author":"JG Stanley","year":"1981","journal-title":"Aquaculture"},{"issue":"3A","key":"pcbi.1012483.ref014","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1051\/rnd:19800415","article-title":"Thermal induction of diploid gynogenesis and triploidy in the eggs of the rainbow trout (Salmo gairdneri Richardson).","volume":"20","author":"D. Chourrout","year":"1980","journal-title":"Reprod Nutr D\u00e9velop"},{"issue":"1\u20134","key":"pcbi.1012483.ref015","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1016\/0044-8486(83)90179-5","article-title":"Production of all-female triploid rainbow trout","volume":"30","author":"RF Lincoln","year":"1983","journal-title":"Aquaculture"},{"issue":"7","key":"pcbi.1012483.ref016","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1046\/j.1365-2109.2001.00568.x","article-title":"Covariation between diploid and triploid progenies from common breeders in rainbow trout, Oncorhynchus mykiss (Walbaum): Familial covariation between di- and triploid trout.","volume":"32","author":"JM Blanc","year":"2001","journal-title":"Aquaculture Research"},{"issue":"1","key":"pcbi.1012483.ref017","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/S0044-8486(00)00438-5","article-title":"Family differences in relative growth of diploid and triploid Atlantic salmon (Salmo salar L.).","volume":"192","author":"GW Friars","year":"2001","journal-title":"Aquaculture"},{"key":"pcbi.1012483.ref018","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1016\/j.aquaculture.2016.08.036","article-title":"Response to five generations of selection for growth performance traits in rainbow trout (Oncorhynchus mykiss).","volume":"465","author":"TD Leeds","year":"2016","journal-title":"Aquaculture"},{"key":"pcbi.1012483.ref019","article-title":"Parentage assignment with genomic markers: a major advance for understanding and exploiting genetic variation of quantitative traits in farmed aquatic animals.","author":"M Vandeputte","year":"2014","journal-title":"Front Genet"},{"issue":"13","key":"pcbi.1012483.ref020","doi-asserted-by":"crossref","first-page":"4181","DOI":"10.1093\/nar\/gkp552","article-title":"Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances","volume":"37","author":"T. LaFramboise","year":"2009","journal-title":"Nucleic Acids Research"},{"key":"pcbi.1012483.ref021","doi-asserted-by":"crossref","first-page":"104","DOI":"10.3389\/fpls.2018.00104","article-title":"Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP) Array.","volume":"9","author":"Q You","year":"2018","journal-title":"Front Plant Sci"},{"issue":"1","key":"pcbi.1012483.ref022","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1186\/s12859-018-2433-6","article-title":"A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids","volume":"19","author":"GS Pereira","year":"2018","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"pcbi.1012483.ref023","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1093\/bioinformatics\/bti741","article-title":"A genotype calling algorithm for affymetrix SNP arrays","volume":"22","author":"N Rabbee","year":"2006","journal-title":"Bioinformatics"},{"issue":"12","key":"pcbi.1012483.ref024","doi-asserted-by":"crossref","first-page":"1598","DOI":"10.1093\/bioinformatics\/bts180","article-title":"optiCall: a robust genotype-calling algorithm for rare, low-frequency and common variants","volume":"28","author":"TS Shah","year":"2012","journal-title":"Bioinformatics"},{"issue":"20","key":"pcbi.1012483.ref025","doi-asserted-by":"crossref","first-page":"2741","DOI":"10.1093\/bioinformatics\/btm443","article-title":"A genotype calling algorithm for the Illumina BeadArray platform","volume":"23","author":"YY Teo","year":"2007","journal-title":"Bioinformatics"},{"issue":"1","key":"pcbi.1012483.ref026","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s12711-020-00534-w","article-title":"Genotype calling of triploid offspring from diploid parents","volume":"52","author":"KE Grashei","year":"2020","journal-title":"Genet Sel Evol"},{"issue":"1","key":"pcbi.1012483.ref027","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":"RE Voorrips","year":"2011","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"pcbi.1012483.ref028","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1186\/s12859-019-2703-y","article-title":"FitTetra 2.0 \u2013improved genotype calling for tetraploids with multiple population and parental data support","volume":"20","author":"K Zych","year":"2019","journal-title":"BMC Bioinformatics"},{"key":"pcbi.1012483.ref029","doi-asserted-by":"crossref","first-page":"739068","DOI":"10.1016\/j.aquaculture.2022.739068","article-title":"Genome-wide association study and genomic prediction of tolerance to acute hypoxia in rainbow trout","volume":"565","author":"M Prchal","year":"2023","journal-title":"Aquaculture"},{"issue":"3","key":"pcbi.1012483.ref030","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1111\/1755-0998.12337","article-title":"The development and characterization of a 57K single nucleotide polymorphism array for rainbow trout","volume":"15","author":"Y Palti","year":"2015","journal-title":"Molecular Ecology Resources"},{"issue":"1","key":"pcbi.1012483.ref031","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1186\/s12711-019-0468-4","article-title":"Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding","volume":"51","author":"J D\u2019Ambrosio","year":"2019","journal-title":"Genetics Selection Evolution"},{"key":"pcbi.1012483.ref032","doi-asserted-by":"crossref","first-page":"941340","DOI":"10.3389\/fgene.2022.941340","article-title":"Development of a High-Density 665 K SNP Array for Rainbow Trout Genome-Wide Genotyping.","volume":"13","author":"M Bernard","year":"2022","journal-title":"Front Genet."},{"key":"pcbi.1012483.ref033","article-title":"Rmixmod: A MIXture MODelling R package. In: 1\u00e8res Rencontres R","author":"R. Lebret","year":"2012","journal-title":"Bordeaux, France"},{"key":"pcbi.1012483.ref034","volume-title":"R: A Language and Environment for Statistical Computing","author":"R Core Team","year":"2023"},{"key":"pcbi.1012483.ref035","unstructured":"Affymetrix. Axiom Genotyping Solution."},{"key":"pcbi.1012483.ref036","article-title":"APIS: an updated parentage assignment software managing triploids induced from diploid parents. McCallion A, editor. G3: Genes, Genomes","volume":"jkae143","author":"J Roche","year":"2024","journal-title":"Genetics"},{"issue":"1","key":"pcbi.1012483.ref037","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1186\/1297-9686-44-36","article-title":"An accurate formula to calculate exclusion power of marker sets in parentage assignment","volume":"44","author":"M. Vandeputte","year":"2012","journal-title":"Genet Sel Evol"},{"issue":"1","key":"pcbi.1012483.ref038","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1002\/ppp3.10313","article-title":"Pedigree reconstruction for triploid apple cultivars using single nucleotide polymorphism array data.","volume":"5","author":"NP Howard","year":"2023","journal-title":"Plants People Planet."},{"issue":"2","key":"pcbi.1012483.ref039","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1002\/wics.147","article-title":"ggplot2: ggplot2","volume":"3","author":"H. Wickham","year":"2011","journal-title":"WIREs Comp Stat."}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1012483","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,10,4]],"date-time":"2024-10-04T00:00:00Z","timestamp":1728000000000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1012483","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,4]],"date-time":"2024-10-04T17:34:34Z","timestamp":1728063274000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1012483"}},"subtitle":[],"editor":[{"given":"Feixiong","family":"Cheng","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2024,9,24]]},"references-count":39,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2024,9,24]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1012483","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1012483","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,9,24]]}}}