{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T14:59:14Z","timestamp":1786978754750,"version":"build-2736575974"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T00:00:00Z","timestamp":1785283200000},"content-version":"vor","delay-in-days":209,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100014103","name":"Key Research and Development Program of Shandong Province","doi-asserted-by":"publisher","award":["2024CXPT071-1"],"award-info":[{"award-number":["2024CXPT071-1"]}],"id":[{"id":"10.13039\/100014103","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Basic Research Fund of the State Key Laboratory of Mariculture Biobreeding and Sustainable Goods","award":["BRESG-JB202602"],"award-info":[{"award-number":["BRESG-JB202602"]}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2022YFD2400202"],"award-info":[{"award-number":["2022YFD2400202"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32273129"],"award-info":[{"award-number":["32273129"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012428","name":"Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences","doi-asserted-by":"publisher","award":["2025XT0701"],"award-info":[{"award-number":["2025XT0701"]}],"id":[{"id":"10.13039\/501100012428","id-type":"DOI","asserted-by":"publisher"}]},{"name":"the Science and Technology Innovation Team Project of the Chinese Academy of Fishery Sciences","award":["2023TD27"],"award-info":[{"award-number":["2023TD27"]}]},{"name":"the earmarked fund for the China Agriculture Research System","award":["CARS-48"],"award-info":[{"award-number":["CARS-48"]}]},{"name":"the Taishan Scholars Program; and the Hainan Seed Industry Laboratory","award":["B25H1QC03"],"award-info":[{"award-number":["B25H1QC03"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Pedigrees support relatedness control, mate allocation, inbreeding monitoring, and diversity assessment, but large breeding populations are often curated, analyzed, and visualized using separate tools and data structures. This fragmentation complicates routine analysis and reporting, particularly in high-fecundity systems with extensive full-sib structure, irregular pedigree depth, and repeated cohort-based evaluation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present visPedigree, a software package for large breeding pedigrees built around a new tidyped object model. It integrates pedigree standardization, structural validation, candidate-centered tracing, pedigree statistics, inbreeding and partial inbreeding analysis, founder- and ancestor-based diversity summaries, effective population size estimation, relationship matrices, and scalable visualization. The package also provides Shannon\/Hill-based diversity measures, the pedhalflife() temporal diagnostic, and compact visualization of full-sib-dominated subsets. In a giant freshwater prawn pedigree, it produced an interpretable ancestry overview and quantified recent diversity erosion. Simulated benchmarks showed that representative workflows completed within seconds for pedigrees containing up to one million individuals on a standard laptop.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>visPedigree is implemented in the R language and is freely available at https:\/\/cran.r-project.org\/package=visPedigree, with documentation at https:\/\/luansheng.github.io\/visPedigree\/.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioadv\/vbag210","type":"journal-article","created":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T11:14:41Z","timestamp":1785237281000},"source":"Crossref","is-referenced-by-count":0,"title":["visPedigree: a comprehensive R package for tidying, analyzing, and visualizing breeding pedigrees"],"prefix":"10.1093","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5220-1870","authenticated-orcid":false,"given":"Sheng","family":"Luan","sequence":"first","affiliation":[{"name":"State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao, Shandong 266071,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Kong","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao, Shandong 266071,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhenglong","family":"Xia","sequence":"additional","affiliation":[{"name":"Jiangsu Shufeng Prawn Breeding Co., Ltd. , Gaoyou 225600,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ziyi","family":"Kang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao, Shandong 266071,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guangfeng","family":"Qiang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao, Shandong 266071,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kun","family":"Luo","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao, Shandong 266071,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"Sui","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao, Shandong 266071,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,7,29]]},"reference":[{"key":"2026081710023148300_vbag210-B1","author":"Antonov","year":"2023"},{"key":"2026081710023148300_vbag210-B2","doi-asserted-by":"publisher","author":"Barrett","year":"2026","DOI":"10.32614\/CRAN.package.data.table"},{"key":"2026081710023148300_vbag210-B3","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1186\/1297-9686-29-1-5","article-title":"The value of using probabilities of gene origin to measure genetic variability in a population","volume":"29","author":"Boichard","year":"1997","journal-title":"Genet Sel Evol"},{"key":"2026081710023148300_vbag210-B4","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1017\/S0016672399004449","article-title":"Interrelations between effective population size and other pedigree tools for the management of conserved populations","volume":"75","author":"Caballero","year":"2000","journal-title":"Genet Res"},{"key":"2026081710023148300_vbag210-B5","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1186\/1297-9686-34-4-409","article-title":"An indirect approach to the extensive calculation of relationship coefficients","volume":"34","author":"Colleau","year":"2002","journal-title":"Genet Sel Evol"},{"key":"2026081710023148300_vbag210-B6","first-page":"1","article-title":"The igraph software package for complex network research","volume":"1695","author":"Cs\u00e1rdi","year":"2006","journal-title":"Int J Complex Syst"},{"key":"2026081710023148300_vbag210-B7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.18637\/jss.v040.i08","article-title":"Rcpp: seamless R and C++ integration","volume":"40","author":"Eddelbuettel","year":"2011","journal-title":"J Stat Soft"},{"key":"2026081710023148300_vbag210-B8","doi-asserted-by":"publisher","first-page":"1054","DOI":"10.1016\/j.csda.2013.02.005","article-title":"RcppArmadillo: accelerating R with high-performance C++ linear algebra","volume":"71","author":"Eddelbuettel","year":"2014","journal-title":"Comput Stat Data Anal"},{"key":"2026081710023148300_vbag210-B9","first-page":"1193","article-title":"A software tool for the graphical visualization of large and complex populations","volume":"30","author":"Garbe","year":"2003","journal-title":"Yi Chuan Xue Bao"},{"key":"2026081710023148300_vbag210-B10","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1111\/j.1753-5131.2010.01011.x","article-title":"The first family-based breeding program in aquaculture","volume":"2","author":"Gjedrem","year":"2010","journal-title":"Rev Aquac"},{"key":"2026081710023148300_vbag210-B11","doi-asserted-by":"publisher","first-page":"69","DOI":"10.2307\/2529339","article-title":"A simple method for computing the inverse of a numerator relationship matrix used in prediction of breeding values","volume":"32","author":"Henderson","year":"1976","journal-title":"Biometrics"},{"key":"2026081710023148300_vbag210-B12","doi-asserted-by":"publisher","first-page":"427","DOI":"10.2307\/1934352","article-title":"Diversity and evenness: a unifying notation and its consequences","volume":"54","author":"Hill","year":"1973","journal-title":"Ecology"},{"key":"2026081710023148300_vbag210-B13","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1111\/j.2006.0030-1299.14714.x","article-title":"Entropy and diversity","volume":"113","author":"Jost","year":"2006","journal-title":"Oikos"},{"key":"2026081710023148300_vbag210-B14","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1002\/zoo.1430080203","article-title":"Analysis of founder representation in pedigrees: founder equivalents and founder genome equivalents","volume":"8","author":"Lacy","year":"1989","journal-title":"Zoo Biol"},{"key":"2026081710023148300_vbag210-B15","doi-asserted-by":"publisher","first-page":"btaf329","DOI":"10.1093\/bioinformatics\/btaf329","article-title":"Pedixplorer: a bioconductor package to streamline pedigree design and visualization","volume":"41","author":"Le N\u00e9zet","year":"2025","journal-title":"Bioinformatics"},{"key":"2026081710023148300_vbag210-B16","doi-asserted-by":"publisher","first-page":"564","DOI":"10.1093\/bioinformatics\/btab599","article-title":"purgeR: inbreeding and purging in pedigreed populations","volume":"38","author":"L\u00f3pez-Cortegano","year":"2022","journal-title":"Bioinformatics"},{"key":"2026081710023148300_vbag210-B17","doi-asserted-by":"publisher","first-page":"305","DOI":"10.1186\/1297-9686-24-4-305","article-title":"Computing inbreeding coefficients in large populations","volume":"24","author":"Meuwissen","year":"1992","journal-title":"Genet Sel Evol"},{"key":"2026081710023148300_vbag210-B18","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1111\/j.1439-0388.2005.00538.x","article-title":"A fast algorithm for computing inbreeding coefficients in large populations","volume":"122","author":"Sargolzaei","year":"2005","journal-title":"J Anim Breed Genet"},{"key":"2026081710023148300_vbag210-B19","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1159\/000363105","article-title":"The kinship2 R package for pedigree data","volume":"78","author":"Sinnwell","year":"2014","journal-title":"Hum Hered"},{"key":"2026081710023148300_vbag210-B20","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1109\/TSMC.1981.4308636","article-title":"Methods for visual understanding of hierarchical system structures","volume":"11","author":"Sugiyama","year":"1981","journal-title":"IEEE Trans Syst Man Cybern"},{"key":"2026081710023148300_vbag210-B21","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1186\/s12859-018-2450-5","article-title":"Optimum contribution selection for animal breeding and conservation: the R package optiSel","volume":"20","author":"Wellmann","year":"2019","journal-title":"BMC Bioinformatics"},{"key":"2026081710023148300_vbag210-B22","doi-asserted-by":"publisher","first-page":"792","DOI":"10.1111\/j.2041-210X.2012.00213.x","article-title":"nadiv: an R package to create relatedness matrices for estimating non-additive genetic variances in animal models","volume":"3","author":"Wolak","year":"2012","journal-title":"Methods Ecol Evol"}],"container-title":["Bioinformatics Advances"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformaticsadvances\/advance-article-pdf\/doi\/10.1093\/bioadv\/vbag210\/70351714\/vbag210.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformaticsadvances\/article-pdf\/6\/1\/vbag210\/70351714\/vbag210.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformaticsadvances\/article-pdf\/6\/1\/vbag210\/70351714\/vbag210.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T14:02:38Z","timestamp":1786975358000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformaticsadvances\/article\/doi\/10.1093\/bioadv\/vbag210\/8746876"}},"subtitle":[],"editor":[{"given":"Michael","family":"DeGiorgio","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026]]},"references-count":22,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1,7]]}},"URL":"https:\/\/doi.org\/10.1093\/bioadv\/vbag210","relation":{},"ISSN":["2635-0041"],"issn-type":[{"value":"2635-0041","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026]]},"published":{"date-parts":[[2026]]},"article-number":"vbag210"}}