{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,4]],"date-time":"2026-07-04T02:02:42Z","timestamp":1783130562868,"version":"3.54.6"},"reference-count":65,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2020,8,27]],"date-time":"2020-08-27T00:00:00Z","timestamp":1598486400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Cosmo Art &amp; Science","award":["Cosmo F 1792"],"award-info":[{"award-number":["Cosmo F 1792"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>Genetic variability of Polish Lowland Sheepdog (PON) population was evaluated using both pedigree and genomic data. The analyzed pedigree encompassed 8628 PONs, including 153 individuals genotyped on the Illumina CanineHD BeadChip. Runs of homozygosity (ROH) were defined for homozygous stretches extending over 60 to 4300 kb. The inbreeding coefficients FPed based on pedigree data and FROH50 based on ROHs were at 0.18 and 0.31. The correlation between both was 0.41 but 0.52 when excluding animals with less than seven complete generations. The realized effective population size (Ne\u00af) was 22.2 with an increasing trend over years. Five PONs explained 79% of the genetic diversity of the reference population. The effective population size derived from linkage disequilibrium measured by r\u00b2 was 36. PANTHER analysis of genes in ROHs shared by \u226550% of the PONs revealed four highly over- or underrepresented biological processes. One among those is the 7.35 fold enriched \u201cforelimb morphogenesis\u201d. Candidate loci for hip dysplasia and patent ductus arteriosus were discovered in frequently shared ROHs. In conclusion, the inbreeding measures of the PONs were high and the genetic variability small compared to various dog breeds. Regarding Ne\u00af, PON population was minimally endangered according to the European Association for Animal Production.<\/jats:p>","DOI":"10.3390\/ani10091520","type":"journal-article","created":{"date-parts":[[2020,8,28]],"date-time":"2020-08-28T09:17:08Z","timestamp":1598606228000},"page":"1520","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Genetic Variability in Polish Lowland Sheepdogs Assessed by Pedigree and Genomic Data"],"prefix":"10.3390","volume":"10","author":[{"given":"Paula Wiebke","family":"Michels","sequence":"first","affiliation":[{"name":"Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover (Foundation), 30559 Hannover, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3516-836X","authenticated-orcid":false,"given":"Ottmar","family":"Distl","sequence":"additional","affiliation":[{"name":"Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover (Foundation), 30559 Hannover, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,8,27]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1439-0388.2006.00565.x","article-title":"Genetic variability in French dog breeds assessed by pedigree data","volume":"123","author":"Leroy","year":"2006","journal-title":"J. Anim. Breed. Genet."},{"key":"ref_2","first-page":"593","article-title":"Population structure and inbreeding from pedigree analysis of purebred dogs","volume":"179","author":"Calboli","year":"2008","journal-title":"Genet. Soc. Am."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Wiener, P., S\u00e1nchez-Molano, E., Clements, D.N., Woolliams, J.A., Haskell, M.J., and Blott, S.C. (2017). Genomic data illuminates demography, genetic structure and selection of a popular dog breed. BMC Genom., 18.","DOI":"10.1186\/s12864-017-3933-x"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1038\/hdy.2015.17","article-title":"Measuring individual inbreeding in the age of genomics: Marker-based measures are better than pedigrees","volume":"115","author":"Kardos","year":"2015","journal-title":"Heredity"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1080\/01652176.1992.9694350","article-title":"The relationship between homozygosity and the occurrence of specific diseases in Bouvier Belge des Flandres dogs in the Netherlands: Inbreeding and disease in the bouvier dog","volume":"14","author":"Ubbink","year":"1992","journal-title":"Vet. Q."},{"key":"ref_6","unstructured":"(2020, April 23). Statistic of Born Dogs in VDH. Available online: https:\/\/www.vdh.de\/ueber-den-vdh\/welpenstatistik\/."},{"key":"ref_7","unstructured":"R\u00e4ber, H. (1993). Enzyklop\u00e4die der Rassehunde, Franckh-Kosmos Verlag."},{"key":"ref_8","unstructured":"(2020, April 23). FCI Breeds Nomenclature. Available online: http:\/\/www.fci.be\/en\/nomenclature\/POLISH-LOWLAND-SHEEPDOG-251.html."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1016\/j.tvjl.2011.06.020","article-title":"A genealogical survey of Australian registered dog breeds","volume":"189","author":"Shariflou","year":"2011","journal-title":"Vet. J."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Bell, J., Cavanagh, K., Tilley, L., and Smith, F.W. (2012). Veterinary Medical Guide to Dog and Cat Breeds, Teton NewMedia.","DOI":"10.1201\/b16185"},{"key":"ref_11","unstructured":"(2020, July 24). Polish Lowland Sheepdog Statistics. Available online: https:\/\/www.ofa.org\/diseases\/breed-statistics#detail."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1111\/vop.12284","article-title":"Progressive retinal atrophy in the Polski Owczarek Nizinny dog: A clinical and genetic study","volume":"19","author":"Svensson","year":"2016","journal-title":"Vet. Ophthalmol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1111\/j.1439-0388.2005.00512.x","article-title":"A note on ENDOG: A computer program for analysing pedigree information","volume":"122","author":"Goyache","year":"2005","journal-title":"J. Anim. Breed. Genet."},{"key":"ref_14","first-page":"49","article-title":"Genetic variability of French dairy breeds estimated from pedigree information","volume":"14","author":"Maignel","year":"1996","journal-title":"Interbull Bull."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1093\/oxfordjournals.jhered.a109824","article-title":"Inbreeding and pedigree structure in Standardbred horses","volume":"74","author":"MacCluer","year":"1983","journal-title":"J. Hered."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1017\/S0003356100039271","article-title":"A note on selection differential and generation length when generations overlap","volume":"24","author":"James","year":"1977","journal-title":"Anim. Sci."},{"key":"ref_17","doi-asserted-by":"crossref","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":"ref_18","doi-asserted-by":"crossref","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":"ref_19","unstructured":"Boichard, D. (2020, January 19\u201323). PEDIG: A fortran package for pedigree analysis suited for large populations. Proceedings of the 7th World Congress on Genetics Applied to Livestock Production, Montpellier, France."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1111\/j.1365-2052.2010.02079.x","article-title":"Mating practices and the dissemination of genetic disorders in domestic animals, based on the example of dog breeding","volume":"42","author":"Leroy","year":"2011","journal-title":"Anim. Genet."},{"key":"ref_21","doi-asserted-by":"crossref","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":"ref_22","doi-asserted-by":"crossref","first-page":"1192","DOI":"10.2527\/jas1978.4651192x","article-title":"The relation of livestock breeding to theories of evolution","volume":"46","author":"Wright","year":"1978","journal-title":"J. Anim. Sci."},{"key":"ref_23","doi-asserted-by":"crossref","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":"ref_24","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1023\/A:1019956205473","article-title":"Analysis of genetic diversity for the management of conserved subdivided populations","volume":"3","author":"Caballero","year":"2002","journal-title":"Conserv. Genet."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1111\/j.1439-0388.2009.00810.x","article-title":"Improving the estimation of realized effective population sizes in farm animals","volume":"126","author":"Cervantes","year":"2009","journal-title":"J. Anim. Breed. Genet."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1111\/j.1439-0388.2010.00881.x","article-title":"Estimation of effective population size from the rate of coancestry in pedigreed populations","volume":"128","author":"Cervantes","year":"2011","journal-title":"J. Anim. Breed. Genet."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1186\/1297-9686-40-4-359","article-title":"Individual increase in inbreeding allows estimating effective sizes from pedigrees","volume":"40","author":"Cervantes","year":"2008","journal-title":"Genet. Sel. Evol."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Pfahler, S., and Distl, O. (2015). Effective Population Size, Extended Linkage Disequilibrium and Signatures of Selection in the Rare Dog Breed Lundehund. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0122680"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"s13742-015","DOI":"10.1186\/s13742-015-0047-8","article-title":"Second-generation PLINK: Rising to the challenge of larger and richer datasets","volume":"4","author":"Chang","year":"2015","journal-title":"GigaScience"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"19942","DOI":"10.1073\/pnas.0710021104","article-title":"Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia","volume":"104","author":"Lencz","year":"2007","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Purfield, D.C., Berry, D.P., McParland, S., and Bradley, D.G. (2012). Runs of homozygosity and population history in cattle. BMC Genet., 13.","DOI":"10.1186\/1471-2156-13-70"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Howrigan, D.P., Simonson, M.A., and Keller, M.C. (2011). Detecting autozygosity through runs of homozygosity: A comparison of three autozygosity detection algorithms. BMC Genom., 12.","DOI":"10.1186\/1471-2164-12-460"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s40575-020-00082-y","article-title":"Demographic assessment of the Dalmatian dog\u2013effective population size, linkage disequilibrium and inbreeding coefficients","volume":"7","author":"Vasiliadis","year":"2020","journal-title":"Canine Med. Genet."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1534\/g3.118.200836","article-title":"Fine-scale resolution of runs of homozygosity reveal patterns of inbreeding and substantial overlap with recessive disease genotypes in domestic dogs","volume":"9","author":"Sams","year":"2019","journal-title":"G3 Genes Genomes Genet."},{"key":"ref_35","unstructured":"(2019, May 15). FCI-Rassestandard Polski Owczarek Nizinny (Polski Owczarek Nizinny (PON)). Available online: https:\/\/www.vdh.de\/welpen\/mein-welpe\/polski-owczarek-nizinny-pon."},{"key":"ref_36","unstructured":"R Core Team (2020). R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing. Version 3.6.3."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1016\/j.ajhg.2008.08.007","article-title":"Runs of homozygosity in European populations","volume":"83","author":"McQuillan","year":"2008","journal-title":"Am. J. Hum. Genet."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1086\/519795","article-title":"PLINK: A tool set for whole-genome association and population-based linkage analyses","volume":"81","author":"Purcell","year":"2007","journal-title":"Am. J. Hum. Genet."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1016\/0040-5809(71)90011-6","article-title":"Linkage disequilibrium and homozygosity of chromosome segments in finite populations","volume":"2","author":"Sved","year":"1971","journal-title":"Theor. Popul. Biol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1111\/1755-0998.12442","article-title":"NetView P: A network visualization tool to unravel complex population structure using genome--wide SNPs","volume":"16","author":"Steinig","year":"2016","journal-title":"Mol. Ecol. Resour."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Neuditschko, M., Khatkar, M.S., and Raadsma, H.W. (2012). NetView: A high-definition network-visualization approach to detect fine-scale population structures from genome-wide patterns of variation. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0048375"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: A software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"D419","DOI":"10.1093\/nar\/gky1038","article-title":"PANTHER version 14: More genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools","volume":"47","author":"Mi","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_44","unstructured":"McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, MD) (2020, August 12). Online Mendelian Inheritance in Man, OMIM\u00ae. Available online: https:\/\/omim.org\/."},{"key":"ref_45","unstructured":"Sydney School of Veterinary Science (2020, August 12). Online Mendelian Inheritance in Animals, OMIA. Available online: https:\/\/omia.org\/browse\/."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"720","DOI":"10.1007\/s00335-005-0004-4","article-title":"Quantitative trait loci for hip dysplasia in a crossbreed canine pedigree","volume":"16","author":"Todhunter","year":"2005","journal-title":"Mamm. Genome"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1002\/jor.24178","article-title":"Gene expression in hip soft tissues in incipient canine hip dysplasia and osteoarthritis","volume":"37","author":"Todhunter","year":"2019","journal-title":"J. Orthop. Res."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1016\/j.ygeno.2007.04.004","article-title":"A random model for mapping imprinted quantitative trait loci in a structured pedigree: An implication for mapping canine hip dysplasia","volume":"90","author":"Liu","year":"2007","journal-title":"Genomics"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1007\/s00335-007-9071-z","article-title":"Mapping quantitative trait loci for canine hip dysplasia in German Shepherd dogs","volume":"18","author":"Marschall","year":"2007","journal-title":"Mamm. Genome"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1094","DOI":"10.2460\/ajvr.70.9.1094","article-title":"Evaluation of quantitative trait loci for hip dysplasia in Labrador Retrievers","volume":"70","author":"Phavaphutanon","year":"2009","journal-title":"Am. J. Vet. Res."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1007\/s00335-014-9507-1","article-title":"Multiple loci associated with canine hip dysplasia (CHD) in German shepherd dogs","volume":"25","author":"Fels","year":"2014","journal-title":"Mamm. Genome"},{"key":"ref_52","doi-asserted-by":"crossref","unstructured":"Fels, L., and Distl, O. (2014). Identification and Validation of Quantitative Trait Loci (QTL) for Canine Hip Dysplasia (CHD) in German Shepherd Dogs. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0096618"},{"key":"ref_53","unstructured":"Johns Hopkins University, Baltimore, MD (2020, August 12). Online Mendelian Inheritance in Man, OMIM\u00ae. Available online: https:\/\/omim.org\/entry\/601667?search=601667&highlight=601667."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1111\/j.1365-2052.2008.01842.x","article-title":"Genetic diversity of dog breeds: Within--breed diversity comparing genealogical and molecular data","volume":"40","author":"Leroy","year":"2009","journal-title":"Anim. Genet."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1111\/j.1439-0388.2010.00851.x","article-title":"Population structure and genetic diversity of worldwide Nova Scotia Duck Tolling Retriever and Lancashire Heeler dog populations","volume":"127","year":"2010","journal-title":"J. Anim. Breed. Genet."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1111\/jbg.12031","article-title":"Measuring inbreeding and inbreeding depression on pig growth from pedigree or SNP-Derived metrics","volume":"130","year":"2013","journal-title":"J. Anim. Breed. Genet."},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Zhang, Q., Calus, M.P., Guldbrandtsen, B., Lund, M.S., and Sahana, G. (2015). Estimation of inbreeding using pedigree, 50k SNP chip genotypes and full sequence data in three cattle breeds. BMC Genet., 16.","DOI":"10.1186\/s12863-015-0227-7"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"4697","DOI":"10.3168\/jds.2012-6435","article-title":"Evaluation of inbreeding depression in Holstein cattle using whole-genome SNP markers and alternative measures of genomic inbreeding","volume":"96","author":"Bjelland","year":"2013","journal-title":"J. Dairy Sci."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1046\/j.1439-0388.1999.00210.x","article-title":"Inbreeding in populations with incomplete pedigrees","volume":"116","author":"Lutaaya","year":"1999","journal-title":"J. Anim. Breed. Genet."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"2967","DOI":"10.3168\/jds.S0022-0302(03)73894-6","article-title":"Effect of incomplete pedigrees on estimates of inbreeding and inbreeding depression for days to first service and summit milk yield in Holsteins and Jerseys","volume":"86","author":"Cassell","year":"2003","journal-title":"J. Dairy Sci."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1097\/01.LAB.0000082383.40635.FE","article-title":"Altered expression of angiopoietins during blood-brain barrier breakdown and angiogenesis","volume":"83","author":"Nourhaghighi","year":"2003","journal-title":"Lab. Investig."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.5713\/ajas.2012.12048","article-title":"Estimation of effective population size in the Sapsaree: A Korean native dog (Canis familiaris)","volume":"25","author":"Alam","year":"2012","journal-title":"Asian Australas. J. Anim. Sci."},{"key":"ref_63","unstructured":"DGfZ (1991). Empfehlungen zur Erhaltung genetischer Vielfalt bei einheimischen Nutztieren. Z\u00fcchtungskunde, 63, 426\u2013430."},{"key":"ref_64","unstructured":"Bijma, P. (2000). Long-Term Genetic Contributions: Prediction of Rates of Inbreeding and Genetic Gain in Selected Populations, Department of Animal Sciences, Wageningen University."},{"key":"ref_65","unstructured":"Simon, D.L., and Buchenauer, D. (1993). Genetic Diversity of European Livestock Breeds, Wageningen Pers."}],"container-title":["Animals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2615\/10\/9\/1520\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T10:03:54Z","timestamp":1760177034000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2615\/10\/9\/1520"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,8,27]]},"references-count":65,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2020,9]]}},"alternative-id":["ani10091520"],"URL":"https:\/\/doi.org\/10.3390\/ani10091520","relation":{},"ISSN":["2076-2615"],"issn-type":[{"value":"2076-2615","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,8,27]]}}}