{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T10:15:31Z","timestamp":1790072131598,"version":"4.0.1"},"reference-count":47,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2020,10,17]],"date-time":"2020-10-17T00:00:00Z","timestamp":1602892800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"ALLICE ; APIS-GENE ; GdivSelGen","award":["none"],"award-info":[{"award-number":["none"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>In the management of dairy cattle breeds, two recent trends have arisen that pose potential threats to genetic diversity: the use of reproductive technologies (RT) and a reduction in the number of bulls in breeding schemes. The expected outcome of these changes, in terms of both genetic gain and genetic diversity, is not trivial to predict. Here, we simulated 15 breeding schemes similar to those carried out in large French dairy cattle breeds; breeding schemes differed with respect to their dimensions, the intensity of RT use, and the type of RT involved. We found that intensive use of RT resulted in improved genetic gain, but deteriorated genetic diversity. Specifically, a reduction in the interval between generations through the use of ovum pick-up and in vitro fertilization (OPU-IVF) resulted in a large increase in the inbreeding rate both per year and per generation, suggesting that OPU-IVF could have severe adverse effects on genetic diversity. To achieve a given level of genetic gain, the scenarios that best maintained genetic diversity were those with a higher number of sires\/bulls and a medium intensity of RT use or those with a higher number of female donors to compensate for the increased intensity of RT.<\/jats:p>","DOI":"10.3390\/ani10101903","type":"journal-article","created":{"date-parts":[[2020,10,17]],"date-time":"2020-10-17T05:45:51Z","timestamp":1602913551000},"page":"1903","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Intensified Use of Reproductive Technologies and Reduced Dimensions of Breeding Schemes Put Genetic Diversity at Risk in Dairy Cattle Breeds"],"prefix":"10.3390","volume":"10","author":[{"given":"Anna-Charlotte","family":"Doublet","sequence":"first","affiliation":[{"name":"ALLICE, 149 rue de Bercy, 75012 Paris, France"},{"name":"Universit\u00e9 Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gwendal","family":"Restoux","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S\u00e9bastien","family":"Fritz","sequence":"additional","affiliation":[{"name":"ALLICE, 149 rue de Bercy, 75012 Paris, France"},{"name":"Universit\u00e9 Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Balberini","sequence":"additional","affiliation":[{"name":"AURIVA-Elevage, 61 Chemin des Hoteaux, 69126 Brindas, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guillaume","family":"Fayolle","sequence":"additional","affiliation":[{"name":"Groupe UMOTEST, Les Soudani\u00e8res, 01250 Ceyz\u00e9riat, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chris","family":"Hoz\u00e9","sequence":"additional","affiliation":[{"name":"ALLICE, 149 rue de Bercy, 75012 Paris, France"},{"name":"Universit\u00e9 Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8359-0760","authenticated-orcid":false,"given":"Denis","family":"Lalo\u00eb","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6493-2892","authenticated-orcid":false,"given":"Pascal","family":"Croiseau","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,10,17]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"5160","DOI":"10.3168\/jds.2010-3308","article-title":"Rates of inbreeding and genetic diversity in Canadian Holstein and Jersey cattle","volume":"94","author":"Stachowicz","year":"2011","journal-title":"J. Dairy Sci."},{"key":"ref_2","first-page":"459","article-title":"Effectiveness of selection on progeny performance as a supplement to earlier culling in livestock","volume":"69","author":"Dickerson","year":"1944","journal-title":"J. Agric. Res."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"61","DOI":"10.2527\/1999.77161x","article-title":"The importance of genetic diversity in livestock populations of the future","volume":"77","author":"Notter","year":"1999","journal-title":"J. Anim. Sci."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1111\/age.12178","article-title":"Inbreeding depression in livestock species: Review and meta-analysis","volume":"45","author":"Leroy","year":"2014","journal-title":"Anim. Genet."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1186\/s12711-014-0071-7","article-title":"Identification of genomic regions associated with inbreeding depression in Holstein and Jersey dairy cattle","volume":"46","author":"Pryce","year":"2014","journal-title":"Genet. Sel. Evol."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Eynard, S.E., Windig, J.J., Hiemstra, S.J., and Calus, M.P.L. (2016). Whole-genome sequence data uncover loss of genetic diversity due to selection. Genet. Sel. Evol., 48.","DOI":"10.1186\/s12711-016-0210-4"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1186\/s12711-019-0495-1","article-title":"The impact of genomic selection on genetic diversity and genetic gain in three French dairy cattle breeds","volume":"51","author":"Doublet","year":"2019","journal-title":"Genet. Sel. Evol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"E177","DOI":"10.3168\/jds.S0022-0302(01)70213-5","article-title":"Controlling Inbreeding in Modern Breeding Programs","volume":"84","author":"Weigel","year":"2001","journal-title":"J. Dairy Sci."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.livsci.2015.01.014","article-title":"Genomic selection strategies to optimize the use of multiple ovulation and embryo transfer schemes in dairy cattle breeding programs","volume":"174","author":"Bouquet","year":"2015","journal-title":"Livest. Sci."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1331","DOI":"10.3168\/jds.2015-9437","article-title":"Reproductive technologies combine well with genomic selection in dairy breeding programs","volume":"99","author":"Thomasen","year":"2016","journal-title":"J. Dairy Sci."},{"key":"ref_11","unstructured":"Maignel, L., Boichard, D., and Verrier, E. (1996). Genetic variability of French dairy breeds estimated from pedigree information. Interbull Bull., 49."},{"key":"ref_12","unstructured":"Le M\u00e9zec, P., Danchin-Burge, C., and Moureaux, S. (2019, January 21). Davantage de diversit\u00e9 avec la g\u00e9nomique? plut\u00f4t non.... Available online: http:\/\/idele.fr\/contact\/publication\/idelesolr\/recommends\/les-programmes-de-selection-et-de-diffusion-de-taureaux-dia-a-lere-de-la-genomique-et-leurs-effets.html."},{"key":"ref_13","first-page":"235","article-title":"Cr\u00e9ation d\u2019un observatoire de la VARiabilit\u00e9 g\u00e9n\u00e9tique des RUMinants et des Equid\u00e9s (VARUME)","volume":"55","author":"Danvy","year":"2017","journal-title":"Innov. Agron."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Eynard, S.E., Windig, J.J., Leroy, G., van Binsbergen, R., and Calus, M. (2015). The effect of rare alleles on estimated genomic relationships from whole genome sequence data. BMC Genet., 16.","DOI":"10.1186\/s12863-015-0185-0"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"597","DOI":"10.3168\/jds.2019-16974","article-title":"Genotyping more cows increases genetic gain and reduces rate of true inbreeding in a dairy cattle breeding scheme using female reproductive technologies","volume":"103","author":"Thomasen","year":"2020","journal-title":"J. Dairy Sci."},{"key":"ref_16","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_17","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s12711-018-0385-y","article-title":"Trends in genome-wide and region-specific genetic diversity in the Dutch-Flemish Holstein\u2013Friesian breeding program from 1986 to 2015","volume":"50","author":"Doekes","year":"2018","journal-title":"Genet. Sel. Evol."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Forutan, M., Ansari Mahyari, S., Baes, C., Melzer, N., Schenkel, F.S., and Sargolzaei, M. (2018). Inbreeding and runs of homozygosity before and after genomic selection in North American Holstein cattle. BMC Genom., 19.","DOI":"10.1186\/s12864-018-4453-z"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1111\/jbg.12374","article-title":"van der Optimizing female allocation to reproductive technologies considering merit, inbreeding and cost in nucleus breeding programmes with genomic selection","volume":"136","author":"Granleese","year":"2019","journal-title":"J. Anim. Breed. Genet."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1111\/j.1439-0388.2011.00958.x","article-title":"Genomic selection strategies in dairy cattle breeding programmes: Sexed semen cannot replace multiple ovulation and embryo transfer as superior reproductive technology","volume":"129","author":"Pedersen","year":"2012","journal-title":"J. Anim. Breed. Genet."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"5455","DOI":"10.3168\/jds.2010-3256","article-title":"Deterministic models of breeding scheme designs that incorporate genomic selection","volume":"93","author":"Pryce","year":"2010","journal-title":"J. Dairy Sci."},{"key":"ref_22","unstructured":"S\u00f8rensen, A.C., and S\u00f8rensen, M.K. (2009, January 21\u201324). Inbreeding Rates in Breeding Programs with Different Strategies for Using Genomic Selection. Proceedings of the 2009 Interbull Meeting, Barcelona, Spain."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"458","DOI":"10.3168\/jds.2013-6599","article-title":"Genomic selection strategies in a small dairy cattle population evaluated for genetic gain and profit","volume":"97","author":"Thomasen","year":"2014","journal-title":"J. Dairy Sci."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1017\/S000335610003035X","article-title":"The possible use of superovulation and embryo transfer in cattle to increase response to selection","volume":"21","author":"Land","year":"1975","journal-title":"Anim. Sci."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1341","DOI":"10.1016\/S0093-691X(01)00486-1","article-title":"Embryo production by ovum pick up from live donors","volume":"55","author":"Galli","year":"2001","journal-title":"Theriogenology"},{"key":"ref_26","unstructured":"Pook, T. (2018). MoBPS: Simulation of Breeding Programs, R Package. version 1.0.2."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Pook, T., Schlather, M., and Simianer, H. (2020). MoBPS-Modular Breeding Program Simulator. G3 Genes Genomes Genet.","DOI":"10.1101\/829333"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Arias, J.A., Keehan, M., Fisher, P., Coppieters, W., and Spelman, R. (2009). A high density linkage map of the bovine genome. BMC Genet., 10.","DOI":"10.1186\/1471-2156-10-18"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1186\/1297-9686-33-3-209","article-title":"The distribution of the effects of genes affecting quantitative traits in livestock","volume":"33","author":"Hayes","year":"2001","journal-title":"Genet. Sel. Evol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1534\/g3.117.1117","article-title":"Which Individuals to Choose to Update the Reference Population? Minimizing the Loss of Genetic Diversity in Animal Genomic Selection Programs","volume":"8","author":"Eynard","year":"2018","journal-title":"G3 Bethesda Md"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1016\/S0301-6226(02)00092-1","article-title":"A proposal of criteria of robustness analysis in genetic evaluation","volume":"80","author":"Phocas","year":"2003","journal-title":"Livest. Prod. Sci."},{"key":"ref_32","unstructured":"Mardia, K.V., Kent, J.T., and Bibby, J.M. (1979). Multivariate Analysis, Academic Press. Probability and Mathematical Statistics."},{"key":"ref_33","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_34","doi-asserted-by":"crossref","first-page":"6091","DOI":"10.1111\/mec.12560","article-title":"Using genomic tools to maintain diversity and fitness in conservation programmes","volume":"22","author":"Villanueva","year":"2013","journal-title":"Mol. Ecol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"7","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_36","unstructured":"Purcell, S., and Chang, C. (2020, October 17). PLINK 1.9, Available online: www.cog-genomics.org\/plink\/1.9\/."},{"key":"ref_37","unstructured":"R Core Team (2019). R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing."},{"key":"ref_38","unstructured":"Lenth, R., Singmann, H., Love, J., Buerkner, P., and Herve, M. (2020). emmeans: Estimated Marginal Means, aka Least-Squares Means, R package. Available online: https:\/\/CRAN.R-project.org\/package=emmeans."},{"key":"ref_39","unstructured":"Hothorn, T., Bretz, F., Westfall, P., Heiberger, R.M., Schuetzenmeister, A., and Scheibe, S. (2020). multcomp: Simultaneous Inference in General Parametric Models, R package. Available online: https:\/\/CRAN.R-project.org\/package=multcomp."},{"key":"ref_40","unstructured":"FAO (2000). Secondary Guidelines for the National Farm Animal Genetic Resources Management Plans: Management of Small Populations at Risk, FAO."},{"key":"ref_41","unstructured":"AETE (2020, October 17). Commercial Embryo Transfer Activity in Europe 2018, Available online: https:\/\/www.aete.eu\/publications\/statistics\/."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1046\/j.1439-0442.2000.00327.x","article-title":"The Effect of Repeated Follicular Puncture on Ovarian Function in Dairy Heifers","volume":"47","author":"Petyim","year":"2000","journal-title":"J. Vet. Med. Ser. A"},{"key":"ref_43","first-page":"118","article-title":"Transvaginal Ultrasound-guided Ovum Pick-up(OPU) in Cattle","volume":"18","author":"Qi","year":"2013","journal-title":"J. Biomim. Biomater. Tissue Eng."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1111\/j.1439-0531.2006.00833.x","article-title":"Ovum Pick-up in Dairy Heifers: Does it Affect Animal Well-being?","volume":"42","author":"Petyim","year":"2007","journal-title":"Reprod. Domest. Anim."},{"key":"ref_45","unstructured":"B\u00e9rodier, M., Berg, P., Meuwissen, T., Brochard, M., and Ducrocq, V. (2019, January 26\u201330). Improving mating plans at herd level using genomic information. Proceedings of the Annual Meeting of the European Association for Animal Production (EAAP), Ghent, Belgium."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"934","DOI":"10.2527\/1997.754934x","article-title":"Maximizing the response of selection with a predefined rate of inbreeding","volume":"75","author":"Meuwissen","year":"1997","journal-title":"J. Anim. Sci."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1186\/s12711-015-0151-3","article-title":"Increased genetic gains in sheep, beef and dairy breeding programs from using female reproductive technologies combined with optimal contribution selection and genomic breeding values","volume":"47","author":"Granleese","year":"2015","journal-title":"Genet. Sel. Evol."}],"container-title":["Animals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2615\/10\/10\/1903\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T10:23:02Z","timestamp":1760178182000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2615\/10\/10\/1903"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,10,17]]},"references-count":47,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2020,10]]}},"alternative-id":["ani10101903"],"URL":"https:\/\/doi.org\/10.3390\/ani10101903","relation":{},"ISSN":["2076-2615"],"issn-type":[{"value":"2076-2615","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,10,17]]}}}