{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,5]],"date-time":"2026-03-05T11:56:25Z","timestamp":1772711785885,"version":"3.50.1"},"reference-count":49,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2025,1,26]],"date-time":"2025-01-26T00:00:00Z","timestamp":1737849600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Instituto Nacional de Investigaci\u00f3n Agropecuaria","award":["INIA_CL_40"],"award-info":[{"award-number":["INIA_CL_40"]}]},{"name":"Instituto Nacional de Investigaci\u00f3n Agropecuaria","award":["INIA_CL_38"],"award-info":[{"award-number":["INIA_CL_38"]}]},{"name":"Instituto Nacional de Investigaci\u00f3n Agropecuaria","award":["CSIC_I+D_2018_287"],"award-info":[{"award-number":["CSIC_I+D_2018_287"]}]},{"name":"Instituto Nacional de Investigaci\u00f3n Agropecuaria","award":["772787"],"award-info":[{"award-number":["772787"]}]},{"name":"Comisi\u00f3n Sectorial de Investigaci\u00f3n Cient\u00edfica, CSIC, Universidad de la Rep\u00fablica","award":["INIA_CL_40"],"award-info":[{"award-number":["INIA_CL_40"]}]},{"name":"Comisi\u00f3n Sectorial de Investigaci\u00f3n Cient\u00edfica, CSIC, Universidad de la Rep\u00fablica","award":["INIA_CL_38"],"award-info":[{"award-number":["INIA_CL_38"]}]},{"name":"Comisi\u00f3n Sectorial de Investigaci\u00f3n Cient\u00edfica, CSIC, Universidad de la Rep\u00fablica","award":["CSIC_I+D_2018_287"],"award-info":[{"award-number":["CSIC_I+D_2018_287"]}]},{"name":"Comisi\u00f3n Sectorial de Investigaci\u00f3n Cient\u00edfica, CSIC, Universidad de la Rep\u00fablica","award":["772787"],"award-info":[{"award-number":["772787"]}]},{"name":"European Union","award":["INIA_CL_40"],"award-info":[{"award-number":["INIA_CL_40"]}]},{"name":"European Union","award":["INIA_CL_38"],"award-info":[{"award-number":["INIA_CL_38"]}]},{"name":"European Union","award":["CSIC_I+D_2018_287"],"award-info":[{"award-number":["CSIC_I+D_2018_287"]}]},{"name":"European Union","award":["772787"],"award-info":[{"award-number":["772787"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Infection by gastrointestinal nematodes (GINs) in sheep is a significant health issue that affects animal welfare and leads to economic losses in the production sector. Genetic selection for parasite resistance has shown promise in improving animal health and productivity. This study aimed to determine if incorporating genomic data into genetic prediction models currently used in Uruguay could improve the accuracy of breeding value estimations for GIN resistance in the Australian Merino breed. This study compared the accuracy of breeding value predictions using the BLUP (Best Linear Unbiased Prediction) and ssGBLUP (single-step genomic BLUP) models on partial and complete data sets, including 32,713 phenotyped and 3238 genotyped animals. The quality of predictions was evaluated using a linear regression method, focusing on 145 rams. The inclusion of genomic data increased the average individual accuracies by 4% for genotyped and phenotyped animals. For animals with genomic and non-phenotyped data, the accuracy improvement reached 8%. Of these, one group of animals that benefited from an ssGBLUP evaluation came from a facility with a strong connection to the informative nucleus and showed an average increase of 20% in their individual accuracy. Additionally, ssGBLUP slightly outperformed BLUP in terms of prediction quality. These findings demonstrate the potential of genomic information to improve the accuracy of breeding value predictions for parasite resistance in sheep. The integration of genomic data, particularly in non-phenotyped animals, offers a promising tool for enhancing genetic selection in Australian Merino sheep to improve resistance to gastrointestinal parasites.<\/jats:p>","DOI":"10.3390\/genes16020159","type":"journal-article","created":{"date-parts":[[2025,1,27]],"date-time":"2025-01-27T04:59:10Z","timestamp":1737953950000},"page":"159","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Accuracy of Genomic Predictions for Resistance to Gastrointestinal Parasites in Australian Merino Sheep"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8200-4117","authenticated-orcid":false,"given":"Brenda","family":"Vera","sequence":"first","affiliation":[{"name":"Sistema Ganadero Extensivo, INIA Las Brujas, Ruta 48, km 10, Canelones 90200, Uruguay"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elly A.","family":"Navajas","sequence":"additional","affiliation":[{"name":"Sistema Ganadero Extensivo, INIA Las Brujas, Ruta 48, km 10, Canelones 90200, Uruguay"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1510-0456","authenticated-orcid":false,"given":"Elize","family":"Van Lier","sequence":"additional","affiliation":[{"name":"Departamento de Producci\u00f3n Animal y Pasturas, Facultad de Agronom\u00eda, Universidad de la Rep\u00fablica, Avda. Garz\u00f3n 780, Montevideo 12900, Uruguay"},{"name":"Estaci\u00f3n Experimental Facultad de Agronom\u00eda Salto, Ruta 31, km 21, Salto 50000, Uruguay"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1340-367X","authenticated-orcid":false,"given":"Beatriz","family":"Carracelas","sequence":"additional","affiliation":[{"name":"Sistema Ganadero Extensivo, INIA Las Brujas, Ruta 48, km 10, Canelones 90200, Uruguay"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pablo","family":"Peraza","sequence":"additional","affiliation":[{"name":"Sistema Ganadero Extensivo, INIA Las Brujas, Ruta 48, km 10, Canelones 90200, Uruguay"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0091-3956","authenticated-orcid":false,"given":"Gabriel","family":"Ciappesoni","sequence":"additional","affiliation":[{"name":"Sistema Ganadero Extensivo, INIA Las Brujas, Ruta 48, km 10, Canelones 90200, Uruguay"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,1,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/0304-4017(95)00908-6","article-title":"The Prevalence of Anthelmintic Resistance in Nematode Parasites of Sheep in Southern Latin America: Uruguay","volume":"62","author":"Nari","year":"1996","journal-title":"Vet. Parasitol."},{"key":"ref_2","unstructured":"Castells, D. (2008). Evaluaci\u00f3n de Resistencia de Ovinos Corriedale a los Nematodos en Uruguay: Heredabilidad y Correlaciones Gen\u00e9ticas el Recuento de Huevos de Nematodos Caracter\u00edsticas Productivas. [Master\u2019s Thesis, UDELAR]."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1186\/s12711-023-00797-z","article-title":"A Comprehensive Analysis of the Genetic Diversity and Environmental Adaptability in Worldwide Merino and Merino-Derived Sheep Breeds","volume":"55","author":"Ceccobelli","year":"2023","journal-title":"Genet. Sel. Evol."},{"key":"ref_4","first-page":"706","article-title":"Estimation of Changes in Herd Environment","volume":"32","author":"Henderson","year":"1949","journal-title":"J. Dairy Sci."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1819","DOI":"10.1093\/genetics\/157.4.1819","article-title":"Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps","volume":"157","author":"Meuwissen","year":"2001","journal-title":"Genetics"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"skaa101","DOI":"10.1093\/jas\/skaa101","article-title":"Current Status of Genomic Evaluation","volume":"98","author":"Misztal","year":"2020","journal-title":"J. Anim. Sci."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/1297-9686-44-33","article-title":"Accuracy of Pedigree and Genomic Predictions of Carcass and Novel Meat Quality Traits in Multi-Breed Sheep Data Assessed by Cross-Validation","volume":"44","author":"Daetwyler","year":"2012","journal-title":"Genet. Sel. Evol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1333","DOI":"10.1017\/S1751731117003688","article-title":"Invited Review: Genomic Selection for Small Ruminants in Developed Countries: How Applicable for the Rest of the World?","volume":"12","author":"Mrode","year":"2018","journal-title":"Animal"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"3375","DOI":"10.2527\/jas.2011-4557","article-title":"Components of the Accuracy of Genomic Prediction in a Multi-Breed Sheep Population","volume":"90","author":"Daetwyler","year":"2012","journal-title":"J. Anim. Sci."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.3168\/jds.2013-7135","article-title":"Assessment of Accuracy of Genomic Prediction for French Lacaune Dairy Sheep","volume":"97","author":"Baloche","year":"2014","journal-title":"J. Dairy Sci."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Dodds, K.G., Auvray, B., Newman, S.-A.N., and McEwan, J.C. (2014). Genomic Breed Prediction in New Zealand Sheep. BMC Genet., 15.","DOI":"10.1186\/s12863-014-0092-9"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1111\/jbg.12771","article-title":"Including Genotypic Information in Genetic Evaluations Increases the Accuracy of Sheep Breeding Values","volume":"140","author":"Kaseja","year":"2023","journal-title":"J. Anim. Breed. Genet."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Cunha, S.M.F., Willoughby, O., Schenkel, F., and C\u00e1novas, \u00c1. (2024). Genetic Parameter Estimation and Selection for Resistance to Gastrointestinal Nematode Parasites in Sheep\u2014A Review. Animals, 14.","DOI":"10.3390\/ani14040613"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1186\/s13071-014-0598-z","article-title":"First Report of Monepantel Haemonchus contortus Resistance on Sheep Farms in Uruguay","volume":"7","author":"Mederos","year":"2014","journal-title":"Parasit. Vectors"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/j.vetpar.2012.03.037","article-title":"Anthelmintic Resistance in Sheep Farms: Update of the Situation in the American Continent","volume":"189","year":"2012","journal-title":"Vet. Parasitol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1093\/jas\/sky404.407","article-title":"PSI-30 Identifying Key Regulator Genes Associated with Parasite Resistance and Their Link with Climate Conditions in Sheep","volume":"96","author":"Dixon","year":"2018","journal-title":"J. Anim. Sci."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"743","DOI":"10.3168\/jds.2009-2730","article-title":"Hot Topic: A Unified Approach to Utilize Phenotypic, Full Pedigree, and Genomic Information for Genetic Evaluation of Holstein Final Score1","volume":"93","author":"Aguilar","year":"2010","journal-title":"J. Dairy Sci."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Vera, B., Navajas, E.A., Peraza, P., Carracelas, B., Van Lier, E., and Ciappesoni, G. (2024). Genomic Regions Associated with Resistance to Gastrointestinal Parasites in Australian Merino Sheep. Genes, 15.","DOI":"10.20944\/preprints202406.0134.v1"},{"key":"ref_19","unstructured":"Viljoen, G., Garcia Podesta, M., and Boettcher, P. (July, January 28). Breeding for Sheep Parasite Resistance in Extensive Production Systems in Uruguay: From Phenotype to Genotype. Proceedings of the International Symposium on Sustainable Animal Production and Health, Vienna, Austria."},{"key":"ref_20","first-page":"177","article-title":"Some Modifications of the McMaster Helminth Egg-Counting Technique and Apparatus","volume":"21","author":"Whitlock","year":"1948","journal-title":"J. Counc. Sci. Ind. Res. Aust."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Sargolzaei, M., Chesnais, J.P., and Schenkel, F.S. (2014). A New Approach for Efficient Genotype Imputation Using Information from Relatives. BMC Genom., 15.","DOI":"10.1186\/1471-2164-15-478"},{"key":"ref_22","unstructured":"Misztal, I., Tsuruta, S., Strabel, T., Auvray, B., Druet, T., and Lee, D.H. (2002, January 19\u201323). BLUPF90 and Related Programs (BGF90). Proceedings of the 7th World Congress on Genetics Applied to Livestock Production, Montpellier, France."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"2287","DOI":"10.3168\/jds.2009-2773","article-title":"Selection and Management of DNA Markers for Use in Genomic Evaluation","volume":"93","author":"Wiggans","year":"2010","journal-title":"J. Dairy Sci."},{"key":"ref_24","first-page":"215","article-title":"Residual Maximum Likelihood Estimation of (Co) Variance Components in Multivariate Mixed Linear Models Using Average Information","volume":"49","author":"Jensen","year":"1997","journal-title":"J. Indian Soc. Agric. Stat."},{"key":"ref_25","unstructured":"Henderson, C.R. (1963). Selection Index and Expected Genetic Advance. Statistical Genetics and Plant Breeding, National Academy of Sciences, National Research Council Publication."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/1297-9686-42-2","article-title":"Genomic Prediction When Some Animals Are Not Genotyped","volume":"42","author":"Christensen","year":"2010","journal-title":"Genet. Sel. Evol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"4414","DOI":"10.3168\/jds.2007-0980","article-title":"Efficient Methods to Compute Genomic Predictions","volume":"91","author":"VanRaden","year":"2008","journal-title":"J. Dairy Sci."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1111\/jbg.12470","article-title":"Effects of Ignoring Inbreeding in Model-Based Accuracy for BLUP and SSGBLUP","volume":"137","author":"Aguilar","year":"2020","journal-title":"J. Anim. Breed. Genet."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1186\/s12711-018-0426-6","article-title":"Semi-Parametric Estimates of Population Accuracy and Bias of Predictions of Breeding Values and Future Phenotypes Using the LR Method","volume":"50","author":"Legarra","year":"2018","journal-title":"Genet. Sel. Evol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1111\/jbg.12507","article-title":"Validation of Single-Step GBLUP Genomic Predictions from Threshold Models Using the Linear Regression Method: An Application in Chicken Mortality","volume":"138","author":"Bermann","year":"2021","journal-title":"J. Anim. Breed. Genet."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1016\/j.smallrumres.2016.03.006","article-title":"Is It Feasible to Select Humid Sub-Tropical Merino Sheep for Faecal Egg Counts?","volume":"137","author":"Benavides","year":"2016","journal-title":"Small Rumin. Res."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1016\/j.livsci.2013.07.011","article-title":"Estimates of Genetic Parameters for Worm Resistance, Wool and Growth Traits in Merino Sheep of Uruguay","volume":"157","author":"Ciappesoni","year":"2013","journal-title":"Livest. Sci."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1017\/S1357729800054497","article-title":"Genetic Relationships between Faecal Egg Count and Production Traits in Commercial Merino Sheep Flocks","volume":"79","author":"Pollott","year":"2004","journal-title":"Anim. Sci."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"516","DOI":"10.5713\/ajas.19.0816","article-title":"Genetic Evaluation of Sheep for Resistance to Gastrointestinal Nematodes and Body Size Including Genomic Information","volume":"34","author":"Torres","year":"2020","journal-title":"Anim. Biosci."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1017\/S1357729800014995","article-title":"Selection of Merino Sheep for Resistance to Haemonchus contortus: Genetic Variation","volume":"62","author":"Woolaston","year":"1996","journal-title":"Anim. Sci."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/j.livprodsci.2004.09.003","article-title":"A Review of Genetic Parameter Estimates for Wool, Growth, Meat and Reproduction Traits in Shee","volume":"92","author":"Safari","year":"2005","journal-title":"Livest. Prod. Sci."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/1297-9686-44-4","article-title":"The Importance of Information on Relatives for the Prediction of Genomic Breeding Values and the Implications for the Makeup of Reference Data Sets in Livestock Breeding Schemes","volume":"44","author":"Clark","year":"2012","journal-title":"Genet. Sel. Evol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1565","DOI":"10.1017\/S1751731112000742","article-title":"Single-Step Methods for Genomic Evaluation in Pigs","volume":"6","author":"Christensen","year":"2012","journal-title":"Anim. Int. J. Anim. Biosci."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"2653","DOI":"10.2527\/jas.2014-8836","article-title":"Genetic Evaluation Using Single-Step Genomic Best Linear Unbiased Predictor in American Angus1","volume":"93","author":"Lourenco","year":"2015","journal-title":"J. Anim. Sci."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1017\/S001667231100022X","article-title":"Bias in Genomic Predictions for Populations under Selection","volume":"93","author":"Vitezica","year":"2011","journal-title":"Genet. Res."},{"key":"ref_41","unstructured":"Spelman, R.J., Keehan, M.D., Obolonkin, V., Winkelman, A.M., Johnson, D.L., and Harris, B. (2010, January 1\u20136). Application of Genomic Selection in the New Zealand Dairy Cattle Industry. Proceedings of the 9th World Congress on Genetics Applied to Livestock Production, Leipzig, Germany."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"659","DOI":"10.3168\/jds.2014-8560","article-title":"Application of Genomic Evaluation to Dairy Cattle in New Zealand","volume":"98","author":"Winkelman","year":"2015","journal-title":"J. Dairy Sci."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"3200","DOI":"10.3168\/jds.2013-7745","article-title":"Within- and across-Breed Genomic Predictions and Genomic Relationships for Western Pyrenees Dairy Sheep Breeds Latxa, Manech, and Basco-B\u00e9arnaise","volume":"97","author":"Legarra","year":"2014","journal-title":"J. Dairy Sci."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1186\/s12711-020-00567-1","article-title":"Bias and Accuracy of Dairy Sheep Evaluations Using BLUP and SSGBLUP with Metafounders and Unknown Parent Groups","volume":"52","author":"Macedo","year":"2020","journal-title":"Genet. Sel. Evol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"6346","DOI":"10.3168\/jds.2019-18033","article-title":"Exploring the Inclusion of Genomic Information and Metafounders in Latxa Dairy Sheep Genetic Evaluations","volume":"103","author":"Legarra","year":"2020","journal-title":"J. Dairy Sci."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1186\/1297-9686-43-26","article-title":"Accuracy of Multi-Trait Genomic Selection Using Different Methods","volume":"43","author":"Calus","year":"2011","journal-title":"Genet. Sel. Evol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1513","DOI":"10.1534\/genetics.112.144246","article-title":"Multiple-Trait Genomic Selection Methods Increase Genetic Value Prediction Accuracy","volume":"192","author":"Jia","year":"2012","journal-title":"Genetics"},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Song, H., Zhang, J., Zhang, Q., and Ding, X. (2019). Using Different Single-Step Strategies to Improve the Efficiency of Genomic Prediction on Body Measurement Traits in Pig. Front. Genet., 9.","DOI":"10.3389\/fgene.2018.00730"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"2439","DOI":"10.3168\/jds.2021-20860","article-title":"Removing Data and Using Metafounders Alleviates Biases for All Traits in Lacaune Dairy Sheep Predictions","volume":"105","author":"Macedo","year":"2022","journal-title":"J. Dairy Sci."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/16\/2\/159\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,8]],"date-time":"2025-10-08T10:36:41Z","timestamp":1759919801000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/16\/2\/159"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,1,26]]},"references-count":49,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2025,2]]}},"alternative-id":["genes16020159"],"URL":"https:\/\/doi.org\/10.3390\/genes16020159","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,1,26]]}}}