{"id":10147,"date":"2026-04-09T08:43:19","date_gmt":"2026-04-09T08:43:19","guid":{"rendered":"https:\/\/www.proefschriftmaken.nl\/portfolio\/renzo-bonifazi\/"},"modified":"2026-04-23T07:42:18","modified_gmt":"2026-04-23T07:42:18","slug":"renzo-bonifazi","status":"publish","type":"us_portfolio","link":"https:\/\/www.proefschriftmaken.nl\/en\/portfolio\/renzo-bonifazi\/","title":{"rendered":"Renzo Bonifazi"},"content":{"rendered":"","protected":false},"excerpt":{"rendered":"","protected":false},"author":8,"featured_media":12860,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"us_portfolio_category":[45],"class_list":["post-10147","us_portfolio","type-us_portfolio","status-publish","has-post-thumbnail","hentry","us_portfolio_category-new-template"],"acf":{"naam_van_het_proefschift":"International genetic and genomic evaluations of beef cattle","samenvatting":"Er is geen Nederlandse samenvatting beschikbaar. De Engelse samenvatting vind je <a href=\"https:\/\/www.proefschriftmaken.nl\/en\/portfolio\/renzo-bonifazi\/\">hier<\/a>.","summary":"Animal breeding aims to improve a population for a series of economic and societal relevant traits. This goal is achieved by selecting the best animals at such traits from the current generation to be the parents of the next generation. National breeding organizations help farmers to make this selection decision by ranking animals according to their genetic values. In cattle, advancements in reproductive technologies such as artificial insemination led to major genetic improvements by allowing superior bulls with desired genetic characteristics to have thousands of offspring. Thanks to such technologies, breeders could access the genetic material of superior bulls from foreign countries. However, animals\u2019 estimated breeding values (EBV) are not directly comparable across countries due to differences in scales and genetic bases, trait and model definitions and the possible presence of genotype-by-environment interactions caused by different environmental conditions between countries. Thus, breeders needed methods to compare and rank domestic sires with foreign ones, leading to the creation of so-called international evaluations.\n\nInternational evaluations jointly analyse all national data to compute an international EBV (EBV INT) and account for differences across countries by modelling the same trait recorded in different countries as different correlated traits. The resulting EBV INT are expressed on the same country scale as the EBV computed from national evaluations (EBV NAT), facilitating the comparison of domestic and foreign sires and worldwide trading of the genetic material of elite sires. International beef cattle evaluations led by Interbeef (a working group of the International Committee for Animal Recording) currently involve 15 countries worldwide, five breeds and three traits. Current Interbeef evaluations only use national phenotypes and pedigree data. Beef cattle international evaluations face various challenges mainly related to three aspects: i) the estimation of across-country genetic correlations; ii) the inclusion of national genomic information, and iii) the lack of an official procedure for participating countries to integrate the EBV INT back into their national evaluations. By addressing these challenges, this thesis aimed to improve and further develop methodologies for beef cattle international evaluations.\n\nIn Chapter 2, we provided up-to-date insights on the impact of Interbeef pedigree-based evaluations from a national perspective, considering both small and large participating countries. We evaluated how international evaluations impact the EBV\u2019s reliabilities of domestic animals and the number and origin of so-called publishable sires, i.e. sires with EBV INT that are publishable in other countries\u2019 scales. On average across countries, international evaluations increased the reliability of domestic animals\u2019 EBV by 9.6 and 8.3 percentage points for direct EBV and maternal EBV, respectively, due to the inclusion of information from relatives recorded in other countries. International evaluations allow small countries to access a larger panel of elite foreign sires with an EBV INT directly expressed on their country scale and increase the EBV\u2019s reliabilities of domestic animals. For large countries, international evaluations provide EBV INT for their elite sires on the scale of all participating countries, facilitating their comparison with foreign sires and helping to better promote their genetic material abroad.\n\nAcross-country genetic correlations (r g) are key for international evaluations as they model how the information from animals recorded in foreign countries contributes to the animals\u2019 EBV INT. In beef cattle, there is usually a low level of connectedness between populations due to the low usage of artificial insemination. These low levels of connectedness and the presence of maternal effects make the estimation of across-country r g challenging; lack of convergence of the estimated parameters and high standard errors of r g are often experienced. Given the low level of connectedness, using simultaneously all data available for the estimation process would be preferred, but it is unfeasible due to computational constraints. In Chapter 3, we first quantified the existing level of genetic connectedness in Limousin cattle across eight European populations. We then estimated across-country r g using a multi-trait approach that simultaneously fits data from all countries. We showed that estimating all 120 across-country r g required for the Interbeef evaluations is feasible with a multi-trait approach but requires a long computation time. Therefore, we investigated four scenarios that implemented data sub-setting to select the most connected herds from the largest population while keeping a multi-trait estimation approach. These scenarios reduced the computational time up to five-fold of that required using all data. The estimated across-country r g from scenarios with data sub-setting had larger associated standard errors and were smaller, albeit close, than those obtained when using all data. Data sub-setting mainly impacted within-country and between-country direct-maternal r g (r dm).\n\nChapter 4 investigated the impact of ignoring, i.e. replacing estimated values with 0, within-country and between-country estimated r dm on the EBV INT in pedigree-based Interbeef evaluations. Within-country r dm are often reported to be negative in beef cattle. Between-country r dm are currently assumed to be 0 in Interbeef evaluations as they are difficult to estimate. We compared EBV INT from a model that used both within-country and between-country r dm with EBV INT from models that ignored between-country r dm or both within-country and between-country r dm. Results showed that the current practice of ignoring between-country r dm had no or limited impact on the ranking of animals\u2019 direct and maternal EBV INT, respectively. Moreover, there was no re-ranking for publishable sires and the top 100 publishable sires. These results were likely due to the estimated between-country r dm being close to zero on average. On the other hand, ignoring both within-country and between-country r dm gave considerable re-ranking in all groups of animals evaluated, suggesting that within-country r dm should not be ignored in international evaluations.\n\nIn Chapter 5, we developed and investigated the benefits of single-step international evaluations for beef cattle. At the national level, genomic evaluations are increasingly adopted. However, the feasibility and the benefits of including genomic information in beef cattle international evaluations are unknown. Using Limousin weaning weight data from 7 European countries, we implemented a single-step single nucleotide polymorphism BLUP (ssSNPBLUP) international evaluation that jointly analyses national phenotypes, genotypes and pedigree information. The ssSNPBLUP international evaluations led to higher accuracy than either current pedigree-based international evaluations or national evaluations (both pedigree-based and genomic-based), whilst giving similar or slightly reduced level and dispersion bias. Implementing single-step international evaluations was beneficial for both large and small countries and for countries with different amounts of genotypes available at the national level. On average across countries, moving from pedigree-based international to ssSNPBLUP international evaluations led to increases in population accuracies of 13.7% and 25.8% for direct and maternal EBV, respectively. Moreover, the international single-step approach increased the accuracies for non-genotyped animals and for countries without genotypes at the national level. The developed ssSNPBLUP international evaluation can be applied to other traits and breeds evaluated by Interbeef and will allow participating countries to enlarge existing national reference populations and improve the accuracy of national (genomic) evaluations.\n\nIn Chapter 6, we developed a generalized procedure to integrate publishable sires\u2019 EBV INT computed either from pedigree-based or single-step beef cattle international evaluations into national evaluations. National and international evaluations use different sources of information to compute animals\u2019 EBV. Thus, animals\u2019 EBV NAT and EBV INT may differ and using only one of the two EBV leads to the loss of information contained only in the discarded EBV. The integration procedure allows combining and propagating international information (i.e. EBV INT and its reliability) to all animals included in the national evaluations, resulting in a blended EBV. In this procedure, publishable sires\u2019 information are de-regressed one-bull-at-the-time and included in national evaluations as additional phenotypes next to up-to-date national data. We validated the integration procedure using the Italian pedigree-based national evaluations for Limousin weaning weight as a case study. The integration procedure increased the model adequacy of national evaluations for publishable sires, while giving similar or higher predictivity for the EBV of publishable sires\u2019 domestic offspring. The procedure performed well for integrating either pedigree-based or single-step international information into national evaluations. The integration procedure has low computational costs and can be easily implemented by countries participating in Interbeef evaluations without relying on specific software, making its application to existing national evaluations straightforward.\n\nChapter 7 is divided into three parts and expands the results of this thesis to a broader context. In the first part, I proposed a general standard procedure to estimate across-country r g in current Interbeef evaluations using a multi-trait approach that simultaneously fits data from all countries. I discussed the different steps of the procedure and how data could be subset for the estimation process while maintaining a multi-trait approach. In the second part, I discussed how genomic data available from national evaluations can be used to estimate across-country r g and measure connectedness between populations. Using simulation, I showed that genomic data can aid the estimation of r g between disconnected and weakly connected countries. Furthermore, genomic data can help to reduce both the standard errors associated with the estimated r g and the amount of data required for the estimation process. I also discussed measures that can capture increases in connectedness between populations due to genomic data and that can be used to identify connected subsets of herds when estimating across-country r g. Among these measures, I showed that the coefficient of determination can detect increases in connectedness between populations due to genomic data and I discussed possible approaches to compute them in Interbeef. In the last part of this chapter, I discussed the modelling of missing parental information using genetic groups as a model improvement for Interbeef evaluations. I discussed the definition of genetic groups in current pedigree-based evaluations and its extensions to future single-step evaluations. Based on initial results, I showed that genetic groups can help to reduce level bias in pedigree-based evaluations, mainly for direct EBV INT. Further research should investigate how to implement genetic groups in single-step international evaluations.","auteur":"Renzo Bonifazi","auteur_slug":"renzo-bonifazi","publicatiedatum":"16 september 2022","taal":"EN","url_flipbook":"https:\/\/ebook.proefschriftmaken.nl\/ebook\/renzobonifazi?iframe=true","url_download_pdf":"","url_epub":"","ordernummer":"FTP-202604090839","isbn":"978-94-6447-281-3","doi_nummer":"","naam_universiteit":"Wageningen University","afbeeldingen":12860,"naam_student:":"","binnenwerk":"","universiteit":"Wageningen University","cover":"","afwerking":"","cover_afwerking":"","design":""},"_links":{"self":[{"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/us_portfolio\/10147","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/us_portfolio"}],"about":[{"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/types\/us_portfolio"}],"author":[{"embeddable":true,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/users\/8"}],"replies":[{"embeddable":true,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/comments?post=10147"}],"version-history":[{"count":1,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/us_portfolio\/10147\/revisions"}],"predecessor-version":[{"id":10148,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/us_portfolio\/10147\/revisions\/10148"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/media\/12860"}],"wp:attachment":[{"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/media?parent=10147"}],"wp:term":[{"taxonomy":"us_portfolio_category","embeddable":true,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/us_portfolio_category?post=10147"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}