Development of genomic predictions for Angus cattle in Brazil incorporating genotypes from related American sires

Campos, Gabriel Soares; Cardoso, F. F.; Gomes, Claudia Cristina Gulias; Domingues, R.; Regitano, L. C. de A.; Oliveira, M. C. de S.; Oliveira, Henrique Nunes de; Carvalheiro, Roberto; Albuquerque, Lúcia Galvão de; Miller, Stephen; Misztal, I.; Lourenço, Daniela

doi:10.1093/jas/skac009

Cited by 3 publications

(8 citation statements)

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“…These results confirm that the use of large reference populations enables to achieve high weaning weight accuracies for both direct and maternal EBV in young animals. In contrast with the results of our study, both Jang et al [ 67 ] and Campos et al [ 66 ] reported values of dispersion for weaning weight that were mostly within the 0.85–1.15 interval, except for pedigree evaluations of total maternal in Campos et al [ 66 ].…”

Section: Discussioncontrasting

confidence: 99%

“…In ssSNPBLUP NAT , was on average 0.31 for direct EBV (ranging from 0.25 for CZE to 0.38 for CHE) and 0.21 for maternal EBV (ranging from 0.17 for CZE to 0.27 for CHE) (Table 7 ). In Brazilian Angus, Campos et al [ 66 ] conducted pedigree and genomic evaluations for growth traits using ssGBLUP [ 7 , 8 ] with about 1600 genotyped animals. For weaning weight gain, the average across validation groups was 0.39 for direct effect and 0.30 for total maternal (weaning weight and tick count) for PBLUP, and 0.45 for direct effect and 0.37 for total maternal for ssGBLUP.…”

Section: Discussionmentioning

confidence: 99%

“…These values are in agreement with our results for countries such as CHE and smaller for other countries such as CZE. These differences could be due to the use of a multi-variate model in combination with other growth traits (birth weight and post-weaning weight) in Campos et al [ 66 ] as well as differences in population structure and trait definition. Recently, Jang et al [ 67 ] reported LR estimates for genomic predictions of weaning weight in American Angus using a large reference population of about 180,000 genotyped animals and over 2,4 million weaning weight phenotypes.…”

Section: Discussionmentioning

confidence: 99%

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International single-step SNPBLUP beef cattle evaluations for Limousin weaning weight

et al. 2022

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Background Compared to national evaluations, international collaboration projects further improve accuracies of estimated breeding values (EBV) by building larger reference populations or performing a joint evaluation using data (or proxy of them) from different countries. Genomic selection is increasingly adopted in beef cattle, but, to date, the benefits of including genomic information in international evaluations have not been explored. Our objective was to develop an international beef cattle single-step genomic evaluation and investigate its impact on the accuracy and bias of genomic evaluations compared to current pedigree-based evaluations. Methods Weaning weight records were available for 331,593 animals from seven European countries. The pedigree included 519,740 animals. After imputation and quality control, 17,607 genotypes at a density of 57,899 single nucleotide polymorphisms (SNPs) from four countries were available. We implemented two international scenarios where countries were modelled as different correlated traits: an international genomic single-step SNP best linear unbiased prediction (SNPBLUP) evaluation (ssSNPBLUPINT) and an international pedigree-based BLUP evaluation (PBLUPINT). Two national scenarios were implemented for pedigree and genomic evaluations using only nationally submitted phenotypes and genotypes. Accuracies, level and dispersion bias of EBV of animals born from 2014 onwards, and increases in population accuracies were estimated using the linear regression method. Results On average across countries, 39 and 17% of sires and maternal-grand-sires with recorded (grand-)offspring across two countries were genotyped. ssSNPBLUPINT showed the highest accuracies of EBV and, compared to PBLUPINT, led to increases in population accuracy of 13.7% for direct EBV, and 25.8% for maternal EBV, on average across countries. Increases in population accuracies when moving from national scenarios to ssSNPBLUPINT were observed for all countries. Overall, ssSNPBLUPINT level and dispersion bias remained similar or slightly reduced compared to PBLUPINT and national scenarios. Conclusions International single-step SNPBLUP evaluations are feasible and lead to higher population accuracies for both large and small countries compared to current international pedigree-based evaluations and national evaluations. These results are likely related to the larger multi-country reference population and the inclusion of phenotypes from relatives recorded in other countries via single-step international evaluations. The proposed international single-step approach can be applied to other traits and breeds.

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Section: Discussioncontrasting

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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International single-step SNPBLUP beef cattle evaluations for Limousin weaning weight

et al. 2022

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“…Our values are in agreement to those of these authors for countries like CHE and smaller for other countries like CZE. Differences with our study could be due to the usage of a multi-variate model in combination with other growth traits (birth weight and post-weaning weight) in Campos et al (2022) as well as differences in population structure and trait definition. Recently, Jang et al (2022) reported LR estimates for genomic predictions of weaning weight in American Angus using a large reference population of about 180,000 genotyped animals and over 2,4 million weaning weight phenotypes.…”

Section: Benefits Of International Single-step Genomic Evaluationsmentioning

confidence: 72%

“…In ssSNPBLUP NAT , 𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎 � � was on average 0.31 for direct EBV (ranging from 0.25 of CZE to 0.38 of CHE) and 0.21 for maternal EBV (ranging from 0.17 of CZE to 0.27 of CHE) (Table 5.7). In Brazilian Angus, Campos et al (2022) conducted pedigree and genomic evaluations for growth traits using ssGBLUP (Christensen and Lund 2010;Aguilar et al 2010) with about 1,600 genotyped animals. For weaning weight gain, the average 𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎 � � across validation groups was 0.39 for direct effect and 0.30 for total maternal (weaning weight and tick count) for PBLUP, and 0.45 for direct effect and 0.37 for total maternal for ssGBLUP.…”

Section: Benefits Of International Single-step Genomic Evaluationsmentioning

confidence: 99%

International genetic and genomic evaluations of beef cattle

Bonifazi¹

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. International genetic and genomic evaluations of beef cattle.PhD thesis, Wageningen University, the Netherlands.In cattle, advancements in reproductive technologies such as artificial insemination allowed breeders to access the genetic material of superior bulls from foreign countries. However, animals' estimated breeding values (EBV) computed from different national evaluations 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. International evaluations account for such differences by jointly analysing all national data and modelling the same trait recorded in different countries as different correlated traits. The resulting international EBV (EBV INT ) facilitate the comparison of domestic and foreign sires and worldwide trading of their genetic material. This thesis aimed to improve and further develop methodologies for international beef cattle evaluations (Interbeef) by addressing various challenges, mainly related to: i) the estimation of across-country genetic correlations (r g ) and their impact on the EBV INT ; ii) the inclusion of national genomic information; and iii) the development of an official procedure for participating countries to integrate the distributed EBV INT back into their national evaluations. First, I showed that both large and small participating countries benefit from current Interbeef pedigree-based evaluations. Second, I showed the feasibility of estimating across-country r g using a multi-trait approach that simultaneously fits data from all countries and proposed data sub-setting strategies to improve computational time. Third, I showed that the current practice of assuming across-country direct-maternal r g to be 0 has limited impact on the EBV INT of animals of interest such as publishable sires, i.e., sires that meet Interbeef publications rules. On the other hand, assuming zero within-country direct-maternal r g impacts the EBV INT of such animals. Fourth, I developed international genomic evaluations for beef cattle using a single-step SNPBLUP approach (ssSNPBLUP). International ssSNPBLUP evaluations lead to higher accuracies compared to both current international pedigree evaluations and either national pedigree or genomic evaluations, while keeping similar or slightly reduced level and dispersion bias. Finally, I developed a generalized procedure to integrate pedigree-based or singlestep EBV INT of publishable sires into national evaluations. The procedure can be easily implemented with current software. Compared to national evaluations without integration, the integration reduces level bias, gives similar dispersion, and increases accuracies of publishable sires' EBV INT . Overall, this thesis contributes to the development of international evaluations of beef cattle.

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Genomic analysis of inbreeding level, kinship and breed relationships in Creole cattle from South America

Marcuzzi,

Calcaterra,

Loza Vega

et al. 2024

Animal Genetics

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The conservation of animal genetic resources refers to measures taken to prevent the loss of genetic diversity in livestock populations, including the protection of breeds from extinction. Creole cattle populations have suffered a drastic reduction in recent decades owing to absorbent crosses or replacement with commercial breeds of European or Indian origin. Genetic characterization can serve as a source of information for conservation strategies to maintain genetic variation. The objective of this work was to evaluate the levels of inbreeding and kinship through the use of genomic information. A total of 903 DNAs from 13 cattle populations from Argentina, Bolivia and Uruguay were genotyped using an SNP panel of 48 K. Also, a dataset of 76 K SNPs from Peruvian Creole was included. Two inbreeding indices (FROH and Fhat2) and kinship relationships were calculated. In addition, effective population size (Ne), linkage disequilibrium, population composition and phylogenetic relationships were estimated. In Creole cattle, FROH ranged from 0.14 to 0.03, and Fhat2 was close to zero. The inferred Ne trends exhibited a decline toward the present for all populations, whereas Creole cattle presented a lower magnitude of Ne than foreign breeds. Cluster analysis clearly differentiated the taurine and Zebu components (K2) and showed that Bolivian Creole cattle presented Zebu gene introgression. Despite the population reduction, Creole populations did not present extreme values of consanguinity and kinship and maintain high levels of genetic diversity. The information obtained in this work may be useful for planning conservation programmes for these valuable local animal genetic resources.

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Development of genomic predictions for Angus cattle in Brazil incorporating genotypes from related American sires

Cited by 3 publications

References 53 publications

International single-step SNPBLUP beef cattle evaluations for Limousin weaning weight

International single-step SNPBLUP beef cattle evaluations for Limousin weaning weight

International genetic and genomic evaluations of beef cattle

Genomic analysis of inbreeding level, kinship and breed relationships in Creole cattle from South America

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