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Oliveira CS, Camargo LSA, da Silva MVGB, Saraiva NZ, Quintão CC, Machado MA. Embryo biopsies for genomic selection in tropical dairy cattle. Anim Reprod 2023; 20:e20230064. [PMID: 37547565 PMCID: PMC10399131 DOI: 10.1590/1984-3143-ar2023-0064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 06/21/2023] [Indexed: 08/08/2023] Open
Abstract
Genomic selection has transformed the livestock industry, enabling early-life selection of animals. Biopsy sampling of pre-implantation embryos has been described since 1968. However, it was only after 2010, with the advancement of molecular biology techniques such as whole genomic amplification and SNP Chips, that next-generation sequencing became commercially available for bovine embryos. It is now possible to make decisions about which embryos to transfer not only based on recipients' availability or embryo morphology but also on genomic estimates. This technology can be implemented for a wide spectrum of applications in livestock. In this review, we discuss the use of embryo biopsy for genomic selection and share our experience with Gir and Girolando Brazilian breeding programs, as well as future goals for implementing it in Brazilian bovine in vitro embryo production practices.
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Oliveira CS, Silva MVGBD, Quintão CC, Otto PI, Alonso RV, Feres LF, Panetto JCDC, Machado MA, Camargo LSDA. Imputation accuracy for genomic selection using embryo biopsy samples in Gir. Reprod Biol 2023; 23:100765. [PMID: 37150127 DOI: 10.1016/j.repbio.2023.100765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 04/09/2023] [Accepted: 04/10/2023] [Indexed: 05/09/2023]
Abstract
The aim of this study was to establish a platform for genomic selection of in vitro-fertilized (IVF) Gir embryos. Multiple displacement amplification (MDA)-based embryo biopsy samples were genotyped, and genomic estimated breeding values (GEBV) for milk yield (305MY) were calculated. The concordance of GEBV and accuracy between embryo biopsies and the respective liveborn were assessed. Imputation was performed using two panels (Z-Chip and Bovine HD, Illumina) based on a database of 73,110 lactating cow's database and pedigree files from 147,131 animals. Biopsied embryos had similar pregnancy rates (39% vs 40%), pregnancy loss rates (18% vs 20%), and pregnancy length compared to Control embryos. After genotyping, low call rate means were detected for biopsy samples compared to the respective calf samples (0.80 vs 0.98). Imputation presented 0.83 (Z-Chip) and 0.96 (HD) accuracy (CORRanim). Embryo GEBV accuracy levels were higher in BovineHD imputation (0.82) than Z-Chip imputation (0.55) or no imputation (0.62), and the correlation between embryo/calf pairs' accuracy was 0.85 for BovineHD imputation, 0.11 for Z-Chip imputation, and 0.02 for no imputation. GEVB estimates correlation between embryo/calf pairs was 0.87 for BovineHD imputation, 0.80 for Z-Chip imputation, and 0.41 before imputation. The call rate of embryo samples did not affect the correlation between embryo/calf pairs for accuracy and GEBV before and after BovineHD imputation. Embryos obtained on the same farm presented GEBV 305MY differences of up to 800 kg, emphasizing the expected impact of embryo genomic selection for the Gir breed.
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Affiliation(s)
- Clara Slade Oliveira
- Embrapa Dairy Cattle, 610 Eugenio do Nascimento Ave., Juiz de Fora, MG 36038-330, Brazil.
| | | | | | - Pamela Itajara Otto
- Embrapa Dairy Cattle, 610 Eugenio do Nascimento Ave., Juiz de Fora, MG 36038-330, Brazil; Department of Animal Science, Universidade Federal de Santa Maria, 1000 Roraima Ave., Santa Maria, RS 97105-900, Brazil
| | | | - Luiz Fernando Feres
- Jose do Rosario Vellano University (UNIFENAS), MG 179Rd., Alfenas, MG 37132-440, Brazil
| | | | - Marco Antonio Machado
- Embrapa Dairy Cattle, 610 Eugenio do Nascimento Ave., Juiz de Fora, MG 36038-330, Brazil
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