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.

ABSTRACT Genomic selection has been a valuable tool for increasing the rate of genetic improvement in purebred dairy cattle populations. However, there also are many large populations of crossbred dairy cattle in the world, and multi-breed genomic evaluations may be a valuable tool for improving rates of genetic gain in those populations. Multi-breed models are an extension of single-breed genomic models in which a genomic relationship matrix is used to account for the breed origin of alleles in the population, as well as allele frequency differences between breeds. Most studies have found little benefit from multi-breed evaluations for pure breeds that have large reference populations. However, breeds with small reference populations may benefit from inclusion in a multi-breed evaluation without adversely affecting evaluations for purebred performance. Most research has been conducted in taurine breeds, so additional research is needed to determine the value of multi-breed reference populations for composite and synthetic breeds that include both indicine and taurine cattle adapted to tropical climates.

O objetivo neste estudo foi avaliar a estrutura genética da população de bovinos da raça Girolando no Brasil. Analisou-se o arquivo de pedigree de 26.969 animais, composto de 3.031 machos e 23.938 fêmeas. O nível de conteúdo de informação do pedigree na geração atual foi 61%, mostrando ser de qualidade moderada. O coeficiente de endogamia médio e o coeficiente de relação médio da população Girolando foram 0,11 e 0,13%, respectivamente. O tamanho efetivo da população, considerando a geração completa traçada, foi 188, acima do nível crítico. Do total de 9.457 ancestrais que contribuíram para a população de referência, 457 explicaram 50% da variabilidade genética da população. O número efetivo de fundadores foi 551 e o de ancestrais 393. O intervalo médio de geração foi de 5,26 anos, sendo ligeiramente maior nas trilhas gaméticas mãe-filho e pai-filha. A partir dos coeficientes estimados, pode-se concluir que a endogamia nos rebanhos da raça Girolando foi de pequena magnitude e que as práticas de acasalamento foram adequadas durante o período avaliado. No entanto, é importante continuar com o monitoramento desses coeficientes a fim de prevenir perda de variabilidade genética

The aim of this study was to evaluate the population structure of Girolando cattle in Brazil. The pedigree file contained 26,969 individuals, from which 3,031 were males and 23,938 were females. The average level of completeness of the pedigree in the current generation was of reasonable quality (61%). Inbreeding and average relatedness coefficients were low: 0.11 and 0.13%, respectively. Estimates of effective population size considering the full generations traced was 188, which is above the critical level range. The number of ancestors that contributed to the reference population was 9,457 animals, from which 457 explained 50% of the genetic variability of the population. The effective number of founders and the effective number of ancestors in this population were, respectively, 551 and 393. The average generation interval was 5.26 years, slightly higher in genetic pathways dam-son and sire-daughter. The inbreeding in the Girolando breed was of small magnitude, indicating that the current practices of mating were adequate during the study period. However, it is important to continue monitoring these coefficients in order to prevent loss of genetic variability

The identification of regions that have undergone selection is one of the principal goals of theoretical and applied evolutionary genetics. Such studies can also provide information about the evolutionary processes involved in shaping genomes, as well as physical and functional information about genes/genomic regions. Domestication followed by breed formation and selection schemes has allowed the formation of very diverse livestock breeds adapted to a wide variety of environments and with special characteristics. The advances in genomics in the last five years have enabled the development of several methods to detect selection signatures and have resulted in the publication of a considerable number of studies involving livestock species. The aims of this review are to describe the principal effects of natural/artificial selection on livestock genomes, to present the main methods used to detect selection signatures and to discuss some recent results in this area. This review should be useful also to research scientists working with wild animals/non-domesticated species and plant biologists working with breeding and evolutionary biology.

O objetivo deste trabalho foi avaliar a associação dos polimorfismos dos genes bGH, IGF-1 e PIT-1 com características de peso e ganho de peso numa população F2 de bovinos (Gir x Holandês), pela técnica de PCR-RFLP. As freqüências alélicas A e B, do gene PIT-1, e dos genótipos AA, AB e BB, nas populações parentais foram semelhantes entre si, mas diferentes das freqüências nas populações cruzadas F1 e F2, para esse gene. Quanto ao gene bGH, os animais da raça Holandesa apresentaram freqüência de 100% para o alelo E e os animais da raça Gir, 92% para o alelo F, resultando em alta freqüência de indivíduos heterozigotos nas populações F1 e F2. Quanto ao gene IGF-1, todos os animais da raça Holandesa eram heterozigotos (AB) e, nos animais Gir, a maioria dos indivíduos foi de homozigotos (AA), o que resultou em alta freqüência do alelo A nas populações F1 e F2. Foram encontradas associações significativas do alelo A do gene PIT-1 com as características de peso aos 60, 205, 365 dias e ganho de peso do nascimento aos 60 dias. Em bGH, observou-se efeito significativo do alelo E para peso aos 365 dias e ganho de peso do nascimento aos 60 dias, enquanto o efeito do alelo A do IGF-1 foi significativo somente para peso ao nascimento. Os alelos identificados podem ser usados como marcadores no melhoramento animal.

The objective of this work was to evaluate the association between polymorphisms of bGH, IGF-1 and PIT-1 genes with weight and weight gain traits in a bovine F2 population derived from Holstein x Gyr crosses, using the PCR-RFLP technique. Allelic frequencies A and B of PIT-1 gene and AA, AB, and BB genotypes were similar between parental populations but different from F1 and F2 crossed populations. For the bGH gene, Holstein animals showed allelic frequency of 100% for E allele, while Gyr animals showed allelic frequency of 92% for F allele, resulting in high frequency of heterozygous animals in F1 and F2 populations. For the IGF-1 gene, all Holstein were heterozygous (AB) and most Gyr were homozygous (AA), resulting in a high frequency of A allele in F1 and F2 populations. Significant associations were found between PIT-1 allele A with traits weight at 60, 205 and 365 days and weight gain from birth to 60 days. For IGF-1, significant association was found between A allele and birth weight. For bGH gene, significant associations were found between E allele and 365 days weight and weight gain from birth to 60 days. The selected alleles could be used as markers in animal breeding for these traits.

Foram estudados os registros da idade ao primeiro parto (IPP), intervalo de partos (IDP) e período de serviço (PSERV) provenientes das cinco primeiras lactações de 1.406 vacas do ecótipo Mantiqueira, filhas de 113 reprodutores, com partos entre os anos de 1977 e 1997, do Arquivo de Escrituração Zootécnica do Pólo Regional do Vale do Paraíba da Agência Paulista de Tecnologia dos Agronegócios da Secretaria de Agricultura e Abastecimento do Estado de São Paulo (NPZGJRA/IZ/APTA/SAA-SP), no município de Pindamonhangaba. Os modelos usados para obtenção das médias dos quadrados mínimos incluíram, além dos efeitos aleatórios de reprodutor e do erro, os efeitos fixos de ano e estação de nascimento (IPP) ou ano e estação de parto (IDP e PSERV) e idade ao parto. Para a obtenção dos parâmetros genéticos pela metodologia REML, em análises de uni e bicaracterísticas, foram utilizados modelos que ajustavam os efeitos fixos de ano-estação e idade da vaca ao parto, além dos efeitos aleatórios de animal e do erro. As médias ajustadas ± erros-padrão foram: 45,60 ± 8,14 meses para a IPP; 460,56 ± 122,05 dias para o IDP; e 181,44 ± 110,31 dias para o PSERV. As herdabilidades foram: 0,13; 0,01; e 0,01, respectivamente, para IPP, IDP e PSERV.

The reproductive performance of Mantiqueira cows were analyzed using data of records of age of first calving (IPP), calving interval (IDP) and days open (PSERV). These data were the first five lactations of 1406 cows of Mantiqueira ecotype consisting of daughters of 113 sires, with calving from 1952 to 1997, from the Paraiba Valley Regional Center of Research in São Paulo State (APTA/SAA-SP) breeding program. Models to obtain least square means included fixed effects for year and season of birth (for IPP) or calving (for IDP and PSERV) and age, in addition to the random effect of sire and error. The models to obtain genetic parameters by REML methodology included fixed effects for year-season and age, in addition to the random effects of animal and error. The least square means ± standard error were 45.60 ± 8.14 months to the IPP, 460.56 ± 122.05 days to the IDP and 181.44 ± 110.31 days to the PSERV. Estimated values of heritabilities were: 0.13 (IPP), 0.01 (IDP), and 0.01 (PSERV).

Por meio de análises uni e bicaracterísticas entre a produção total de leite (PL), produção de gordura (PROG), porcentagem de gordura (PERG), duração da lactação (DL) e período seco (PSECO), objetivou-se, com este trabalho, estimar parâmetros genéticos utilizando-se registros provenientes das cinco primeiras lactações de 1.406 vacas do ecótipo Mantiqueira, filhas de 113 reprodutores, com partos entre os anos de 1977 e 1997, pertencentes ao programa de melhoramento do Pólo Regional do Vale do Paraíba da Agência Paulista de Tecnologia dos Agronegócios da Secretaria de Agricultura e Abastecimento do Estado de São Paulo (APTA/SAA-SP), no município de Pindamonhangaba. Os modelos usados para obtenção das médias dos quadrados mínimos incluíram os efeitos fixos de ano e estação de parto e idade ao parto, além dos efeitos aleatórios de reprodutor e do erro. Para a obtenção dos parâmetros genéticos pela metodologia REML foram utilizados os modelos que ajustavam os efeitos fixos de ano-estação e idade da vaca ao parto, além dos efeitos aleatórios de animal e do erro. As médias ajustadas ± erros-padrão foram: 1863,31 ± 1047,19 kg para a PL; 76,59 ± 31,92 kg para a PROG; 3,43 ± 0,64 % para PERG; 231,72 ± 91,30 dias para DL; e 256,40 ± 180,29 dias para o PSECO. As herdabilidades foram: 0,25; 0,09; 0,00; 0,16 e 0,06, respectivamente, para PL, PROG, PERG, DL e PSECO. As correlações genéticas entre PL e PROG ou PERG foram, respectivamente, de 0,36 e -0,02. De acordo com os resultados obtidos, pode-se inferir que há variação genética aditiva entre vacas para produção de leite.

Mantiqueira ecotype breed cows were analyzed to estimate genetic parameters for productive traits using single and multiple traits analysis of total milk production (PL), fat production (PROG), fat percentage (PERG), lactation length (DL) and days dry (PSECO). Records of the first five lactations of 1,406 cows from 113 sires with calving between 1977 and 1997 from the Paraiba Valley Regional Center of Research from São Paulo State (APTA/SAA-SP) breeding program were used. Models to obtain least square means included fixed effects for year and season of calving and age of calving, in addition to random effect of sire and error. The models to obtain the genetic parameters by REML methodology included fixed effects for year-season and age, in addition to random effects of animal and error. Least square means ± standard error were 1863,31 ± 1047,19 kg (PL); 76,59 ± 31,92 kg (PROG); 3,43 ± 0,64 % (PERG); 231,72 ± 91,30 days (DL); and 256,40 ± 180,29 days (PSECO). Estimated values of heritabilities were: 0.25 (PL); 0.09 (PROG); 0.00 (PERG); 0.16 (DL) and 0.06 (PSECO). Genetic correlations of PL with PROG and PERG were 0.36 and 0.02, respectively. These results suggest an additive genetic variation among cows to milk yield.