Influence of variance component estimates on genomic predictions for growth and reproductive-related traits in Nellore cattle.

This study aimed to estimate variance components (VCs) for growth and reproductive traits in Nellore cattle using two relationship matrices (pedigree relationship A matrix and pedigree plus genomic relationship H matrix), and records collected before and after genomic selection (GS) implementation. The study also evaluated how genomic breeding values (GEBV) are affected by variance components and discarding old records. The analysed traits were weight at 120 days (W120), weight and scrotal circumference at 450 days (W450 and SC450, respectively). Three datasets were used to estimate VCs, including all phenotypic information (All) or records for animals born before or after GS implementation (Before or After datasets, respectively). Both relationship matrices were considered for VC estimation, the A matrix was used in all three datasets and VC from each combination were named as A_Before, A_After, and A_All). The H was used in two datasets: H_All and H_After. Different VCs were used for GEBV prediction through ssGBLUP. This step used two possible Datasets, using all available phenotypic data (Dataset 1) or just records collected since GS implementation (Dataset 2). Validation was conducted using accuracy, bias and dispersion according to the LR method and prediction accuracy from corrected phenotypes. The heritability of all traits increased from A_Before to A_After, while estimates for A_All were intermediary. In the previous order, the estimates were 0.16, 0.17, and 0.15 for W120; 0.31, 0.39, and 0.35 for W450; 0.35, 0.47, and 0.41 for SC. For W450 and SC, using the H matrix reduced the heritability (0.33 and 0.32 for W450; 0.41 and 0.38 for SC for H_After and H_All, respectively). For W120, Dataset1 and VCs from A_After showed the highest accuracy for direct and maternal GEBV (0.953 and 0.868). For W450, Dataset 1 and VC from H_After allowed the highest accuracy (0.854) but use Dataset 2 and same VC source yield similar value (0.846). For SC, Dataset 2 with VC from H_After showed the highest accuracy (0.925). To use Dataset 2 does not cause important changes in bias or dispersion with respect to Dataset 1. The VC and genetic parameters changed for W120, W450, and SC450, using records before or after the GS implementation. For W450 and SC450, genetic variance and heritability estimates increased with the use of GS. For W120, genomic predictions were more accurate using A for VC estimation. Accuracy gains were observed for W450 and SC450 using H in VC estimation and/or discarding records before GS. It is possible to discard phenotypic records before GS implementation without generating bias or dispersion in the GEBV of young candidates.

Phylogenetic analysis of the partial sequences of the env and tax BLV genes reveals the presence of genotypes 1 and 3 in dairy herds of Antioquia, Colombia.

Bovine leukemia virus (BLV) is a retrovirus that primarily infects dairy cows. Although few studies have also used the tax gene, phylogenetic studies of BLV use mostly the env gene. The aim of this work was to establish the circulating genotypes of BLV in specialized dairy cattle from Antioquia, Colombia. Twenty blood samples from Holstein Friesian cows were collected, and their DNA was isolated. A PCR was performed for a partial region of the env and tax genes. A phylogenetic analysis was carried out using the maximum likelihood and Bayesian methods for both genes. Nineteen sequences were identified as genotype 1 by env and tax genes. Only one sequence was clustered with genotype 3 and had the highest proportion of different nucleotide sites compared to other strains. Four amino acid substitutions in the 134 amino acid residue fragment of the Env protein were identified in the Colombian sequences, and three new amino acid substitutions were reported in the 296 amino acid residue fragment of the Tax protein. R43K (Z finger), A185T (Activation domain), and L105F changes were identified in the genotype 3 sample. This genotype has been reported in the United States, Japan, Korea, and Mexico, but so far, not in Colombia. The country has a high rate of imported live animals, semen, and embryos, especially from the United States. Although it is necessary to evaluate samples from other regions of the country, the current results indicate the presence of two BLV genotypes in specialized dairy herds.

Genome-wide association study for reproduction traits in Colombian Creole Blanco Orejinegro cattle.

The profitability of the beef cattle production system relies heavily on reproductive traits. Unfortunately, certain traits, such as age at first calving (AFC), calving interval (CI), and gestation length (GL), can pose challenges in traditional breeding programs because of their low heritability (0.01-0.12) and sex-limited characteristics. Another important aspect is the conservation of the genetic resources of animals adapted to the Colombian regions, which implies the preservation and rational use of the creole breeds in the country market. Therefore, this study aimed to identify genomic regions in the creole cattle breed Blanco Orejinegro (BON) that influence the reproductive traits in females. The dataset comprised 439 animals and 118,116 single-nucleotide polymorphisms' (SNPs) markers. The GS3 program was used to identify the SNP effects employing the BAYES Cπ methodology. The number of SNPs with effect for AFC was 25, 1527 for CI, and 23 for GL. Some of the genes found associated with reproductive and growth traits as well as immune response and environmental adaptation ECE1, EPH, EPHB2, SMARCAL1, IGFBP5, IGFBP2, FCGRT, EGFR, MUL1, PINK1, STPG1, CNGB1, TGFB1, OXTR, IL22RA1, MYOM3, OXTR, CNR2, HIVEP3, CTPS1, CXCL8, FCGRT, MREG, TMEM169, PECR, and MC1R. Our results evidenced a high contribution of the genetic architecture of the Colombian creole cattle breed Blanco Orejinegro that may impact should be included in implementing genetic improvement and conservation programs.

Genetic-quantitative uni- and bi-trait analysis for growth traits in the Colombian creole breed Blanco Orejinegro (BON).

The Blanco Orejinegro (BON) is a Colombian creole cattle breed that is not genetically well characterized for growth traits. The aim of this work was to estimate genetic parameters for birth weight (BW), weaning weight (WW), yearling weight (YW), daily weight gain between birth and weaning (DWG), time to reach 120 kg of live weight (T120), and time to reach 60% of adult weight (T60%), and establish the selection criteria for growth traits in the BON population of Colombia. Genealogical and phenotypic information for BW, WW, YW, DWG, T120, and T60% traits of BON animals from 14 Colombian herds were used. These traits were analyzed with the AIREML method in a uni- and bi-trait animal model including the maternal effect for BW, WW, DWG, and T120. The direct heritability estimates values were 0.22 ± 0.059 (BW), 0.20 ± 0.057 (WW), 0.20 ± 0.153 (YW), 0.17 ± 0.07 (DWG), 0.26 (T120), and 0.44 ± 0.03 (T60%). The maternal heritability estimates values were 0.14 ± 0.040 (BW), 0.15 ± 0.039 (WW), 0.25 ± 0.06 (DWG), and 0.16 (T120). The direct genetic correlations were high ( >|0.60|) among all the traits, except between T60% with BW, WW, YW, and DWG (ranged from - 0.02 to - 0.51), all in a favorable direction. The results showed that there is genetic variation in the growth traits associated with the additive genetic effect, and they might respond to selection processes. Furthermore, genetic gains would improve through selection, especially for YW and T60% when WW is used as criterion.

Antibody seropositivity for Neospora caninum in Blanco Orejinegro cattle in Colombia and factors associated with the infection.

Neosporosis is a parasitic disease that causes abortions and economic losses in bovine production systems, but no studies have been found concerning its effect on the Creole cattle breed, Blanco Orejinegro (BON). The aim of this research was to establish the serological status of Colombian BON cattle against Neospora caninum and to determine the factors associated with seropositivity. Blood samples were taken from 363 animals from 13 herds in six states of Colombia, and analyzed by indirect ELISA using a commercial test. Information on sex, herd, generation group, and state was recorded. A survey was carried out with 26 questions related to productive, reproductive, and health factors per herd. A logistic regression analysis was performed and the ORs for significantly associated variables were estimated using the R software. General seropositivity of 73.5% (95% CI 68.6-77.9%) was obtained, and sex, age group, and herd were the variables significantly associated with seropositivity (p < 0.05). For the sex variable, seroprevalence levels of 79.6% (95% CI 74.3-84.1%) were recorded for females and 54.5% (95% CI 43.6-65.1%) for males. Herd seroprevalence varied between 58.3 and 95.8%, and the last generation showed the lowest positivity (51.2%, 95% CI 42.1-60.2%). The inadequate disposal of fetuses was a risk factor, while carrying out serological tests to new animals that enter the herd, the use of new gloves and palpation utensils for each animal, supplementation, and stabling were stated as protective factors. No effect of positivity was found in the last calving interval. The implementation of bovine neosporosis control programs to support breeding and conservation programs of the BON breed in Colombia is recommended.

Presence of bovine leukemia virus genotypes 1 and 3 in antioquia, colombia / Presencia de los genotipos 1 y 3 del virus de la leucosis bovina en antioquia, colombia

SUMMARY Bovine leukemia virus (BLV) is an immunosuppressant retrovirus that primarily affects dairy livestock, its target cells are B lymphocytes in which it integrates its genome infecting cattle for life. It is important to identify the distribution of the BLV in the region and to reconstruct its evolutionary history through phylogenetic trees, for the province of Antioquia this is the first report of the BLV genotypes. The aim of this study was to identify the genotype of BLV circulating in dairy cattle of different regions of the province of Antioquia, Colombia. DNA was extracted from 8 Holstein cows. Nested PCR was performed to amplify a fragment of 444 pb of the env gene. The env viral gene codes for surface protein gp51, gene is highly conserved and it is used for phylogenetic analysis. Obtained amplicons were sequenced, manually aligned in MEGA V7 program, and compared to 53 viral env gene sequences registered in GenBank. Phylogenetic analysis was performed by Maximum Likelihood and Bayesian methods. Two circulating genotypes were found: the most common genotype was 1, found in seven samples; they grouped with sequences from EE. UU, Argentina and Japan; only one sample was classified as genotype 3 and was grouped with samples from EE. UU and Japan. At least two genotypes (1 and 3) of BLV are circulating in Antioquia; however, more cattle and herds should be evaluated to elucidate the diversity and distribution of BLV in Colombia.

RESUMEN El virus de la leucosis bovina (BLV) es un retrovirus inmuno-supresor que afecta, principalmente, al ganado lechero; sus células diana son los linfocitos B, en los cuales, integra su genoma, infectando al ganado de por vida. Es importante identificar la distribución del BLV en la región y reconstruir su historia evolutiva, a través de árboles filogenéticos; para el departamento de Antioquia, este es el primer reporte de los genotipos del BLV. El objetivo de este estudio fue identificar el genotipo de BLV que circula en ganado lechero de diferentes regiones del departamento de Antioquia, Colombia. Se extrajo ADN de 8 vacas Holstein. Se realizó una PCR anidada, para amplificar un fragmento del gen env de 444 pb. El gen env viral codifica la proteína de superficie gp51, altamente conservado y es usado en análisis filogenéticos. Los amplicones obtenidos se secuenciaron, se alinearon manualmente en el programa MEGA V7 y se compararon con 53 secuencias del gen env viral, registradas en GenBank. El análisis filogenético, se realizó por métodos de Máxima Verosimilitud y Bayesianos. Se encontraron dos genotipos circulantes: el genotipo más común fue 1, hallado en siete muestras, agrupadas con secuencias de EE. UU, Argentina y Japón; solo una muestra se clasificó como genotipo 3 y se agrupó con muestras de EE. UU y Japón. Al menos dos genotipos (1 y 3) de BLV están circulando en Antioquia; sin embargo, se deben evaluar más bovinos y hatos para elucidar la diversidad y la distribución de BLV en Colombia.

Asociación del orden de parto y del componente racial con la prevalencia de mastitis clínica en un hato lechero especializado ubicado en el trópico alto de Colombia / Association of birth order and racial component with the prevalence of clinical mastitis in a specialized dairy herd located in the high tropics of Colombia / Associação da ordem de parto e do componente racial com a prevalência de mastite clínica em um rebanho leiteiro especializado situado no trópico alto da Colômbia

Resumen Introducción: conocer las variables asociadas a la prevalencia de mastitis clínica (PMC) ayuda a diseñar medidas de control más eficientes. Objetivos: cuantificar la PMC en un hato de especialización lechera, de acuerdo con la influencia del orden de parto (OP) y el efecto del componente racial (CR). Materiales y métodos: se realizó un estudio transversal, mediante el cual se calculó la PMC según el OP (1, 2, 3, 4, 5 y 6 o más), la probabilidad condicional (PC), la PMC para cada CR y la PMC según el OP para cada CR. Se realizó prueba de x2. Resultados: se observó una PMC global de 15 %. Se estableció una relación directamente proporcional entre el OP y la PMC. Las prevalencias calculadas fueron 9,9; 10,9; 12,2; 21,6; 21,7 y 21,4 %, para los OP 1, 2, 3, 4, 5 y 6 o más, respectivamente, con diferencias estadísticas significativas. La PC varió entre 9 % (1 y 2 OP) y 22,8 % (3 y 4 OP). Se observó una PMC de 16,7 % para la holstein (H), 8,9 % para el F1 de H por blanco orejinegro (BON) y de 9,4 % para la 3/4H x 1/4BON, sin diferencias significativas. No obstante, al comparar la H con los cruces por BON, sin importar el porcentaje del componente racial BON, se observaron diferencias estadísticas significativas. Conclusiones: la PMC incrementa con el aumento del OP; por tanto, los programas de vigilancia de la enfermedad deben intensificarse en vacas mayores. La raza BON aporta un factor de rusticidad a sus cruces que disminuye la PMC.

Abstract Introduction: The knowledge of the variables associated with the prevalence of clinical mastitis (PCM) can help to design more efficient control measures. Objectives: To quantify PCM in a specialized dairy herd, according to the influence ofbirth order (BO) and the effect of racial component (RC). Materials and methods: A transversal study was carried out to calculate PCM according to BO (1, 2, 3, 4, 5, and 6, or more), conditional probability (CP), PCM for each RC, and PCM according to BO for each RC. The x2 test was performed. Results: An overall PCM of 15% was observed. A directly proportional relationship was established between BO and PCM. The calculated prevalences were 9.9, 10.9, 12.2, 21.6, 21.7, and 21.4% for BO 1, 2, 3, 4, 5, and 6 or more, respectively, with significant statistical differences. CP varied between 9% (BO 1 and 2) and 22.8% (BO 3 and 4). A PCM of 16.7% was observed for Holstein (H) cows, 8.9% for Holstein F1 with Blanco Orejinegro cows (BON), and 9.4% for % H x V BON, with no significant differences. However, when comparing H with BON crosses, regardless of the percentage of the BON racial components, significant statistical differences were observed. Conclusions: PCM increases with increased BO; therefore, disease surveillance programs should be intensified in older cows. The BON breed contributes a rusticity factor to its crosses that decreases PCM.

Resumo Introdução: conhecer as variáveis associadas à prevalência de mastite clínica (PMC) ajuda a desenhar medidas de controle mais eficientes. Objetivos: quantificar a PMC em um rebanho de especialização leiteira, de acordo com a influência da ordem de parto (OP) e o efeito do componente racial (CR). Materiais e métodos: se realizou um estudo transversal, mediante o qual se calculou a PMC segundo o OP (1, 2, 3, 4, 5 e 6 ou mais), a probabilidade condicional (PC), a PMC para cada CR e a PMC segundo o OP para cada CR. Realizou-se exame de x2. Resultados: se observou uma PMC global de 15 %. Se estabeleceu uma relação diretamente proporcional entre o OP e a PMC. As prevalências calculadas foram 9,9; 10,9; 12,2; 21,6; 21,7 e 21,4 %, para os OP 1, 2, 3, 4, 5 e 6 ou mais respectivamente, com diferenças estatísticas significativas. A PC variou entre 9 % (1 e 2 OP) e 22,8 % (3 e 4 OP). Observou-se uma PMC de 16,7 % para a Holstein (H), 8,9 % para o F1 de H por branco orelhas negras (BON) e de 9,4 % para a 3/4H x 1/4BON, sem diferenças significativas. Não obstante, al comparar a H com os cruzamentos por BON, sem importar a porcentagem do componente racial BON, se observaram diferenças estatísticas significativas. Conclusões: a PMC incrementa com o aumento do OP; portanto, os programas de vigilância da doença devem intensificar-se em vacas mais velhas. A raça BON proporciona um fator de rusticidade aos seus cruzamentos que diminui a PMC.