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.

Association of the MC4R gene with growth traits and meat quality in Colombian hair sheep.

Objective: The objective of this study was to associate the 1016G > A variant of the melanocortin-4 receptor gene with lamb's weight, growth, and meat quality in the Colombian hair sheep breed. Materials and Methods: A total of 168 lambs, weights were measured at birth weight (BW), at weaning adjusted weaning weight (AWW), at 6 months [adjusted weight (AW180)], at slaughter adjusted slaughter weight (ASW), daily weight gain preweaning daily gain (preWDG), and postweaning daily gain (postWDG) weaning, and after slaughter, pH, texture, and cook-loss (CL) in the longissimus thoracis et lumborum (LTL) muscle according to the American Meat Science Association methodology. The 1016G > A genotypes were obtained by sequencing. Genotypic and allele frequencies, heterozygosities, and Hardy-Weinberg equilibrium (HWE) were estimated. Using a generalized linear model, the genotype and the allelic substitution effect were associated with the evaluated traits. Results: The heterozygous genotype (0.48) and G allele (0.61) were the most frequent. Heterozygosities were similar (0.47), indicating HWE. The genotype affected the BW (p < 0.05), with a higher value for the GG genotype (2.69 kg). AWW (12.75 kg), AW180 (19.67 kg), and ASW (31.21 kg) weights and daily weight gain (preWDG = 115.41 gm; postWDG = 96.16 gm) were not associated. Average pH, Warner-Bratzler shear force, and CL were 5.75 units, 49.46 N, and 32.02%, with no genotype effect. The G > A substitution only affected BW at -388 gm (p < 0.05). Conclusion: The 1016G > A variant is polymorphic and affects the BW but not other growth traits or the meat quality of the LTL muscle.

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.

Genomic characterization of the nucleus for conservation of the Chino Santandereano breed using SNP markers.

The Chino Santandereano (CHS) creole cattle breed has undergone an adaptation process of more than 500 years to the Colombian mountainous tropics. Despite its advantages, the breed has been replaced by specialized cattle that put it at risk of extinction. The aim of this work was to estimate the genomic diversity and population structure of the nucleus of conservation of the CHS breed. Thirty-seven CHS and 20 Brahman animals were genotyped due to the possible introgression of genes with the GGP Bovine LD v3 chip. Quality control was performed, and linkage disequilibrium (LD), effective population size (Ne), ROH segments, homozygosity, and genomic inbreeding in the breed were estimated. Subsequently, 50 K genomic information of the Holstein (n = 30) and Romosinuano (n = 8) breeds were included to estimate the minor allele frequency (MAF) with common markers and constructing the graphs of the principal component analysis (PCA). Pairwise FSTs were estimated and a neighbor-joining tree was constructed using the IBS matrix. Admixture was used with k = 2 to 10 for the racial composition. LD (r2) was found up to a distance of 0.13 Mb, r2 > 0.3 at a distance of 340.3 kb, and Ne of 32 ± 1. ROH inbreeding was 5.36 ± 0.86%, with a higher contribution from recent inbreeding (4.55%). The PCA showed that the creole breeds were closer together, and the Brahman was more distant. The admixture analysis suggested k = 5 possible ancestral groups and shows that within the CHS breed, there seem to be two different groups with little Holstein and Brahman introgression. The genetic diversity parameters obtained in this work show minimal diversity in this breed and reinforce the need to protect this resource and the conservation banks.

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.

Correction to: High throughput transcriptome analysis of coffee reveals prehaustorial resistance in response to Hemileia vastatrix infection.

All the transcriptome sequencing data mentioned in the original article is publicly available at the National Center of Biotechnology Information (NCBI).

High throughput transcriptome analysis of coffee reveals prehaustorial resistance in response to Hemileia vastatrix infection.

KEY MESSAGE: We provide a transcriptional profile of coffee rust interaction and identified putative up regulated resistant genes Coffee rust disease, caused by the fungus Hemileia vastatrix, is one of the major diseases in coffee throughout the world. The use of resistant cultivars is considered to be the most effective control strategy for this disease. To identify candidate genes related to different mechanism defense in coffee, we present a time-course comparative gene expression profile of Caturra (susceptible) and Híbrido de Timor (HdT, resistant) in response to H. vastatrix race XXXIII infection. The main objectives were to obtain a global overview of transcriptome in both interaction, compatible and incompatible, and, specially, analyze up-regulated HdT specific genes with inducible resistant and defense signaling pathways. Using both Coffea canephora as a reference genome and de novo assembly, we obtained 43,159 transcripts. At early infection events (12 and 24 h after infection), HdT responded to the attack of H. vastatrix with a larger number of up-regulated genes than Caturra, which was related to prehaustorial resistance. The genes found in HdT at early hours were involved in receptor-like kinases, response ion fluxes, production of reactive oxygen species, protein phosphorylation, ethylene biosynthesis and callose deposition. We selected 13 up-regulated HdT-exclusive genes to validate by real-time qPCR, which most of them confirmed their higher expression in HdT than in Caturra at early stage of infection. These genes have the potential to assist the development of new coffee rust control strategies. Collectively, our results provide understanding of expression profiles in coffee-H. vastatrix interaction over a time course in susceptible and resistant coffee plants.

Effects of some production factors on the content of kappa-casein in the milk of cows from different herds in Risaralda (Colombia) / Efecto de algunos factores productivos sobre el contenido de kappa-caseína en leche de vacas de diferentes hatos en Risaralda (Colombia) / Efeito de alguns fatores produtivos sobre o conteúdo de kappa-caseína no leite de vacas de diferentes rebanhos no departamento de Risaralda na Colômbia

K-casein is one of the most important milk proteins by their relationship to traits associated with the cheese production. Therefore, the aim of this study was to determine the relationship between some production traits and kappa casein content in the milk of cows in eight herds from Pereira, Risaralda. 48 milk samples from cows were analysed for k-casein content by polyacrylamide gel electrophoresis in one dimension (SDS-PAGE Triazine) and were taken the effect of the breed, the supplementation, calving number, days in milk and milk yield. The information was evaluated using a generalized linear model using R software with agricolae and car libraries (R Core Team). The mean of k-casein was 3.55 g/L and the coefficient of variation was 19.3%, the coefficient of variation for milk production was 40.3%. The traits evaluated was only significant (p<0.05) the type of supplementation and. Was found, an inverse relation of k-casein with the number of calving, although it was not significant, this may be due to number of calving it is indicative of the age of the cow and the racial component of the generation.

La k-caseína es una de las proteínas más importantes de la leche por su relación con diferentes características asociadas a la producción de quesos. Por lo anterior, el objetivo de este trabajo fue determinar la relación entre algunas características productivas y el contenido de kappa caseína de la leche de vacas en ocho hatos del Municipio de Pereira, Risaralda. Para esto, se tomaron muestras de leche de 48 vacas de diferente tipo racial, las que se les determinó el contenido de k-caseína mediante electroforesis en gel de poliacrilamida en una dimensión (Triacina SDS-PAGE) y se determinó el efecto que ejerce el grupo racial, el tipo de suplementación, el número de parto, los días en lactancia, y el volumen de leche producido. La información fue evaluada mediante un modelo lineal generalizado, usando el software R mediante las librerías agricolae y car (R Core Team). Se encontró un valor medio de k-caseína de 3,55 g/L y un coeficiente de variación del 19,3%, el coeficiente de variación para la producción de leche fue de 40,3%. De los caracteres evaluadas sólo fue significativo (p<0,05) el tipo de suplementación. Además, se encontró una relación inversa entre el contenido de k-caseína con el número de parto, aunque no fue significativa, esto se puede deber a que el número de partos es un indicativo de la edad de la vaca y el componente racial de la generación.

A k-caseína é uma das proteínas mais importantes do leite por sua relação com diferentes características associadas a produção de queijos. Pelo anterior, o objetivo deste trabalho foi determinar a relação entre algumas características produtivas e o conteúdo de kappa caseína do leite de vacas em oito rebanhos do município de Pereira, Risaralda. Para isto, tomaram-se amostras de leite de 48 vacas de diferente tipo racial, nas quais determinou-se o conteúdo de k-caseína mediante eletroforese em gel de poliacrilamida em uma dimens ão (Triacina SDS-PAGE) e determinou-se o efeito que exerce o grupo racial, o tipo de suplementação, o número de parto, os dias em lactação e o volume do leite produzido. A informação foi avaliada mediante um modelo linear generalizado usando o software R mediante as livrarias agricolae e car (R Core Team). Encontrou-se um valor médio de k-caseína de 3,55 g/L e um coeficiente de variação de 19,3%, o coeficiente de variação para a produção do leite foi de 40,3%. Dos caracteres avaliados só foi significativo (p<0,05) o tipo de suplementação. Além, encontrou-se uma relação inversa entre o conteúdo de k-caseína com o número de parto, ainda que não foi significativa, isto pode-se dever a que o número de partos é um indicativo da idade da vaca e o componente racial da geração.

Comparison of nonlinear models to describe growth in Blanco Orejinegro (BON) cattle / Comparación de modelos no lineales para describir el crecimiento en ganado Blanco Orejinegro (BON) / Comparação de modelos não lineares para descrever o crescimento em gado Blanco Orejinegro (BON)

BON cattle is an important genetic resource. It is necessary to describe the productive behavior of BON to improve the use of this breed. The objective of this study was to determine the model that best fit BON growth. Nonlinear models (Gompertz, logistic, Brody and von Bertalanffy) were compared to determine the one with the best fit and estimate the parameters for each model. Brody showed the best fit, with the lowest sum of squared errors (SQE) for both Akaike information criterion (AIC) and Bayesian information criterion (BIC). Brody parameters were β0 (mature weight: 590 kg) and β2 (maturity index: 0.00153 ± 0.0000042 kg/day). The maturity index was similar and in some cases higher to that found in some crosses of commercial beef cattle, highlighting the precocity of BON, which reaches about 52.9% maturity at 12 months. Additionally, the age BON reaches 75% maturity was approximately 708 days, which shows its precocity and growth potential. This results highlight the importance of this breed as a valuable genetic resource for cattle farming in the tropics.

El ganado BON constituye un recurso genético y ganadero de gran importancia, por lo que describir su comportamiento productivo es necesario para garantizar su utilización. El objetivo del presente trabajo fue determinar el modelo que mejor se ajustara al crecimiento del ganado BON, por lo que se compararon diferentes modelos no lineales (Gompertz, Logístico, de Brody y de Von Bertalanffy), con el fin de determinar el que mejor se ajusta y estimar los parámetros para cada uno. El modelo que mejor se ajustó al crecimiento del BON fue el de Brody, mostrando menores valores de sumatoria de cuadrados del error (SQE), de AIC y de BIC. Por otra parte, los parámetros hallados para el modelo de Brody fueron: β0 , interpretado como el peso maduro, de 590 kg y el parámetro β2 , correspondiente con el índice de madurez, de 0,00153 ± 0,0000042 kg/día. El índice de madurez fue similar y en algunos casos superior al encontrado en algunos cruces y ganados de carne comerciales, lo que resalta la precocidad que presenta el ganado BON, que alcanza aproximadamente 52,9% de madurez a los 12 meses. Adicionalmente, se encontró que la edad a la cual el BON alcanza el 75% de madurez fue de 708 días aproximadamente, lo que muestra su precocidad y capacidad de crecimiento. Lo expuesto anteriormente resalta la importancia del ganado BON como un recurso genético y productivo para los programas de producción bovina en el trópico.

O gado BON, constitui um recurso genético e de produção de grande importância, pelo qual, descrever seu comportamento e desempenho produtivo e mostrar suas fortalezas é necessário para garantir sua utilização. O objetivo do presente trabalho foi determinar o modelo que melhor tivesse ajuste não linear (Gompertz, Logístico, de Brody e de Von Bertalanffy), com o fim de determinar o modelo que melhor se ajustasse e estimar os parâmetros para cada um deles. O modelo que melhor se ajustou ao crescimento do gado BON foi o de Brody, apresentando menores valores na somatória de quadrados do erro (SQE), de AIC e de BIC. Por outro lado, os parâmetros encontrados para o modelo de Brody foram: β0, interpretado como o peso maduro, de 590 kg e o parâmetro β2, que corresponde com o índice de maturidade, de 0,00153 ± 0,0000042 kg/dia. O índice de maturidade foi similar e em alguns casos até superior ao encontrado em alguns cruzamentos e gados de corte não registrados, o que ressalta a precocidade que apresenta o gado BON, que consegue aproximadamente 52,9% de maturidade aos 365 dias (12 meses). Adicionalmente, encontrou-se que a idade na qual o gado BON consegue o 75% de maturidade foi de 708 dias (23,6 meses) aproximadamente, o que demostra sua precocidade e capacidade de crescimento. O exposto anteriormente ressalta a importância do gado BON como um recurso genético com boas qualidades produtivas e reprodutivas para os programas de produção bovina no tropico.