Frequency of genotypic markers for genetic disorders, colour, polledness, and major genes in Blanco Orejinegro cattle.

The purpose of this work was to establish DNA marker frequencies for genetic disorders, colour, horned/polled trait, and major genes of importance for productive and reproductive traits in Blanco Orejinegro (BON) cattle. The Blanco Orejinegro breed is a Colombian creole breed characterized by a white hair coat on black skin with black ears, black hair on the middle part of the legs, and absence of horns. We genotyped 420 animals of Colombia, 70 with the GGP-Bovine 150 K chip and 350 with the GGP-Bovine 50 K chip. The markers were associated with 50 genetic diseases, 52 major gene variants related to productive traits, and 12 variants related to coat coloration, presence of horns, and adaptation, selected from the information contained in the chips. Genotype frequencies were estimated using the R statistical program. Genetic disorder annotations were derived using the Online Mendelian Inheritance in Animals tool (OMIA) and the average inbreeding coefficient (F) (n = 7799) using the MTDFNRM program. Carriers were found for 16 of the genetic disorders evaluated but with low frequencies (0.24 to 2.46%); no homozygous animals were found for the disorders. Carriers were associated with disorders such as bovine leukocyte adhesion deficiency (BLAD), deficiency of uridine monophosphate synthase (DUMPS), syndactyly, and epidermolysis bullosa (EB). The F was 4.41%. Concerning the genes associated with colour (TYR, MC1R, and PMEL), alleles related to black pigmentation, the absence of horns (polledness), and slick coat (an adaptive trait) were highly frequent (> 81.90%). Markers associated with milk production and quality, yellow fat, and fertility showed variable frequencies, indicating selection potential. Allele frequency of genetic disorders in BON cattle was low, suggesting few genetic disorder problems, with syndactyly being the most frequent condition. The markers associated with colour and polledness were almost fixed, with a frequency at or near 100%. Production and reproduction markers showed variability for selection.

Diversity analysis, runs of homozygosity and genomic inbreeding reveal recent selection in Blanco Orejinegro cattle.

Blanco Orejinegro (BON) cattle have 500 years of adaptation to the Colombian tropic, but little is known about their genetic history. Our aim was to estimate levels of linkage disequilibrium (LD), effective population size (Ne), genomic inbreeding for runs of homozygosity (FROH ), genomic relation matrix (FGRM ), excess of homozygotes (FHOM ) and pedigree information (FPEDCOMP ) and to characterize the runs of homozygosity (ROH), searching for selection signatures. A total of 419 BON animals were genotyped, 70 with a 150K chip and 349 with a 50K chip. Next, an imputation to 50K was performed, and, after editing, databases of 40K were obtained. The PLINK v1.90 and R programs were used to estimate LD, ROH, FROH and FHOM . The SNeP v1.1 program was used to obtain Ne, and PreGSf90 was used to elaborate the scaled G matrix. The MTDFNRM program was used to estimate FPEDCOMP . The LD mean as r2 at 1 Mb was 0.21 (r2  > 0.30 at a distance of 96.72kb), and Ne was 123 ± 1. A total of 7,652 homozygous segments were obtained, with a mean of 18.35 ± 0.55 ROH/animal. Most of the genome was covered by long ROHs (ROH>8 Mb  = 4.86%), indicating significant recent inbreeding. The average inbreeding coefficient for FPEDCOM , FGRM , FHOM and FROH was 4.41%, 4.18%, 5.58% and 6.78%, respectively. The highest correlation was observed between FHOM and FROH (0.95). ROH hotspots/islands were defined using the extreme values of a box plot that was generated, and correspond to QTLs related to milk yield (55.11%), external appearance (13.47%), production (13.30%), reproduction (8.15%), health (5.24%) and meat carcass (4.74%).

Variance and covariance components and genetic parameters for fat and protein yield of first-lactation Holstein cows using random regression models / Componentes de varianza y covarianza y parámetros genéticos para grasa y proteína láctea en vacas Holstein de primera lactancia mediante modelos de regresión aleatoria / Componentes de variância e covariância e parâmetros genéticos para gordura e proteína do leite em vacas da raça Holandesa de primeira lactação por meio de modelos de regressão aleatória

Background: the genetic parameters of the lactation curve in dairy cattle can be analyzed as longitudinal data using Random Regression Models (RRM). Objective: to estimate the (co) variance components and genetic parameters for fat (F) and protein (P) yield in first lactation Holstein cows of Antioquia (Colombia) by RRM based on Legendre polynomials. Methods: monthly F and P records (9,479) from 1,210 first-lactation Holstein cows were used. Twenty-two and 24 RRM were used for F and P, respectively, with different orthogonal Legendre-polynomial orders to estimate the fixed-curve population coefficients and predict direct-genetic additive and permanent environment effects. The models considered homogeneous and heterogeneous residual variances of 5, 7, and 10 classes. Results: the best fit for F was the fourth order model for the population fixed-curve and the additive genetic effect, and the third order for the permanent environment with seven heterogeneous variances. The best fit for P was the fifth order model for the population fixed-curve and the additive genetic and permanent environmental effects with five heterogeneous variances. The variance for the animals' genetic, phenotypic, permanent environment, and residual effects for both F and P decreased as lactation progressed. F and P heritabilities were between 0.13 and 0.38, and 0.12 and 0.32, respectively. Conclusion: first-birth animals can be selected in Antioquia for F and P characteristics. Selection should be done preferably at the beginning of lactation since they reach the highest heritability values at this time.

Antecedentes: los parámetros genéticos de la curva de lactancia en ganado de leche pueden ser analizados como datos longitudinales usando Modelos de Regresión Aleatoria (RRM). Objetivo: estimar mediante RRM basados en polinomios de Legendre componentes de (co) varianza y parámetros genéticos para producción de grasa (F) y proteína (P) láctea en vacas Holstein de primera lactancia de Antioquia (Colombia). Métodos: se incluyeron 9.479 registros mensuales de F y P pertenecientes a 1.210 vacas Holstein de primera lactancia. Para F y P se usaron 22 y 24 RRM respectivamente, con diferentes órdenes de polinomio ortogonal de Legendre para estimar los coeficientes de la curva fija de la población, la predicción de los efectos genético aditivo directo y del ambiente permanente. Los modelos consideraron varianzas residuales homogéneas y heterogéneas de 5, 7 y 10 clases. Resultados: para F, el mejor modelo fue el de cuarto orden para la curva fija de la población y el efecto genético aditivo, y de tercer orden para el ambiente permanente con siete varianzas heterogéneas. Para P, el modelo que presentó mejor ajuste fue el de quinto orden para la curva fija de la población, el efecto genético aditivo y el ambiente permanente y 5 varianzas heterogéneas. Para ambas características las varianzas genética aditiva directa, fenotípica, de ambiente permanente y residual disminuyeron a medida que avanzaba la lactancia. Las heredabilidades para F y P estuvieron entre 0,13 y 0,38, y entre 0,12 y 0,32, respectivamente. Conclusión: es posible realizar la selección para F y P en animales de primer parto en el departamento de Antioquia, preferiblemente al inicio de la lactancia, ya que ambas características presentan heredabilidades altas en esta etapa.

Antecedentes: os parâmetros genéticos da produção de leite podem ser estimados usando Modelos de Regressão Aleatória (RRM). Objetivo: estimar por RRM com base em polinômios de Legendre os componentes de variância e covariância e os parâmetros genéticos para produção de gordura (F) e proteína (P) em vacas leiteiras de primeira lactação da raça holandesa em rebanhos de Antioquia, Colômbia. Métodos: foram avaliadas 9.479 registros mensais de F e P pertencentes a 1.210 vacas. Para F e P foram usados 22 e 24 RRM, respectivamente, com diferentes ordens de polinomiais ortogonais de Legendre para estimar os coeficientes da curva fixa da população, os efeitos genéticos aditivo direito, do ambiente permanente e residual. Os modelos consideraram variâncias residuais homogêneas e heterogêneas de 5, 7 e 10 classes. Resultados: para F, o melhor modelo foi o de quarta ordem para a curva fixa da população e o efeito genético aditivo, e de terceira ordem para o ambiente permanente com sete variâncias heterogêneas. Para P, o modelo que forneceu o melhor ajuste foi do quinto ordem para a curva fixa da população, o efeito genético aditivo e de ambiente permanente, e com 5 variâncias heterogêneas. Para ambas as características as variâncias genética aditiva direita, fenotípica e residual diminuíram no tempo. As herdabilidades para F e P ficaram entre 0,13 e 0,38 e entre 0,12 e 0,32, respectivamente. Conclusão: é possível fazer a seleção de animais da raça holandesa para F e P, de preferência no início da lactação, pois as duas características têm altas herdabilidades.