Genetic parameters of growth traits and carcass weight of New Zealand white rabbits in a tropical dry forest area.

OBJECTIVE: The objective of this study was to estimate the heritability (h 2), repeatability (r), and correlations (ryiyi ) in some traits of zootechnical interest in a population of New Zealand white rabbits of a tropical dry forest area. MATERIALS AND METHODS: Three mating groups were formed, each one of 1 male and 70 females. The traits evaluated were litter size at birth (LB), born alive (BA), born dead (BD), litter weight born alive (LW), litter weight at weaning (LWW), weaning weight (WW), slaughter weight (SW), and carcass weight (CW). Weaning took place at 42 days, and the fattening phase lasted 60 ± 3 days. A descriptive statistical study was carried out on the study variables. Paternal heritability was estimated ( h f 2 ) and maternal ( h m 2 ), repeatability, rabbit index IC, and Pearson's correlations (ryiyi ) between traits. The descriptive statistics showed high variation for the BD traits. RESULTS: The values of the productivity found were similar to those presented in studies around the world. h 2 presented magnitudes between low and medium. h f 2 ranged between 0.09 and 0.42 and between 0.11 and 0.45 for h m 2 . In general, the values of h m 2 were higher than the values of h f 2 . The r values for the traits LB, BA, LW, LWW, and SW presented low magnitude, while it was medium for WW and CW. From the values of r, IC was calculated for each of the rabbits, allowing their categorization, which will be used in future selection plans. ryiyi among the variables ranged from -0.01 to 0.860. They were generally positive and mostly not significant (p > 0.05); they took a magnitude from low to moderate, except for the correlation between LB and BA. CONCLUSION: The production of rabbits under tropical conditions is similar to other reports. The genetic parameters evaluated were medium-to-low, indicating a robust non-additive gene and/or environmental effect.

Polymorphisms in TLR4 Gene Associated With Somatic Cell Score in Water Buffaloes (Bubalus bubalis).

Considering the importance of the diseases affecting the productive performance of animals in the dairy industry worldwide, it is necessary to implement tools that help to control and limit the occurrence of such diseases. As the increased somatic cell counts (SCC) are a direct expression of the inflammatory process, they are candidates to become the usual parameter for assessing udder health regarding milk quality and for monitoring mastitis incidences. Toll-Like Receptors are membrane proteins that play a key role in immunity, recognizing pathogens and, subsequently, activating immune responses. The present study was conducted to identify single nucleotide polymorphisms in the TLR4 gene of buffaloes and to analyze its associations with somatic cell counts. DNA samples of 120 Murrah buffaloes were used. The whole coding region of the TLR4 gene was amplified by polymerase chain reaction reactions and sequenced for polymorphism scanning. A total of 13 polymorphisms were identified for the sequenced regions of the TLR4, most of which are in the coding region. The association with the somatic cell score was highly significant (p < 0.001) for all identified polymorphisms of TLR4 gene (g.54621T>A, g.54429G>T, g.54407T>A, g.46616C>A, g.46613T>G, g.46612A>G, g.46611C>A, g.46609T>G, g.46541C>G, g.46526C>A, g.46516T>C, g.46376C>T, g.46372T>C). Therefore, it is suggested that the markers of the TLR4 gene can be used as molecular markers for mastitis resistance in buffaloes, due to their association with somatic cell counts.

Linkage Disequilibrium-Based Inference of Genome Homology and Chromosomal Rearrangements Between Species.

The aim of this study was to analyze the genomic homology between cattle (Bos taurus) and buffaloes (Bubalus bubalis) and to propose a rearrangement of the buffalo genome through linkage disequilibrium analyses of buffalo SNP markers referenced in the cattle genome assembly and also compare it to the buffalo genome assembly. A panel of bovine SNPs (single nucleotide polymorphisms) was used for hierarchical, non-hierarchical and admixture cluster analyses. Thus, the linkage disequilibrium information between markers of a specific panel of buffalo was used to infer chromosomal rearrangement. Haplotype diversity and imputation accuracy of the submetacentric chromosomes were also analyzed. The genomic homology between the species enabled us to use the bovine genome assembly to recreate a buffalo genomic reference by rearranging the submetacentric chromosomes. The centromere of the submetacentric chromosomes exhibited high linkage disequilibrium and low haplotype diversity. It allowed hypothesizing about chromosome evolution. It indicated that buffalo submetacentric chromosomes are a centric fusion of ancestral acrocentric chromosomes. The chronology of fusions was also suggested. Moreover, a linear regression between buffalo and cattle rearranged assembly and the imputation accuracy indicated that the rearrangement of the chromosomes was adequate. When using the bovine reference genome assembly, the rearrangement of the buffalo submetacentric chromosomes could be done by SNP BTA (chromosome of Bos taurus) calculations: shorter BTA (shorter arm of buffalo chromosome) was given as [(shorter BTA length - SNP position in shorter BTA)] and larger BTA length as [shorter BTA length + (larger BTA length - SNP position in larger BTA)]. Finally, the proposed linkage disequilibrium-based method can be applied to elucidate other chromosomal rearrangement events in other species with the possibility of better understanding the evolutionary relationship between their genomes.

Genome-wide association study applied to type traits related to milk yield in water buffaloes (Bubalus bubalis).

This research aimed to estimate genetic parameters for milk yield and type traits [withers height (WH), croup height (CH), body length (BL), croup length (CL), iliac width (ILW), ischial width (ISW), and thoracic circumference] in Murrah buffaloes and to identify genomic regions related to type traits by applying a single-step genome-wide association study. Data used to estimate the genetic parameters consisted of 601 records of milk yield in the first lactation and the aforementioned type traits. For the single-step genome-wide association study, 322 samples genotyped with a 90K Axiom Buffalo Genotyping array (Thermo Fisher Scientific, Santa Clara, CA) were used. Bivariate analysis revealed that heritability for milk yield (kg) at 305 d was 0.31 ± 0.11, whereas it ranged from 0.22 ± 0.07 to 0.34 ± 0.09 for the studied conformation traits. Based on the percentages of genetic variance explained by windows of 10 markers, there were 16 genomic regions explaining more than 0.5% of the variance for WH, CH, BL, CL, ILW, ISW, and thoracic circumference. Between those regions, 4 were associated with more than 1 trait, suggesting pleiotropic roles for some genes of Bos taurus autosome (BTA) 12 on CL and WH, BTA13 on ISW and ILW, BTA23 on CH and BL, and BTA28 on ISW and BL. Most of these regions coincide with known quantitative trait loci for milk traits. Thus, further studies based on sequence data will help to validate the association of this region with type traits and likely identify the causal mutations.

Genotype-environment interaction for age at first calving in buffaloes, using the reaction norm model.

The objective of this study was to evaluate the genotype-environment interaction effect on age at first calving in buffaloes. The records were analysed using two approaches: (a) standard animal model and (b) reaction norm model. For the reaction norm analysis, two environmental gradients were formed, using age of first calving or milk yield group contemporary average. The results showed differences in the heritability estimates when using the two approaches. The reaction norm model indicated high heritability in more favourable environments and low magnitude genetic correlations between extreme environments. Based on our findings, we verified the significance of the genotype-environment interaction effect on age at first calving in buffaloes.

Polymorphisms in oxytocin and α1a adrenergic receptor genes and their effects on production traits in dairy buffaloes.

The use of molecular markers may auxiliary the buffalo breeding. The oxytocin (OXT) and the adrenergic receptor α1A (ADRA1A) may be involved in milk ejection in ruminants. The aim of this study was to verify the existence of polymorphisms in the OXT and ADRA1A genes and their associations with milk production traits. A total of 220 buffaloes were genotyped using PCR-RFLP for both genes. The SNP identified in the ADRA1A gene was associated with protein percentage in dairy buffaloes. This is the first report of such association in the literature, which has not been studied in other species.

Random regression models for milk, fat and protein in Colombian Buffaloes / Modelos de regresión aleatoria para leche, grasa y proteína en búfalos de Colombia

Objective. Covariance functions for additive genetic and permanent environmental effects and, subsequently, genetic parameters for test-day milk (MY), fat (FY) protein (PY) yields and mozzarella cheese (MP) in buffaloes from Colombia were estimate by using Random regression models (RRM) with Legendre polynomials (LP). Materials and Methods. Test-day records of MY, FY, PY and MP from 1884 first lactations of buffalo cows from 228 sires were analyzed. The animals belonged to 14 herds in Colombia between 1995 and 2011. Ten monthly classes of days in milk were considered for test-day yields. The contemporary groups were defined as herd-year-month of milk test-day. Random additive genetic, permanent environmental and residual effects were included in the model. Fixed effects included the contemporary group, linear and quadratic effects of age at calving, and the average lactation curve of the population, which was modeled by third-order LP. Random additive genetic and permanent environmental effects were estimated by RRM using third- to- sixth-order LP. Residual variances were modeled using homogeneous and heterogeneous structures. Results. The heritabilities for MY, FY, PY and MP ranged from 0.38 to 0.05, 0.67 to 0.11, 0.50 to 0.07 and 0.50 to 0.11, respectively. Conclusions. In general, the RRM are adequate to describe the genetic variation in test-day of MY, FY, PY and MP in Colombian buffaloes.

Objetivo. Fueron estimadas funciones de covariancia para los efectos genéticos aditivos y de ambiente permanente, y posteriormente fueron estimados los parámetros genéticos para la producción de leche en el día del control (PDC) para leche (MY), grasa (FY), proteína (PY) y producción de queso mozzarella (MP), usando modelos de regresión aleatoria (RRM) mediante Polinomios Ortogonales de Legendre (LP) en búfalos de Colombia. Materiales y Métodos. Fueron analizados 1884 registros de PDC de primeras lactancias para MY, FY, PY y MP, hijas de 228 reproductores. Los registros procedían de 14 rebaños entre 1995 y 2011. Para las PDC fueron consideradas 10 clases mensuales de días en lactancia. Los grupos contemporáneos fueron definidos como rebaño-año-mes de control. Fueron incluidos en el modelo efectos aleatorios genético aditivo, de ambiente permanente y residual. Los efectos fijos incluidos fueron grupo contemporáneo, efecto lineal y cuadrático de edad al parto, y curva promedia de la lactancia de la población, la cual fue modelada por un LP de tercera orden. Los efectos aleatorios genético aditivo y de ambiente permanente fueron estimados por RRM mediante LP de tercero a sexto orden. Las variancias residuales fueron modeladas usando estructuras homogéneas y heterogéneas. Resultados. Las heredabilidades para MY, FY, PY y MP variaron de 0.38 a 0.05, 0.67 a 0.11, 0.50 a 0.07 y 0.50 a 0.11, respectivamente. Conclusiones. En general, los RRM son adecuados para describir la variación genética para la PDC de MY, FY, PF y MP en búfalos de Colombia.

Polymorphisms in the MTRN1A gene and their effects on the productive and reproductive traits in buffaloes.

The main environmental factor that affects the regulation of reproductive seasonality is photoperiod through its effects on melatonin secretion. The melatonin receptor MTRN1A appears to be involved in regulating the reproductive seasonality and milk production in the period. The aim of this study was to identify polymorphisms in the MTRN1A gene and their possible associations with milk, fat and protein productions, fat and protein percentages, age at first calving, and first calving interval in buffaloes. Three genotypes (CC, CT, and TT) were identified by PCR-RFLP, and there was a significant association with protein percentage (P < 0.0001). Further studies are necessary to better understand the influence of melatonin gene and their receptors in the productive functions of buffaloes.

Estimation of genetic parameters for test-day milk yield in first calving buffaloes / Estimación de parámetros genéticos para producción de leche en el día de control en búfalas de primer parto / Estimação de parâmetros genéticos para produção do leite no dia do controle em búfalas de primeiro parto

Background: the milk yield records measured along lactation provide an example of repeated measures; the random regression models are an appealing approach to model repeated measures and to estimate genetic parameters. Objective: to estimate the genetic parameters by modeling the additive genetic and the residual variance for test-day milk yield in first calving buffaloes. Methods: 3,986 test-day data from 1,246 first lactations of crossbred buffalo daughters of 23 sires and 391 dams between 1997 and 2008 from five farms were used. The model included the genetic and permanent environment additive as the random effect and the contemporary group (year, month of test-day) and age at calving as covariable (linear) fixed effects. The fixed (third order) and random (third to ninth order) regressions were obtained by Legendre polynomials. The residual variances were modeled with a homogeneous structure and various heterogeneous classes. The variance components were estimated using the WOMBAT statistical program (Meyer, 2006). Results: according to the likelihood ratio test, the best model included four variance classes, considering Legendre polynomials of the fourth order for permanent environment and additive genetic effects. The heritabilities estimates were low, varying from 0.0 to 0.14. The estimates of genetic correlations were high and positive among PDC1 and PDC8, except for PCD9, which was negative. This indicates that for any of the selection criteria adopted, the indirect genetic gain is expected for all lactation curves, except for PCD9. Conclusion: heterogeneity of residual variances should be considered in models whose goal is to examine the alterations of variances according to day of lactation.

Antecedentes: los registros de producción de leche medidos a lo largo de la lactancia son un ejemplo de medidas repetidas, los modelos de regresión aleatoria presentan un enfoque atractivo para modelar medidas repetidas y para estimar parámetros genéticos. Objetivo: estimar parámetros genéticos a través de la modelación de la varianza genética y residual para producción de leche en el día de control en búfalas de primer parto. Métodos: fueron analizados 3986 controles de producción de leche en la primera lactancia de 1246 búfalas, hijas de 391 hembras y 23 toros, durante los años 1997 hasta 2008 en 5 fincas. El modelo incluyó como efectos aleatorios genético aditivo y de ambiente permanente, como efectos fijos grupo contemporáneo compuesto por mes, año de control y la covariable de la edad de la búfala al parto (lineal). Las regresiones fijas (3er orden) y aleatorias (3er a 9no orden) fueron obtenidas mediante polinomios de Legendre. Las varianzas residuales fueron modeladas con una estructura homogénea y varias clases heterogéneas. Los componentes de varianza fueron estimados utilizando el programa WOMBAT. Resultados: de acuerdo con la prueba de la razón de verosimilitud, el mejor modelo fue con 4 clases de varianzas residuales, siendo considerado un polinomio de Legendre de cuarto orden para el efecto de ambiente permanente y genético aditivo. Las heredabilidades fueron bajas, variando desde 0,00 hasta 0,14. Las correlaciones genéticas fueron altas y positivas entre los PDC1 a PDC8, excepto en el PDC9 que fue negativo con respecto a los demás controles. Conclusiones: es necesario considerar la heterogeneidad de varianzas residuales en los modelos estudiados, con el fin de modelar los cambios en las variaciones respecto a los días en lactancia.

Antecedentes: os registros da produção do leite medidos ao longo da lactação, apresentam um exemplo de medidas repetidas. Os modelos de regressão aleatória apresentam abordagem atraente para modelar medidas repetidas e estimar parâmetros genéticos. Objetivo: estimar parámetros genéticos mediante a modelação das variâncias genéticas e residual da produção do leite no dia do controle em búfalas de primeiro parto. Métodos: foram analisados 3986 controles de produção de leite em primeiras lactações de 1246 búfalas, filhas de 391 fêmeas e 23 touros, entre 1997 e 2008 em 5 fazendas. No modelo foram incluídos como efeitos aleatórios o genético aditivo e ambiente permanente, e como fixos o grupo contemporâneo (mês e ano de controle) e a covariável a idade da búfala ao parto (Lineal). As regressões fixas (3° ordem) e aleatórias (3° a 9° ordem) foram obtidas mediante polinômios ortogonais de Legendre. As variâncias residuais foram modeladas mediante estruturas homogêneas e diferentes classes heterogêneas. Os componentes de variância foram estimadas mediante o software WOMBAT. Resultados: de acordo com a prova da máxima verossimilhança, o melhor modelo foi com 4 classes de variâncias residuais, sendo considerado polinômios de Legendre de quarto ordem para o efeito de ambiente permanente e genético aditivo. As herdabilidades foram baixas, variando desde 0,00 até 0,14. As correlações genéticas foram altas e positivas entre o PDC1 e PDC8, a exceção do PDC9 que apresentou valores negativos com respeito aos outros controles. Conclusões:é necessário considerar heterogeneidade de variâncias nos modelos estudados, tentando modelar as mudanças nas variações respeito aos dias em lactação.

Multiple-trait random regression models for the estimation of genetic parameters for milk, fat, and protein yield in buffaloes.

In this study, genetic parameters for test-day milk, fat, and protein yield were estimated for the first lactation. The data analyzed consisted of 1,433 first lactations of Murrah buffaloes, daughters of 113 sires from 12 herds in the state of São Paulo, Brazil, with calvings from 1985 to 2007. Ten-month classes of lactation days were considered for the test-day yields. The (co)variance components for the 3 traits were estimated using the regression analyses by Bayesian inference applying an animal model by Gibbs sampling. The contemporary groups were defined as herd-year-month of the test day. In the model, the random effects were additive genetic, permanent environment, and residual. The fixed effects were contemporary group and number of milkings (1 or 2), the linear and quadratic effects of the covariable age of the buffalo at calving, as well as the mean lactation curve of the population, which was modeled by orthogonal Legendre polynomials of fourth order. The random effects for the traits studied were modeled by Legendre polynomials of third and fourth order for additive genetic and permanent environment, respectively, the residual variances were modeled considering 4 residual classes. The heritability estimates for the traits were moderate (from 0.21-0.38), with higher estimates in the intermediate lactation phase. The genetic correlation estimates within and among the traits varied from 0.05 to 0.99. The results indicate that the selection for any trait test day will result in an indirect genetic gain for milk, fat, and protein yield in all periods of the lactation curve. The accuracy associated with estimated breeding values obtained using multi-trait random regression was slightly higher (around 8%) compared with single-trait random regression. This difference may be because to the greater amount of information available per animal.

Growth Curves and Genetic Parameters in ColombianBuffaloes (Bubalus bubalis Artiodactyla, Bovidae) / Curvas de crecimiento y parámetros genéticos en búfalos (Bubalus bubalisArtiodactyla, Bovidae) en Colombia / Curvas de crescimento e parâmetros genéticos em búfalos (Bubalus bubalisArtiodactyla, Bovidae) na Colômbia

Non-linear mathematical functions proposed by Brody, Gompertz, Richards, Bertalanffy and Verhulstwere compared in several buffalo production systems in Colombia. Herds were located in three provinces:Antioquia, Caldas, and Cordoba. Growth was better described by the curves proposed by Brody andGompertz. Using the datasets from herds from Caldas, heritabilities for traits such as weaning weight(WW), weight and maturity at one year of age (WY and MY, respectively), age at 50% and 75% of maturity(A50% and A75%, respectively), adult weight (β0), and other characteristics, were also estimated. Directand maternal heritabilities for WW were 0.19 and 0.12, respectively. Direct heritabilities for WY, MY,A50%, A75% and β0 were 0.39, 0.15, 0.09, 0.20 and 0.09, respectively. The genetic correlation for β0 andWY was -0.47, indicating that selection for heavy weight at one year of age will lead to lower weight at adultage. These data suggest that selection based on maturity traits can generate changes in characteristics ofeconomic importance in beef–type buffalo farms.

Funciones matemáticas no lineales propuestas por Brody, Gompertz, Richards, Bertalanffy y Verhulst fueron utilizadas para describir el crecimiento en búfalos provenientes de tres regiones de Colombia (Antioquia,Caldas y Córdoba). Las funciones que mejor describieron el crecimiento fueron Brody y Gompertz. Con labase de datos de la región de Caldas, fueron estimadas las heredabilidades para las características peso aldestete (PD), peso y madurez al año de edad (PA y MA, respectivamente), edad al 50% y 75% de madurez(I50% y I75%, respectivamente), peso adulto (β0), y otras características. Las heredabilidades directa ymaterna para PD fueron: 0.19 y 0.12, respectivamente. Las heredabilidades directas para PA, MA, I50%,I75% y β0 fueron 0.39, 0.15, 0.09, 0.20 y 0.09, respectivamente. La correlación genética para β0 y PA fue-0.47, indicando que al seleccionar animales por peso al año, tendríamos animales con mayor peso adulto.Las características de madurez pueden ser utilizadas en programas de mejoramiento genético en procura debúfalos mas eficientes en sistemas de producción colombianos.

Funções matemáticas não lineares propostas por Brody, Gompertz, Richards, Bertalanffy e Verhulstforam utilizadas para descrever o crescimento em búfalos provenientes de três regiões da Colômbia (Antioquia, Caldas e Córdoba). As funções que melhor descreveram o crescimento foram Brody e Gompertz.Com a base de dados da região de Caldas, foram estimadas as herdabilidades para as características pesoao desmame (PD), peso e maturidade ao ano de idade (PA e MA, respectivamente), idade ao 50% e 75% dematuridade (I50% e I75%, respectivamente), peso adulto (β0), e outras características. As herdabilidadesdireita e materna para PD foram: 0.19 e 0.12, respectivamente. As herdabilidades direitas para PA, MA,I50%, I75% e β0 foram 0.39, 0.15, 0.09, 0.20 e 0.09, respectivamente. A correlação genética para β0 e PA foi-0.47, indicando que ao selecionar animais por peso ao ano, teríamos animais com maior peso adulto. Ascaracterísticas de maturidade podem ser utilizadas em programas de melhoramento genético em procurade búfalos mais eficientes em sistemas de produção colombianos.