Background R is a multi-platform statistical software and an object oriented programming language. The package archive network for R provides CRAN repository that features over 15,000 free open source packages, at the time of writing this article (https://cran.r-project.org/web/packages, accessed in October 2019). The package is introduced in this article. The purpose of this package is providing functions for checking and processing the pedigree, calculation of the additive genetic relationship matrix and its inverse, which are used to study the population structure and predicting the genetic merit of animals. Calculation of the dominance relationship matrix and its inverse are also covered. A concept in animal breeding is genetic groups, which is about the inequality of the average genetic merits for groups of unknown parents. The package provides functions for the calculation of the matrix of genetic group contributions (Q). Calculating Q is computationally demanding, and depending on the size of the pedigree and the number of genetic groups, it might not be feasible using personal computers. Therefore, a computationally optimised function and its parallel processing alternative are provided in the package. Results Using sample data, outputs from different functions of the package were presented to illustrate a real experience of working with the package. Conclusions The presented R package is a free and open source tool mainly for quantitative geneticists and ecologists, who deal with pedigree data. It provides numerous functions for handling pedigree data, and calculating various pedigree-based matrices. Some of the functions are computationally optimised for large-scale data.

ObjectiveFrom a review of published information on genetic association studies, a meta-analysis was conducted to determine the influence of the genes κ-casein (CSN3) and β-lactoglobulin (LGB) on milk yield traits in Holstein, Jersey, Brown Swiss, and Fleckvieh.MethodsThe GLIMMIX procedure was used to analyze milk production and percentage of protein and fat in milk. Models included the main effects and all their possible two-way interactions; not estimable effects and non-significant (p>0.05) two-way interactions were dropped from the models. The three traits analyzed used Poisson distribution and a log link function and were determined with the Interactive Data Analysis of SAS software. Least square means and multiple mean comparisons were obtained and performed for significant main effects and their interactions (p<0.0255).ResultsInteraction of breed by gene showed that Holstein and Fleckvieh were the breeds on which CSN3 (6.01%±0.19% and 5.98%±0.22%), and LGB (6.02%±0.19% and 5.70%±0.22%) have the greatest influence. Interaction of breed by genotype nested in the analyzed gene indicated that Holstein and Jersey showed greater influence of the CSN3 AA genotype, 6.04%±0.22% and 5.59%±0.31% than the other genotypes, while LGB AA genotype had the largest influence on the traits analyzed, 6.05%±0.20% and 5.60%±0.19%, respectively. Furthermore, interaction of type of statistical model by genotype nested in the analyzed gene indicated that CSN3 and LGB genes had similar behavior, maintaining a difference of more than 7% across analyzed genotypes. These results could indicate that both Holstein and Jersey have had lower substitution allele effect in selection programs that include CSN3 and LGB genes than Brown Swiss and Fleckvieh.ConclusionBreed determined which genotypes had the greatest association with analyzed traits. The mixed model based in Bayesian or Ridge Regression was the best alternative to analyze CSN3 and LGB gene effects on milk yield and protein and fat percentages.

El objetivo fue evaluar el rendimiento, la composición bromatológica y producción de biogás in vitro con fertilización orgánica e inorgánica, para determinar la edad de corte óptimo del pasto Megathyrsus maximus (Jacq.) B.K. Simon & S.W.L. Jacobs cv. aruana. Los tratamientos fueron: fertilización con composta, lombricomposta, composta más lixiviado y fertilización química. El diseño experimental fue bloques completos al azar, en arreglo de medidas repetidas en el tiempo con tres repeticiones, se realizaron muestreos a los 20, 35, 50, 65, 80 y 95 días después del corte (DDC) de uniformización. Las variables evaluadas fueron acumulación de materia seca, composición morfológica, altura, fibra detergente neutro, fibra detergente acido, materia orgánica, proteína cruda, cenizas y producción de biogás in vitro. Los mayores rendimientos fueron a los 80 DDC con los tratamientos químico y composta más lixiviado con 24 013 y 10 974 kg MS ha?1, respectivamente. En los tratamientos orgánicos se encontró mayor relación hoja: tallo comparado con el químico en todas las fechas evaluadas. Los tratamientos mostraron descenso del porcentaje de proteína cruda conforme avanzó la edad de rebrote. A los 50 y 95 DDC, el pasto aruana fertilizado con lombricomposta o composta más lixiviado produjeron 2.8 y 2.0 veces mayor biogás que el fertilizado con químico o composta. La fecha óptima de corte para el pasto aruana para el tratamiento químico y composta más lixiviado es a los 50 y 65 DDC, mientras que para lombricomposta y composta es a los 65 DDC.

<p><strong>Background</strong>. Ripe papaya that does not meet standards for human consumption has the potential to be ensiled with star grass as a moisture absorber, which has the potential as an unconventional ruminant feed. <strong>Objective</strong>. To determine the quality, nutritional, and <em>in</em> <em>vitro</em> fermentative characteristics of silages made with milled ripe papaya (<em>Carica</em> <em>papaya</em> L) and star (<em>Cynodon</em> <em>nlemfluensis</em>) grass hay as moisture absorber, adding three levels of molasses during 21 and 28 days of lactic fermentation. <strong>Methodology</strong>. The silos (1.5 Kg) were made with 75% ripe papaya, 25% star grass hay, added with 2% urea and 0, 3 and 6% cane molasses; the silos were fermented for 21 and 28 d. The quality characteristics (pH, lactic acid (LA), ammonia nitrogen (N-NH₃) and dry matter (DM)), chemical characteristics (crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF) and ashes (As)) and <em>in</em> <em>vitro</em> fermentation (partial and accumulated production of biogas and methane (CH₄), degradation of dry matter (DDM) and degradation of neutral detergent fiber (DNDF) were evaluated). The statistical analysis was a 3x2 factorial arrangement within a completely randomized design, using level of molasses addition and fermentation time as factors. <strong>Results</strong>. pH, LA, CP and partial biogas at 24 and 48 h showed interaction between factors (p&lt;0.05). Silages with 0% molasses showed lower content of DM, As, accumulated biogas, partial CH₄ at 24 h, DDM; as well as, higher NDF, partial CH₄ at 72 h. The silages with 6% molasses presented higher DM, As, partial CH₄ at 24 h, accumulated CH₄ and DDM; in addition, lower NDF, ADF, partial CH₄ at 72 h. Silages with 21 d had lower N-NH₃, NDF, Ce, Biogas and accumulated CH₄, partial CH₄ at 24 h and 72 h than at 28 d (p&lt;0.05). The highest pH value was in silages with 28 d and 6% molasses and the highest LA in 28 d silages with 0% molasses (p&lt;0.05). <strong>Implications</strong>. Ripe papaya silage does not require cane molasses as an additive; there is no effect on the opening of the silos at 21 or 28 d of lactic fermentation. <strong>Conclusion</strong>. Silage made with ripe papaya and star grass hay as moisture absorber, with urea does not require sugar cane molasses as an additive to maintain its quality, chemical and <em>in</em> <em>vitro</em> fermentation characteristics, which allows inferring that it is an unconventional alternative in the feeding of ruminants.</p>

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