Genome-Wide SNP Signal Intensity Scanning Revealed Genes Differentiating Cows with Ovarian Pathologies from Healthy Cows.

Hypoplasia and ovarian cysts are the most common ovarian pathologies in cattle. In this genome-wide study we analyzed the signal intensity of 648,315 Single Nucleotide Polymorphisms (SNPs) and identified 1338 genes differentiating cows with ovarian pathologies from healthy cows. The sample consisted of six cows presenting an ovarian pathology and six healthy cows. SNP signal intensities were measured with a genotyping process using the Axiom Genome-Wide BOS 1 SNPchip. Statistical tests for equality of variance and mean were applied to SNP intensities, and significance p-values were obtained. A Benjamini-Hochberg multiple testing correction reveled significant SNPs. Corresponding genes were identified using the Bovine Genome UMD 3.1 annotation. Principal Components Analysis (PCA) confirmed differentiation. An analysis of Copy Number Variations (CNVs), obtained from signal intensities, revealed no evidence of association between ovarian pathologies and CNVs. In addition, a haplotype frequency analysis showed no association with ovarian pathologies. Results show that SNP signal intensity, which captures not only information for base-pair genotypes elucidation, but the amount of fluorescence nucleotide synthetization produced in an enzymatic reaction, is a rich source of information that, by itself or in combination with base-pair genotypes, might be used to implement differentiation, prediction and diagnostic procedures, increasing the scope of applications for Genotyping Microarrays.

High density LD-based structural variations analysis in cattle genome.

Genomic structural variations represent an important source of genetic variation in mammal genomes, thus, they are commonly related to phenotypic expressions. In this work, ∼ 770,000 single nucleotide polymorphism genotypes from 506 animals from 19 cattle breeds were analyzed. A simple LD-based structural variation was defined, and a genome-wide analysis was performed. After applying some quality control filters, for each breed and each chromosome we calculated the linkage disequilibrium (r2) of short range (≤ 100 Kb). We sorted SNP pairs by distance and obtained a set of LD means (called the expected means) using bins of 5 Kb. We identified 15,246 segments of at least 1 Kb, among the 19 breeds, consisting of sets of at least 3 adjacent SNPs so that, for each SNP, r2 within its neighbors in a 100 Kb range, to the right side of that SNP, were all bigger than, or all smaller than, the corresponding expected mean, and their P-value were significant after a Benjamini-Hochberg multiple testing correction. In addition, to account just for homogeneously distributed regions we considered only SNPs having at least 15 SNP neighbors within 100 Kb. We defined such segments as structural variations. By grouping all variations across all animals in the sample we defined 9,146 regions, involving a total of 53,137 SNPs; representing the 6.40% (160.98 Mb) from the bovine genome. The identified structural variations covered 3,109 genes. Clustering analysis showed the relatedness of breeds given the geographic region in which they are evolving. In summary, we present an analysis of structural variations based on the deviation of the expected short range LD between SNPs in the bovine genome. With an intuitive and simple definition based only on SNPs data it was possible to discern closeness of breeds due to grouping by geographic region in which they are evolving.

Effect of magnesium oxide (MgO) addition in diets for lactating holstein cows / Efecto de la adición de óxido de magnesio (MgO) en dietas para vacas holstein en lactación

It was evaluated the effect of magnesium oxide (MgO) addition in diets for Holstein cows on milk production and quality. Nineteen Holstein cows in second third of lactation were assigned to two treatments (T), with 9 and 10 animals. Both treatments were similar for days in lactation and milk yield. Cows were assigned at random to two treatments (T) groups: T1 received 0.2% and T2 received 0.4% of MgO. The MgO (alkalinizing agent) was mixed with a commercial concentrate and offered in feed bunk with total diet, which consisted of 9 kg/d of concentrate plus alfalfa hay fed ad libitum. Total diet was offered three times a day (0600; 1200 and 1700 h). The experimental period was of 30 d, with other 30 for adaptation. Milk production (kg/d) and milk quality (fat, protein, and total solids) were evaluated. Data were analyzed using the statistical package SAS through of a randomized block design. Animals on T2 (0.40% MgO) produced 2.85 kg/d more milk (P<0.50) than those on T1 (0.20% MgO). The fat, protein and total solids content in milk were higher (P<0.05) in T1 than in T2. It is concluded that the addition of 0.4% MgO in diets for lactating dairy cows resulted in milk production increased, although there was a small reduction in milk quality, compared with 0.2% MgO supplementation.

Se evaluó el efecto de adición de óxido de magnesio (MgO) en dietas para vacas Holstein sobre la producción y calidad de la leche. Diecinueve vacas Holstein en el segundo tercio de lactancia fueron asignadas a dos tratamientos (T), con 9 y 10 animales. Ambos tratamientos fueron similares para días de lactancia y producción de leche. Las vacas fueron asignadas al azar a dos grupos o tratamientos (T): T1 recibió 0,2%, y T2 recibió 0,4% de MgO. El MgO (agente alcalinizante) se mezcló con un concentrado comercial y se ofreció en el comedero junto con la dieta total, la cual consistió de 9 kg/d del concentrado mas heno de alfalfa ad libitum. La dieta total se ofreció 3 veces al día (06000, 1200 and 1700 h). El periodo experimental fue de 30 d, con otros 30 d de adaptación. Se evaluó la producción de leche (kg/d) y la calidad de la leche (grasa, proteína, y sólidos totales). Los datos se analizaron por medio del paquete estadístico SAS en un diseño de bloques al azar. Los animales en T2 (0,4% MgO) produjeron más leche (2,5 kg/d; P<0,05) que aquellos en T1 (0,20% MgO). El contenido de grasa, proteína, y sólidos totales en leche fue más alto (P<0,05) en T1 que en T2. Se concluye que la adición de 0,40% de MgO en dietas para vacas lactantes incrementa la producción de leche, sin embargo puede haber una pequeña reducción en la calidad de la leche, comparado con la suplementación de 0,20% de MgO.