Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits.

Background: The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (F), genomic relationship matrix (F), and pedigree-based coefficient (F).

Results: The average number of ROH per animal was 55.

Genotype imputation in a tropical crossbred dairy cattle population.

The objective of this study was to investigate different strategies for genotype imputation in a population of crossbred Girolando (Gyr × Holstein) dairy cattle. The data set consisted of 478 Girolando, 583 Gyr, and 1,198 Holstein sires genotyped at high density with the Illumina BovineHD (Illumina, San Diego, CA) panel, which includes ∼777K markers. The accuracy of imputation from low (20K) and medium densities (50K and 70K) to the HD panel density and from low to 50K density were investigated.

Kernel-based variance component estimation and whole-genome prediction of pre-corrected phenotypes and progeny tests for dairy cow health traits.

Prediction of complex trait phenotypes in the presence of unknown gene action is an ongoing challenge in animals, plants, and humans. Development of flexible predictive models that perform well irrespective of genetic and environmental architectures is desirable. Methods that can address non-additive variation in a non-explicit manner are gaining attention for this purpose and, in particular, semi-parametric kernel-based methods have been applied to diverse datasets, mostly providing encouraging results.

Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array.

Background: Btau_4.0 and UMD3.1 are two distinct cattle reference genome assemblies.

Development of a nomenclature system for a canine STR multiplex reagent kit.

Despite the popularity of dogs in US households, canine DNA evidence remains largely untapped in forensic investigations partially because of the absence of well-defined forensic short tandem repeats (STRs), lack of standardized and validated PCR protocols, STR reagent kits, and poorly developed nomenclature. A nomenclature system was established based on internationally recognized recommendations for human forensic STRs for a recently developed canine STR reagent kit. Representative alleles were sequenced from each of the 18 STRs and the sex-typing marker included in the kit.

Canine population data generated from a multiplex STR kit for use in forensic casework.

Canine biological specimens are often part of the physical evidence from crime scenes. Until now, there have been no validated canine-specific forensic reagent kits available. A multiplex genotyping system, comprising 18 short tandem repeats (STRs) and a sex-linked zinc finger locus for gender determination, was developed for generating population genetic data assessing the weight of canine forensic DNA profiles.

Developmental validation of short tandem repeat reagent kit for forensic DNA profiling of canine biological material.

Aim: To develop a reagent kit that enables multiplex polymerase chain reaction (PCR) amplification of 18 short tandem repeats (STR) and the canine sex-determining Zinc Finger marker.

Methods: Validation studies to determine the robustness and reliability in forensic DNA typing of this multiplex assay included sensitivity testing, reproducibility studies, intra- and inter-locus color balance studies, annealing temperature and cycle number studies, peak height ratio determination, characterization of artifacts such as stutter percentages and dye blobs, mixture analyses, species-specificity, case type samples analyses and population studies.

Results: The kit robustly amplified domesticated dog samples and consistently generated full 19-locus profiles from as little as 125 pg of dog DNA.

Thermoregulatory responses of Holstein and Brown Swiss heat-stressed dairy cows to two different cooling systems.

Thirty-seven Holstein and 26 Brown Swiss dairy cows were used to evaluate the effect of two different cooling systems on physiological and hormonal responses during the summer. A control group of cows had access only to shade (C). A second group was cooled with spray and fans (S/F) and the third group was under an evaporative cooling system called Korral Kool (KK).