Emerging issues in genomic selection

Genomic selection (GS) is now practiced successfully across many species. However, many questions remain, such as long-term effects, estimations of genomic parameters, robustness of genome-wide association study (GWAS) with small and large datasets, and stability of genomic predictions. This study summarizes presentations from the authors at the 2020 American Society of Animal Science (ASAS) symposium. The focus of many studies until now is on linkage disequilibrium between two loci. Ignoring higher-level equilibrium may lead to phantom dominance and epistasis. The Bulmer effect leads to a reduction of the additive variance; however, the selection for increased recombination rate can release anew genetic variance. With genomic information, estimates of genetic parameters may be biased by genomic preselection, but costs of estimation can increase drastically due to the dense form of the genomic information. To make the computation of estimates feasible, genotypes could be retained only for the most important animals, and methods of estimation should use algorithms that can recognize dense blocks in sparse matrices. GWASs using small genomic datasets frequently find many marker-trait associations, whereas studies using much bigger datasets find only a few. Most of the current tools use very simple models for GWAS, possibly causing artifacts. These models are adequate for large datasets where pseudo-phenotypes such as deregressed proofs indirectly account for important effects for traits of interest. Artifacts arising in GWAS with small datasets can be minimized by using data from all animals (whether genotyped or not), realistic models, and methods that account for population structure. Recent developments permit the computation of P-values from genomic best linear unbiased prediction (GBLUP), where models can be arbitrarily complex but restricted to genotyped animals only, and single-step GBLUP that also uses phenotypes from ungenotyped animals. Stability was an important part of nongenomic evaluations, where genetic predictions were stable in the absence of new data even with low prediction accuracies. Unfortunately, genomic evaluations for such animals change because all animals with genotypes are connected. A top-ranked animal can easily drop in the next evaluation, causing a crisis of confidence in genomic evaluations. While correlations between consecutive genomic evaluations are high, outliers can have differences as high as 1 SD. A solution to fluctuating genomic evaluations is to base selection decisions on groups of animals. Although many issues in GS have been solved, many new issues that require additional research continue to surface.     

Differentially expressed genes identified through RNA‐seq with extreme values of principal components for beef fatty acid in Nelore cattle

The aim of this study was to identify differentially expressed genes (DEG) in the Longissimus thoracis muscle of Nelore cattle related to fatty acid (FA) profile through RNA sequencing and principal component analysis (PCA). Two groups of 10 animals each were selected containing PC1 and PC2 extreme DEG values (HIGH × LOW) for each FA group. The intramuscular fat (IMF) was compared between cluster groups by ANOVA, and only the sum of monounsaturated FA (MUFA) and ω3 showed significant differences (p < .05). Interestingly, the highest percentage (95%) of phenotypic variation explained by the sum of the first two PC was observed for ω3, which also displayed the lowest number of DEG (n = 1). The lowest percentage (59%) was observed for MUFA, which also revealed the largest number of DEG (n = 66). Since only MUFA and ω3 exhibited significant differences between cluster groups, we can conclude that the differences observed for the remaining groups are not due to the percentage of IMF. Several genes that have been previously associated with meat quality and FA traits were identified as DEG in this study. The functional analysis revealed one KEGG pathway and eight GO terms as significant (p < .05), in which we highlighted the purine metabolism, glycolytic process, adenosine triphosphate binding and bone development. These results strongly contribute to the knowledge of the biological mechanisms involved in meat FA profile of Nelore cattle.     

Production,chemical composition,and fatty acid profile of milk from buffaloes fed with cupuaçu (Theobroma grandiflorum) cake and murumuru (Astrocaryum murumuru) cake in the Eastern Amazon

The objective was to evaluate the effect of concentrate supplementation using by-products of the Amazonian industry on milk production, milk composition, and milk fatty acid profile of dairy buffaloes. Twelve lactating buffaloes (544.5 ± 35.6 kg, 6.4 ± 2.2 years old, 59 ± 6 days in milk) were allotted in a pasture of Mombaça grass and managed under rotational grazing (4 days occupancy/28 days rest). A 3 × 3 Latin square was adopted, and each animal alternately received three supplementary treatments based on corn bran + soybean meal or cupuaçu cake or murumuru cake for 21 days per treatment. Murumuru cake increased the levels of lauric acid and myristic acid in the milk (p < 0.05). Murumuru cake reduced the unsaturated fatty acid contents in the milk compared with animals fed control diet or cupuaçu cake (24.27% vs. 25.24% vs. 25.08%). The n-6/n-3 ratio was 2.6, 1.97, and 2.0 in the control, cupuaçu, and murumuru groups, respectively. Based on this parameter, cakes made from cupuaçu as well as murumuru could be considered to be adequate for inclusion in dairy water buffalo feed. However, the murumuru cake addition requires some caution because its use induces the secretion of higher levels of lauric and myristic fatty acids that are related to human cardiovascular disease.     

Multiple generalized follicular cysts in a stallion

This case report describes a case of multiple follicular cysts in a 4-year-old Spanish purebred stallion. The lesions ranged in size from 0.5 to 3 cm in diameter, and were firm, well circumscribed and nonpruritic. They developed over a 2-year period with a generalized distribution affecting all body regions. Five nodules were removed and histopathologically corresponded to simple epidermal cysts (infundibular and isthmus-catagen) with squamous epithelium and a keratin filled cavity. Lesions were not evident at birth but their number, early age of detection, slow growth and lack of previous trauma suggested that they were congenital. To the authors' knowledge, this condition has not previously been reported either in young horses or in Spanish purebred horses.     

Canine bartonellosis: serological and molecular prevalence in Brazil and evidence of co-infection with Bartonella henselae and Bartonella vinsonii subsp. berkhoffii

The purpose of this study was to determine the serological and molecular prevalence of Bartonella spp. infection in a sick dog population from Brazil. At the S?o Paulo State University Veterinary Teaching Hospital in Botucatu, 198 consecutive dogs with clinicopathological abnormalities consistent with tick-borne infections were sampled. Antibodies to Bartonella henselae and Bartonella vinsonii subsp. berkhoffii were detected in 2.0% (4/197) and 1.5% (3/197) of the dogs, respectively. Using 16S-23S rRNA intergenic transcribed spacer (ITS) primers, Bartonella DNA was amplified from only 1/198 blood samples. Bartonella seroreactive and/or PCR positive blood samples (n=8) were inoculated into a liquid pre-enrichment growth medium (BAPGM) and subsequently sub-inoculated onto BAPGM/blood-agar plates. PCR targeting the ITS region, pap31 and rpoB genes amplified B. henselae from the blood and/or isolates of the PCR positive dog (ITS: DQ346666; pap31 gene: DQ351240; rpoB: EF196806). B. henselae and B. vinsonii subsp. berkhoffii (pap31: DQ906160; rpoB: EF196805) co-infection was found in one of the B. vinsonii subsp. berkhoffii seroreactive dogs. We conclude that dogs in this study population were infrequently exposed to or infected with a Bartonella species. The B. henselae and B. vinsonii subsp. berkhoffii strains identified in this study are genetically similar to strains isolated from septicemic cats, dogs, coyotes and human beings from other parts of the world. To our knowledge, these isolates provide the first Brazilian DNA sequences from these Bartonella species and the first evidence of Bartonella co-infection in dogs.     

Measuring versus estimating net radiation and soil heat flux: Impact on Penman–Monteith reference ET estimates in semiarid regions

The standardized ASCE Penman–Monteith and FAO-56 equations were used to estimate reference evapotranspiration (ET₀) using estimated and measured net radiation (R_n) and soil heat flux (G), based on hourly and daily meteorological data. The estimates were evaluated against lysimeter measurements. The results indicate that using measured or estimated values of R_n and G can have significant effect on the accuracy of the ET₀ estimations, especially when calculations were made on an hourly basis. The FAO-56 version performed very well during the irrigation season on a daily basis. The use of measured R_n and G did not improve ET₀ estimation on a daily basis, therefore, the use of estimated R_n and G appears to be dependable when calculations are based on 24-h weather data. When daily ET₀ was calculated from hourly estimations, the results were different depending on the version used. The ASCE version was more accurate, especially when R_n and G were measured. Therefore, measurement of R_n and G may have potential to improve estimation only when daily ET₀ is calculated from hourly estimations. The PM FAO-56 version was always a little less accurate than the ASCE version. For hourly calculations, using a constant surface resistance (as in FAO-56 version), the PM method underpredicted for high evaporative demand and vice versa. The ASCE version performed better than PM FAO-56 version when R_n and G were measured and estimated. Therefore, ASCE version tended to provide quite accurate values of hourly ET₀, even using estimated values of R_n and G. As conclusion, the methods proposed by FAO-56 for estimating R_n and G tended to produce accurate estimates for daily and hourly ET₀ under semiarid conditions and can be used with some degree of confidence for estimating ET₀. In addition, results suggest that the ASCE standardized equation on an hourly basis improved the accuracy of ET₀ estimation with respect to the FAO-56 version.     

Near-Infrared Spectroscopy Coupled with Chemometrics Tools: A Rapid and Non-Destructive Alternative on Soil Evaluation

Near-infrared (NIR) spectroscopy is a rapid, non-destructive and accurate technique for analyzing a wide variety of samples, thus, the growing interest of using this technique in soil science. The objective of this study was to evaluate the potential of NIR spectroscopy to predict organic carbon (OC), total nitrogen (TN), available phosphorus (P) and available potassium (K) in the soil. NIR spectra from 20 cm³ of soil samples were acquired on the range of 750 to 2500 nm in diffuse reflectance mode, resolution of 16 cm^?1 and 64 scans. Eight models of calibration/validation were constructed. Calibration and validation models showed that the predictive potential of NIR varied with the specific soil property (OC, TN, P and K) under evaluation and according to the methodology employed in the model construction (cross-validation or test set). Good prediction models were obtained for OC and TN content based on the statistical parameters. Test set methodology was able to predict soil OC, TN, P, and K better than cross-validation methodology.     

Nutritional value of Pavlova spp. (Prymnesiophyceae) for spat of the Cortez oyster Crassostrea corteziensis during late-nursery culturing at the hatchery

Three Pavlova species were evaluated for their nutritional value as diets for growth and survival of the Cortez oyster Crassostrea corteziensis spat during late‐nursery cultivation at a hatchery. Microalgae were provided as monospecific diets (Pavlova salina, P. sp. C50 and P. sp. C53) and in binary combinations of diets 1+2, 1+3 and 2+3 at 80–90 × 10³ cells mL^?1 for 21 days. Juveniles experienced high survival rates and grew well with all dietary treatments, but binary diets yielded greater survival and growth of spat. From the three binary treatments, Diet 6 (P. sp. C50 and P. sp. C53) promoted significantly (P<0.001) fastest growth of juveniles in shell height (0.19 mm day^?1), shell length (0.14 mm day^?1), total wet weight (0.04 g day^?1) and dry weight of meat biomass (0.024 g day^?1). For all shell dimensions, the lowest growth rates occurred with Diets 2 (P. sp. C56 alone) and 3 (P. sp. C50 alone). These results highlight the importance of testing microalgal diets for bivalve spat rather than just relying on published nutritional values.