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.     

Use of genomic recursions and algorithm for proven and young animals for single‐step genomic BLUP analyses – a simulation study

The purpose of this study was to examine accuracy of genomic selection via single‐step genomic BLUP (ssGBLUP) when the direct inverse of the genomic relationship matrix ( G ) is replaced by an approximation of G ^?1 based on recursions for young genotyped animals conditioned on a subset of proven animals, termed algorithm for proven and young animals (APY). With the efficient implementation, this algorithm has a cubic cost with proven animals and linear with young animals. Ten duplicate data sets mimicking a dairy cattle population were simulated. In a first scenario, genomic information for 20k genotyped bulls, divided in 7k proven and 13k young bulls, was generated for each replicate. In a second scenario, 5k genotyped cows with phenotypes were included in the analysis as young animals. Accuracies (average for the 10 replicates) in regular EBV were 0.72 and 0.34 for proven and young animals, respectively. When genomic information was included, they increased to 0.75 and 0.50. No differences between genomic EBV (GEBV) obtained with the regular G ^?1 and the approximated G ^?1 via the recursive method were observed. In the second scenario, accuracies in GEBV (0.76, 0.51 and 0.59 for proven bulls, young males and young females, respectively) were also higher than those in EBV (0.72, 0.35 and 0.49). Again, no differences between GEBV with regular G ^?1 and with recursions were observed. With the recursive algorithm, the number of iterations to achieve convergence was reduced from 227 to 206 in the first scenario and from 232 to 209 in the second scenario. Cows can be treated as young animals in APY without reducing the accuracy. The proposed algorithm can be implemented to reduce computing costs and to overcome current limitations on the number of genotyped animals in the ssGBLUP method.     

Characterization and growth conditions of Vibrio parahaemolyticus strains with different virulence degrees that cause acute hepatopancreatic necrosis disease in Litopenaeus vannamei

The phenotypic characteristics and growth kinetics at several temperatures, salinities, and pH values of three Vibrio parahaemolyticus (Vp) strains with different virulence and one nonpathogenic strain were evaluated. Independent of the virulence of the strain, a high metabolic diversity was found, which yielded different colored phenotypes on the CHROMagar? Vibrio. All strains were resistant to ampicillin and carbenicillin, and Vp AHPND+ organisms were the most sensitive to enrofloxacin. The exponential growth of Vp strains started at 1–2 hr of incubation, although no relationship was observed between the bacterial density and degree of virulence. Moreover, the growth of the most virulent strain was independent of the nutrients in the incubation media during the initial hour postinoculation. No strain grew at 4°C in 0% NaCl and pH 4, but only Vp AHPND+ grew at 44°C. For all strains, the lag phase was proportional to the NaCl concentration, and the growth was better at pH 8–9. However, the Vp AHPND? strain displayed a greater variability, was more sensitive to extreme conditions, and showed a lag phase of 9 hr independent of the pH.     

Biocultural Diversity of Sarangani Province,Philippines: An Ethno-Ecological Analysis

This paper discussed effects of lowland-associated influences on upland ecology, food security and biocultural diversity in the Sarangani farming communities of the Philippines. In the uplands of Sarangani Province, the conservation of traditional rice varieties, the centrality of rice in tribal life, and the continued observance of planting rituals attest to its cultural significance and convey a common desire for cultural preservation and community solidarity. Economic and socio-political pressures had transformed tribal communities, although vestiges of traditional farming systems are still being practiced in remote sitios(villages). Changing land use patterns had also resulted in shrinking farm sizes and consequently in food insecurity in the Sarangani uplands. Extractive industries(i.e. logging, mining and charcoal making) and swidden farming were observed to cause widespread environmental degradation, while modern agriculture had undermined the capacity of indigenous peoples to survive because of their complete dependence on lands and resources. With the reality that cultural and biological diversities are inextricably linked, trans-disciplinary strategies coupling indigenous knowledge systems with scientific knowledge should, therefore, be instituted to save the Sarangani upland ecosystem, the indigenous peoples and their tribal resources.     

Effect of emerged shipment on the physiological condition of the adductor muscle in adult giant lion's paw scallop Nodipecten subnodosus (Sowerby 1835)

Currently, there is an increasing interest in shipping live adult scallops to markets and broodstock to hatcheries; nevertheless, information about the shipping effect on live scallops physiology is very scarce. In a previous study, a method in emersion was developed to ship scallop seed out of water, but it was not known whether this method is useful to transport adult organisms. As a consequence, the purpose of this study was to evaluate the effects of transportation by the emersion method on the physiological status of the adductor muscle of adult giant lion's paw scallop. Live specimens were packaged in a container and transported in emersion for 11 h. Six scallops were frozen in a farm and a similar number were frozen as soon as they arrived to the laboratory. Physiological indices were determined in each lot and the survival was estimated 24 h after re‐immersion. As a result of the transportation, a significant loss (P<0.05) of total carbohydrates, glycogen, adenosine 5′‐triphosphate and adenilated energetic charge, and a significant increase (P<0.05) in the free amino acids concentration were observed. Eighty‐eight per cent survival was achieved; therefore, we conclude that this method is appropriate for shipping live adult scallops of Nodipecten subnodosus.     

Status and distribution of the Mediterranean monk seal Monachus monachus on the Cabo Blanco peninsula (Western Sahara-Mauritania) in 1993–1994

The current geographical distribution of the Mediterranean monk seal Monachus monachus colony inhabiting the Cabo Blanco peninsula (Western Sahara-Mauritania) is described. Its distribution range has apparently not changed since surveys conducted in 1984–1988. Sightings of adults on the Tarf el Guerguerat coast, 20 km north of the known breeding caves, suggests the existence of other possible breeding groups further north. Two caves used by the seals are described for the first time. A review of historical trends in cave occupation by seals made it possible (1) to locate the so-called ‘maternity cave’, last reported in 1949; and (2) to establish that the colony, since its discovery, has occupied at least eight caves, five of which have collapsed. An index of population size based on counts of individuals of identified morphological types indicates that, during 1993–1994, the colony was composed of c.113–165 individuals (excluding pups), a larger number than previously assumed. Counting of seals at times of maximum haul-out is proposed as a tool to monitor population trends, although it is considered unreliable for estimating absolute numbers.     

Consumer willingness to pay price premiums for environmentally certified wood products in the U.S.

Since its inception nearly 15 years ago, environmental certification has become an important issue in the wood products industry. One research question that has been examined is the potential willingness for supply chain participants to pay a premium for certified products or raw materials to offset certification costs. This study examines stated willingness to pay for four wood products from the perspective of U.S. consumers. Data was collected in 1995 and 2005 from the population of U.S. residential consumers to detect changes in willingness to pay for certified wood products along time and increase the statistical strength of the model. Results of an ordered probit model suggest that higher probabilities of paying a premium are associated to consumers who seek out certified products and who believe certification can lessen environmental impacts such as tropical deforestation. There is also a strong relationship between respondent income and willingness-to-pay. Despite the current industry structure in the U.S. that has adopted a mass-certification strategy that does not place price premiums on certified products, results suggest that such premiums may exist for imported certified tropical wood products. Analysis of marginal effects suggests consumers' willingness to pay a 10% premium for three of the four certified items studied. Niche markets may potentially be exploited in the U.S. and price premiums captured by wood products manufacturers in tropical regions and/or American importers.     

Neotropical Bats from Costa Rica harbour Diverse Coronaviruses

Bats are hosts of diverse coronaviruses (CoVs) known to potentially cross the host–species barrier. For analysing coronavirus diversity in a bat species‐rich country, a total of 421 anal swabs/faecal samples from Costa Rican bats were screened for CoV RNA‐dependent RNA polymerase (RdRp) gene sequences by a pancoronavirus PCR. Six families, 24 genera and 41 species of bats were analysed. The detection rate for CoV was 1%. Individuals (n = 4) from four different species of frugivorous (Artibeus jamaicensis, Carollia perspicillata and Carollia castanea) and nectivorous (Glossophaga soricina) bats were positive for coronavirus‐derived nucleic acids. Analysis of 440 nt. RdRp sequences allocated all Costa Rican bat CoVs to the α‐CoV group. Several CoVs sequences clustered near previously described CoVs from the same species of bat, but were phylogenetically distant from the human CoV sequences identified to date, suggesting no recent spillover events. The Glossophaga soricina CoV sequence is sufficiently dissimilar (26% homology to the closest known bat CoVs) to represent a unique coronavirus not clustering near other CoVs found in the same bat species so far, implying an even higher CoV diversity than previously suspected.     

Insights into an undescribed high-elevation lake (6,170 m a.s.l.) on Volcán Llullaillaco: A physical and microbiological view

1. High elevation lakes are extreme ecosystems and serve as sentinels of various global changes.
2. An expedition to Volcán Llullaillaco in 1996 discovered an unstudied high-elevation lake (6,170 m a.s.l.) that probably was formed as a result of the past eruptive events or climatic processes such as glacial retreat in the lake basin.
3. This article describes an initial physical characterization of the lake and its microbial communities derived from two sampling expeditions in 2013 and 2016.
4. The microbial community in the lake, with an area between 1.2 and 1.4 ha and a depth of 6.8 m, was dominated by Proteobacteria, Actinobacteria and Haloarchaea. In addition, 26 bacterial isolates were identified within the genera Subtercola, Xylophilus, Rhodanobacter, Mesorhizobium and Pseudomonas.
5. Lago Llullaillaco is one of the highest recorded lakes in the world, and this study highlights the unique microbial diversity of this aquatic ecosystem and the importance of its preservation to understand the complex biological processes under polyextreme conditions.

     

Distribution of alpha‐neoendorphin,ACTH (18–39) and beta‐endorphin (1–27) in the alpaca brainstem

Using an immunocytochemical technique, we have studied in the alpaca brainstem the distribution of immunoreactive structures containing prodynorphin (alpha‐neoendorphin)‐ and pro‐opiomelanocortin (adrenocorticotrophin hormone (18–39) (ACTH), beta‐endorphin (1–27))‐derived peptides. No peptidergic‐immunoreactive cell body was observed. Immunoreactive fibres were widely distributed, although in most of the brainstem nuclei the density of the peptidergic fibres was low or very low. In general, the distribution of the immunoreactive fibres containing the peptides studied was very similar. A close anatomical relationship occurred among the fibres containing alpha‐neoendorphin, ACTH or beta‐endorphin (1–27), suggesting a functional interaction among the three peptides in many of the brainstem nuclei. The number of fibres belonging to the prodynorphin system was higher than that of the pro‐opiomelanocortin system. A moderate/low density of immunoreactive fibres was observed in 65.11% (for alpha‐neoendorphin (1–27)), 18.18% (for ACTH) and 13.95% (for beta‐endorphin) of the brainstem nuclei/tracts. In the alpaca brainstem, a high density of immunoreactive fibres was not observed. The neuroanatomical distribution of the immunoreactive fibres suggests that the peptides studied are involved in auditory, motor, gastric, feeding, vigilance, stress, respiratory and cardiovascular mechanisms, taste response, sleep‐waking cycle and the control of pain transmission.