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.     

Mortality induced by drifting longline hooks and branchlines in loggerhead sea turtles,estimated through observation in captivity

• 1. Drifting longlines are considered a major threat to endangered sea turtle populations worldwide. However, for a number of reasons, the mortality rate of captured turtles is not known with any certainty.
• 2. Information on 409 loggerhead turtles (Caretta caretta), collected during the day‐to‐day activities of a turtle rescue centre in Lampedusa island, central Mediterranean, in the period 2001–2005 has been analysed.
• 3. Observations indicate that: (i) drifting longlines are a major cause of mortality for sea turtles in the area; (ii) in addition to the hook, the piece of line attached to it (branchline) can easily cause death if it is long enough and well‐anchored; (iii) hooks and branchlines cause death in the short and long term, respectively; (iv) a turtle with a hook in the lower oesophagus/stomach has a very low chance of surviving the combined effect of hook and branchline; (v) the mortality of turtles with a hook in the mouth or higher oesophagus is probably important, though less than that of turtles with a hook in the lower oesophagus/stomach; (vi) in the study fishery, the average mortality of a turtle caught by a drifting longline is probably much higher than 30%.
• 4. Without specific investigations on the mortality of turtles with hooks in the mouth or higher oeasophagus, which are usually removed, the mortality induced by drifting longlines will remain unknown, preventing a full understanding of the effect on population growth and the real effectiveness of conservation measures such as use of different hooks and fishing depths, and proposals for adequate fishery management measures.
• 5. The number of turtles captured by drifting longlines should be drastically reduced, and because of the above uncertainty and the socio‐economic importance of the fishery sector, an ecosystem‐based management scheme should be promoted that is not limited to addressing only the turtle issue.

Copyright © 2007 John Wiley & Sons, Ltd.     

Assessment of potential trade‐off between maternal colouration and offspring quality in the ornamental “red cherry” shrimp Neocaridina davidi (Bouvier)

Maternal colouration based on carotenoids has been proposed to negatively affect offspring quality in several taxa, since females might trade off their limited carotenoid resources between body colouration and eggs. This study investigated in the ornamental “red cherry” shrimp (Neocaridina davidi) the relationship between maternal colouration and female reproductive performance, as well as offspring quality. Females selected displayed a broad array of body colour, from less coloured to intensely red coloured and were paired with transparent males. The first two spawning events of each female were studied and compared. The number of newly hatched juveniles was associated to maternal weight, but not to maternal colouration. Offspring quality was measured in terms of survival at the end of the 90‐day growth period, weight and length increment for 0–30 days and 30–60 days periods, and protein, lipid and glycogen contents in 30‐day‐old offspring. Yet, neither of these variables was associated to maternal colouration. These results indicate that there is no trade‐off between maternal colouration and offspring quality in this species. Furthermore, no association was found between maternal and offspring colouration, evaluated at a similar age. However, body colouration in 180‐day old females was significantly higher than in 90‐day‐old females, indicating that female colouration is strongly influenced by age.