Whole-genome sequencing of two captive black soldier fly populations: Implications for commercial production.

Black soldier fly (BSF; Hermetia illucens) is a promising insect species for food and feed production as its larvae can convert different organic waste to high-value protein. Selective breeding is one way to optimize production, but the potential of breeding is only starting to be explored and not yet utilized for BSF. To assist in monitoring a captive population and implementing a breeding program, genomics tools are imperative. We conducted whole genome sequencing of two captive populations separated by geographical distance - Denmark (DK) and Texas, USA (TX). Various population genetics analyses revealed a moderate genetic differentiation between two populations. Moreover, we observed higher inbreeding in the DK population, and the detection of a subpopulation within DK population aligned well with the recent foundation of the DK population from two captive populations. Additionally, we generated gene ontology annotation and variants annotation for wider potential applications. Our findings establish a robust marker set for research in population genetics, facilitating the monitoring of inbreeding and laying the groundwork for practical breeding programs for BSF.

Estimation of genetic parameters for the implementation of selective breeding in commercial insect production.

BACKGROUND: There is a burgeoning interest in using insects as a sustainable source of food and feed, particularly by capitalising on various waste materials and by-products that are typically considered of low value. Enhancing the commercial production of insects can be achieved through two main approaches: optimising environmental conditions and implementing selective breeding strategies. In order to successfully target desirable traits through selective breeding, having a thorough understanding of the genetic parameters pertaining to those traits is essential. In this study, a full-sib half-sib mating design was used to estimate variance components and heritabilities for larval size and survival at day seven of development, development time and survival from egg to adult, and to estimate correlations between these traits, within an outbred population of house flies (Musca domestica), using high-throughput phenotyping for data collection. RESULTS: The results revealed low to intermediate heritabilities and positive genetic correlations between all traits except development time and survival to day seven of development and from egg to adulthood. Surprisingly, larval size at day seven exhibited a comparatively low heritability (0.10) in contrast to development time (0.25), a trait that is believed to have a stronger association with overall fitness. A decline in family numbers resulting from low mating success and high overall mortality reduced the amount of available data which resulted in large standard errors for the estimated parameters. Environmental factors made a substantial contribution to the phenotypic variation, which was overall high for all traits. CONCLUSIONS: There is potential for genetic improvement in all studied traits and estimates of genetic correlations indicate a partly shared genetic architecture among the traits. All estimates have large standard errors. Implementing high-throughput phenotyping is imperative for the estimation of genetic parameters in fast developing insects, and facilitates age synchronisation, which is vital in a breeding population. In spite of endeavours to minimise non-genetic sources of variation, all traits demonstrated substantial influences from environmental components. This emphasises the necessity of thorough attention to the experimental design before breeding is initiated in insect populations.

Selection for social genetic effects in purebred pigs improves behaviour and handling of their crossbred progeny.

BACKGROUND: In commercial pig production, reduction of harmful social behavioural traits, such as ear manipulation and tail biting, is of major interest. Moreover, farmers prefer animals that are easy to handle. The aim of this experiment was to determine whether selection on social breeding values (SBV) for growth rate in purebred pigs affects behaviour in a weighing crate, lesions from ear manipulation, and tail biting of their crossbred progeny. Data were collected on crossbred F1 pigs allocated to 274 pens, which were progeny of purebred Landrace sows and Yorkshire boars from a DanBred nucleus herd. RESULTS: Behaviour in the weighing crate scored on a three-level scale showed that groups of pigs with high SBV for growth rate were significantly calmer than groups of pigs with low SBV (P < 0.027). When the mean SBV in the group increased by 1 unit, the proportion of pigs that obtained a calmer score level was increased by 14%. A significant (p = 0.04), favourable effect of SBV was found on both the number of pigs with ear lesions in the group and the mean number of ear lesions per pig. For a 1 unit increase in mean SBV, the mean number of lesions per pig decreased by 0.06 from a mean of 0.98. Individual severity of ear lesions conditional upon the number of ear lesions was also significantly affected (p = 0.05) by the mean SBV in the group. In groups for which the mean SBV increased by 1 unit, the proportion of pigs that were observed with a lower severity score was increased by 20% on a three-level scale. Most pigs received no tail biting injuries and no effect of SBV was observed on the tail injury score. CONCLUSIONS: After 7 weeks in the finisher unit, crossbred progeny with high SBV were calmer in the weighing crate and had fewer ear lesions. These results indicate that selection of purebred parents for SBV for growth rate will increase welfare in their crossbred progeny by decreasing the number of ear lesions and making them easier to handle.

Selection for social genetic effects in purebreds increases growth in crossbreds.

BACKGROUND: Average daily gain (ADG) in pigs is affected by both direct and social genetic effects (SGE). However, selection for SGE in purebreds has not conclusively been shown to improve ADG in crossbreds, and it is unknown whether SGE in purebreds are equal to those in crossbreds. Moreover, SGE may reflect dominance related behaviour, which is affected by the variation in body weight within a group. Therefore, we hypothesized that (a) there is a positive effect of parent average SGE estimated in purebred pigs on phenotypic ADG in crossbred offspring, and (b) there is an interaction between SGE on ADG and standard deviation in starting weight of pigs within the group. We also hypothesized that (c) social genetic variance for ADG exists in crossbred pigs, and (d) there is a favourable genetic correlation between SGE on ADG in purebred and crossbred pigs. RESULTS: We found a statistically significant interaction between the standard deviation in starting weight and SGE within groups, and conditioning on the mean standard deviation in starting weight, we found a favourable regression coefficient (0.37 ± 0.21) of ADG in crossbreds on SGE in purebreds. Variances for SGE were small in both Landrace (L) and Yorkshire (Y), and higher for SGE in both the dam and sire component of crossbred YL. The genetic correlations between SGE in purebreds and the dam or sire component of SGE in crossbreds were also favourable (0.52 ± 0.48 and 0.34 ± 0.42, respectively), although not significantly different from 0. CONCLUSIONS: We confirmed that there is a positive effect of SGE estimated using purebred information on phenotypic ADG in crossbreds, and that the largest effect is achieved when the within-group variation in starting weight is small. Our results indicate that social genetic variance in crossbreds exists and that there is a favourable genetic correlation between social genetic effects in purebreds and crossbreds. Collectively, our results indicate that selection for SGE on ADG in purebreds in a nucleus farm environment with little competition for resources can improve ADG in crossbreds in a commercial environment.

Pedigree relationships to control inbreeding in optimum-contribution selection realise more genetic gain than genomic relationships.

BACKGROUND: We tested the premise that optimum-contribution selection with pedigree relationships to control inbreeding (POCS) realises at least as much true genetic gain as optimum-contribution selection with genomic relationships (GOCS) at the same rate of true inbreeding. METHODS: We used stochastic simulation to estimate rates of true genetic gain realised by POCS and GOCS at a 0.01 rate of true inbreeding in three breeding schemes with best linear unbiased predictions of breeding values based on pedigree (PBLUP) and genomic (GBLUP) information. The three breeding schemes differed in number of matings and litter size. Selection was for a single trait with a heritability of 0.2. The trait was controlled by 7702 biallelic quantitative-trait loci (QTL) that were distributed across a 30-M genome. The genome contained 54,218 biallelic markers that were used in GOCS and GBLUP. A total of 6012 identity-by-descent loci were placed across the genome in base populations. Unique alleles at these loci were used to calculate rates of true inbreeding. Breeding schemes were run for 10 discrete generations. Selection candidates were genotyped and phenotyped before selection. RESULTS: POCS realised more true genetic gain than GOCS at a 0.01 rate of true inbreeding in all combinations of breeding scheme and prediction method. POCS realised 14 to 33% more true genetic gain than GOCS with PBLUP in the three breeding schemes. It realised 1.5 to 5.7% more true genetic gain than GOCS with GBLUP. CONCLUSIONS: POCS realised more true genetic gain than GOCS because it managed expected genetic drift without restricting selection at QTL. By contrast, GOCS penalised changes in allele frequencies at markers that were generated by genetic drift and selection. Because these marker alleles were in linkage disequilibrium with QTL alleles, GOCS restricted changes in allele frequencies at QTL. This provides little incentive to use GOCS and highlights that we have more to learn before we can control inbreeding using genomic relationships in selective-breeding schemes. Until we can do so, POCS remains a worthy method of optimum-contribution selection because it realises more true genetic gain than GOCS at the same rate of true inbreeding.

Patent Ethics: The Misalignment of Views Between the Patent System and the Wider Society.

Concerns have been voiced about the ethical implications of patenting practices in the field of biotechnology. Some of these have also been incorporated into regulation, such as the European Commission Directive 98/44 on the legal protection of biotechnological inventions. However, the incorporation of ethically based restrictions into patent legislation has not had the effect of satisfying all concerns. In this article, we will systematically compare the richness of ethical concerns surrounding biotech patenting, with the limited scope of ethical concerns actually addressed in the patent system. As sources of our analyses we will use literature and document studies and a survey with important stakeholders and experts related to Norwegian patenting in the aquacultural biotechnology sector. We will structure the analyses with an ethical matrix, developed for this purpose. Showing the misalignment of the discussions within and outside the patent system, we suggest that an important reason for the ethical controversy still surrounding patenting is that ethical questions keep being framed in a narrow way within the system. Until a richer set of ethical considerations is addressed head-on within the patent system, the patent system will continue to evoke academic and interest group criticism, potentially contributing to a legitimacy crisis of the whole system.

The Effect of Using Organic or Conventional Sires on Genetic Gain in Organic Pigs: A Simulation Study.

Current organic pig-breeding programs use pigs from conventional breeding populations. However, there are considerable differences between conventional and organic production systems. This simulation study aims to evaluate how the organic pig sector could benefit from having an independent breeding program. Two organic pig-breeding programs were simulated: one used sires from a conventional breeding population (conventional sires), and the other used sires from an organic breeding population (organic sires). For maintaining the breeding population, the conventional population used a conventional breeding goal, whereas the organic population used an organic breeding goal. Four breeding goals were simulated: one conventional breeding goal, and three organic breeding goals. When conventional sires were used, genetic gain in the organic population followed the conventional breeding goal, even when an organic breeding goal was used to select conventional sires. When organic sires were used, genetic gain followed the organic breeding goal. From an economic point of view, using conventional sires for breeding organic pigs is best, but only if there are no genotype-by-environment interactions. However, these results show that from a biological standpoint, using conventional sires biologically adapts organic pigs for a conventional production system.

Contrasting Manual and Automated Assessment of Thermal Stress Responses and Larval Body Size in Black Soldier Flies and Houseflies.

Within ecophysiological and genetic studies on insects, morphological and physiological traits are commonly assessed and phenotypes are typically obtained from manual measurements on numerous individuals. Manual observations are, however, time consuming, can introduce observer bias and are prone to human error. Here, we contrast results obtained from manual assessment of larval size and thermal tolerance traits in black soldier flies (Hermetia illucens) and houseflies (Musca domestica) that have been acclimated under three different temperature regimes with those obtained automatically using an image analysis software (Noldus EthoVision XT). We found that (i) larval size estimates of both species, obtained by manual weighing or by using the software, were highly correlated, (ii) measures of heat and cold tolerance using manual and automated approaches provided qualitatively similar results, and (iii) by using the software we obtained quantifiable information on stress responses and acclimation effects of potentially higher ecological relevance than the endpoint traits that are typically assessed when manual assessments are used. Based on these findings, we argue that automated assessment of insect stress responses and largescale phenotyping of morphological traits such as size will provide new opportunities within many disciplines where accurate and largescale phenotyping of insects is required.

Development and validation of a capillary electrophoresis-indirect photometric detection method for the determination of the non-UV-absorbing 1,4-dideoxy-1,4-imino-D-arabinitol in active pharmaceutical ingredients, solutions and tablets using an internal standard.

A high speed, selective, and robust capillary electrophoresis (CE) method with high capacity was developed and validated for determination of assay of 1,4-dideoxy-1,4-imino-D-arabinitol in active pharmaceutical ingredients, solutions, and tablets during the development work at preclinical and Phase I and II clinical studies. 1,4-Dideoxy-1,4-imino-D-arabinitol, tartrate has (almost) no UV absorption. Therefore, the developed CE method for quantification was based on indirect UV detection. A cation CE principle was chosen using an electrolyte at pH 4.0 containing dimethyldiphenylphosphonium hydroxide, which has a strong UV absorbance. The quantification was performed using internal standard technique, by which piperidine was used as internal standard. The method was validated. The validation results showed that the CE method was suitable for the assay (and dissolution) analysis.