Forward - Green Virtual Enterprises and Their Breeding Environments: Sustainable Manufacturing, Logistics and Consumption

Part 9: Innovation Networks

Neotropical Copestylum Macquart (Diptera: Syrphidae) Breeding in Fruits and Flowers, Including 7 New Species

Ten species of Copestylum (Diptera: Syrphidae) were reared from fruits and flowers in Costa Rica, Ecuador and Trinidad. Seven were new and in this paper, we describe them, their development sites and the third stage larva and/or the puparium of all ten species. One new synonym is proposed, Copestylum pinkusi (Curran) [= Copestylum cinctiventre (Curran)]. Similarities and differences between these new and other Copestylum species, suggest they separate into two groups, referred to as the Vagum and Cinctiventre species groups. Features characterising these groups for both adult and early stages are assessed. Each species was also distinguished using adult and early stage characters. Within the Vagum group, adults were more disparate morphologically than the larval stage; this was reversed in the Cinctiventre group. Adult colour patterns are probably cryptic in function and for disguise. Vagum species have disruptive marks, while the Cinctiventre species have reflective colours. Biologically, the groups are almost distinguished by larval development sites. Vagum species use predominantly fruits and have a larval stage that is relatively generalised in form and habit. Cinctiventre species are confined to developing in flowers and the larva is more specialised. A key to both adult and early stages of all ten species is provided.

Genome selection in fruit breeding: application to table grapes.

Genomic selection (GS) has recently been proposed as a new selection strategy which represents an innovative paradigm in crop improvement, now widely adopted in animal breeding. Genomic selection relies on phenotyping and high-density genotyping of a sufficiently large and representative sample of the target breeding population, so that the majority of loci that regulate a quantitative trait are in linkage disequilibrium with one or more molecular markers and can thus be captured by selection. In this study we address genomic selection in a practical fruit breeding context applying it to a breeding population of table grape obtained from a cross between the hybrid genotype D8909-15 (Vitis rupestris × Vitis arizonica/girdiana), which is resistant to dagger nematode and Pierce?s disease (PD), and ?B90-116?, a susceptible Vitis vinifera cultivar with desirable fruit characteristics. Our aim was to enhance the knowledge on the genomic variation of agronomical traits in table grape populations for future use in marker-assisted selection (MAS) and GS, by discovering a set of molecular markers associated with genomic regions involved in this variation. A number of Quantitative Trait Loci (QTL) were discovered but this method is inaccurate and the genetic architecture of the studied population was better captured by the BLasso method of genomic selection, which allowed for efficient inference about the genetic contribution of the various marker loci. The technology of genomic selection afforded greater efficiency than QTL analysis and can be very useful in speeding up the selection procedures for agronomic traits in table grapes.

Marker-assisted selection integrated to the embrapa common bean breeding program.

The establishment of a specific Marker-Assisted Selection Facility at the Embrapa Rice and Beans Biotechnology Laboratory, in 2014, has better supported the routine analysis with molecular markers demanded by the Embrapa Common Bean Breeding Program. In addition, it has also supported other Embrapa plant breeding programs, such as rice and cotton.

Genome-Wiide estimates of coancestry, in breeding and effective population size in the Spanish Holstein population

Estimates of effective population size in the Holstein cattle breed have usually been low despite the large number of animals that constitute this breed. Effective population size is inversely related to the rates at which coancestry and inbreeding increase and these rates have been high as a consequence of intense and accurate selection. Traditionally, coancestry and inbreeding coefficients have been calculated from pedigree data. However, the development of genome-wide single nucleotide polymorphisms has increased the interest of calculating these coefficients from molecular data in order to improve their accuracy. In this study, genomic estimates of coancestry, inbreeding and effective population size were obtained in the Spanish Holstein population and then compared with pedigree-based estimates. A total of 11,135 animals genotyped with the Illumina BovineSNP50 BeadChip were available for the study. After applying filtering criteria, the final genomic dataset included 36,693 autosomal SNPs and 10,569 animals. Pedigree data from those genotyped animals included 31,203 animals. These individuals represented only the last five generations in order to homogenise the amount of pedigree information across animals. Genomic estimates of coancestry and inbreeding were obtained from identity by descent segments (coancestry) or runs of homozygosity (inbreeding). The results indicate that the percentage of variance of pedigree-based coancestry estimates explained by genomic coancestry estimates was higher than that for inbreeding. Estimates of effective population size obtained from genome-wide and pedigree information were consistent and ranged from about 66 to 79. These low values emphasize the need of controlling the rate of increase of coancestry and inbreeding in Holstein selection programmes.

Past, present and future of epigenetics applied to livestock breeding

This article reviews the concept of Lamarckian inheritance and the use of the term epigenetics in the field of animal genetics. Epigenetics was first coined by Conrad Hal Waddington (1905–1975), who derived the term from the Aristotelian word epigenesis. There exists some controversy around the word epigenetics and its broad definition. It includes any modification of the expression of genes due to factors other than mutation in the DNA sequence. This involves DNA methylation, post-translational modification of histones, but also linked to regulation of gene expression by non-coding RNAs, genome instabilities or any other force that could modify a phenotype. There is little evidence of the existence of transgenerational epigenetic inheritance in mammals, which may commonly be confounded with environmental forces acting simultaneously on an individual, her developing fetus and the germ cell lines of the latter, although it could have an important role in the cellular energetic status of cells. Finally, we review some of the scarce literature on the use of epigenetics in animal breeding programs.

Triticale breeding program for fusarium head blight resistance.

2016

Migration strategy and pathogen risk: non-breeding distribution drives malaria prevalence in migratory waders

Pathogen exposure has been suggested as one of the factors shaping the myriad of migration strategies observed in nature. Two hypotheses relate migration strategies to pathogen infection: the 'avoiding the tropics hypothesis' predicts that pathogen prevalence and transmission increase with decreasing non-breeding (wintering) latitude, while the "habitat selection hypothesis" predicts lower pathogen prevalence in marine than in freshwater habitats. We tested these scarcely investigated hypotheses by screening wintering and resident wading shorebirds (Charadriiformes) for avian malaria blood parasites (Plasmodium and Haemoproteus spp.) along a latitudinal gradient in Australia. We sequenced infections to determine if wintering migrants share malaria parasites with local shorebird residents, and we combined prevalence results with published data in a global comparative analysis. Avian malaria prevalence in Australian waders was 3.56% and some parasite lineages were shared between wintering migrants and residents, suggesting active transmission at wintering sites. In the global dataset, avian malaria prevalence was highest during winter and increased with decreasing wintering latitude, after controlling for phylogeny. The latitudinal gradient was stronger for waders that use marine and freshwater habitats (marine + freshwater) than for marine-restricted species. Marine + freshwater wader species also showed higher overall avian malaria parasite prevalence than marine-restricted species. By combining datasets in a global comparative analysis, we provide empirical evidence that migratory waders avoiding the tropics during the non-breeding season experience a decreased risk of malaria parasite infection. We also find global support for the hypothesis that marine-restricted shorebirds experience lower parasite pressures than shorebirds that also use freshwater habitats. Our study indicates that pathogen transmission may be an important driver of site selection for non-breeding migrants, a finding that contributes new knowledge to our understanding of how migration strategies evolve.

Sex-specific arrival times on the breeding grounds: hybridizing migratory skuas provide empirical support for the role of sex ratios

In migratory animals, protandry (earlier arrival of males on the breeding grounds) prevails over protogyny (females preceding males). In theory, sex differences in timing of arrival should be driven by the operational sex ratio, shifting toward protogyny in female-biased populations. However, empirical support for this hypothesis is, to date, lacking. To test this hypothesis, we analyzed arrival data from three populations of the long-distance migratory south polar skua (Catharacta maccormicki). These populations differed in their operational sex ratio caused by the unidirectional hybridization of male south polar skuas with female brown skuas (Catharacta antarctica lonnbergi). We found that arrival times were protandrous in allopatry, shifting toward protogyny in female-biased populations when breeding in sympatry. This unique observation is consistent with theoretical predictions that sex-specific arrival times should be influenced by sex ratio and that protogyny should be observed in populations with female-biased operational sex ratio.

How does nest box temperature affect nestling growth rate and breeding success in a parrot?

Climate change is predicted to affect many species by reducing range, habitat suitability and breeding success. Cavity-nesting species, already threatened by deforestation and declining natural hollows, may be particularly at risk because they are limited in nest-site location, and climatic alterations may further reduce usability of natural cavities. It is therefore essential to determine how cavity-users may be affected. We recorded internal nest box temperatures and modelled the relationships of four temperature parameters (relating to mean temperature, variability in temperature, low temperature extremes and high temperature extremes) with breeding success and nestling growth in an Australian cavity-nesting parrot, the Crimson Rosella (Platycercus elegans). We found that less extreme low temperatures resulted in heavier nestlings; however, higher mean temperatures tended to result in lighter nestlings. Greater temperature variability tended to reduce fledging success; however, no temperature variables had a clear effect on clutch size or hatching success. Our findings indicate that there may be a complex relationship between nestling growth and temperature, and although less extreme cold temperatures may benefit nestlings, continued increases in mean temperature and variability may have negative consequences.

The adaptive significance of provisioning and foraging coordination between breeding partners.

Sexual conflict over parental care relies on the fundamental assumption that parents do not share the cost of their partner's effort on future reproduction. However, this is unlikely to be true whenever partners breed together more than once. In that case, individuals should try to optimize the cost and benefits for the pair, rather than only for themselves. Here we seek to establish whether the synchronization of parents' provisioning visits to the nest could fulfill this function. We conducted a brood-size manipulation experiment on wild zebra finches to test whether nest visit synchrony was flexible and beneficial for nestlings' growth, while controlling for the confounding effects of pair "quality" and synchrony away from the nest during foraging. Using a network of readers to track parents at nests and feeding stations, we found that nest visit synchrony responded directly to the brood manipulation and increased with brood size. Synchrony at the nest and while foraging were correlated, but the latter better predicted nestling mass, possibly because it was associated with more regular provisioning patterns. Our findings suggest that parental coordination could indeed play an important role in partners' investment decisions, underpinning the evolution of the most prominent mating system in birds.

Energetic consequences of time-activity budgets for a breeding seabird

How animals allocate their time to different behaviours has important consequences for their overall energy budget and reflects how they function in their environment. This potentially affects their ability to successfully reproduce, thereby impacting their fitness. We used accelerometers to record time-activity budgets of 21 incubating and chick-rearing kittiwakes (Rissa tridactyla) on Puffin Island, UK. These budgets were examined on a per day and per foraging trip basis. We applied activity-specific estimates of energy expenditure to the kittiwakes' time-activity budgets in order to identify the costs of variation in their allocation of time to different behaviours. Estimates of daily energy expenditure for incubating kittiwakes averaged 494 ± 20 kJ d-1 while chick-rearing birds averaged 559 ± 11 kJ d-1. Time-activity budgets highlighted that kittiwakes did not spend a large proportion of their time flying during longer foraging trips, or during any given 24-h period. With time spent flying highlighted as the driving factor behind elevated energy budgets, this suggests behavioural compensation resulting in a possible energetic ceiling to their activities. We also identified that kittiwakes were highly variable in the proportion of time they spent either flying or on the water during foraging trips. Such variation meant that using forage trip duration alone to predict energy expenditure gave a mean error of 19% when compared to estimates incorporating the proportion of a foraging trip spent flying. We have therefore highlighted that trip duration alone is not an accurate indicator of energy expenditure.

Placement of re-nests following predation: are birds managing risk?

Nest predation is the most important source of reproductive failure for many bird species, thus placing nests in 'safe' locations that minimise predation risk is paramount to maximising fitness. After a nest predation event, some species have been shown to manage the risk of nest predation for subsequent re-nesting attempts by moving to a new location, placing re-nests in areas with increased cover, or changing the height above ground at which the re-nest is placed. The extent to which this is an adaptive behaviour for birds in general is not yet clear, as existing studies are almost exclusively restricted to northern hemisphere species and species that do not breed cooperatively. Here, we examined the re-nesting behaviour of Bell Miners (Manorina melanophrys), a species of honeyeater endemic to Australia that is both multi-brooded and also frequently re-nests soon after nesting failure; females can build up to five nests in a breeding season. We tested if these females managed within-season nest predation risk by changing nest site characteristics (height from ground and distance between nests) between successive nesting attempts. We found that female miners did indeed manage predation risk by reducing the height from the ground at which they placed re-nests following predation events, but contrary to our second prediction we found no difference in distances moved to re-nest after females experienced nest predation or successfully rearing young.

Somewhat saved : a captive breeding programme for two endemic Christmas Island lizard species, now extinct in the wild

As with many islands, Christmas Island in the Indian Ocean has suffered severe biodiversity loss. Its terrestrial lizard fauna comprised five native species, of which four were endemic. These were abundant until at least the late 1970s, but four species declined rapidly thereafter and were last reported in the wild between 2009 and 2013. In response to the decline, a captive breeding programme was established in August 2009. This attempt came too late for the Christmas Island forest skink Emoia nativitatis, whose last known individual died in captivity in 2014, and for the non-endemic coastal skink Emoia atrocostata. However, two captive populations are now established for Lister's gecko Lepidodactylus listeri and the blue-tailed skink Cryptoblepharus egeriae. The conservation future for these two species is challenging: reintroduction will not be possible until the main threats are identified and controlled.

Evaluation of breeding strategies for polledness in dairy cattle using a newly developed simulation framework for quantitative and Mendelian traits

Background: Intensified selection of polled individuals has recently gained importance in predominantly horned dairy cattle breeds as an alternative to routine dehorning. The status quo of the current polled breeding pool of genetically-closely related artificial insemination sires with lower breeding values for performance traits raises questions regarding the effects of intensified selection based on this founder pool. Methods: We developed a stochastic simulation framework that combines the stochastic simulation software QMSim and a self-designed R program named QUALsim that acts as an external extension. Two traits were simulated in a dairy cattle population for 25 generations: one quantitative (QMSim) and one qualitative trait with Mendelian inheritance (i.e. polledness, QUALsim). The assignment scheme for qualitative trait genotypes initiated realistic initial breeding situations regarding allele frequencies, true breeding values for the quantitative trait and genetic relatedness. Intensified selection for polled cattle was achieved using an approach that weights estimated breeding values in the animal best linear unbiased prediction model for the quantitative trait depending on genotypes or phenotypes for the polled trait with a user-defined weighting factor. Results: Selection response for the polled trait was highest in the selection scheme based on genotypes. Selection based on phenotypes led to significantly lower allele frequencies for polled. The male selection path played a significantly greater role for a fast dissemination of polled alleles compared to female selection strategies. Fixation of the polled allele implies selection based on polled genotypes among males. In comparison to a base breeding scenario that does not take polledness into account, intensive selection for polled substantially reduced genetic gain for this quantitative trait after 25 generations. Reducing selection intensity for polled males while maintaining strong selection intensity among females, simultaneously decreased losses in genetic gain and achieved a final allele frequency of 0.93 for polled. Conclusions: A fast transition to a completely polled population through intensified selection for polled was in contradiction to the preservation of high genetic gain for the quantitative trait. Selection on male polled genotypes with moderate weighting, and selection on female polled phenotypes with high weighting, could be a suitable compromise regarding all important breeding aspects.