Potential of genomic selection for improvement of resistance to ostreid herpesvirus in Pacific oyster (Crassostrea gigas)

In genomic selection (GS), genome-wide SNP markers are used to generate genomic estimated breeding values for selection candidates. The application of GS in shellfish looks promising and has the potential to help in dealing with one of the main issues currently affecting Pacific oyster production worldwide, which is the 'summer mortality syndrome'. This causes periodic mass mortality in farms worldwide and has mainly been attributed to a specific variant of the ostreid herpesvirus (OsHV-1). In the current study, we evaluated the potential of genomic selection for host resistance to OsHV-1 in Pacific oysters, and compared it with pedigree-based approaches. An OsHV-1 disease challenge was performed using an immersion-based virus exposure treatment for oysters for 7 days. A total of 768 samples were genotyped using the medium-density SNP array for oysters. A GWAS was performed for the survival trait using a GBLUP approach in blupf90 software. Heritability ranged from 0.25 ± 0.05 to 0.37 ± 0.05 (mean ± SE) based on pedigree and genomic information respectively. Genomic prediction was more accurate than pedigree prediction, and SNP density reduction had little impact on prediction accuracy until marker densities dropped below approximately 500 SNPs. This demonstrates the potential for GS in Pacific oyster breeding programmes, and importantly, demonstrates that a low number of SNPs might suffice to obtain accurate genomic estimated breeding values, thus potentially making the implementation of GS more cost effective.

Assessment of genetic diversity and population structure in cultured Australian Pacific oysters

The recent development of Pacific oyster (Crassostrea gigas) SNP genotyping arrays has allowed detailed characterisation of genetic diversity and population structure within and between oyster populations. It also raises the potential of harnessing genomic selection for genetic improvement in oyster breeding programmes. The aim of this study was to characterise a breeding population of Australian oysters through genotyping and analysis of 18 027 SNPs, followed by comparison with genotypes of oyster sampled from Europe and Asia. This revealed that the Australian populations had similar population diversity (H_E ) to oysters from New Zealand, the British Isles, France and Japan. Population divergence was assessed using PCA of genetic distance and revealed that Australian oysters were distinct from all other populations tested. Australian Pacific oysters originate from planned introductions sourced from three Japanese populations. Approximately 95% of these introductions were from geographically, and potentially genetically, distinct populations from the Nagasaki oysters assessed in this study. Finally, in preparation for the application of genomic selection in oyster breeding programmes, the strength of LD was evaluated and subsets of loci were tested for their ability to accurately infer relationships. Weak LD was observed on average; however, SNP subsets were shown to accurately reconstitute a genomic relationship matrix constructed using all loci. This suggests that low-density SNP panels may have utility in the Australian population tested, and the findings represent an important first step towards the design and implementation of genomic approaches for applied breeding in Pacific oysters.

Compositional response of Amazon forests to climate change

Most of the planet's diversity is concentrated in the tropics, which includes many regions undergoing rapid climate change. Yet, while climate-induced biodiversity changes are widely documented elsewhere, few studies have addressed this issue for lowland tropical ecosystems. Here we investigate whether the floristic and functional composition of intact lowland Amazonian forests have been changing by evaluating records from 106 long-term inventory plots spanning 30 years. We analyse three traits that have been hypothesized to respond to different environmental drivers (increase in moisture stress and atmospheric CO₂ concentrations): maximum tree size, biogeographic water-deficit affiliation and wood density. Tree communities have become increasingly dominated by large-statured taxa, but to date there has been no detectable change in mean wood density or water deficit affiliation at the community level, despite most forest plots having experienced an intensification of the dry season. However, among newly recruited trees, dry-affiliated genera have become more abundant, while the mortality of wet-affiliated genera has increased in those plots where the dry season has intensified most. Thus, a slow shift to a more dry-affiliated Amazonia is underway, with changes in compositional dynamics (recruits and mortality) consistent with climate-change drivers, but yet to significantly impact whole-community composition. The Amazon observational record suggests that the increase in atmospheric CO₂ is driving a shift within tree communities to large-statured species and that climate changes to date will impact forest composition, but long generation times of tropical trees mean that biodiversity change is lagging behind climate change.

Host-limited dynamics of autoparasitoids

Autoparasitoids, an important class of intraguild predators used in classical biological control, have a unique biology. Females develop as primary endoparasitoids of scale insects and whiteflies. Males develop at the expense of conspecific or heterospecific parasitoid prepupae. To evaluate the effect of autoparasitism on host suppression, system stability, and parasitoid coexistence, stage-structured differential equation models are developed and analysed. For a host-parasitoid system, autoparasitism stabilizes host-parasitoid oscillations generated by developmental delays of the parasitoid. In host-autoparasitoid-primary parasitoid systems, a distinction between obligate (i.e. parasitoid only attacks conspecifics for the production of males) and facultative (i.e. parasitoid attacks conspecifics and heterospecifics for the production of males) autoparasitism is drawn. Coexistence between an obligate autoparasitoid and primary parasitoid occurs if and only if the autoparasitoid can invade at lower host densities than the primary parasitoid, and the primary parasitoid can suppress the host to a lower equilibrium density than the autoparasitoid. When coexistence occurs, the primary parasitoid determines the host equilibrium abundance. Interactions between facultative autoparasitoids and primary parasitoids can lead to a priority effect, and, less likely, to coexistence. When coexistence occurs, the invasion of the facultative autoparasitoid into the host-primary parasitoid system raises the equilibrium density of the host. In either coexistence scenario, the invasion of an autoparasitoid can stabilize an unstable host-primary parasitoid system. The analysis concludes by showing that the introduction of an autoparasitoid to a host-primary parasitoid system can improve host suppression in the short-term despite possible long-term disruption.

Inoculum Densities of Fusarium oxysporum f. sp. vasinfectum and Meloidogyne incognita in Relation to the Development of Fusarium Wilt and the Phenology of Cotton Plants (Gossypium hirsutum)

ABSTRACT Development of Fusarium wilt in upland cotton (Gossypium hirsutum) usually requires infections of plants by both Meloidogyne incognita and Fusarium oxysporum f. sp. vasinfectum. In this study, the soil densities of M. incognita and F. oxysporum f. sp. vasinfectum and the incidence of Fusarium wilt in three field sites were determined in 1982-1984. Multiple regression analysis of percent incidence of Fusarium wilt symptoms on population densities of M. incognita and F. oxysporum f. sp. vasinfectum yielded a significant fit (R (2) = 0.64) only on F. oxysporum f. sp. vasinfectum. Significant t-values for slope were also obtained for the interaction of M. incognita and F. oxysporum f. sp. vasinfectum, but densities of M. incognita and F. oxysporum f. sp. vasinfectum were also related on a log(10) scale. The physiological time of appearance of first foliar symptoms of Fusarium wilt, based on a degree-days threshold of 11.9 degrees C (53.5 degrees F), was used as a basis for determining disease progress curves and the phenology of cotton plant growth and development. Effects of Fusarium wilt on plant height and boll set were determined in three successive years. Increases in both of these plant characteristics decreased or stopped before foliar symptoms were apparent. Seed cotton yields of plant cohorts that developed foliar wilt symptoms early in the season (before 2,000 F degree-days) were variable but not much different in these years. This contrasted with cohorts of plants that first showed foliar symptoms late in the season (after 2,400 F degree-days) and cohorts of plants that showed no foliar symptoms of wilt. Regression analyses for 1982-1984 indicated moderate to weak correlations (r = 0.16-0.74) of the time of appearance of the first foliar symptoms and seed cotton yields.