II. Horticultural performance of ‘Honeycrisp’ grown on a genetically diverse set of rootstocks under Western New York climatic conditions

A field experiment with 31 rootstocks representing a genetically diverse group of rootstocks featuring ‘Honeycrisp’ as the scion was planted in 2010 at Geneva, NY USA. Rootstocks included three from the Malling series (UK), nine from the Budagovsky series (Russia), 16 from the Cornell Geneva series (USA) and three from the Pillnitz series (Germany). Over the first 8 years (2010–2017) we measured final tree size (trunk cross-sectional area: TCA) and cumulative yield. In the last 4 years we measured fruit soluble solids, bitter pit incidence, biennial bearing, and leaf zonal chlorosis. Tree size varied dramatically with the largest trees on B.70-20-20 and smallest trees on B.71-7-22. Setting the most vigorous rootstock at 100% we categorized rootstocks into 5 size categories: sub-dwarfing class (10–25%), dwarfing class (25–35%), semi-dwarfing class (35–50%), semi-vigorous category (50–70%) and vigorous class (70–100%). Cumulative yield varied 8 fold between the highest yielding rootstock (CG.3001) and the lowest yielding rootstock (B.71-7-22). We calculated theoretical yield per ha by multiplying cumulative yield per tree by a theoretical optimal tree density (trees/ha) based on tree size (TCA). The dwarfing rootstocks G.814, G.41TC, G.11 and B.10 had the highest yields per hectare while the most vigorous rootstocks B.70.20.20 and B.71-7-22 were the least productive. Theoretical cumulative yields varied from a high of 400 t/ha to a low of 50 t/ha, an 8-fold difference. Rootstock also influenced the incidence of bitter pit with the lowest levels of bitter pit with the rootstocks B.10, CG.2034, B.71-7-22, G.41N, CG.4003, G.202N, G.214, and Supporter 3. Considering bitter pit, yield, and optimum tree density, the theoretical yield of bitter pit free fruit varied from a high of 340 t/ha to a low of 35 t/ha, almost a 10-fold difference. The dwarfing rootstocks B.10, G.11, G.41TC, G.214 and G.814 had the highest yields per hectare of bitter pit free fruit. Rootstocks B.9 and M.26 had significantly lower cumulative bitter pit free yield/ha. These data indicate that rootstock not only has a large influence on mature tree cumulative yield but also bitter pit incidence which combine to create a large economic impact of rootstock choice on the long-term economic result of an orchard. This leads to the need for “designer rootstocks” which combine the rootstock characteristics needed to maximize the economic potential of each scion cultivar.info:eu-repo/semantics/acceptedVersio

Natural fruitlet abscission as related to apple tree carbon balance estimated with the MaluSim model

Apple trees produce many more flower clusters than needed for a full crop, but natural early season flower and fruitlet abscission drastically reduce the final fruit number. Natural fruit abscission varies significantly year to year. There have been attempts to try to model apple fruit abscission in the past. However, due to the great complexity of a perennial crop system in a dynamic environment with significant plant manipulations, regulatory processes and controlling environmental variables have been difficult to elucidate. In 1995, a field trial was planted at the New York State Agricultural Experiment Station in Geneva, New York with 3 apple cultivars (‘Delicious’, ‘Gala’, and ‘McIntosh’). Beginning in 2000 and for 18 years thereafter, we recorded the natural whole-season fruit abscission of untreated trees that received no chemical or hand thinning. We also estimated early season patterns of carbohydrate supply-to-demand each year with a carbon balance model. These data were used to correlate tree carbon balance status and other environmental variables with natural fruit abscission responses. In general terms, natural set, defined as final fruit/flower cluster, of ‘Gala’ averaged ˜1 fruit for each flower cluster (fruit set = 0.9), whereas fewer fruits were set on ‘Delicious’ and ‘McIntosh’ (fruit set = 0.7 and 0.6, respectively). Fruit set of ‘Gala’ was less variable than of ‘Delicious’ or ‘McIntosh’, and there was a clear pattern for decreasing fruit set when the number of initial flower clusters per tree increased. Fruit weight was less dependent on fruit number for ‘Delicious’ and ‘McIntosh’ than for ‘Gala’. Multiple regression models indicated that number of flower clusters per tree and average carbohydrate balance between 0–60 degree days (DD) after bloom and 300–360 DD after bloom were the main significant variables that explained 60–80% of the variability in natural fruit set or final fruit number. For ‘Delicious’, temperatures of the previous fall also explained a significant amount of variation in final fruit set and final fruit number. For ‘Gala’, carbon balance from bloom to shortly after petal fall and when fruits were about 18 mm were the two main periods, which were more sensible to carbohydrate deficiency triggering fruit abscission. A later susceptible period was also observed for ‘McIntosh’, suggesting a larger thinning window for this cultivar.info:eu-repo/semantics/acceptedVersio

Modelling physiological and environmental factors regulating relative fruit set and final fruit numbers in apple trees

Chemical thinning of apple (Malus domestica Borkh.) has been practised for 50 years but it remains an unpredictable part of apple production with large variations from year to year and within years. Carbohydrate availability to support young fruitlet growth may play a significant role in apple tree response to chemical thinners, especially when the carbohydrate supply is the limiting factor for fruit growth. To address the carbohydrate component, we have tested the MaluSim model that integrates many environmental and tree physiological factors as a tool to predict chemical thinner response. The model suggests that carbon supply-to-demand variations may explain some of the great variations in thinning spray response. Relative fruit set and final fruit number per tree were affected by the carbohydrate balance within 2 days before the spray and up to 5 days after. There was a period, 15–29 days after bloom that thinners showed higher action. The greater the carbohydrate supply relative to demand, the greater the relative set and the final fruit number. This suggested that carbohydrate supply-demand balance may be a baseline for thinner responses, and that integrative modelling of these balances can be useful in understanding variation in thinning responses. Apple relative fruit set and final fruit number per tree could be modelled relatively well with consideration of initial flower density, the carbohydrate balance model, and cumulative growing degree-days since bloom.info:eu-repo/semantics/acceptedVersio

Unifying Gene Expression Measures from Multiple Platforms Using Factor Analysis

In the Cancer Genome Atlas (TCGA) project, gene expression of the same set of samples is measured multiple times on different microarray platforms. There are two main advantages to combining these measurements. First, we have the opportunity to obtain a more precise and accurate estimate of expression levels than using the individual platforms alone. Second, the combined measure simplifies downstream analysis by eliminating the need to work with three sets of expression measures and to consolidate results from the three platforms

The genomes of two key bumblebee species with primitive eusocial organization

Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation

Reconstructing an Ancestral Mammalian Immune Supercomplex from a Marsupial Major Histocompatibility Complex

The first sequenced marsupial genome promises to reveal unparalleled insights into mammalian evolution. We have used theMonodelphis domestica (gray short-tailed opossum) sequence to construct the first map of a marsupial major histocompatibility complex (MHC). The MHC is the most gene-dense region of the mammalian genome and is critical to immunity and reproductive success. The marsupial MHC bridges the phylogenetic gap between the complex MHC of eutherian mammals and the minimal essential MHC of birds. Here we show that the opossum MHC is gene dense and complex, as in humans, but shares more organizational features with non-mammals. The Class I genes have amplified within the Class II region, resulting in a unique Class I/II region. We present a model of the organization of the MHC in ancestral mammals and its elaboration during mammalian evolution. The opossum genome, together with other extant genomes, reveals the existence of an ancestral “immune supercomplex” that contained genes of both types of natural killer receptors together with antigen processing genes and MHC genes

Put My Skills to Use? Understanding the Joint Effect of Job Security and Skill Utilization on Job Satisfaction Between Skilled Migrants and Australian Born Workers in Australia

The topic of skilled migrants has gained importance in the past decade as they are increasingly becoming one of the main drivers for labor supply in developed countries like Australia. Although there is research on skilled migrants, most have been studied from the perspectives of (un)employment, wage and over-education. Some evidence suggests that skilled migrants are often less satisfied with their job compared to their local counterparts, yet little is known about why these differences exist. Using a nationally representative sample of Australian workers, we examine how two important job characteristics, job security and skill utilization, exert their differential interaction effect on job satisfaction for skilled migrants and Australian born workers. We found a differential moderation effect between job security and skill utilization for skilled migrants and Australian born workers. For skilled migrants, high job security did not lead to positive reaction (i.e., job satisfaction), as this effect was dependent on their skill utilization; while such moderation effect was not present for Australian born workers. This study highlights the need to take a more fine-tuned approach by understanding target sample groups (e.g., skilled migrants) when study the relationship between key job characteristics and job satisfaction. Furthermore, it highlights the importance for organizations to revisit their human resource management strategies and policies to recognize the needs for enhancing skill utilization for skilled migrants

Finding the missing honey bee genes: lessons learned from a genome upgrade

BACKGROUND: The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes. RESULTS: Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data. CONCLUSIONS: Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.Funding for the project was provided by a grant to RG from the National Human Genome Research Institute, National Institutes of Health (NHGRI, NIH) U54 HG003273. Contributions from members of the CGE lab were supported by Agriculture and Food Research Initiative Competitive grant no. 2010- 65205-20407 from the USDA National Institute of Food Agriculture. AKB was supported by a Clare Luce Booth Fellowship at Georgetown University

Staphylococcus aureus Panton-Valentine Leukocidin Contributes to Inflammation and Muscle Tissue Injury

Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) threatens public health worldwide, and epidemiologic data suggest that the Panton-Valentine Leukocidin (PVL) expressed by most CA-MRSA strains could contribute to severe human infections, particularly in young and immunocompetent hosts. PVL is proposed to induce cytolysis or apoptosis of phagocytes. However, recent comparisons of isogenic CA-MRSA strains with or without PVL have revealed no differences in human PMN cytolytic activity. Furthermore, many of the mouse studies performed to date have failed to demonstrate a virulence role for PVL, thereby provoking the question: does PVL have a mechanistic role in human infection? In this report, we evaluated the contribution of PVL to severe skin and soft tissue infection. We generated PVL mutants in CA-MRSA strains isolated from patients with necrotizing fasciitis and used these tools to evaluate the pathogenic role of PVL in vivo. In a model of necrotizing soft tissue infection, we found PVL caused significant damage of muscle but not the skin. Muscle injury was linked to induction of pro-inflammatory chemokines KC, MIP-2, and RANTES, and recruitment of neutrophils. Tissue damage was most prominent in young mice and in those strains of mice that more effectively cleared S. aureus, and was not significant in older mice and mouse strains that had a more limited immune response to the pathogen. PVL mediated injury could be blocked by pretreatment with anti-PVL antibodies. Our data provide new insights into CA-MRSA pathogenesis, epidemiology and therapeutics. PVL could contribute to the increased incidence of myositis in CA-MRSA infection, and the toxin could mediate tissue injury by mechanisms other than direct killing of phagocytes