A comparison of deformed wing virus in deformed and asymptomatic honey bees

Deformed wing virus (DWV) in association with Varroa destructor is currently attributed to being responsible for colony collapse in the western honey bee (Apis mellifera). The appearance of deformed individuals within an infested colony has long been associated with colony losses. However, it is unknown why only a fraction of DWV positive bees develop deformed wings. This study concerns two small studies comparing deformed and non-deformed bees. In Brazil, asymptomatic bees (no wing deformity) that had been parasitised by Varroa as pupae had higher DWV loads than non-parasitised bees. However, we found no greater bilateral asymmetry in wing morphology due to DWV titres or parasitisation. As expected, using RT-qPCR, deformed bees were found to contain the highest viral loads. In a separate study, next generation sequencing (NGS) was applied to compare the entire DWV genomes from paired symptomatic and asymptomatic bees from three colonies on two different Hawaiian islands. This revealed no consistent differences between DWV genomes from deformed or asymptomatic bees, with the greatest variation seen between locations, not phenotypes. All samples, except one, were dominated by DWV type A. This small-scale study suggests that there is no unique genetic variant associated with wing deformity; but that many DWV variants have the potential to cause deformit

Vertical and Horizontal Transmission of Cell Fusing Agent Virus in Aedes aegypti

Cell fusing agent virus (CFAV) is an insect-specific flavivirus (ISF) found in Aedes aegypti mosquitoes. ISFs have demonstrated the ability to modulate the infection or transmission of arboviruses such as dengue, West Nile, and Zika viruses. It is thought that vertical transmission is the main route for ISF maintenance in nature. This has been observed with CFAV, but there is evidence of horizontal and venereal transmission in other ISFs. Understanding the route of transmission can inform strategies to spread ISFs to vector populations as a method of controlling pathogenic arboviruses. We crossed individually reared male and female mosquitoes from both a naturally occurring CFAV-positive Ae. aegypti colony and its negative counterpart to provide information on maternal, paternal, and horizontal transmission. RT-PCR was used to detect CFAV in individual female pupal exuviae and was 89% sensitive, but only 42% in male pupal exuviae. This is a possible way to screen individuals for infection without destroying the adults. Female-to-male horizontal transmission was not observed during this study. However, there was a 31% transmission rate from mating pairs of CFAV-positive males to negative female mosquitoes. Maternal vertical transmission was observed with a filial infection rate of 93%. The rate of paternal transmission was 85% when the female remained negative, 61% when the female acquired CFAV horizontally, and 76% overall. Maternal and paternal transmission of CFAV could allow the introduction of this virus into wild Ae. aegypti populations through male or female mosquito releases, and thus provides a potential strategy for ISF-derived arbovirus control

Superinfection exclusion and the long-term survival of honey bees in Varroa-infested colonies

Over the past 50 years, many millions of European honey bee (Apis mellifera) colonies have died as the ectoparasitic mite, Varroa destructor, has spread around the world. Subsequent studies have indicated that the mite's association with a group of RNA viral pathogens (Deformed Wing Virus, DWV) correlates with colony death. Here, we propose a phenomenon known as superinfection exclusion that provides an explanation of how certain A. mellifera populations have survived, despite Varroa infestation and high DWV loads. Next-generation sequencing has shown that a non-lethal DWV variant 'type B' has become established in these colonies and that the lethal 'type A' DWV variant fails to persist in the bee population. We propose that this novel stable host-pathogen relationship prevents the accumulation of lethal variants, suggesting that this interaction could be exploited for the development of an effective treatment that minimises colony losses in the future.The ISME Journal advance online publication, 27 October 2015; doi:10.1038/ismej.2015.186

Japanese courage: a genetic analysis of complex traits in medaka fish and humans

This thesis primarily explores how an individual's genes interact with the genes of their social companions to create differences in behaviour, using the Japanese medaka fish as a model organism. Chapter 1 sets out the introduction to the diverse topics covered in this thesis, and is followed by five substantive chapters. Chapter 2 describes several genomic characteristics of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel, which comprises 80 inbred lines of medaka that were bred from a wild population from the city of Kiyosu, southern Japan. In this chapter I plot the inbreeding trajectory of the MIKK panel and analyse a number of genomic characteristics relevant to its utility for the genetic mapping of complex traits, including: the panel's evolutionary relationship with other previously-established inbred medaka strains; the degree of homozygosity in the inbred lines; the rate of linkage disequilibrium decay across the panel; and the genomic repeats and structural variation present in their genomes. In Chapter 3, I use a custom behavioural assay to characterise and classify bold-shy behaviours in 5 previously-established inbred medaka strains. I describe the assay, assess its robustness against confounding factors, and apply a hidden markov model (HMM) to classify the fishes' behaviours across a spectrum of boldness-shyness based on the individuals' distance and angle of travel between pre-defined time intervals. I describe how the strains differ in their behaviours over the course of the assay (a "direct genetic effect") and how the behaviour of a single "reference" strain (*iCab*) differs in the presence of different strains (an "indirect genetic effect"). In Chapter 4, I describe the bioinformatic processes and genetic association models that I used to map the variants associated with variation in the period of somite development, based on an F2-cross between the southern Japanese iCab strain, and the northern Japanese Kaga strain. In Chapter 5, I explain how I ran the custom behavioural assay described in Chapter 3 over the MIKK panel to identify lines that diverge in both their own bold-shy behaviours (the direct genetic effect) and the extent to which they transmit those behaviours onto their tank partners (the indirect genetic effect). I then describe how I used those divergent lines as the parental lines in a multi-way F2-cross to identify the genetic variants associated with both direct and indirect genetic effects. Finally, in Chapter 6, I turn to humans to compare and rank all complex traits in the GWAS Catalog based on the extent to which their associated alleles vary across global populations, using the Fixation Index (FST) as a metric, and the 1000 Genomes dataset as a sample of global genetic variation. I set out the bioinformatic pipelines used to process the data, present the distributions of FST for trait-associated alleles across the genome, and use the Kolmogorov-Smirnov test to compare the distributions of FST across different traits. Altogether, this thesis describes some of the genomic characteristics of both medaka fish and humans, and how those variations relate to differences in complex traits, with a particular focus on the genetic causes of adaptive behaviours and the transmission of those behaviours onto one's social companions.EMBL International PhD Programm

The Australian National Mango Breeding Program - In search of improved cultivars for the new millennium

The Australian mango industry is predominantly based on a single cultivar Kensington Pride. Although this cultivar is popular in the domestic market, it has a number of limitations, which impact greatly on the economics of production. Problems such as excessive tree vigour, unreliable flowering and poor fruit-set result in low and irregular cropping. Fruit quality of Kensington Pride also suffers from short shelf life, susceptibility to sap burn, inconsistency in development of red blush and internal physiological disorders. Although chemical means aimed at overcoming some of these limitations have been useful, cultivar research and breeding are being looked at for more sustainable and long term solutions. The Australian National Mango Breeding Program was initiated in year 1994 as a joint project between four Australian state and federal agricultural organisations to develop superior genotypes. In most crosses, Kensington Pride was used as one of the parents and crossed with a range of Floridian, Indian and Asian cultivars. Emasculation and hand pollination was used to evolve over 1800 crosses involving 33 parental combinations with 40 to 50 each in most of the crosses. These hybrids are being evaluated in two different environmental conditions, one in the humid tropical climate of Darwin and the other in the dry milder tropical conditions of Mareeba district in Queensland. Results from the early phases of the program are presented together with some promising early outcomes and plans for the future. Over 300 progenies fruited by year 2000, of which six outstanding crosses have been selected for regional testing. The project will also generate valuable information on inheritance of various traits for future breeding work

Inheritance of fruit characters in hybrid mangoes produced through controlled pollination

Mango fruit quality attributes have been evaluated in hybrids produced by the Australian National Mango Breeding Program. Since its inception in 1994 the program has generated more than 1800 hybrids from 33 parental combinations using controlled pollination methods. Characterisation of the fruit was carried out by assessing 24 internal and external attributes and an estimate was made of the heritabilities of characters for which the data were either quantitative or were scored on an evenly ordered hedonic scale. Analysis of the data indicated that many important fruit quality aspects such as fruit weight, fruit shape, ground skin colour, fruit width and pulp depth have high heritabilities, and can therefore be readily selected in a breeding programme. For non-ordered traits scored in discrete categories (blush colour, bloom, lenticel colour, embryo type and flavour), an estimate was made of data consistency from multiple scores for individual hybrids at different times and locations. A relatively high consistency value was recorded for fruit flavour, and in combinations involving Kensington Pride, between 24% and 47% of hybrids were scored as having Kensington Pride flavour. The embryo type of hybrids was also recorded and the data are discussed in the context of polyembrony being controlled by a single dominant gene

INHERITANCE OF FRUIT CHARACTERS IN HYBRID MANGOES PRODUCED THROUGH CONTROLLED POLLINATION

Mango fruit quality attributes have been evaluated in hybrids produced by the Australian National Mango Breeding Program. Since its inception in 1994 the program has generated more than 1800 hybrids from 33 parental combinations using controlled pollination methods. Characterisation of the fruit was carried out by assessing 24 internal and external attributes and an estimate was made of the heritabilities of characters for which the data were either quantitative or were scored on an evenly ordered hedonic scale. Analysis of the data indicated that many important fruit quality aspects such as fruit weight, fruit shape, ground skin colour, fruit width and pulp depth have high heritabilities, and can therefore be readily selected in a breeding programme. For non-ordered traits scored in discrete categories (blush colour, bloom, lenticel colour, embryo type and flavour), an estimate was made of data consistency from multiple scores for individual hybrids at different times and locations. A relatively high consistency value was recorded for fruit flavour, and in combinations involving Kensington Pride, between 24% and 47% of hybrids were scored as having Kensington Pride flavour. The embryo type of hybrids was also recorded and the data are discussed in the context of polyembrony being controlled by a single dominant gene