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Almond ('Prunus dulcis') is the only nut crop of the Rosaceae. As one of the earliest species to bloom in spring, almond trees can experience severe crop loss due to late frosts and unfavourable climatic conditions. The Australian almond breeding program is one of the world's major almond breeding programs and has developed a genetic linkage map. One of the objectives of the project is to investigate the inheritance of flowering time. The flowering time of a 'Nonpareil' × 'Lauranne' population was evaluated for two years. The proportion of buds and flowers at seven stages of bud and flower development were recorded for each tree using the same procedures in each of two years. A proportional odds logistic model was used to analyse the data, considering the timing of development of buds and flowers as a latent variable that was estimated for each tree on each occasion recorded. These estimates of flower timing were then used in QTL analysis of flowering time. The goal of this project is to identify genetic markers useful in breeding for altered flowering time in almond.

Almond (Prunus dulcis) is the only nut crop of the Rosaceae. As one of the earliest species to bloom in spring, almond trees can experience severe crop loss due to late frosts and unfavourable climatic conditions. The Australian almond breeding program is one of the world's major almond breeding programs and has developed a genetic linkage map. One of the objectives of the project is to investigate the inheritance of flowering time. The flowering time of a 'Nonpareil' x 'Lauranne' population was evaluated for two years. The proportion of buds and flowers at seven stages of bud and flower development were recorded for each tree using the same procedures in each of two years. A proportional odds logistic model was used to analyse the data, considering the timing of development of buds and flowers as a latent variable that was estimated for each tree on each occasion recorded. These estimates of flower timing were then used in QTL analysis of flowering time. The goal of this project is to identify genetic markers useful in breeding for altered flowering time in almond.

Wild pollinators are becoming more valuable to global agriculture as the commercial honeybee industry is increasingly affected by disease and other stressors. Perennial tree crops are particularly reliant on insect pollination, and are often pollen limited. Research on how different tree crop production systems influence the richness and abundance of wild pollinators is, however, limited. We investigated, for the first time, the richness and abundance of potential wild pollinators in commercial temperate almond orchards in Australia, and compared them to potential pollinator communities in proximate native vegetation. We quantified ground cover variables at each site and assessed the value of ground cover on the richness and abundance of potential wild pollinators in commercial almond systems focussing on three common taxa: bees, wasps and flies. More insects were caught in orchards with living ground cover than in native vegetation or orchards without ground cover, although overall species richness was highest in native vegetation. Percent ground cover was positively associated with wasp richness and abundance, and native bee richness, but flies showed no association with ground cover. The strongest positive relationship was between native bee abundance and the richness of ground cover plants. Our results suggest that maintaining living ground cover within commercial almond orchards could provide habitat and resources for potential wild pollinators, particularly native bees. These insects have the potential to provide a valuable ecosystem service to pollinator-dependent crops such as almond.

Background: Despite a high genetic similarity to peach, almonds ('Prunus dulcis') have a fleshless fruit and edible kernel, produced as a crop for human consumption. While the release of peach genome v1.0 provides an excellent opportunity for almond genetic and genomic studies, well-assessed segregating populations and the respective saturated genetic linkage maps lay the foundation for such studies to be completed in almond. Results: Using an almond intraspecific cross between 'Nonpareil' and 'Lauranne' (N × L), we constructed a moderately saturated map with SSRs, SNPs, ISSRs and RAPDs. The N × L map covered 591.4 cM of the genome with 157 loci. The average marker distance of the map was 4.0 cM. The map displayed high synteny and colinearity with the 'Prunus' T × E reference map in all eight linkage groups (G1-G8). The positions of 14 mapped gene-anchored SNPs corresponded approximately with the positions of homologous sequences in the peach genome v1.0. Analysis of Mendelian segregation ratios showed that 17.9% of markers had significantly skewed genotype ratios at the level of P < 0.05. Due to the large number of skewed markers in the linkage group 7, the potential existence of deleterious gene(s) was assessed in the group. Integrated maps produced by two different mapping methods using JoinMap® 3 were compared, and their high degree of similarity was evident despite the positional inconsistency of a few markers. Conclusions: We presented a moderately saturated Australian almond map, which is highly syntenic and collinear with the 'Prunus' reference map and peach genome V1.0. Therefore, the well-assessed almond population reported here can be used to investigate the traits of interest under Australian growing conditions, and provides more information on the almond genome for the international community.

Developed recently, high resolution melting (HRM) analysis is an efficient, accurate and inexpensive method for distinguishing DNA polymorphisms. HRM has been used to identify mutations in human genes, and to detect SNPs, INDELs and microsatellites in plants. However, its capacity to discriminate DNA variants in the context of complex haplotypes involving INDEL as well as SNP variants has not been examined until now. In this study, we genotyped an almond (Prunus dulcis (Mill.) D. A. Webb, syn. Prunus amygdalus Batsch) pseudotestcross mapping population that showed segregation of complex haplotypes associated with CYP79D16 promoter sequence. The 175 bp region in question included a 7 bp INDEL and 3 SNPs, and manifested as three different haplotypes in the parents. Thus, with one homozygous and one heterozygous parent, two relevant genotypes were identified in the mapping population. Although the population displayed monomorphism with respect to the INDEL and one of the SNPs, HRM was sufficiently sensitive to distinguish genotypes on the basis of the two informative SNPs, and the resulting data were used to map CYP79D16 to linkage group 6 of the almond genome. Thus the capacity of HRM to resolve genotypes arising from complex haplotypes has been demonstrated, and this has important implications for the design of efficient HRM markers for various genetic applications including mapping, population studies and biodiversity analyses.

The almond, ['Prunus dulcis' (Mill) D.A. Webb syn. 'P. amygdalus' Batsch] is an important nut crop belonging to the family Rosaceae. Almond consumption has shown steady growth during the last decades due to the increased awareness of its excellent flavour, nutritional value and health benefits. The Australian climate provides great potential for growing almonds and the Australian almond breeding program was initiated in 1997 to develop cultivars better suited to growing conditions and to meet market demands. The construction of a genetic linkage map for one of the breeding populations (Nonpareil x Lauranne) was a part of this breeding program. This population comprised 181 individuals, of which 93 were used for map construction and quantitative trait loci (QTL) analysis in this study. Important traits that were investigated included flowering time, flower structures in relation to fruit set and autogamy and shell and kernel traits.

The dataset consists of six tabs (each referring to a data chapter of the thesis). Data related to this dataset was collected online from Scopus research database (Chapter 2), and in the field from Lake Powell, Victoria, Australia (Chapter 5), and from the East-North Coast of New South Wales, Australia (chapters 3, 4, 6, and 7). Each tab has a spreadsheet with data from each thesis research chapter, and the content of each tab is explained below:

Chapter 2: A review of honey bee (Apis mellifera L.) interactions with other pollinators. The dataset consists of information extracted from reviewed articles, such as the title of the article, the authors, the year of publication, the country in which the research was performed, the place of study (i.e., open fields, or enclosed areas like glasshouses, cages, etc.), whether the study aimed to test competition or not, whether the study found and/or discussed competition or not, the type of interaction (i.e., direct or indirect) between honey bees and other species, the main methods used to perform the research, the interacting species with honey bees, and the behaviour performed by honey bees during the interaction.

Chapter 3: Observation of birds foraging on raspberry orchards. The dataset consists of the number of instances insectivorous or nectarivorous birds were seen perched on cages containing brown blowflies, within a raspberry orchard block. The first column is the days since flies were released inside cages until birds were seen inside the same cages, column two is the number of observational hours on each day of data collection, the following four columns have the bird species name and the number of individuals of each species, and the last column is the total number of individuals.

Chapter 4: Effectiveness of brown honeyeater (Lichmera indistincta) in pollinating blueberry flowers compared to insect pollinators. The dataset consists of stigmas collected after a single visit by one pollinator species. The first column is the pollinator ID, the second column is the identification of the stigma sampled, and the last column is the number of conspecific (i.e., blueberry) pollen grains deposited.

Chapter 5: Pollen collection by honey bee hives in almond orchards. The data consists of pollen pellets removed from different hives placed in almond orchards for pollination. The first column is the almond flower abundance during the flowering season (measures were always taken from the same tree branch throughout the study period), column two is the day of data collection (11 days in total), column three is the apiary identification, column four is the hive identification, column five is the heterospecific pollen richness (number of species), column six is the abundance of heterospecific pollen, column seven is the weight of heterospecific pollen collected from each hive, column eight is the weight of almond pollen collected from each hive, column nine is the total weight.

Chapter 6: Impacts of protective nets on pollen flow in blueberry orchards. The dataset consists of analyses of pollen deposition on blueberry stigmas under different netting treatments. The first column is the blueberry plant variety stigma was sampled from, column two the orchard block identification, column three is the netting treatment (i.e., covered - block completely covered by nets, partially - block partially covered by nets with sides open, and open - no nets), column four is the week of data collection (seven weeks in total), column five is the abundance of blueberry flower within each block (measures were always taken from the same blueberry plant), column six is the conspecific pollen abundance, column seven is the heterospecific pollen abundance on the stigmas, column eight is the heterospecific pollen richness in the stigmas, column nine is the point of data collection within the orchards (i.e., edge or center), and the last column is the number of non-blueberry flowers present in the remnant vegetation surrounding the orchard blocks.

Chapter 7: Effects of multiple visits on pollen deposition in blueberry, blackberry, and raspberry flowers. The dataset consists of pollen deposition analyses after multiple visits by different insect taxa in blueberry, blackberry, and raspberry flowers. The first column is the sample identification, column two is the crop species (i.e., Rubus sp - raspberry, rabbiteye - blueberry, or blackberry), column three is the crop species variety, column four is the block identification, column five is the date of sample collection, column six is the row number within the block that the sample was collected from, column seven is the identification tag used for the sample during collection, column eight is the total number if visits received by the sample (i.e., stigma), column nine is the combination of species that visited the stigma (i.e., MX - mix of species, SB - stingless bees, HB - honey bees, CR - carpenter bees), column ten is the number of conspecific pollen counted on the stigma, column eleven is the number of heterospecific pollen counted on the stigma, column twelve is the richness of heterospecific pollen counted on the stigma, column thirteen is the total visit duration time in seconds, column fourteen to thirty four is the visit duration of each subsequent visit.

Five years of research on interrelationships between fauna use of almond plantations and native vegetation in north-western Victoria shows that almond plantations have a strong influence on fauna dynamics and in some cases may provide important habitat for threatened species.

1 Homogeneous tree crop plantations can adversely impact wild pollinator communities by limiting the temporal continuity of food and the availability of nesting sites. Identifying how structural differences between plantations and natural vegetation influence pollinator communities is necessary for ecological management of agroecosystems. 2 Communities of potential wild pollinators (native bees, wasps, flies) were compared between monoculture almond plantations and native vegetation in a semi-arid region of southern Australia, before, during and after the late winter almond flowering period. Abundance and richness of each insect group were related to site heterogeneity and keystone structural resources at each site, focusing on food and nesting resources. 3 Relationships with site heterogeneity varied between taxa and across months. Native bee abundance and richness were strongly associated with specific keystone resources, despite showing no association with site heterogeneity. 4 The present study highlights the value of focusing on biologically meaningful resources when investigating relationships between insects and habitat, rather than on generalized heterogeneity metrics. The results suggest that maintaining keystone resources in agroecosystems can support the conservation of insects and ecosystem services, especially in areas where homogeneous agricultural systems overlap dynamic natural ecosystems.

Peach and almond have been considered as model species for the family Rosaceae and other woody plants. Consequently, mapping and characterisation of genes in these species has important implications. High-resolution melting (HRM) analysis is a recent development in the detection of SNPs and other markers, and proved to be an efficient and cost-effective approach. In this study, we aimed to map genes corresponding to known proteins in other species using the HRM approach. Prunus unigenes were searched and compared with known proteins in the public databases. We developed single-nucleotide polymorphism (SNP) markers, polymorphic in a mapping population produced from a cross between the cloned cultivars Nonpareil and Lauranne. A total of 12 SNP-anchored putative genes were genotyped in the population using HRM, and mapped to an existing linkage map. These genes were mapped on six linkage groups, and the predicted proteins were compared to putative orthologs in other species. Amongst those genes, four were abiotic stress-responsive genes, which can provide a starting point for construction of an abiotic resistance map. Two allergy and detoxification related genes, respectively, were also mapped and analysed. Most of the investigated genes had high similarities to sequences from closely related species such as apricot, apple and other eudicots, and these are putatively orthologous. In addition, it was shown that HRM can be an effective means of genotyping populations for the purpose of constructing a linkage map. Our work provides basic genomic information for the 12 genes, which can be used for further genetic and functional studies.

Molecular breeding is the use of genetic manipulation at the DNA molecular level to improve traits of interest in plants and to shorten the time for developing new crop varieties to be brought to the market. In traditional plant breeding, genetic variation and characterization are usually identified by visual selection of morphological traits. However, with the development of molecular biology, the problems related to environmental factors and, in some cases, the slow development process, might be solved by the use of molecular markers. 'DNA marker' is a term used to refer to a specific DNA variation between individuals that has been found to be associated with a certain characteristic. These different DNA or genetic variants are known as alleles. Thus, the use of DNA markers to define the genotype and predict the performance of a plant is a powerful aid to plant breeding. Molecular breeding implies molecular marker-assisted selection (MAS), which is a strategy to facilitate the exploitation of existing genetic diversity in breeding populations and therefore, in combination with linkage maps and genomics, can be used to improve a whole range of desirable traits.

Homogenization of agricultural landscapes affects ecological processes and biodiversity and can affect the community composition of ecosystem service providers. These effects can have particular impact in landscapes dominated by monocultures of pollinator-dependent tree crop plantations, which create both spatial and temporal homogeneity at the landscape scale. I looked for associations between the proportion of nearby unmanaged vegetation and potential wild pollinator groups collected within flowering almond orchards in two types of landscape. In the Complex landscape, characterized by a heterogeneous mosaic of multiple crops, semi-natural grassland and natural woodland, insect pollinator groups were not associated with unmanaged vegetation. In the Simple landscape, dominated by monoculture almond plantations, most pollinator groups showed positive relationships with the two unmanaged vegetation types (grassland and woodland). In particular, all wild bee and all but one hoverfly individual were found in remnant native vegetation patches within almond plantations, rather than within rows of almond trees. More research is necessary to identify how structural differences created in monoculture landscapes, between crops and the native vegetation they encroach on, influence ecological communities and the provision of ecosystem services.

The secondary metabolite amygdalin is a cyanogenic diglucoside that at high concentrations is associated with intense bitterness in seeds of the Rosaceae, including kernels of almond ('Prunus dulcis' (Mill.), syn. 'Prunus amygdalus' D.A. Webb Batsch). Amydalin is a glucoside of prunasin, itself a glucosider of 'R'-mandelonitrile (a cyanohydrin). Here we report the isolation of an almond enzyme (UGT85A19) that stereo-selectively gucosylates 'R'-mandelonitrile to produce prunasin. In a survey of developing kernels from seven bitter and 11 non-bitter genotypes with polyclonal antibody raised to UGT85A19, the enzyme was found to accumulate to higher levels in the bitter types in later development. This differential accumulation of UGT85A19 is associated with more than three-fold greater mandelonitrile glucosyltrajsferase activity in bitter kernels compared with non-bitter types, and transcriptional regulation was demonstrated using quantitative-PCR analysis. UGT85A19 and its encoding transcript were most concentrated in the testa (seed coat) of the kernel compared with the embryo, and prunasin and amygdalin were differentially compartmentalised in these tissues. Prunasin was confined to the testa and amygdalin was confined to the embryo. These results are consisted with the seed coat being an important site of synthesis of prunasin as a precursor of amygdalin accumulation in the kernel. The presence of UGT85A19 in the kernel and other tissues of both bitter and non-bitter types indicates that its expression is unlikely to be a control point for amygdalin accumulation and suggests additional roles for the enzyme in almond metabolism.

In 1999, we presented our work at XI GREMPA on conservation of almond (Prunus dulcis) germplasm by cryopreservation of almond shoot tips. "Nonpareil", "Ne Plus Ultra" and an almond-peach hybrid rootstock, Prunus dulcis "Titan" x P. persica "Nemaguard" were successfully cryopreserved for 6 months using a one-step vitrification technique. That work has since been extended to test for plant viability and genetic integrity after storage under liquid nitrogen for up to 2 years. Mean survival of shoot tips was 80% for "Ne Plus Ultra", 54% for "Nonpareil", and 78% for the hybrid rootstock, and there were no significant differences in survival between 3 days and 2 years. Genetic stability was tested by comparing DNA from the original trees, with leaves regrown from tissue culture, and from leaves regrown from cryopreserved shoot tips. Some changes in the structure and methylation of the DNA were found that were probably related to the in vitro culture process. These changes may have affected agronomic performance. Fruit and kernel characteristics have been monitored and compared to authentic non-preserved cultivars.