Bradley C. Campbell

Transgenic Plants for Abiotic Stress Resistance

Modern agricultural crop production relies on the growth of a few of the worlds plant species selected for their superior qualities and suitability as food, animal feed, fiber or industrial end uses. Centuries of selection and, more recently, scientific breeding for adaptation to biotic and abiotic stresses have been necessary to improve yield, yield stability, and product quality in agricultural species.

The Macroecology of Airborne Pollen in Australian and New Zealand Urban Areas

The composition and relative abundance of airborne pollen in urban areas of Australia and New Zealand are strongly influenced by geographical location, climate and land use. There is mounting evidence that the diversity and quality of airborne pollen is substantially modified by climate change and land-use yet there are insufficient data to project the future nature of these changes. Our study highlights the need for long-term aerobiological monitoring in Australian and New Zealand urban areas in a systematic, standardised, and sustained way, and provides a framework for targeting the most clinically significant taxa in terms of abundance, allergenic effects and public health burden.

IRAP, a retrotransposon-based marker system for the detection of somaclonal variation in barley

The retrotransposon-based marker system, inter-retrotransposon amplified polymorphism (IRAP), and inter-simple sequence repeats (ISSRs) were used to detect somaclonal variation induced by tissue culture. IRAPs use a single primer designed to amplify out from the 5′ LTR sequence of the BARE-1 retrotransposon combined with a degenerate 3′ anchor, similar to that of ISSR primers. We analysed DNA polymorphisms in 147 primary regenerants and parental controls from three cultivars of barley (Hordeum vulgare). The ISSR marker system generated an average of 218 bands per primer, with 29 polymorphisms of which 12 were novel non-parental bands. In comparison, the IRAP system generated an average of 121 bands per primer, with 15 polymorphisms of which nine were novel non-parental bands. Polymorphism detected for IRAP and ISSR markers was more than twofold higher in Golden Promise than Mackay and Tallon cultivars. However, there was no significant difference in the frequency of novel non-parental bands. Cluster analysis revealed that the level of polymorphism and genetic variability detected was comparable between IRAP and ISSR markers. This suggests that retrotransposon-based marker systems, such as IRAP, based on retrotransposons such as BARE-1, are valuable tools for the detailed characterisation of mutation profiles that arise during tissue culture. Their use should improve our understanding of processes influencing mutation and somaclonal variation and allow for the design of methods that yield fewer genome changes in applications where maintaining clonal integrity is important.

Differences in grass pollen allergen exposure across Australia

Objective: Allergic rhinitis and allergic asthma are important chronic diseases posing serious public health issues in Australia with associated medical, economic, and societal burdens. Pollen are significant sources of clinically relevant outdoor aeroallergens, recognised as both a major trigger for, and cause of, allergic respiratory diseases. This study aimed to provide a national, and indeed international, perspective on the state of Australian pollen data using a large representative sample.

Whole-Genome Analysis of Candidate genes Associated with Seed Size and Weight in Sorghum bicolor Reveals Signatures of Artificial Selection and Insights into Parallel Domestication in Cereal Crops

Seed size and seed weight are major quality attributes and important determinants of yield that have been strongly selected for during crop domestication. Limited information is available about the genetic control and genes associated with seed size and weight in sorghum. This study identified sorghum orthologs of genes with proven effects on seed size and weight in other plant species and searched for evidence of selection during domestication by utilizing resequencing data from a diversity panel. In total, 114 seed size candidate genes were identified in sorghum, 63 of which exhibited signals of purifying selection during domestication. A significant number of these genes also had domestication signatures in maize and rice, consistent with the parallel domestication of seed size in cereals. Seed size candidate genes that exhibited differentially high expression levels in seed were also found more likely to be under selection during domestication, supporting the hypothesis that modification to seed size during domestication preferentially targeted genes for intrinsic seed size rather than genes associated with physiological factors involved in the carbohydrate supply and transport. Our results provide improved understanding of the complex genetic control of seed size and weight and the impact of domestication on these genes.

Domestication and the storage starch biosynthesis pathway: signatures of selection from a whole sorghum genome sequencing strategy.

Summary Next‐generation sequencing of complete genomes has given researchers unprecedented levels of information to study the multifaceted evolutionary changes that have shaped elite plant germplasm. In conjunction with population genetic analytical techniques and detailed online databases, we can more accurately capture the effects of domestication on entire biological pathways of agronomic importance. In this study, we explore the genetic diversity and signatures of selection in all predicted gene models of the storage starch synthesis pathway of Sorghum bicolor, utilizing a diversity panel containing lines categorized as either ‘Landraces’ or ‘Wild and Weedy’ genotypes. Amongst a total of 114 genes involved in starch synthesis, 71 had at least a single signal of purifying selection and 62 a signal of balancing selection and others a mix of both. This included key genes such as STARCH PHOSPHORYLASE 2 (SbPHO2, under balancing selection), PULLULANASE (SbPUL, under balancing selection) and ADP‐glucose pyrophosphorylases (SHRUNKEN2, SbSH2 under purifying selection). Effectively, many genes within the primary starch synthesis pathway had a clear reduction in nucleotide diversity between the Landraces and wild and weedy lines indicating that the ancestral effects of domestication are still clearly identifiable. There was evidence of the positional rate variation within the well‐characterized primary starch synthesis pathway of sorghum, particularly in the Landraces, whereby low evolutionary rates upstream and high rates downstream in the metabolic pathway were expected. This observation did not extend to the wild and weedy lines or the minor starch synthesis pathways.

Whole Genome Sequencing Reveals Potential New Targets for Improving Nitrogen Uptake and Utilization in Sorghum bicolor

Nitrogen (N) fertilizers are a major agricultural input where more than 100 million tons are supplied annually. Cereals are particularly inefficient at soil N uptake, where the unrecovered nitrogen causes serious environmental damage. Sorghum bicolor (sorghum) is an important cereal crop, particularly in resource-poor semi-arid regions, and is known to have a high NUE in comparison to other major cereals under limited N conditions. This study provides the first assessment of genetic diversity and signatures of selection across 230 fully sequenced genes putatively involved in the uptake and utilization of N from a diverse panel of sorghum lines. This comprehensive analysis reveals an overall reduction in diversity as a result of domestication and a total of 128 genes displaying signatures of purifying selection, thereby revealing possible gene targets to improve NUE in sorghum and cereals alike. A number of key genes appear to have been involved in selective sweeps, reducing their sequence diversity. The ammonium transporter (AMT) genes generally had low allelic diversity, whereas a substantial number of nitrate/peptide transporter 1 (NRT1/PTR) genes had higher nucleotide diversity in domesticated germplasm. Interestingly, members of the distinct race Guinea margaritiferum contained a number of unique alleles, and along with the wild sorghum species, represent a rich resource of new variation for plant improvement of NUE in sorghum.

Sorghum Genetic Transformation by Particle Bombardment

Particle bombardment transformation describes the acceleration of high-velocity microparticles coated with exotic genes through the plant-protective cell walls, in order for the introduced genes to be integrated into the host genome. This technique has proven to be an effective and versatile approach towards plant genetic modification in preceding decades. Particle bombardment has been successfully applied to cereals including rice, maize, wheat, barley, and sorghum. Historically, sorghum has been considered as one of the most recalcitrant major crops with regard to successful genetic transformation; however, tremendous progress has been made in recent years. Transformation efficiency by particle bombardment has now improved from approximately 1 % to in excess of 20 % utilizing an optimized tissue culture and DNA delivery system. The protocol described in this chapter routinely generates transformants at 10-25 % efficiency within sorghum genotype Tx430. The process generally takes 11-16 weeks from initiation of immature embryos to planting of transformants. This protocol covers the operation of both the Bio-Rad PDS-1000/He System and particle inflow gun. Three factors are crucial to an efficient particle bombardment transformation system: (1) an efficient tissue culture system, (2) a highly efficient DNA delivery system, and (3) an effective selection strategy.

Dynamic ecological observations from satellites inform aerobiology of allergenic grass pollen

Allergic diseases, including respiratory conditions of allergic rhinitis (hay fever) and asthma, affect up to 500 million people worldwide. Grass pollen are one major source of aeroallergens globally. Pollen forecast methods are generally site-based and rely on empirical meteorological relationships and/or the use of labour-intensive pollen collection traps that are restricted to sparse sampling locations. The spatial and temporal dynamics of the grass pollen sources themselves, however, have received less attention. Here we utilised a consistent set of MODIS satellite measures of grass cover and seasonal greenness (EVI) over five contrasting urban environments, located in Northern (France) and Southern Hemispheres (Australia), to evaluate their utility for predicting airborne grass pollen concentrations. Strongly seasonal and pronounced pollinating periods, synchronous with satellite measures of grass cover greenness, were found at the higher latitude temperate sites in France (46-50° N. Lat.), with peak pollen activity lagging peak greenness, on average by 2-3weeks. In contrast, the Australian sites (34-38° S. Lat.) displayed pollinating periods that were less synchronous with satellite greenness measures as peak pollen concentrations lagged peak greenness by as much as 4 to 7weeks. The Australian sites exhibited much higher spatial and inter-annual variations compared to the French sites and at the Sydney site, broader and multiple peaks in both pollen concentrations and greenness data coincided with flowering of more diverse grasses including subtropical species. Utilising generalised additive models (GAMs) we found the satellite greenness data of grass cover areas explained 80-90% of airborne grass pollen concentrations across the three French sites (p<0.001) and accounted for 34 to 76% of grass pollen variations over the two sites in Australia (p<0.05). Our results demonstrate the potential of satellite sensing to augment forecast models of grass pollen aerobiology as a tool to reduce the health and socioeconomic burden of pollen-sensitive allergic diseases.

Rice-cold tolerance across reproductive stages

Abstract. Cold temperature stress at the reproductive stage, particularly at booting and flowering stages can cause significant reductions in rice (Oryza sativa L.) yield particularly at high latitudes and elevation. Although genotypic variation for cold tolerance is known to exist, the tolerance mechanisms and genotypic consistency across the stages are yet to be understood for segregating populations. Three experiments were conducted under controlled temperature glasshouse conditions to determine floral characteristics that were associated with cold tolerance at the flowering stage and to determine genotypic consistency at the booting and flowering stages. Twenty F5 Reiziq × Lijiangheigu lines from two extreme phenotypic bulks selected for cold tolerance at booting stage in the F2 generation were utilised. Spikelet sterility under cold stress at booting was significantly correlated with spikelet sterility under cold stress at flowering (r = 0.62**) with five lines identified as cold tolerant across reproductive stages. There was also a positive correlation (r = 0.47*) between spikelet sterility under cold stress at booting at the F5 and at the F2 generation. The quantitative trait loci (QTL; qLTSPKST10.1) previously identified on chromosome 10 contributing to spikelet sterility within the F2 generation, was also identified in the F5 generation. Additionally, genomic regions displaying significant segregation between the progenies contrasting for their cold tolerance response phenotype were identified on chromosomes 5 and 7 with Lijiangheigu as allelic donor and an estimated reduction in spikelet sterility of 25% and 27%, respectively. Although genotypic variation in spikelet sterility at the booting stage was not related to the development rate for heading or flowering, those cold-tolerant genotypes at the flowering stage were the quickest to complete flowering. Cold-tolerant genotypes at the flowering stage had larger numbers of dehisced anthers and subsequently pollen number on stigma, which contributed to reduced spikelet sterility. It is concluded that enhanced anther dehiscence plays a significant role in improved cold tolerance at the flowering stage.