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The Batley research group works in several areas associated with second generation sequencing, genetic and genomic variation analysis and the application of molecular genetic markers. We work with a range of species, mostly in collaboration with a range of national and international research groups.

Current projects include:

Understanding the co-evolution of Brassica- blackleg interaction

Blackleg disease, caused by the fungus Leptospheria maculans, is the most important fungal disease of Brassica crops world-wide. The newly available genome sequence for Brassica and L. maculans provide the resources to study the co-evolution of this plant and pathogen. We aim to apply a novel genetic approach to identify the genes underlying this plant-pathogen interaction, and assess their prevalence in different geographic and agronomic conditions. An understanding of the co-evolution of genes responsible for virulence and resistance will lead to improved plant protection strategies for Brassica canola and provide a model to understand plant-pathogen interactions in other major Australian crops. We aim to characterise the evolution and conservation of disease resistance genes in cultivated and wild Brassicas, using next-generation sequencing technology for their identification, and to assess their potential for crop improvement. An understanding of the evolution of genes responsible resistance will lead to improved plant protection strategies for Brassica crops. We have identified candidate genes (Tollenaere et al., 2012) which are currently undergoing validation. Current work is also focussing on identification of novel Avr genes, through resequencing blackleg isolates, and gaining an understanding of the genetic diversity of the pathogen.

Research team: Manuel Zander, Reece Tollenaere, Salman Alamery, Fabian Inturissi, Satomi Hayashi and Dhwani Patel

Characterising genetic variation in Brassica napus

The aim of this project was to develop and establish a robust, rapid and cost effective method for the discovery and validation of SNPs within complex genomes. Over one million SNPs were identified through re-sequencing eight canola varieties. A 6K Illumina infinium array was developed from these SNPs, and screened across a range of lines from the amphidiploid Brassica napus genome, along with an assessment of these SNPs in different Brassica germplasm. This will lead to the identification of SNP markers for important agronomic traits for use in canola breeding and an assessment of linkage disequilibrium in Brassica. The SNPs were contributed towards the public 60K array, which is currently being screened across a range of germplasm for projects including understanding domestication, genome conservation across different species, identification of candidate genes, GWAS, understanding morphological variation and species identification. A further set of over 20 canola varieties have been sequenced as extra resources for these projects and is contributing to studies on Presence/Absence (PAV) analysis and structural variation across the genome.

Research team: Jessica Dalton-Morgan, Satomi Hayashi

Investigating the evolution and conservation of nodulation and mycorrhization genes across the Brassicaceae

Plants have evolved many and complex interactions with bacterial and fungal micro-organisms, from symbiotic relationships which benefit both plant and microbe, to pathogenesis, impacting crop yield and quality. The application of new genome technologies suggest that the evolution of plant signalling mechanisms are conserved, whether the plant is supporting a symbiotic relationship or defending against pathogenic bacteria or fungi. This project will characterise the diversity and evolution of conserved signal network components common to a plant’s response to microbes in wild and cultivated Brassica. A greater understanding of these mechanisms may lead to a model for polyploidisation and an understanding of the function of these genes in non-nodulating, non-mycorrhizal organisms. Initial results have recently been published (Hayward et al., 2012).

Research Team: Alice Hayward, Sarah Lorberg

Epigenetic regulation of important agricultural traits in Brassica napus

Brassica napus (canola/oilseed rape) is the most economically important Brassica crop. Agronomic fitness and hybrid vigour in canola (where hybrids of inbred cultivars show increased fitness relative to their parents) involves an epigenetic DNA modification termed DNA methylation. DNA methylation heritably alters the expression levels of genes and thus can influence multiple processes and traits including flowering time, seed yeild and disease resistance. This project is using next-generation, whole-genome DNA methylation sequencing to associate DNA methylation with the regulation of important agricultural traits and hybrid vigour in canola. This research will pioneer the functional analysis of genome methylation in canola with application for future crop breeding.

Research Team: Satomi Hayashi, Alice Hayward

Mapping recombination blocks in Brassica

We aim to gain a broader insight into genetic variation in Brassica species to understand how recombination varies across the Brassica genomes during crop selection and breeding. Specific emphasis will be placed on determining the role of different recombination blocks and how these vary across the three Brassica genomes. This knowledge may be applied to develop novel crop improvement strategies and the process of assessing recombination blocks can be applied to other agronomically important crop species.

Research Team: Satomi Hayashi

Creating an allohexaploid Brassica species

Canola (Brassica napus) is an important Australian oilseed crop species. However, canola is poorly adapted to many Australian farming environments as it is sensitive to drought, heat and disease. By co-opting methods by which plants have evolved to adapt to changing environments, we propose to pioneer a novel breeding strategy to produce an improved hybrid canola species. Using recent advances in molecular cytogenetics and sequencing technology, we are investigating the natural evolutionary mechanisms by which hybrid species form in Brassica, and attempting to utilize these evolutionary mechanisms to produce new, stable canola crop species, which may thrive in hot and dry Australian conditions. Key areas of investigation include unreduced gamete formation and chromosome behaviour in interspecific Brassica hybrids.

Research Team: Annaliese Mason, Ning Chen

Evolution of species through chromosome change

How do new species form? Previously, most attempts to answer this question have looked at population genetics and ecology, but what underlying changes are taking place at the chromosome level to allow new species to form? Using the agriculturally significant Brassica genus, we aim to investigate how chromosome changes trigger species formation, and what happens to chromosomes and chromosome behaviour during the formation of new hybrid species. Answering these questions will lead to a greater understanding of speciation, and allow us to manipulate these natural evolutionary processes for Brassica crop improvement.

Research Team: Annaliese Mason, Ning Chen