Mark P. Dobrowolski

Three clonal lineages of Phytophthora cinnamomi in Australia revealed by microsatellites

ABSTRACT The genetic structure of populations of Phytophthora cinnamomi, a pathogen of an enormous variety of woody plants, was investigated using microsatellites. Three intensively sampled disease sites in southwest Australia were analyzed along with a large culture collection of Austra-lian isolates and some isolates from elsewhere in the world. The mutation in the four microsatellite loci analyzed revealed spatial patterns at the disease sites that correlated with the age of the infestation. Only three clonal lineages were identified in Australian populations and these same clonal lineages were present in worldwide populations, where it is suggested that a limited number of clonal lineages have spread in most regions. No evidence for sexual reproduction between these clonal lineages in Australia has been found even though the pathogen has the opportunity. Instead, mitotic recombination is frequent within the clonal lineages. The implications of this are discussed.

Phenotypic variation in a clonal lineage of two Phytophthora cinnamomi populations from Western Australia

Seventy-three isolates of Phytophthora cinnamomi were collected from diseased Eucalyptus marginata (jarrah) and Corymbia calophylla (marri) trees in two forest communities in the southwest of Western Australia. Both populations of P. cinnamomi were examined for phenotypic and genotypic variation. Microsatellite DNA analysis showed that all isolates were of the same clonal lineage. We show, for the first time for P. cinnamomi, that morphological and pathogenic variation between populations of the clonal lineage are very broad and continuous. The phenotypes examined included growth rates and colony morphology on potato dextrose agar at different temperatures, sporangial and gametangial morphology, ability to form lesions in detached jarrah and marri stems, and ability to cause deaths of clonal jarrah plants in a glasshouse trial. Phenotype variation was derived asexually. All phenotypes investigated varied independently from one another. Cluster analysis of 24 morphological and pathogenicity phenotypes identified two main clusters of isolates corresponding to each population. The ability to cause deaths in both populations ranged from killing all plants within 59 d to plants being symptomless 182 d after inoculation.

Assessment of genetic diversity in Australian canola (Brassica napus L.) cultivars using SSR markers

Australian canola (Brassica napus L.) has been relatively isolated from the global gene pool and limited knowledge is available for genetic variability based on DNA profiling. In the present study, genetic diversity of recent Australian canola cultivars was determined by simple sequence repeat (SSR) marker analysis. In total, 405 individuals from 48 varieties were genotyped with 18 primer pairs, resulting in 112 polymorphic features. The number of polymorphic features amplified by each SSR primer pair varied from 3 to 16. Analysis of molecular variance (AMOVA) detected 53.7% and 46.3% within- and between-cultivar variation, respectively. Intra-cultivar genetic variability differed according to cultivar. The number of polymorphic features per cultivar varied from 35 (Ag-Spectrum) to 72 (Ag-Insignia), while mean sum of squares (MSS) varied from 6.29 (Tornado TT) to 24.76 (Ag-Emblem). Genetic differentiation of cultivars generally reflected pedigree structure and origin by breeding organisation. Clustering and principal coordinate analysis (PCoA) indicated that the individuals were separated into 4 major groups. The genetic diversity information from this study will be useful for future Australian canola breeding programs.

Functionally associated molecular genetic markers for temperate pasture plant improvement

The key components for implementation of functionally associated genetic markers in perennial ryegrass and white clover breeding have been established. They include: generation of substantial genomic sequence resources; methods for functional analysis and verification of candidate gene status, including transcriptomics and transgenesis; efficient methods for in silico and in vitro discovery and validation of gene-associated SNP loci; evaluation of intra- and inter-population diversity; estimation of SNP haplotype complexity and LD; development of robust protocols for phenotypic analysis of key agronomic traits; design and implementation of experiments for haplotype-phenotype correlation; and development of efficient strategies for gene-based marker deployment in existing germplasm improvement programmes. These processes are mature for perennial ryegrass, and despite the added complexities of genetic architecture in white clover, optimized methods for SNP discovery should be equally effective for the latter species. The strategies are also suitable for other agronomically important temperate forage species, such as the grasses Italian ryegrass, tall fescue (Festuca arundinacea), meadow fescue (Festuca pratensis), cocksfoot (Dactylis glomerata) and timothy (Phleum pratense), as well as the legumes red clover (Trifolium pratense) and lucerne (Medicago sativa).