Lolium rigidum (annual ryegrass), a widespread weed of southern Australian cereal crops, has frequently evolved herbicide resistance. It is commonly found associated with the mutualistic, endophytic fungus, Neotyphodium occultans. The objectives of this study were as follows: (i) determine the occurrence of N. occultans in L. rigidum populations across southern Australia, (ii) evaluate potential associations between infection frequency and herbicide resistance, climatic and topographic variables and (iii) examine genetic diversity of N. occultans from this national collection of L. rigidum using simple sequence repeat markers. By microscopic assessment of seed, we found all seed lots were infected with N. occultans, with highly variable frequencies, ranging from 4% to 98%. Frequencies were higher in New South Wales, South Australia and Victoria (54-62%) than in Western Australia (43%) or Tasmania (17%). A negative association existed between elevation and mean rainfall, and infection frequency. Significant interactions were as follows: mean rainfall (growing season) and state and mean rainfall (growing season) and elevation. Significant associations were found between infection frequency and herbicide mode of action. Infection was lower in seed lots resistant to group B (sulfonylurea and imidazolinone) and higher in seed lots resistant to group D (dinitroaniline) herbicides. Higher infection frequencies were observed in seed lots from earlier years, with the lowest in seed lots recently collected. No significant associations were found with long-term mean temperature or rainfall. Little genetic diversity was observed for N. occultans endophyte in Australian plants. These results provide a benchmark of the relationship of N. occultans with L. rigidum and suggest further research on the role this endophyte has in determining the fitness of L. rigidum under varying conditions of herbicide resistance, rainfall and elevation that may aid in the management of this grass.

Verticillium dahliae is a soil-borne phytopathogen and the causal agent of Verticillium wilt. It affects many agriculturally important crops around the world, including cotton. In Australia, the billion-dollar cotton industry is increasingly impacted by Verticillium wilt. Internationally it has been reported that the defoliating V. dahliae Vegetative Compatibility Group (VCG) 1A causes severe damage to cotton. In Australia however, the non-defoliating VCG2A is causing more severe damage to crops in fields than the defoliating VCG1A. This review examines the current research to understand the Australian V. dahliae situation, including current classification systems, genetic analyses and management strategies. It appears that virulence cannot be defined solely by VCG in Australian Verticillium dahliae isolates causing disease in cotton, and that the industry must continually adapt their practices in order to keep the disease under control.

For 32 years, cotton grown in NSW has been monitored for Verticillium wilt, with isolates of Verticillium dahliae Kleb. stored in the NSW Department of Primary Industries culture collection. An increase in disease severity in the 2013/14 season suggests a more virulent pathogenic strain may have been introduced. Eight V. dahliae isolates were selected for vegetative compatibility group (VCG) analysis using molecular assays and nit mutant testing. Two of the eight isolates were identified as the highly virulent defoliating VCG1A, making this the first record of VCG1A in Australia.

Three decades of disease survey data have shown Verticillium wilt was one of the first major diseases of cotton recorded in the 1984–85 season. Survey reports the mean incidence was 4.1% in the 1984–85 season and rose to 16.6% in the 1989–90 season. Prior to 1984 all commercial varieties of cotton available in Australia were susceptible to bacterial blight and the disease was common. The adoption of the resistant varieties contributed to a dramatic decline in the incidence of bacterial blight and the removal of bacterial blight as a significant pathogen to Australian cotton crops by 1992. Survey results showed the incidence of black root rot increased on farms with a long history of growing cotton during the 1990s. Fusarium wilt of cotton was first reported in New South Wales (NSW) in 1994. The disease is now widespread, being confirmed on 86 NSW farms in six of the eight cotton production areas in NSW. These four significant plant disease ‘problems’ have challenged the cotton industry in NSW. Data provided by the surveys have indicated the relative importance of each of the diseases present and the impact of cultural practices and the adoption of new varieties on disease distribution, incidence and severity. The results have therefore been used to support and justify requests for research funding and have contributed to the development of Integrated Disease Management strategies. The NSW Department of Primary Industries continues to monitor the distribution of disease and the incidence and severity present in commercial cotton crops in all production areas of NSW. The aim of this paper is to highlight four significant cotton diseases in Australia and show relationships between cultural practices and declining and increasing incidence of disease.

Verticillium dahliae, the causal agent of Verticillium wilt, is a soil-borne ascomycete that infects numerous agriculturally important crops globally, including cotton. As a billion-dollar industry, cotton is economically important to Australia and the management of disease such as Verticillium wilt is key for the success of the industry. Internationally, defoliating V. dahliae isolates belonging to Vegetative Compatibility Group (VCG) 1A cause severe damage to cotton, while non-defoliating VCG2A isolates result in significantly less disease. However, in Australia, VCG2A is causing more severe damage to crops in the field than the defoliating VCG1A. This study aimed to replicate field observations in controlled greenhouse conditions. We examined and compared disease symptoms on a range of Australian commercial cotton varieties when inoculated with different V. dahliae VCGs. Seedlings were root dipped in conidial suspensions and assessed over seven weeks. The final disease score, disease over time and root length were analysed. Plant mortality resulted from both V. dahliae VCG1A and VCG2A isolates across all cotton varieties used, confirming that there are virulent VCG2A isolates present in Australia. To our knowledge, although virulent on other plant hosts, V. dahliae VCG2A has not previously been reported to be highly virulent in cotton. We infer that virulence cannot be defined solely by VCG in Australian V. dahliae isolates causing disease in cotton.