Detection methods for virus diseases of pulse crops in Australia.

Abstract

Accurate identification of viruses is critical for resistance breeding and for development of management strategies. We are developing improved diagnostics for the luteoviruses / poleroviruses that commonly affect chickpea and pulse crops in Australia. The Tissue blot immuneassay (TBIA) method is routinely used to screen large numbers of samples for viruses in pulse crops. However, some of the antibodies used in TBIA are known to cross react with multiple viruses. Therefore, we use PCR tests in conjunction with TBIA in virus surveys of chickpea and pulse crops from eastern Australia. We use a multiplex PCR for Turnip yellows virus (TuYV), Bean leaf roll virus (BLRV), Phasey bean mild yellows virus (PBMYV) and Soybean dwarf virus (SbDV)to investigate the importance of each virus and their host range from different locations. Important alternative hosts included Malva parviflora which was commonly found to be infected with TuYV from many locations and Medicago polymorpha was a host for BLRV, PBMYV and SbDV.
We have found pronounced differences in the population of viruses infecting pulse crops across regions and seasons. For example, in northern New South Wales pulse crops, SbDV was the dominant virus in the 2013 season but was relatively rare in 2014. In contrast, there were relatively fewer luteo/polero viruses in 2015 but some large outbreaks of other important aphid-transmitted viruses, Alfalfa mosaic virus (AMV) and Cucumber mosaic virus (CMV) in chickpea crops.
Using the virus species-specific PCRs for luteo / polero viruses, we have confirmed that several antibodies used for TBIA provide false positives for TuYV. In addition, we now know that there are at least three genetically distinct viruses infecting a range of pulse crops that make up a complex previously thought to be BWYV. These distinct virus species or strains all have some degree of genetic similarity to the recognised species Turnip yellows virus (TuYV). We have used next generation sequencing to characterise almost complete genomes of three distinct viruses from this TuYV cluster which may have distinct geographical distributions and host ranges. While our knowledge of these viruses is currently limited, we have confirmed they infect crops of chickpea, faba bean, field pea, lentil and canola.
Further work to clarify the Australian luteovirus / polerovirus complex through molecular techniques and investigate biological differences between virus species is in progress.