Breeding for resistance against soil-borne phytopathogenic fungi unintentionally affects the diversity of viruses and viroids in the Phaseolus vulgaris rhizosphere
A study by Dr Lucas Braga and colleagues in the Ecosystems and Global Change group shows that breeding for resistance against Fusarium oxysporum affects the diversity of viruses and viroids in the rhizosphere.
Plant pathogens are a major threat to crop production, causing up to a third of global yield losses. Resistance breeding is a sustainable and widely-practised strategy to confer protection against such pathogens. However, resistance breeding is challenging given the complex dynamics of plant-pathogen interactions, and often has short-term durability due to pathogen evolution. Many organisms that aid or hinder plant growth live in the in the rhizosphere, including fungi, nematodes, viruses, algae, protozoa, arthropods and bacteria, and the use of resistant varieties may alter its composition and its contribution or otherwise to the plants’ growth. The effects of breeding on plant microbiomes including the rhizosphere have been largely neglected due to the lack of tools that have only recently become available with advances in sequencing technologies and computational methods.
Working in partnership with colleagues from the University of Sao Paulo, Brazil; National Center for Biotechnology Information, USA; Netherlands Institute of Ecology; and Embrapa Meio Ambiente, Brazil, the team used cutting-edge bioinformatic tools to identify and reconstruct genomes of novel viruses and viroids from rhizosphere metatranscriptomes of common bean cultivars with different levels of susceptibility to the fungal root pathogen F. oxysporum. The combination of these methods allowed the team to capture with great resolution the diversity and response of viroids and viruses, including bacteriophages, to breeding for resistance.
‘The effect we observed for viroids, which were about 1.2-times more abundant, on average, in the Fusarium resistant cultivar compared to the susceptible ones, is pretty remarkable,’ said Lucas Braga, study leader.
The results also support that viruses, including Phaseolus vulgaris alphaendornaviruses, and viroids produced in plant cells, can be released by the roots into the rhizosphere.
‘Our findings open a new avenue of research. We show that a better understanding of the role of viruses and viroids in the rhizosphere, as well as their response to plant breeding against soil-borne pathogen, are an important consideration for breeding programmes aimed at improving food security. The next step now is to further study this system to elucidate the mechanisms on how the rhizosphere viruses and viroids affected by breeding can affect plant protection,’ he said.
Read the paper
Braga, L.P.P., Tanentzap, A., Lee, B., Tsai, S.M., Raaijmakers, J.M., Mendes, R., Mendes, L.W. 2023. Diversity of viruses and viroids in the rhizosphere of common bean cultivars differing in resistance to the fungal root pathogen Fusarium oxysporum. Applied Soil Ecology. 190. 2023. https://doi.org/10.1016/j.apsoil.2023.105018
Title image from https://commons.wikimedia.org/wiki/File:%C4%90%E1%BA%ADu_c%C3%B4ve_-Phaseolus_vulgaris.JPG