Abstract
The impact of modern agriculture on the evolutionary trajectory of plant pathogens is a central question for crop sustainability. The Green Revolution replaced traditional rice landraces with high-yielding varieties, creating a uniform selection pressure that allows measuring the effect of such intervention. In this study, we analyzed a unique historical pathogen record to assess the impact of a major resistance gene, Xa4, in the population structure of Xanthomonas oryzae pv. oryzae (Xoo) collected in the Philippines in a span of 40 years. After the deployment of Xa4 in the early 1960s, the emergence of virulent pathogen groups was associated with the increasing adoption of rice varieties carrying Xa4, which reached 80% of the total planted area. Whole genomes analysis of a representative sample suggested six major pathogen groups with distinctive signatures of selection in genes related to secretion system, cell-wall degradation, lipopolysaccharide production, and detoxification of host defense components. Association genetics also suggested that each population might evolve different mechanisms to adapt to Xa4. Interestingly, we found evidence of strong selective sweep affecting several populations in the mid-1980s, suggesting a major bottleneck that coincides with the peak of Xa4 deployment in the archipelago. Our study highlights how modern agricultural practices facilitate the adaptation of pathogens to overcome the effects of standard crop improvement efforts.
Highlights
Supplementary information The online version of this article contains supplementary material, which is available to authorized users.The emergence of plant pathogens in agricultural ecosystems represents a threat to food security
The situation changed in the early 1960s after the International Rice Research Institute (IRRI) was established and the country emerged as a natural laboratory for testing rice varieties during the Green Revolution
The genotypic data input used was a combination of single nucleotide polymorphisms (SNP) and the Roary and Piggy presence–absence matrix
Summary
The situation changed in the early 1960s after the International Rice Research Institute (IRRI) was established and the country emerged as a natural laboratory for testing rice varieties during the Green Revolution This is where semi-dwarf high-yielding varieties, such as IR8 were first bred, tested, and rapidly spread across Asia, replacing traditional landraces [4]. We traced the presence of Xa4 in the overall rice germplasm and showed that continuous deployment reached at least ~80% of the total ricefarming area This massive selection pressure, favored the emergence of Xa4-overcoming groups. We documented how modern breeding schemes were instrumental to shape contemporary pathogen populations This finding is important because it expands our understanding on how to contain emerging pathogens in modern agriculture
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call