Elevational Variation in Diversity of Xanthomonas oryzae pv. oryzae in South‐West China

Abstract

Virulence analysis and two polymerase chain reaction–based assays were used to evaluate the population structure of Xanthomonas oryzae pv. oryzae (Xoo) from different elevations ranging from 150 to 2600 m in south‐west China. Among the 218 isolates of Xoo, 18 pathotypes were identified using six near‐isogenic rice lines, each containing a single resistance gene. Among them, pathotype 9 predominated in low and mid‐elevations was virulent to all resistance genes, including Xa2, Xa3, xa5, xa13, Xa14 and Xa18. However, pathotype 2 was predominant at high elevation and was virulent to Xa18 only. The 18 pathotypes were grouped into four clusters. Isolates belonging to cluster 1 were mainly found at high and mid‐elevations, while those of cluster 4 were mainly found at low elevations. There were significant trends of virulence of isolates from low to high with the elevation from high to low. The ERIC and J3 primers were used to screen the genomes of 218 isolates, and 56 molecular haplotypes were found. Multiple correspondence analyses revealed that 56 haplotypes were divided into four putative genetic lineages. Lineage 2 was the most frequently detected from 150 to 2600 m; it was clearly shown that isolates from high elevation with 80% is much more than from low and mid‐elevation in the lineage. It is intriguing that genetic variation of Xoo is restricted by physical geographical barriers of elevations. This is the first report on the relationship of pathotypic and genotypic diversity of Xoo at different elevations.

Decision tools for bacterial blight resistance gene deployment in rice-based agricultural ecosystems

“…The first aspect of monitoring entails a collection of field strains to understand population genetic structure and local distribution. So far, all markers based on restriction fragment length polymorphism profiling or repeated sequences ( Choi et al, 1998 ; Chen et al, 2012 ; Mishra et al, 2013 ) have not succeeded in describing functional groups or simply are not currently available in high-throughput platforms. However, many large-scale shotgun sequencing projects involving short-reads are underway and would potentially allow us to identify a set of SNP markers for standard use in field genotyping across different regions.…”

New Multilocus Variable-Number Tandem-Repeat Analysis Tool for Surveillance and Local Epidemiology of Bacterial Leaf Blight and Bacterial Leaf Streak of Rice Caused by Xanthomonas oryzae

“…Most of these studies analyzed regional populations of X. oryzae pv. oryzae, mainly using pathogenicity assays and/or restriction fragment length polymorphism (RFLP) profiling (25)(26)(27)(28)(29)(30). For instance, Mishra and coworkers (2013) analyzed more than 1,000 isolates of X. oryzae pv.…”

Population genomics and pathotypic evaluation of the bacterial leaf blight pathogen of rice reveals rapid evolutionary dynamics of a plant pathogen

“…Though resistance breeding of rice had effectively prevented the unprecedented outbreak of BB since 1990s, sporadic outbreaks occurred in different areas of China after the year 2000 (22, 23). Genomic epidemiology analysis indicates that the recent outbreaks in different places were contributed by different lineages or sub-lineages, even some outbreaks from the same places caused by different lineages.…”

“…Since 1980s, BB-resistant rice varieties have been widely planted in China and have significantly reduced the loss caused by BB (19–21). However, sporadic outbreaks have occurred in different areas of China after the year of 2000 (22, 23). It is unknown whether the recent outbreaks relate to changes in the genetics and virulence of the past Xoo populations in China, allowing it to overcome host defenses.…”