Genetic Diversity of Xanthomonas oryzae pv. oryzae in Asia

Abstract

Restriction fragment length polymorphism and virulence analyses were used to evaluate the population structure of Xanthomonas oryzae pv. oryzae, the rice bacterial blight pathogen, from several rice-growing countries in Asia. Two DNA sequences from X. oryzae pv. oryzae, IS1112, an insertion sequence, and avrXa10, a member of a family of avirulence genes, were used as probes to analyze the genomes of 308 strains of X. oryzae pv. oryzae collected from China, India, Indonesia, Korea, Malaysia, Nepal, and the Philippines. On the basis of the consensus of three clustering statistics, the collection formed five clusters. Genetic distances within the five clusters ranged from 0.16 to 0.51, and distances between clusters ranged from 0.48 to 0.64. Three of the five clusters consisted of strains from a single country. Strains within two clusters, however, were found in more than one country, suggesting patterns of movement of the pathogen. The pathotype of X. oryzae pv. oryzae was determined for 226 strains by inoculating five rice differential cultivars. More than one pathotype was associated with each cluster; however, some pathotypes were associated with only one cluster. Most strains from South Asia (Nepal and India) were virulent to cultivars containing the bacterial blight resistance gene xa-5, while most strains from other countries were avirulent to xa-5. The regional differentiation of clusters of X. oryzae pv. oryzae in Asia and the association of some pathotypes of X. oryzae pv. oryzae with single clusters suggested that strategies that target regional resistance breeding and gene deployment are feasible.

Genotypic and Pathotypic Diversity of Xanthomonas oryzae pv. oryzae, the Cause of Bacterial Blight of Rice in Punjab State of India

“…1). These findings agreed with some earlier reports (Adhikari et al 1995) that most of the Xoo strains from Nepal and India were virulent on cultivars possessing BB resistance gene xa5, while the isolates from Indonesia, Korea, Malaysia and Philippines were avirulent.…”

“…However, the characterization of isolates at the molecular level may further help in delineating isolates belonging to the same race or group, studying the pathogenic diversity across the region ⁄ country and monitoring the isolates at the field level. Based on molecular typing, genetic diversity has been reported in the Xoo populations from different rice-growing countries (Leach et al 1992;Nelson et al 1994;Adhikari et al 1995;Ardales et al 1996;George et al 1997;Yashitola et al 1997;Lee et al 1999). In India, the number of reported pathotypes varied from 2 to 11 depending on the number of differential cultivars used (Gupta et al 1986;Reddy and Reddy 1992).…”

Genotypic and Pathotypic Diversity of Xanthomonas oryzae pv. oryzae Strains in Taiwan

“…Although unique information and different levels of population diversity can be revealed by the use of different primers/probes (Louws et al 1994;Nelson et al 1994), our results revealed that REP1R-Dt/REP2-D is not suitable for typing Xoo at the subspecies level. While insertion sequences and transposable elements may have strong impact on the evolution of bacterial genomes (Siguier et al 2014), data from previous studies generally indicated a partial or little relationship between molecular haplotype and pathotype (Nelson et al 1994;Adhikari et al 1995Adhikari et al , 1999Ochiai et al 2000;Li et al 2009). A similar phenomenon was observed in the present study.…”

“…Xa21 is known to confer broad-spectrum resistance to multiple Xoo strains from many countries (Wang et al 1996;Tripathi et al 2014). Xa21 was resistant to almost all Xoo strains collected from Sri Lanka in 1995 (Ochiai et al 2000), from the Punjab state in northern India in 1997 (Singh et al 2003), from13 major ricegrowing provinces in China in 2003 (Li et al 2009), and from 20 different states of India during 2004-2010 (Mishra et al 2013); however its resistance was gradually defeated in northern India (Lore et al 2011), Nepal (Adhikari et al 1999) and Korea (Lee et al 1999). The expression of Xa21 is activated by Xoo infection, but its cognate PAMP, which appears to be a common molecule in Xoo and X. campestris pv.…”

“…Using restriction fragment length polymorphism (RFLP), Leach et al (1992) analysed 98 Xoo strains collected in the Philippines from 1972 to 1988 and found some association between the RFLP patterns and race types. Adhikari et al (1995) compared the RFLP genotypes of 308 Xoo strains in seven Asian countries from 1981 to 1993 and revealed geographical clustering of the bacterial strains. Compared to RFLP fingerprinting, repetitive sequence-based PCR (REP-PCR) is simpler, faster and more economical to detect DNA polymorphisms, particularly for a large number of samples (Vera Cruz et al 1996;George et al 1997).…”