Genetic composition and complexity of virus populations at tungro-endemic and outbreak rice sites

Abstract

We have recently demonstrated the geographic isolation of rice tungro bacilliform virus (RTBV) populations in the tungro-endemic provinces of Isabela and North Cotabato, Philippines. In this study, we examined the genetic structure of the virus populations at the tungro-outbreak sites of Lanao del Norte, a province adjacent to North Cotabato. We also analyzed the virus populations at the tungro-endemic sites of Subang, Indonesia, and Dien Khanh, Vietnam. Total DNA extracts from 274 isolates were digested with EcoRV restriction enzyme and hybridized with a full-length probe of RTBV. In the total population, 22 EcoRV-restricted genome profiles (genotypes) were identified. Although overlapping genotypes could be observed, the outbreak sites of Lanao del Norte had a genotype combination distinct from that of Subang or Dien Khanh but a genotype combination similar to that identified earlier from North Cotabato, the adjacent endemic province. Sequence analysis of the intergenic region and part of the ORF1 RTBV genome from randomly selected genotypes confirms the geographic clustering of RTBV genotypes and, combined with restriction analysis, the results suggest a fragmented spatial distribution of RTBV local populations in the three countries. Because RTBV depends on rice tungro spherical virus (RTSV) for transmission, the population dynamics of both tungro viruses were then examined at the endemic and outbreak sites within the Philippines. The RTBV genotypes and the coat protein RTSV genotypes were used as indicators for virus diversity. A shift in population structure of both viruses was observed at the outbreak sites with a reduced RTBV but increased RTSV gene diversity.

Maize dwarf mosaic virus diversity in the Johnsongrass native reservoir and in maize: evidence of geographical, host and temporal differentiation

“…The northwest (Castilla‐León–Extremadura) and Albacete are areas where maize has been introduced more recently, whilst Lleida, Girona and Andalucía are old maize‐growing areas, and Zaragoza and Huesca have a mixture of both new and old maize‐growing areas. The high diversity and low homogozity values observed in old maize‐growing areas corroborated the fact that old virus populations are associated with traditional cropping areas and vice versa for new cropping areas (Azzam et al. , 2000; Bateson et al.…”

“…ns, non-significant; **significant (P < 0AE01). (Azzam et al, 2000;Bateson et al, 2002;Chin et al, 2007). It should be noted that the genetic flow between Andalucía and surrounding areas may be strongly constrained by mountain barriers.…”

Maize dwarf mosaic virus diversity in the Johnsongrass native reservoir and in maize: evidence of geographical, host and temporal differentiation

“…The northwest (Castilla‐León–Extremadura) and Albacete are areas where maize has been introduced more recently, whilst Lleida, Girona and Andalucía are old maize‐growing areas, and Zaragoza and Huesca have a mixture of both new and old maize‐growing areas. The high diversity and low homogozity values observed in old maize‐growing areas corroborated the fact that old virus populations are associated with traditional cropping areas and vice versa for new cropping areas (Azzam et al. , 2000; Bateson et al.…”

“…ns, non-significant; **significant (P < 0AE01). (Azzam et al, 2000;Bateson et al, 2002;Chin et al, 2007). It should be noted that the genetic flow between Andalucía and surrounding areas may be strongly constrained by mountain barriers.…”

VARIABILITY AND GENETIC STRUCTURE OF PLANT VIRUS POPULATIONS

“…Azzam and co-workers have made a detailed analysis of the population structure of the viruses causing rice tungro in Southeast Asia. When the population structure of both viruses was analyzed in the same sample, population diversity for RTBV and RTSV did not correlate and a significant association was found among types of RTSV and the presence of RTBV (18). The same was found in similar analyses of RTBV (15,18).…”

Molecular characterisation of rice tungro bacilliform virus isolated from Bario, Sarawak

“…One variant may be dominant and easily detected compared to another. A slight change in the dynamic of RTBV populations due to pressure in the environment and green leafhopper populations can lead to an outbreak (Arboleda and Azzam, 2000;Azzam et al, 2000). Phylogenetic analysis showing the genetic relationships between RTBV primary isolates from Bario, Sarawak and other RTBV isolates from SA and SEA available from NCBI GenBank database.…”

Maize dwarf mosaic virus diversity in the Johnsongrass native reservoir and in maize: evidence of geographical, host and temporal differentiation

“…The northwest (Castilla‐León–Extremadura) and Albacete are areas where maize has been introduced more recently, whilst Lleida, Girona and Andalucía are old maize‐growing areas, and Zaragoza and Huesca have a mixture of both new and old maize‐growing areas. The high diversity and low homogozity values observed in old maize‐growing areas corroborated the fact that old virus populations are associated with traditional cropping areas and vice versa for new cropping areas (Azzam et al. , 2000; Bateson et al.…”

“…ns, non-significant; **significant (P < 0AE01). (Azzam et al, 2000;Bateson et al, 2002;Chin et al, 2007). It should be noted that the genetic flow between Andalucía and surrounding areas may be strongly constrained by mountain barriers.…”

VARIABILITY AND GENETIC STRUCTURE OF PLANT VIRUS POPULATIONS

“…Azzam and co-workers have made a detailed analysis of the population structure of the viruses causing rice tungro in Southeast Asia. When the population structure of both viruses was analyzed in the same sample, population diversity for RTBV and RTSV did not correlate and a significant association was found among types of RTSV and the presence of RTBV (18). The same was found in similar analyses of RTBV (15,18).…”

Molecular characterisation of rice tungro bacilliform virus isolated from Bario, Sarawak

“…One variant may be dominant and easily detected compared to another. A slight change in the dynamic of RTBV populations due to pressure in the environment and green leafhopper populations can lead to an outbreak (Arboleda and Azzam, 2000;Azzam et al, 2000). Phylogenetic analysis showing the genetic relationships between RTBV primary isolates from Bario, Sarawak and other RTBV isolates from SA and SEA available from NCBI GenBank database.…”

Maize dwarf mosaic virus diversity in the Johnsongrass native reservoir and in maize: evidence of geographical, host and temporal differentiation

“…The northwest (Castilla‐León–Extremadura) and Albacete are areas where maize has been introduced more recently, whilst Lleida, Girona and Andalucía are old maize‐growing areas, and Zaragoza and Huesca have a mixture of both new and old maize‐growing areas. The high diversity and low homogozity values observed in old maize‐growing areas corroborated the fact that old virus populations are associated with traditional cropping areas and vice versa for new cropping areas (Azzam et al. , 2000; Bateson et al.…”

“…ns, non-significant; **significant (P < 0AE01). (Azzam et al, 2000;Bateson et al, 2002;Chin et al, 2007). It should be noted that the genetic flow between Andalucía and surrounding areas may be strongly constrained by mountain barriers.…”

VARIABILITY AND GENETIC STRUCTURE OF PLANT VIRUS POPULATIONS

“…Azzam and co-workers have made a detailed analysis of the population structure of the viruses causing rice tungro in Southeast Asia. When the population structure of both viruses was analyzed in the same sample, population diversity for RTBV and RTSV did not correlate and a significant association was found among types of RTSV and the presence of RTBV (18). The same was found in similar analyses of RTBV (15,18).…”

Molecular characterisation of rice tungro bacilliform virus isolated from Bario, Sarawak

“…One variant may be dominant and easily detected compared to another. A slight change in the dynamic of RTBV populations due to pressure in the environment and green leafhopper populations can lead to an outbreak (Arboleda and Azzam, 2000;Azzam et al, 2000). Phylogenetic analysis showing the genetic relationships between RTBV primary isolates from Bario, Sarawak and other RTBV isolates from SA and SEA available from NCBI GenBank database.…”