Phylogeography of Rice yellow mottle virus (RYMV) was reconstructed from the coat protein gene sequences of a selection of 173 isolates from the 14 countries of mainland Africa where the disease occurred and from the full sequences of 16 representative isolates. Genetic variation was linked to geographical distribution and not to host species as isolates from wild rice always clustered with isolates from cultivated rice of the same region. Genetic variation was not associated to agro-ecology, viral interference and insect vector species. Distinct RYMV lineages occurred in East, Central and West Africa, although the Central African lineage included isolates from Benin, Togo and Niger at the west, adjacent to countries of the West African lineage. Genetic subdivision at finer geographical scales was apparent within lineages of Central and West Africa, although less pronounced than in East Africa. Physical obstacles, but also habitat fragmentation, as exemplified by the small low-lying island of Pemba offshore Tanzania mainland, explained strain localization. Three new highly divergent strains were found in eastern Tanzania. By contrast, intensive surveys in Cote d’Ivoire and Guinea at the west of Africa did not reveal any new variant. Altogether, this supported the view that the Eastern Arc Mountains biodiversity hotspot was the centre of origin of RYMV and that the virus spread subsequently from east to west across Africa. In West Africa, specific strains occurred in the Inner Niger Delta and suggested it was a secondary centre of diversification. Processes for diversification and dispersion of RYMV are proposed.

Processes of diversification and dispersion of rice yellow mottle virus inferred from large-scale and high-resolution phylogeographical studies.

Rice (Oryza sativa) is a key staple in Tanzania but its productivity is affected by disease infestation, primary among which is the rice yellow mottle virus (RYMV). Tanzania possesses high RYMV densities and several locations including the Eastern Arc Mountains provide suitable habitat fragmentation that facilitates the diversification process of the virus. However, the distribution pattern and diversity of the local strains of RYMV remain largely unknown and this hinders progress in designing interventions. Efforts were, therefore, made to study the pattern and distribution of RYMV. Collection of isolates was made in May; recovery of virus on a susceptible elite line viz. TXD 220-1-3-3-1 was in June-July and molecular analysis was done in September-December 2005. The sequences of the coat protein (CP) gene of 23 isolates, representative of the three strains of RYMV found in Tanzania, were selected from 52 isolates collected from three regions. The phylogenetic analyses of the CP sequences revealed high (14.8%) nucleotide divergence between strains. Strain S6 was the most divergent with an intra- strain nucleotide divergence of 8.8%; this was consistent with its wide distribution in the region and particularly the eastern part of the Tanzania. Isolates of strains S4 were recorded for the first time in the eastern Arc Mountain region. These formed a monophyletic group with the Lake Malawi strain S4 sub-lineage (percentage identity of 95.4 to 96.8%) and differed from the Lake Victoria strain S4 sub-lineage by 4.5%. Coexistence within the same field of S4, S5 and S6 isolates was observed in the eastern Arc Mountains region. Strong competition between strains of RYMV was suspected from the limited distribution and rarity of strain S5. This study confirm speculations that the Eastern Arc Mountain region is the centre of origin of RYMV. Thus, the high viral load in the Eastern Arc Mountain imply that it is a suitable location for strategic studies aimed at designing control interventions against RYMV.

/pdf/distribution-and-diversity-of-local-strains-of-rice-yellow-3ekprcqcoc.pdf

Distribution and diversity of local strains of rice yellow motile virus in Tanzania

Knowledge of rice genetic diversity is necessary to ascertain the germplasm conservation and the development of improved rice genotypes with good quality traits through various breeding programs. The aim of this study was to determine the genetic diversity based on gel consistency and alkali digestion among selected Kenyan and Tanzanian genotypes using SSR markers. PowerMarker version 3.25, GenAlEx version 6.41 and DARwin 6.0.12 statistical software were used to carry out data analysis. The number of alleles per locus ranged from 2 to 4 with an average of 2.75 across the 8 markers used. Polymorphic information content (PIC) ranged from 0.5224 (RM577) to 0.1411 (RM85) with an average of 0.3673 observed across all the markers. Gene diversity ranged from 0.5764 (RM577) to 0.1528 (RM85) with an average of 0.4181 with one rare allele was detected at RM577 loci. Pairwise genetic dissimilarity matrix ranged from ranged from 0.9333 to 0.1818 with the least genetic distance being observed between IR 54 and BS 370 while the highest, 0.9333 being between Saro 5 and IR 2793. The unweighted neighbour joining tree clustered the rice genotypes into three major clusters and subsequent sub clusters hence effectively differentiating the Kenyan and Tanzanian genotypes based on gel consistency and alkali digestion. This clustering was complemented with the findings in the principal coordinate analysis. These results show that determination of genetic diversity using SSR markers cam be successfully achieved. In this study RM577 was the best and most informative SSR marker given it showed the highest PIC, gene diversity and allele per locus. In addition, it’s the only marker that showed a rare allele at 400 bp.

Genetic Diversity Studies on Selected Rice (Oryza sativa L.) Genotypes based on Gel Consistency and Alkali Digestion

Rice yellow mottle genus Sobemovirus is an important disease of rice worldwide. Although the virus attacks both upland and lowland rice cultivars, the latter are worse infected. The disease is spread by insect vectors belonging to the families Chrysomelidae, Coccinelidae, and Tettigonidae. It is also transmitted by domestic cattle (Bos spp.), donkeys (Asinus spp.), grass rats (Arvicanthis niloticus), weed species of the family Poaceae, debris, irrigation water and through mechanical inoculation. Six strains of the virus have been reported so far. Rice yellow mottle virus (RYMV) incidence ranges between 5 and 100% and yield losses vary from 20 to 100%. Effective management includes the use of resistant cultivars, control of insect vectors, good sanitation and integrated pest and production management. This paper reviews the current status of the virus, with emphasis on its geographical distribution, characteristics, strains, symptomatology, diagnosis, transmission, host range and management strategies.

Current status of research on rice yellow mottle Sobemovirus

The triple revolution in biotechnology, computing science, and communication technology has stimulated informatics applications in rice research. This review specifically covers the impact of biology-focused informatics ("bioinformatics") in rice research on the discovery of genotype-phenotype relationships for priority traits, using diverse data sources. Bioinformatics is a scientific discipline lying at the intersection of biology, mathematics, computing science, and information technology. Bioinformatics can be discussed within the following frameworks: • Applications: What kind of research questions can be answered using bioinformatics? • Databases: What data sources and applicable semantic standards (ontology1) are pertinent to answering these research questions? • Protocols, algorithms, and tools: What analysis protocols, computing algorithms, and software tools can be applied to answer these research questions? • Infrastructure: What hardware, software, and networking systems are required to support the above? This review will focus primarily on germplasm-based crop research, although many of the same tools can be applied to current problems in soil microbiology, entomology, and other areas of crop research. Also, some of the design principles of bioinformatics information systems will be useful  for other research fields, such as geographic and agronomic information systems.

Bioinformatics and crop information systems in rice research

Molecular variability and distribution of Rice yellow mottle virus in Tanzania.

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Molecular variability and distribution of Rice yellow mottle virus in Tanzania.