Distribution and diversity of viruses infecting yams (Dioscorea spp.) in Cameroon.

Yam (Dioscorea spp.) is an important food crop cultivated for its edible tubers in Cameroon. Surveys were conducted in Cameroon to determine the incidence and severity of yam mosaic disease and associated viruses in 124 yam farms in four agro-ecological zones in 2014 and 2016. Dioscorea rotundata, D. cayenensis, D. alata, D. Dumetorum and D. bulbifera were most frequently detected yam species in the fields. Symptoms of virus disease were observed on 81.5% of the farms surveyed and the disease incidence ranged from 0 to 96.7%, with an overall mean of 26.5%. Mean symptom severity estimated using a numerical rating scale of 1-5, ranged from 2 to 4.1, with an overall mean of 2.6. Representative set of leaf samples collected from farmers' fields were tested for three viruses known to cause yam mosaic disease in West Africa, viz., Yam mosaic virus (YMV), Yam mild mosaic virus (YMMV) and Cucumber mosaic virus (CMV), using multiplex RT-PCR. YMV and YMMV were detected in 220 (37.2%) of the 591 samples tested and 75% of the farms surveyed. None of the samples tested positive to CMV. Phylogenetic analysis based on the coat protein sequencing of 27 YMV isolates clustered these isolates into three phylogenetic groups. This study demonstrated high prevalence of mosaic disease in yam fields and YMV as main causal agent. Knowledge generated in this study will be useful to augment diagnostic tools and yam mosaic disease control with a view to improve on yam production in Cameroon.

Fine mapping of Msv1, a major QTL for resistance to Maize Streak Virus leads to development of production markers for breeding pipelines.

Msv1 , the major QTL for MSV resistance was delimited to an interval of 0.87 cM on chromosome 1 at 87 Mb and production markers with high prediction accuracy were developed. Maize streak virus (MSV) disease is a devastating disease in the Sub-Saharan Africa (SSA), which causes significant yield loss in maize. Resistance to MSV has previously been mapped to a major QTL (Msv1) on chromosome 1 that is germplasm and environment independent and to several minor loci elsewhere in the genome. In this study, Msv1 was fine-mapped through QTL isogenic recombinant strategy using a large F 2 population of CML206 × CML312 to an interval of 0.87 cM on chromosome 1. Genome-wide association study was conducted in the DTMA (Drought Tolerant Maize for Africa)-Association mapping panel with 278 tropical/sub-tropical breeding lines from CIMMYT using the high-density genotyping-by-sequencing (GBS) markers. This study identified 19 SNPs in the region between 82 and 93 Mb on chromosome 1(B73 RefGen_V2) at a P < 1.00E-04, which coincided with the fine-mapped region of Msv1. Haplotype trend regression identified a haplotype block significantly associated with response to MSV. Three SNPs in this haplotype block at 87 Mb on chromosome 1 had an accuracy of 0.94 in predicting the disease reaction in a collection of breeding lines with known responses to MSV infection. In two biparental populations, selection for resistant Msv1 haplotype demonstrated a reduction of 1.03-1.39 units on a rating scale of 1-5, compared to the susceptible haplotype. High-throughput KASP assays have been developed for these three SNPs to enable routine marker screening in the breeding pipeline for MSV resistance.

Cassava virus diseases: biology, epidemiology, and management.

Cassava (Manihot esculenta Crantz.) is the most important vegetatively propagated food staple in Africa and a prominent industrial crop in Latin America and Asia. Its vegetative propagation through stem cuttings has many advantages, but deleteriously it means that pathogens are passed from one generation to the next and can easily accumulate, threatening cassava production. Cassava-growing continents are characterized by specific suites of viruses that affect cassava and pose particular threats. Of major concern, causing large and increasing economic impact in Africa and Asia are the cassava mosaic geminiviruses that cause cassava mosaic disease in Africa and Asia and cassava brown streak viruses causing cassava brown streak disease in Africa. Latin America, the center of origin and domestication of the crop, hosts a diverse set of virus species, of which the most economically important give rise to cassava frog skin disease syndrome. Here, we review current knowledge on the biology, epidemiology, and control of the most economically important groups of viruses in relation to both farming and cultural practices. Components of virus control strategies examined include: diagnostics and surveillance, prevention and control of infection using phytosanitation, and control of disease through the breeding and promotion of varieties that inhibit virus replication and/or movement. We highlight areas that need further research attention and conclude by examining the likely future global outlook for virus disease management in cassava.

Comparing the regional epidemiology of the cassava mosaic and cassava brown streak virus pandemics in Africa.

The rapid geographical expansion of the cassava mosaic disease (CMD) pandemic, caused by cassava mosaic geminiviruses, has devastated cassava crops in 12 countries of East and Central Africa since the late 1980s. Region-level surveys have revealed a continuing pattern of annual spread westward and southward along a contiguous 'front'. More recently, outbreaks of cassava brown streak disease (CBSD) were reported from Uganda and other parts of East Africa that had been hitherto unaffected by the disease. Recent survey data reveal several significant contrasts between the regional epidemiology of these two pandemics: (i) severe CMD radiates out from an initial centre of origin, whilst CBSD seems to be spreading from independent 'hot-spots'; (ii) the severe CMD pandemic has arisen from recombination and synergy between virus species, whilst the CBSD pandemic seems to be a 'new encounter' situation between host and pathogen; (iii) CMD pandemic spread has been tightly linked with the appearance of super-abundant Bemisia tabaci whitefly vector populations, in contrast to CBSD, where outbreaks have occurred 3-12 years after whitefly population increases; (iv) the CMGs causing CMD are transmitted in a persistent manner, whilst the two cassava brown streak viruses appear to be semi-persistently transmitted; and (v) different patterns of symptom expression mean that phytosanitary measures could be implemented easily for CMD but have limited effectiveness, whereas similar measures are difficult to apply for CBSD but are potentially very effective. An important similarity between the pandemics is that the viruses occurring in pandemic-affected areas are also found elsewhere, indicating that contrary to earlier published conclusions, the viruses per se are unlikely to be the key factors driving the two pandemics. A diagrammatic representation illustrates the temporal relationship between B. tabaci abundance and changing incidences of both CMD and CBSD in the Great Lakes region. This emphasizes the pivotal role played by the vector in both pandemics and the urgent need to identify effective and sustainable strategies for controlling whiteflies on cassava.

First Report of Soybean Witches'-Broom Disease Caused by Group 16SrII Phytoplasma in Soybean in Malawi and Mozambique.

Soybean (Glycine max L.) is an important grain legume cultivated on approximately 1.24 million ha in Africa (1). Malawi ranks fourth in area of production in Africa, with 75,000 ha in 2009 (1). Soybean is also gaining importance in Mozambique and several other southern African countries due to diversification programs. During a field survey conducted in March 2010, soybean plants with phyllody and witches'-broom disorders typical of phytoplasma infection were observed in three of five fields surveyed in Lilongwe (Chitedze Research Station) and Salima (Channa, Chitala) districts in Malawi and three of four fields surveyed in Zambezia Province in Mozambique. Symptoms consisted of shoot proliferation, reduced leaflets, shortened internodes, proliferated auxiliary shoots producing witches'-brooms, virescence, and phyllody. Incidence of symptomatic plants was <1% in Malawi and 10 to 15% in Mozambique. Yield loss was 100% in affected plants. Five leaf samples each from symptomatic and asymptomatic plants were collected from six fields; total genomic DNAs were isolated and used as templates in PCR using phytoplasma-universal primer pair P1 and P7 for 16S-23S ribosomal RNA encoding region (3). PCR amplicons (1,709 bp) were produced from only templates derived from symptomatic plants. Amplicons from a symptomatic plant each from Malawi (Channa, Salima District) and Mozambique (Mutequelse, Zambezia Province) were directly sequenced in both directions and submitted to the GenBank (Accession Nos. HQ840717 and HQ845208). Nucleotide sequences of the two African soybean witches'-broom (SoyWB) phytoplasma strains were 100% identical. The virtual restriction fragment length polymorphism (RFLP) pattern derived from these sequences using iPhyClassifier software (4) was similar to the reference pattern of the 16Sr group II, subgroup C (cactus phytoplasma, Accession No. AJ293216), with a pattern similarity coefficient of 0.99. A BLASTn search revealed that the African SoyWB phytoplasma sequences had a nucleotide sequence identity of 99% with those of soybean phytoplasma from Thailand (Accession No. EF193353), cactus phytoplasma from China (Accession No. EU099561), and several other members of 16SrII group. Phylogenetic analysis revealed the clustering of these strains with members of 16SrII group. In 1984, the occurrence of phyllody and witches'-broom symptoms in soybean in Mozambique was reported (2), however, no comprehensive details on the pathogen are available. To our knowledge, this is the first report of phyllody and witches'-broom disease in soybean in Malawi and the first molecular evidence of association of a 16SrII-C group 'Candidatus phytoplasma' with the disease in Malawi and Mozambique. Phyllody and witches'-broom is a destructive disease, and its widespread occurrence can adversely affect soybean production in sub-Saharan Africa. Identification of alternative hosts and vector species would improve our understanding of the disease's epidemiology and contribute to development of appropriate tactics to prevent escalation of this problem into a major disease. References: (1) FAOSTAT. http://faostat.fao.org/site/567/default.aspx . Retrieved 28 December 2010. (2) P. Plumb-Dhindsa and A. M. Mondjane. Trop. Pest Manage. 30:407, 1984. (3) L. B. Sharmila et al. J. Plant Biochem. Biotech. 13:1, 2004. (4) Y. Zhao et al. Int. J. Syst. Evol. Microbiol. 59:2582, 2009.

Alternate hosts of African cassava mosaic virus and East African cassava mosaic Cameroon virus in Nigeria.

Cassava mosaic disease (CMD) caused by African cassava mosaic virus (ACMV) and East African cassava mosaic Cameroon virus (EACMCV) is the major constraint to cassava production in Nigeria. Sequences of the DNA-A component of ACMV and EACMCV isolates from leguminous plant species (Senna occidentalis, Leucana leucocephala and Glycine max), castor oil plant (Ricinus communis), a weed host (Combretum confertum) and a wild species of cassava (Manihot glaziovii) were determined. All ACMV isolates from these hosts showed 96-98% nucleotide sequence identity with cassava isolates from West Africa. EACMCV was found only in four hosts (S. occidentalis, L. leucocephala, C. confertum, M. glaziovii), and sequences of these isolates showed 96-99% identity with cassava isolates from West Africa. These results provide definitive evidence for the natural occurrence of ACMV and EACMCV in plant species besides cassava.

Identification of cecidophyopsis mites (Acari: Eriophyidae) based on variable simple sequence repeats of ribosomal DNA internal transcribed spacer-1 sequences via multiplex PCR.

A PCR multiplex technique was developed for identifying Cecidophyopsis mites using species-specific differences in rDNA ITS-1 sequences. Four PCR primers derived from ITS-1 were used for the simultaneous amplification (multiplex PCR) of interspecifically variable simple sequence repeats (vSSRs). Mites were identified by electrophoresing PCR products alongside those obtained from plasmids containing ITS copies of known mite species. The multiplex PCR assay was rapid, reproducible and had a sensitivity comparable to sequencing. It was used to identify mite specimens on Ribes from around the world. It also identified a profile from mites on R. rubrum that had no equivalent amongst the known Cecidophyopsis species. Sequence and ecological analysis of this mite suggest that it is a new species of nongall-forming Cecidophyopsis mite.