Settumba B. Mukasa

Unravelling the genetic diversity of the three main viruses involved in Sweet Potato Virus Disease (SPVD), and its practical implications.

SUMMARY Sweetpotato (Ipomoea batatas) is a widely grown food crop, in which the most important diseases are caused by viruses. Genetic variability of three widely distributed sweetpotato viruses was analysed using data from 46 isolates of Sweet potato feathery mottle virus (SPFMV), 16 isolates of Sweet potato mild mottle virus (SPMMV) and 25 isolates of Sweet potato chlorotic stunt virus (SPCSV), of which 19, seven and six isolates, respectively, are newly characterized. Division of SPFMV into four genetic groups (strains) according to phylogenetic analysis of coat protein (CP) encoding sequences revealed that strain EA contained the East African isolates of SPFMV but none from elsewhere. In contrast, strain RC contained ten isolates from Australia, Africa, Asia and North America. Strain O contained six heterogeneous isolates from Africa, Asia and South America. The seven strain C isolates from Australia, Africa, Asia, and North and South America formed a group that was genetically distant from the other SPFMV strains. SPMMV isolates showed a high level of variability with no discrete strain groupings. SPCSV isolates from East Africa were phylogenetically distant to SPCSV isolates from elsewhere. Only from East Africa were adequate data available for different isolates of the three viruses to estimate the genetic variability of their local populations. The implications of the current sequence information and the need for more such information from most sweetpotato-growing regions of the world are discussed in relation to virus diagnostics and breeding for virus resistance.

Sweetpotato Viruses: 15 Years of Progress on Understanding and Managing Complex Diseases

Sweetpotato is a member of the morning glory family that is thought to have originated in Central or South America but also has a secondary center of diversity in the southwest Pacific islands. It is grown in all tropical and subtropical areas of the world and consistently ranks among the 10 most important food crops worldwide on the basis of dry weight produced, yielding about 130 million metric tons per year on about 9 million hectares. Sweetpotato is an important crop for food security. It has been relied on as a source of calories in many circumstances. Vines and/or storage roots can be used for direct human consumption or animal feed. Growing awareness of health benefits attributed to sweetpotato has stimulated renewed interest in the crop. Orange-fleshed cultivars, a source of vitamin A, were introduced to developing countries with hope that they would replace the white-flesh varieties and help alleviate vitamin A deficiencies. In East Africa, sweetpotato virus disease, which is caused by the synergistic interaction of the whitefly-transmitted crinivirus and the aphid-transmitted potyvirus, can cause losses of 80 to 90% in many high-yielding genotypes. During the past 15 years, as molecular methods have been adopted, much has been learned about the composition of the sweetpotato virus complexes, the effects of virus diseases on production systems, the biology of the virus–plant interaction, and management approaches to sweetpotato virus diseases. This article is intended to summarize what has been learned since earlier reviews, integrate knowledge gleaned from experiences in tropical and temperate production systems, and suggest courses of action to develop sustainable management programs for these diseases.

Cassava Brown Streak Virus (Potyviridae) Encodes a Putative Maf/HAM1 Pyrophosphatase Implicated in Reduction of Mutations and a P1 Proteinase That Suppresses RNA Silencing but Contains No HC-Pro

ABSTRACT The complete positive-sense single-stranded RNA genome of Cassava brown streak virus (CBSV; genus Ipomovirus; Potyviridae) was found to consist of 9,069 nucleotides and predicted to produce a polyprotein of 2,902 amino acids. It was lacking helper-component proteinase but contained a single P1 serine proteinase that strongly suppressed RNA silencing. Besides the exceptional structure of the 5′-proximal part of the genome, CBSV also contained a Maf/HAM1-like sequence (678 nucleotides, 226 amino acids) recombined between the replicase and coat protein domains in the 3′-proximal part of the genome, which is highly conserved in Potyviridae. HAM1 was flanked by consensus proteolytic cleavage sites for ipomovirus NIaPro cysteine proteinase. Homology of CBSV HAM1 with cellular Maf/HAM1 pyrophosphatases suggests that it may intercept noncanonical nucleoside triphosphates to reduce mutagenesis of viral RNA.

Incidence of Viruses and Viruslike Diseases of Sweetpotato in Uganda

Sweetpotato plants were surveyed for viruslike diseases and viruses in the four major agroecological zones of Uganda. Testing of 1,260 sweetpotato plants, of which 634 had virus-like symptoms, showed that virus disease incidence ranged from 2.7% (Soroti district, short grassland-savannah zone) to 20% (Mukono district, tall grass-forest mosaic zone). Sweet potato chlorotic stunt virus (SPCSV), Sweet potato feathery mottle virus (SPFMV), Sweet potato mild mottle virus (SPMMV), and sweet potato chlorotic fleck virus (SPCFV) were serologically detected and positive results confirmed by immunocapture reverse transcriptase polymerase chain reaction (IC-RT-PCR) and subsequent sequence analyses of the amplified fragments, except SPCFV, which lacked sequence information. SPCSV and SPFMV were detected in all the 14 districts surveyed, whereas SPMMV and SPCFV were detected in 13 and 8 districts, respectively. Logistic regression analysis revealed that SPCSV and SPFMV, SPFMV and SPMMV, and SPFMV and SPCFV more frequently occurred together than any other virus combinations or as single virus infections. Co-infections of SPCSV with SPFMV and/or SPMMV were associated with more severe and persistent symptoms than infections with each of the viruses alone. Several plants (11%) displaying viruslike symptoms did not react with the virus antisera used, suggesting that more viruses or viruslike agents are infecting sweetpotatoes in Uganda.

Simultaneous virus-specific detection of the two cassava brown streak-associated viruses by RT-PCR reveals wide distribution in East Africa, mixed infections, and infections in Manihot glaziovii

The expanding cassava brown streak disease (CBSD) epidemic in East Africa is caused by two ipomoviruses (genus Ipomovirus; Potyviridae), namely, Cassava brown streak virus (CBSV), and Ugandan cassava brown streak virus (UCBSV) that was described recently. A reverse transcription polymerase chain reaction (RT-PCR) based diagnostic method was developed in this study for simultaneous virus-specific detection of the two viruses. Results showed that CBSV and UCBSV are distributed widely in the highlands (> 1000 m above the sea level) of the Lake Victoria zone in Uganda and Tanzania and also in the Indian Ocean costal lowlands of Tanzania. Isolates of UCBSV from the Lake Victoria zone were placed to two phylogenetic clusters in accordance with their origin in Uganda or Tanzania, respectively. Mixed infections with CBSV and UCBSV were detected in many cassava plants in the areas surveyed. CBSV was also detected in the perennial species Manihot glaziovii (DNA-barcoded in this study) in Tanzania, which revealed the first virus reservoir other than cassava. The method for detection of CBSV and UCBSV described in this study has important applications for plant quarantine, resistance breeding of cassava, and studies on epidemiology and control of CBSD in East Africa.

Some molecular characteristics of three viruses from SPVD-affected sweet potato plants in Egypt

Summary.Sweet potato feathery mottle virus (SPFMV, genus Potyvirus, family Potyviridae), Sweet potato chlorotic stunt virus (SPCSV, genus Crinivirus, family Closteroviridae) and sweet potato virus G (SPVG) were detected in naturally infected sweet potato plants grown in the Delta region in Egypt. Before this study, SPVG was reported only from China. Two isolates of SPFMV and one isolate of SPVG were characterized for the 3′-proximal genomic sequences. Phylogenetic analyses indicated that the SPFMV isolates belong to the ‘russet crack’ strain group (RC). Serological tests using monoclonal antibodies, and phylogenetic analysis of a partial sequence of the Hsp70 gene, indicated that the Egyptian SPCSV belongs to the so-called non-East African strain group of SPCSV.

Molecular genetic analysis of virus isolates from wild and cultivated plants demonstrates that East Africa is a hotspot for the evolution and diversification of Sweet potato feathery mottle virus.

Sweet potato feathery mottle virus (SPFMV, genus Potyvirus) is globally the most common pathogen of cultivated sweet potatoes (Ipomoea batatas; Convolvulaceae). Although more than 150 SPFMV isolates have been sequence‐characterized from cultivated sweet potatos across the world, little is known about SPFMV isolates from wild hosts and the evolutionary forces shaping SPFMV population structures. In this study, 46 SPFMV isolates from 14 wild species of genera Ipomoea, Hewittia and Lepistemon (barcoded for the matK gene in this study) and 13 isolates from cultivated sweet potatoes were partially sequenced. Wild plants were infected with the EA, C or O strain, or co‐infected with the EA and C strains of SPFMV. In East Africa, SPFMV populations in wild species and sweet potato were genetically undifferentiated, suggesting inter‐host transmission of SPFMV. Globally, spatial diversification of the 178 isolates analysed was observed, strain EA being largely geographically restricted to East Africa. Recombination was frequently detected in the 6K2‐VPg‐NIaPro region of the EA strain, demonstrating a recombination ‘hotspot’. Recombination between strains EA and C was rare, despite their frequent co‐infections in wild plants, suggesting purifying selection against strain EA/C recombinants. Positive selection was predicted on 17 amino acids distributed over the entire coat protein in the globally distributed strain C, as compared to only four amino acids in the coat protein N‐terminus of the EA strain. This selection implies a more recent introduction of the C strain and a higher adaptation of the EA strain to the local ecosystem. Thus, East Africa appears as a hotspot for evolution and diversification of SPFMV.

Artificial microRNA-derived resistance to Cassava brown streak disease

Highlights • amiRNAs were produced for imparting resistance to Cassava brown streak disease.• transgenic plants were produced expressing amiRNAs against CBSV and UCBSV.• amiRNAs targeting conserved sequences of P1, NIb and CP genes were efficacious.• levels of resistance to CBSD correlated with accumulation of detectable miRNA.

Genetic variability and evolutionary implications of RNA silencing suppressor genes in RNA1 of sweet potato chlorotic stunt virus isolates infecting sweetpotato and related wild species.

Background The bipartite single-stranded RNA genome of Sweet potato chlorotic stunt virus (SPCSV, genus Crinivirus; Closteroviridae) encodes a Class 1 RNase III (RNase3), a putative hydrophobic protein (p7) and a 22-kDa protein (p22) from genes located in RNA1. RNase3 and p22 suppress RNA silencing, the basal antiviral defence mechanism in plants. RNase3 is sufficient to render sweetpotato (Ipomoea batatas) virus-susceptible and predisposes it to development of severe diseases following infection with unrelated virus. The incidence, strains and gene content of SPCSV infecting wild plant species have not been studied. Methodology/Principal Findings Thirty SPCSV isolates were characterized from 10 wild Ipomoea species, Hewittia sublobata or Lepistemon owariensis (family Convolvulaceae) in Uganda and compared with 34 local SPCSV isolates infecting sweetpotatoes. All isolates belonged to the East African (EA) strain of SPCSV and contained RNase3 and p7, but p22 was not detected in six isolates. The three genes showed only limited genetic variability and the proteins were under purifying selection. SPCSV isolates lacking p22 synergized with Sweet potato feathery mottle virus (SPFMV, genus potyvirus; Potyviridae) and caused severe symptoms in co-infected sweetpotato plants. One SPCSV isolate enhanced accumulation of SPFMV, but no severe symptoms developed. A new whitefly-transmitted virus (KML33b) encoding an RNase3 homolog (<56% identity to SPCSV RNase3) able to suppresses sense-mediated RNA silencing was detected in I. sinensis. Conclusions/Significance SPCSV isolates infecting wild species and sweetpotato in Uganda were genetically undifferentiated, suggesting inter-species transmission of SPCSV. Most isolates in Uganda contained p22, unlike SPCSV isolates characterized from other countries and continents. Enhanced accumulation of SPFMV and increased disease severity were found to be uncoupled phenotypic outcomes of RNase3-mediated viral synergism in sweetpotato. A second virus encoding an RNase3-like RNA silencing suppressor was detected. Overall, results provided many novel and important insights into evolutionary biology of SPCSV.

Prevalence of viruses infecting cowpea in Uganda and their molecular detection

This item can be retrieved directly from the publishers site at http://dx.doi.org/10.5897/AJB11.398