Browsing by Author "Titus Alicai"

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Comparative evolutionary analyses of eight whitefly Bemisia tabaci sensu lato genomes: cryptic species, agricultural pests and plant-virus vectors
(BMC Genomics, 2023-07-19) Lahcen I. Campbell; Joachim Nwezeobi; Sharon L. van Brunschot; Tadeo Kaweesi; Susan E. Seal; Rekha A. R. Swamy; Annet Namuddu; Gareth L. Maslen; Habibu Mugerwa; Irina M. Armean; Leanne Haggerty; Fergal J. Martin; Osnat Malka; Diego Santos‐Garcia; Ksenia Juravel; Shai Morin; Michael E. Stephens; Paul Visendi Muhindira; Paul J. Kersey; M. N. Maruthi; Christopher A. Omongo; Jesús Navas‐Castillo; Elvira Fiallo‐Olivé; Ibrahim Umar Mohammed; Hua‐Ling Wang; Joseph Onyeka; Titus Alicai; John Colvin
Background The group of > 40 cryptic white y species called Bemisia tabaci sensu lato are amongst the world’s worst agricultural pests and plant‐virus vectors. Outbreaks of B. tabaci s.l. and the associated plant‐virus diseases continue to contribute to global food insecurity and social instability, particularly in sub‐Saharan Africa and Asia. Published B. tabaci s.l. genomes have limited use for studying African cassava B. tabaci SSA1 species, due to the high genetic divergences between them. Genomic annotations presented here were performed using the ‘Ensembl gene annotation system’, to ensure that comparative analyses and conclusions reflect biological differences, as opposed to arising from different methodologies underpinning transcript model identification. Results WepresentheresixnewB.tabacis.l.genomesfromAfricaandAsia,andtwore‐annotatedpreviously published genomes, to provide evolutionary insights into these globally distributed pests. Genome sizes ranged between 616—658 Mb and exhibited some of the highest coverage of transposable elements reported within Arthropoda. Many fewer total protein coding genes (PCG) were recovered compared to the previously published B. tabaci s.l. genomes and structural annotations generated via the uniform methodology strongly supported a repertoire of between 12.8—13.2 × 103 PCG. An integrative systematics approach incorporating phylogenomic analysis of nuclear and mitochondrial markers supported a monophyletic Aleyrodidae and the basal positioning of B. tabaci Uganda‐1 to the sub‐Saharan group of species. Reciprocal cross‐mating data and the co‐cladogenesis pattern of the primary obligate endosymbiont ‘Candidatus Portiera aleyrodidarum’ from 11 Bemisia genomes further supported the phylogenetic reconstruction to show that African cassava B. tabaci populations consist of just three biological species. We include comparative analyses of gene families related to detoxification, sugar metabolism, vector competency and evaluate the presence and function of horizontally transferred genes, essential for understanding the evolution and unique biology of constituent B. tabaci. s.l species. Conclusions These genomic resources have provided new and critical insights into the genetics underlying B. tabaci s.l. biology. They also provide a rich foundation for post‐genomic research, including the selection of candidate gene‐ targets for innovative white y and virus‐control strategies.
Detection of cassava brown streak ipomoviruses in aphids collected from cassava plants
(Frontiers in Sustainable Food Systems, 2023-02-08) Sarah Nanyiti; Richard Kabaalu; Titus Alicai; Phillip Abidrabo; Susan E. Seal; Sophie Bouvaine; Andy M. Bailey; Gary D. Foster
Cassava is an important staple food in Africa and a major source of carbohydrates for 800 million people globally. However, cassava suffers severe yield losses caused by many factors including pests and diseases. A devastating disease of cassava is cassava brown streak disease (CBSD) caused by the cassava brown streak ipomoviruses (CBSIs) (family Potyviridae), Cassava brown streak virus (CBSV), and Ugandan cassava brown streak virus (UCBSV). Spread of CBSD is mainly through planting infected stem cuttings used for propagation. Transmission of CBSIs by the insect vector (Bemisia tabaci) has been reported. However, experimental transmission efficiencies of CBSIs are usually low. Recent research has showed the occurrence of a DAG motif associated with aphid transmission in other potyviruses, within the coat protein gene of CBSV. Consequently this study aimed to explore the possibility that besides whiteflies, aphids may transmit CBSIs. Cassava plants were assessed during a survey for occurrence of CBSD and aphids as potential alternative CBSIs vectors. We collected aphids from CBSD-symptomatic and symptomless cassava plants within farmers’ fields in Uganda during April–July 2020. The aphids were analyzed for the presence of CBSIs by reverse transcriptase-polymerase chain reaction (RT-PCR) and to determine aphid species using mitochondrial cytochrome oxidase (mtCOI) barcoding. Unusual aphid infestation of cassava plants was observed at 35 locations in nine districts across Uganda and on 11 other plant species within or adjacent to cassava fields. This is the first report of aphids infesting cassava in Uganda. Molecular analysis of the aphid confirmed presence of three different aphid species in the surveyed cassava fields, namely, Aphis solanella, Aphis fabae mordvilkoi, and Rhopalosiphum sp. mtCOI nucleotide sequences for the aphids in which CBSIs were detected are deposited with Genbank under accession numbers OP223337-40. Both UCBSV and CBSV were detected by RT-PCR in aphids collected from cassava fields with CBSD-affected plants. The CBSIs were detected in 14 aphid samples collected from 19 CBSD- symptomatic cassava plants. These results suggest the ability of aphids to acquire CBSIs, but transmission experiments are required on their vector potential.
Developing a predictive model for an emerging epidemic on cassava in sub-Saharan Africa.
(Scientific Reports, 2023-04-01) David Godding; Richard O. J. H. Stutt; Titus Alicai; Phillip Abidrabo; Geo rey Okao‐Okuja; Christopher A. Gilligan
The agricultural productivity of smallholder farmers in sub‐Saharan Africa (SSA) is severely constrained by pests and pathogens, impacting economic stability and food security. An epidemic of cassava brown streak disease, causing significant yield loss, is spreading rapidly from Uganda into surrounding countries. Based on sparse surveillance data, the epidemic front is reported to be as far west as central DRC, the world’s highest per capita consumer, and as far south as Zambia. Future spread threatens production in West Africa including Nigeria, the world’s largest producer of cassava. Using innovative methods we develop, parameterise and validate a landscape‐scale, stochastic epidemic model capturing the spread of the disease throughout Uganda. The model incorporates real‐ world management interventions and can be readily extended to make predictions for all 32 major cassava producing countries of SSA, with relevant data, and lays the foundations for a tool capable of informing policy decisions at a national and regional scale.
Endemism and Reemergence Potential of the Ipomovirus Sweet Potato Mild Mottle Virus (Family Potyviridae) in Eastern Africa: Half a Century of Mystery
(Phytobiomes Journal, 2022-11-29) Arthur K. Tugume; Deusdedith R. Mbanzibwa; Titus Alicai; Christopher A. Omongo; M. N. Maruthi
Viruses have the ability to frequently colonize new hosts and ecological niches because of their inherently high genetic and evolutionary plasticity. However, a virus may emerge and remain of no or less economic importance until changes in viral or environmental factors dictate its epidemiological status. An example is sweet potato mild mottle virus (SPMMV), which was first reported in the 1970s on sweetpotato in eastern Africa. SPMMV has remained endemic in the region and poorly understood, yet accounting for 60 to 95% of losses, especially in mixed infections. Unlike other sweetpotato viruses which have global incidences, SPMMV has never been confirmed outside eastern Africa. This implicates the region as its center of origin but does not fully account for SPMMV’s exclusive geographic delimitation to eastern Africa. Despite its importance, several mysteries and research gaps surround SPMMV, which decelerate efforts for effective virus disease management in sweetpotato. The aim of this review is to articulate research gaps, propose pivotal scientific directions, and stimulate knowledge generation for better management of virus diseases in sweetpotato. Vector-mediated transmission of SPMMV remains enigmatic. Here, we postulate testable hypotheses to explain SPMMV transmission. Comparisons between SPMMV and cassava brown streak ipomoviruses demonstrate epidemiological “hallmarks” for monitoring SPMMV. Evolutionary forces on SPMMV coupled with the virus’ broad host range imply a “silent build up” of more fit variants in a changing climate, and this could explode into a worse disease conundrum. These information gaps need urgent filling to ease future management of virus disease emergences in sweetpotato.
Flowering and fruit-set in cassava under extended red-light photoperiod supplemented with plant-growth regulators and pruning
(BMC Plant Biology, 2023-06-23) Julius K. Baguma; Settumba B Mukasa; Ephraim Nuwamanya; Titus Alicai; Christopher Omongo; Peter T. Hyde; Tim L. Setter; Mildred Ochwo‐Ssemakula; William Esuma; Michael Kanaabi; Paula Iragaba; Yona Baguma; Robert S. Kawuki
Background Cassava (Manihot esculenta Crantz) is staple food and major source of calories for over 500 million people in sub‐Saharan Africa. The crop is also a source of income for smallholder farmers, and has increasing potential for industrial utilization. However, breeding efforts to match the increasing demand of cassava are impeded by its inability to flower, delayed or unsynchronized flowering, low proportion of female flowers and high fruit abortions. To overcome these sexual reproductive bottlenecks, this study investigated the effectiveness of using red lights to extend the photoperiod (RLE), as a gateway to enhancing flowering and fruit set under field conditions. Materials and methods Panels of cassava genotypes, with non‐ or late and early flowering response, 10 in each case, were subjected to RLE from dusk to dawn. RLE was further evaluated at low (LL), medium (ML) and high (HL) red light intensities, at ~ ≤ 0.5; 1.0 and 1.5PFD (Photon Flux Density) in μmol m−2 s−1 respectively. Additionally, the effect of a cytokinin and anti‐ethylene as plant growth regulators (PGR) and pruning under RLE treatment were examined. Results RLE stimulated earlier flower initiation in all genotypes, by up to 2 months in the late‐flowering genotypes. Height and number of nodes at first branching, particularly in the late‐flowering genotypes were also reduced, by over 50%. Number and proportion of pistillate flowers more than doubled, while number of fruits and seeds also increased. Number of branching levels during the crop season also increased by about three. Earlier flowering in many genotypes was most elicited at LL to ML intensities. Additive effects on flower numbers were detected between RLE, PGR and pruning applications. PGR and pruning treatments further increased number and proportion of pistillate flowers and fruits. Plants subjected to PGR and pruning, developed bisexual flowers and exhibited feminization of staminate flowers. Pruning at first branching resulted in higher pistillate flower induction than at second branching. Conclusions These results indicate that RLE improves flowering in cassava, and its effectiveness is enhanced when PGR and pruning are applied. Thus, deployment of these technologies in breeding programs could significantly enhance cassava hybridizations and thus cassava breeding efficiency and impact.
In silico prediction of candidate gene targets for the management of African cassava whitefly (Bemisia tabaci, SSA1-SG1), a key vector of viruses causing cassava brown streak disease
(PeerJ, 2024-02-23) Tadeo Kaweesi; John Colvin; Lahcen Campbell; Paul Visendi; Gareth Maslen; Titus Alicai; Susan Seal
Whiteflies (Bemisia tabaci sensu lato) have a wide host range and are globally important agricultural pests. In Sub-Saharan Africa, they vector viruses that cause two ongoing disease epidemics: cassava brown streak disease and cassava mosaic virus disease. These two diseases threaten food security for more than 800 million people in Sub-Saharan Africa. Efforts are ongoing to identify target genes for the development of novel management options against the whitefly populations that vector these devastating viral diseases affecting cassava production in Sub-Saharan Africa. This study aimed to identify genes that mediate osmoregulation and symbiosis functions within cassava whitefly gut and bacteriocytes and evaluate their potential as key gene targets for novel whitefly control strategies. The gene expression profiles of dissected guts, bacteriocytes and whole bodies were compared by RNAseq analysis to identify genes with significantly enriched expression in the gut and bacteriocytes. Phylogenetic analyses identified three candidate osmoregulation gene targets: two a-glucosidases, SUC 1 and SUC 2 with predicted function in sugar transformations that reduce osmotic pressure in the gut; and a water-specific aquaporin (AQP1) mediating water cycling from the distal to the proximal end of the gut. Expression of the genes in the gut was enriched 23.67-, 26.54- and 22.30-fold, respectively. Genome-wide metabolic reconstruction coupled with constraint-based modeling revealed four genes (argH, lysA, BCAT & dapB) within the bacteriocytes as potential targets for the management of cassava whiteflies. These genes were selected based on their role and essentiality within the different essential amino acid biosynthesis pathways. A demonstration of candidate osmoregulation and symbiosis gene targets in other species of the Bemisia tabaci species complex that are orthologs of the empirically validated osmoregulation genes highlights the latter as promising gene targets for the control of cassava whitefly pests by in planta RNA interference.
Mutations in DNA polymerase δ subunit 1 co- segregate with CMD2-type resistance to Cassava Mosaic Geminiviruses
(Nature Communications, 2022-07-07) Yi-Wen Lim; Ben N. Mansfeld; Pascal Schläpfer; Kerrigan B. Gilbert; Narayanan N. Narayanan; Weihong Qi; Qi Wang; Zhenhui Zhong; Adam Boyher; Jackson Gehan; Getu Beyene; Zuh-Jyh Daniel Lin; Williams Esuma; Suhua Feng; Christelle Chanez; Nadine Eggenberger; Gerald Adiga; Titus Alicai; Steven E. Jacobsen; Nigel J. Taylor; Wilhelm Gruissem; Rebecca S. Bart
Cassava mosaic disease (CMD) suppresses cassava yields across the tropics. The dominant CMD2 locus confers resistance to cassava mosaic geminiviruses. It has been reported that CMD2-type landraces lose resistance after regeneration through de novo morphogenesis. As full genome bisulfite sequencing failed to uncover an epigenetic mechanism for this loss of resistance, whole genome sequencing and genetic variant analysis was performed and the CMD2 locus was fine-mapped to a 190 kilobase interval. Collectively, these data indicate that CMD2-type resistance is caused by a nonsynonymous, single nucleotide polymorphism in DNA polymerase δ subunit 1 (MePOLD1) located within this region. Virus-induced gene silencing of MePOLD1 in a CMD-susceptible cassava variety produced a recovery phenotype typical of CMD2-type resistance. Analysis of other CMD2-type cassava varieties identified additional candidate resistance alleles within MePOLD1. Genetic variation of MePOLD1, therefore, could represent an important genetic resource for resistance breeding and/or genome editing, and elucidating mechanisms of resistance to geminiviruses.
Resistance of advanced cassava breeding clones to infection by major viruses in Uganda
(Crop Protection, 2018-10-07) Daniel Rogers Mukiibi; Titus Alicai; Robert Kawuki; Geoffrey Okao-Okuja; Fred Tairo; Peter Sseruwagi; Joseph Ndunguru; Elijah Miinda Ateka
Cassava brown streak disease (CBSD) and cassava mosaic disease (CMD) are two viral diseases that cause severe yield losses in cassava of up to 100%, thereby persistently threatening food and income security in sub-Saharan Africa. For effective management of these diseases, there is a critical need to develop and deploy varieties with dual resistance to CBSD and CMD. In this study, we determined the response of advanced breeding lines to field infection by cassava brown streak viruses (CBSVs) and cassava mosaic begomoviruses (CMBs). This aim helped in identifying superior clones for downstream breeding. In total, 220 cassava clones, three in uniform yield trials (UYTs) and 217 in a crossing block trial (CBT), were evaluated for virus and disease resistance. Field data were collected on disease incidence and severity. To detect and quantify CBSVs, 448 and 128 leaf samples from CBSD symptomatic and symptomless plants were analyzed by reverse transcription PCR and real-time quantitative PCR, respectively. In addition, 93 leaf samples from CMD symptomatic plants in the CBT were analyzed by conventional PCR using CMB species-specific primers. In the CBT, 124 (57%) cassava clones did not express CMD symptoms. Of the affected plants, 44 (55%) had single African cassava mosaic virus infection. Single Cassava brown streak virus (CBSV) infections were more prevalent (81.6%) in CBT clones than single Ugandan cassava brown streak virus (UCBSV) infection (3.2%). Of the three advanced clones in the UYT, NAROCASS 1 and NAROCASS 2 had significantly lower (P < 0.05) CBSD severity, incidence, and CBSV load than MH04/0300. In the UYT, only 22% of samples tested had CBSVs, and all showed a negative result for CMBs. The low disease incidence, severity, and viral load associated with NAROCASS 1 and NAROCASS 2 is evidence of their tolerance to both CBSD and CMD. Therefore, these two cassava clones should be utilized in CBSD and CMD management in Uganda, including their utilization as progenitors in further virus resistance breeding.
Validation of KASP markers associated with cassava mosaic disease resistance, storage root dry matter and provitamin A carotenoid contents in Ugandan cassava germplasm
(Frontiers, 2022-11-23) Williams Esuma; Oscar Eyoo; Francisca Gwandu; Settumba Mukasa; Titus Alicai; Alfred Ozimati; Ephraim Nuwamanya; Ismail Rabbi; Robert Kawuki
Introduction: The intrinsic high heterozygosity of cassava makes conventional breeding ineffective for rapid genetic improvement. However, recent advances in next generation sequencing technologies have enabled the use of high- density markers for genome-wide association studies, aimed at identifying single nucleotide polymorphisms (SNPs) linked to major traits such as cassava mosaic disease (CMD) resistance, dry matter content (DMC) and total carotenoids content (TCC). A number of these trait-linked SNPs have been converted to Kompetitive allele-specific polymerase chain reaction (KASP) markers for downstream application of marker assisted selection. Methods: We assayed 13 KASP markers to evaluate their effectiveness in selecting for CMD, DMC and TCC in 1,677 diverse cassava genotypes representing two independent breeding populations in Uganda. Results: Five KASP markers had significant co-segregation with phenotypes; CMD resistance (2), DMC (1) and TCC (2), with each marker accounting for at least 30% of the phenotypic variation. Markers located within the chromosomal regions for which strong marker-trait association loci have been characterised (chromosome 12 markers for CMD, chromosome 1 markers for DMC and TCC) had consistently superior ability to discriminate the respective phenotypes. Discussion: The results indicate varying discriminatory abilities of the KASP markers assayed and the need for their context-based use for MAS, with PSY2_572 particularly effective in selecting for high TCC. Availing the effective KASP markers on cost-effective genotyping platforms could facilitate practical implementation of marker-assisted cassava breeding for accelerated genetic gains for CMD, DMC and provitamin A carotenoids.