Streak Disease Research Articles

Evaluation of Cassava Genotypes for Agronomic Performance, Correlation with CMD and CBSD Parameters and Stability across Alupe, Kakamega and Kibos in Western Kenya

Cassava (Manihot esculenta Crantz) production in sub-Saharan Africa (SSA) is constrained by the two biotic constraints namely, cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). The aim of this study was to evaluate elite cassava genotypes for variation in agronomical traits, correlate them to CMD and CBSD parameters and identify stable genotypes in Alupe, Kakamega and Kibos in Western Kenya. Twenty three (23) elite cassava genotypes that had shown resistance to either one or both of CMD and CBSD in Eastern Africa were evaluated. The trial was conducted using an alpha lattice balanced design with twenty three (23) genotypes, replicated three times at Alupe, Kakamega and Kibos in Western Kenya for an extended cropping cycle between 2016 and 2017. Results showed significant differences (P ≤ 0.05) between genotypes and location (or agro-ecology), but not interaction (P ≥ 0.05), for all the agronomic performance parameters evaluated. All the 23 cassava genotypes evaluated across the three locations had mean cyanide potential levels ranging from of 3.00–6.00 and were therefore, sweet and not bitter. The significant but negative relationship between CMD and CBSD incidence and severity with agronomic performance implied that their relationship was inverse. Confirmation of stability for agronomic performance was achieved through AMMI analysis, using AMMI stability value (ASV). Stable genotypes based on AMMI stability values (ASV) for fresh root yield across Alupe, Kakamega and Kibos were KBH/2002/066, Kibandameno (a local standard check), NASE-18, Kizimbani and NASE-3. These genotypes need to be further evaluated in more environments to assess their wider adaptability and stability.

Effect of Time of Harvesting and Disease Resistance in Reducing Cassava (Manihot esculenta Crantz) Yield Losses by Two Viral Diseases

Cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) are two important biotic constraints for cassava (Manihot esculenta Crantz) production in Eastern and Southern Africa. CMD causes a general decline in yield in affected plants of susceptible cassava varieties but CBSD causes rotting of edible roots.

Genetic diversity and SNP's from the chloroplast coding regions of virus-infected cassava.

Cassava is a staple food crop in sub-Saharan Africa; it is a rich source of carbohydrates and proteins which currently supports livelihoods of more than 800 million people worldwide. However, its continued production is at stake due to vector-transmitted diseases such as Cassava mosaic disease and Cassava brown streak disease. Currently, the management and control of viral diseases in cassava relies mainly on virus-resistant cultivars of cassava. Thus, the discovery of new target genes for plant virus resistance is essential for the development of more cassava varieties by conventional breeding or genetic engineering. The chloroplast is a common target for plant viruses propagation and is also a potential source for discovering new resistant genes for plant breeding. Non-infected and infected cassava leaf samples were obtained from different locations of East Africa in Tanzania, Kenya and Mozambique. RNA extraction followed by cDNA library preparation and Illumina sequencing was performed. Assembling and mapping of the reads were carried out and 33 partial chloroplast genomes were obtained. Bayesian phylogenetic analysis from 55 chloroplast protein-coding genes of a dataset with 39 taxa was performed and the single nucleotide polymorphisms for the chloroplast dataset were identified. Phylogenetic analysis revealed considerable genetic diversity present in chloroplast partial genome among cultivated cassava of East Africa. The results obtained may supplement data of previously selected resistant materials and aid breeding programs to find diversity and achieve resistance for new cassava varieties.

Genomic prediction and quantitative trait locus discovery in a cassava training population constructed from multiple breeding stages

AbstractAssembly of a training population (TP) is an important component of effective genomic selection‐based breeding programs. In this study, we examined the power of diverse germplasm assembled from two cassava (Manihot esculenta Crantz) breeding programs in Tanzania at different breeding stages to predict traits and discover quantitative trait loci (QTL). This is the first genomic selection and genome‐wide association study (GWAS) on Tanzanian cassava data. We detected QTL associated with cassava mosaic disease (CMD) resistance on chromosomes 12 and 16; QTL conferring resistance to cassava brown streak disease (CBSD) on chromosomes 9 and 11; and QTL on chromosomes 2, 3, 8, and 10 associated with resistance to CBSD for root necrosis. We detected a QTL on chromosome 4 and two QTL on chromosome 12 conferring dual resistance to CMD and CBSD. The use of clones in the same stage to construct TPs provided higher trait prediction accuracy than TPs with a mixture of clones from multiple breeding stages. Moreover, clones in the early breeding stage provided more reliable trait prediction accuracy and are better candidates for constructing a TP. Although larger TP sizes have been associated with improved accuracy, in this study, adding clones from Kibaha to those from Ukiriguru and vice versa did not improve the prediction accuracy of either population. Including the Ugandan TP in either population did not improve trait prediction accuracy. This study applied genomic prediction to understand the implications of constructing TP from clones at different breeding stages pooled from different locations on trait accuracy.

Cassava Root Necrosis Disease (CRND): A New Crop Disease Spreading in Western Democratic Republic of Congo and in Some Central African Countries

Cassava is consumed in the Democratic Republic of Congo (DRC) as a staple food for the majority of the Congolese population. This crop is used in several forms: as fufu, chikwangue and pondu; cassava leaves are the most consumed vegetable in the country.
 
 In 2002, cassava root symptoms similar to cassava brown streak disease (CBSD) were reported for the first time in western DRC. PCR assays, using primers specific to Cassava brown streak virus (CBSV), failed to detect or identify any viral pathogens in diseased cassava samples from western DRC. Therefore, next generation sequencing (NGS) techniques were used as they are able to sequence full organism genomes and are widely used for the identification of pathogens responsible for new diseases. The main objective of this study was to identify the pathogens causing root necrosis in western DRC.
 
 Whatman®FTA™ cards were used to collect 12 cassava leaf samples from plants with symptoms indicative of very severe root necrosis, as well as two asymptomatic samples. These 12 samples were sent to Australia at the University of Western Australia in Perth for next generation sequencing (NGS) using the Illumina HiSeq platform. 
 
 Additional bioinformatics tools included Geneious, CLC workbench, ParaKraken and Kaijou software for short DNA sequences. No viruses (including CBSV) were found in any of the DRC samples. These preliminary results confirm all the previous negative results obtained using PCR and CBSV primers. However, NGS analyses did reveal the presence of a number of bacterial and fungal taxa. These will require further investigation and tests such as the Koch Postulates, to establish their specific pathogenic role in cassava.
 
 This is the first scientific evidence that no currently known virus is responsible for the disease which had been referred to previously as ‘CBSD-like disease’. Consequently, the disease found in DRC cassava samples has been designated ‘Cassava Root Necrosis Disease’ or CRND.

How we’ll reengineeer crops for a changing climate

Efforts to improve the genetics of food crops are as old as agriculture. Crossbreeding plants to select for traits is nothing new, but synthetic biology techniques, including CRISPR-Cas9 and other gene-editing systems, have sped up the process and made new approaches possible. As climate change threatens the world’s food-growing systems, plant scientists, industry, and governments hope to use these powerful methods to make plants hardier and land more productive. Here are some of their targets. Resisting disease Researchers say it is not always clear how rising CO2 levels will affect the relationship between crops and disease, but changes in temperature and water availability can make plants more susceptible to disease. The genomes of many bananas and plantains share a dangerous secret that illustrates this: a virus that can cause farmers to lose their harvests. The banana streak disease, which primarily affects the leaves, is activated under stress conditions such as

Sources of black Sigatoka resistance in wild banana diploids

Abstract Black Sigatoka (black leaf streak disease) is caused by the fungus Mycosphaerella fijiensisMorelet. This phytopathogen colonizes banana leaves, resulting in reduced photosynthesis and decreased productivity. Fungicide applications are useful to control black Sigatoka; however, they increase production costs and can have adverse environmental and health impacts. The cultivation of resistant cultivars is regarded as a more economically viable option. The objective of this study was to perform diploid phenotyping in a set of wild banana accessions to identify resistant genotypes. A total of 31 accessions (30 with AA genome and one with AB genome) were phenotyped based on the presence of disease symptoms using a scoring scale. The area under the disease progress curve (AUDPC), the disease severity index (DI), and the disease severity increase index (DII) were estimated. The DII variable proved to be efficient in identifying banana accessions with black Sigatoka resistance. Likewise, the selection index for ranking accessions with moderate black Sigatoka resistance allowed us to identify those genotypes with the highest quantitative resistance. Five diploid accessions (Krasan Saichon, Zebrina, Birmanie, Nº 118, and Tuu Gia) were found to be resistant to this fungal disease; eight accessions (PA Rayong, Pisang Cici, Malaccensis 1, 028003- 01, Microcarpa, Pisang Lidi, Lilin, and Malbut) were moderately resistant.

Incidence, severity and distribution of Cassava brown streak disease in northeastern Democratic Republic of Congo.

Cassava fields were prospected from two provinces of the Democratic Republic of Congo (Ituri and Haut Uélé) to evaluate the ampleness of Cassava brown streak disease (CBSD) infection. CBSD pressure was determined by assessing the incidence, severity, whitefly abundance and distribution of the disease viruses in the surveyed provinces. A duplex RT-PCR was performed for the simultaneous detection of Ugandan Cassava brown streak virus (UCBSV) and Cassava brown streak virus (CBSV) on 56 cassava leaves sampled in the study area. Our results show a high field CBSD incidence contrasted to a low severity in both provinces. CBSD severity was similar in both provinces (mean disease severity 2). High densities of whitefly were recorded in Ituri province (10 adult whiteflies plant−1) than in Haut Uélé where density was 5 adults plant−1. However, no relation has been found between whitefly density and CBSD incidence and severity on cassava leaf, root and stems. Molecular analysis showed the incidence of single infections of UCBSV was greater than single infections of CBSV and mixed infections of UCBSV and CBSV. Disease incidence was greater in Ituri than in Haut Uélé; molecular incidence was lower than field incidence. Our results raise the need for appropriate CBSD control strategies in DRC.

Excellence in Cassava Breeding: Perspectives for the Future

Cassava (Manihot esculenta Crantz) is a major tropical crop. Regarded as an orphan crop a few decades ago, it now receives considerable attention from governments, industry and agencies investing in agricultural research. As a result, the cassava community generates vast amounts of information and develops useful technologies and products. This positions cassava as a key industrial commodity and a reliable food security staple. Significant genetic gains have been achieved through the early 2000s. Gains are particularly noticeable under better agronomic conditions, as was the case for the green revolution of cereals. However, further gains obtained in the past two decades have not been as impressive. Cassava breeding cycle is long, and its multiplication rate slow. Therefore, it takes no less than 8 years to develop a new variety. Cassava breeding is based on the use of heterozygous progenitors which has important drawbacks. One of them is the impossibility to implement conventional back-crossing. Cassava researchers have recently introgressed a single recessive trait (amylose-free starch) into elite varieties. This was unprecedented in cassava and revealed important problems incorporating single genes into elite varieties. In the absence of backcross, the process required essentially the development of new varieties, which exposed strong effects of undesirable genetic linkages. Breeding approaches to overcome the problems of introgressing single-gene traits have been developed and will be implemented to introduce resistance to cassava mosaic disease into SE Asia breeding populations. These methods will also be useful to exploit recently identified immunity to cassava brown streak disease, a serious problem currently restricted to Africa. Trait introgression is an important process in crop breeding and will be more important in the future as gene discovery and editing identify useful genes. This article consolidates and integrates information from cassava and other crops and proposes guidelines to maximize the returns on investments on this important commodity.

Optimal Control Model and Cost Effectiveness Analysis of Maize Streak Virus Pathogen Interaction with Pest Invasion in Maize Plant

ABSTRACT In this paper, we proposed and analyzed an optimal control deterministic model for the dynamics of Maize Streak Virus pathogen interaction with a pest invasion on Maize plant to examine the best strategy for maize streak disease elimination. The Pontryagin’s maximum principle is applied to derive and study the necessary conditions for optimal control strategies. We obtained the Hamiltonian, the adjoint variables, the characterization of the controls and the optimality system. For minimizing the spread of maize streak disease, three controls namely prevention , quarantine and chemical control were incorporated and their impacts were pictorially shown using numerical simulations. We investigated cost-effectiveness using ICER to determine the best strategy. We found that the combination of prevention and quarantine is the best effective strategies in terms of cost as well as health benefits.

Production of virus-free cassava through hot water therapy and two rounds of meristem tip culture

Cassava genetic resources are highly threatened by devastating viral diseases. It is therefore important to conserve the specifically farmer-preferred landraces/cultivars that are highly susceptible. The study assessed the efficiency of hot water therapy and meristem tip culture techniques in the elimination of cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) causal viruses. Stems of symptomatic cassava genotypes confirmed infected with cassava brown streak viruses (CBSV) and cassava mosaic viruses (CMV) were subjected to hot water therapy at varying temperatures (25°C—60°C) followed by two rounds of meristem tip culture (MTC). Data on sprouting in the screen house and response in vitro were recorded and weaned plants were indexed for CMV and CBSV. The results indicated 100% elimination of CMV and a significant reduction in the viral load of CBSV. Thus, these techniques could be integrated into the cassava conservation strategy, for sustainable management of cassava genetic resources.

Pattern of local adaptation to quantitative host resistance in a major pathogen of a perennial crop.

Understanding the mechanisms involved in pathogen adaptation to quantitative resistance in plants has a key role to play in establishing durable strategies for resistance deployment, especially in perennial crops. The erosion of quantitative resistance has been recently suspected in Cuba and the Dominican Republic for a major fungal pathogen of such a crop: Pseudocercospora fijiensis, causing black leaf streak disease on banana. This study set out to test whether such erosion has resulted from an adaptation of P. fijiensis populations, and to determine whether or not the adaptation is local. Almost 600 P. fijiensis isolates from Cuba and the Dominican Republic were sampled using a paired‐population sampling design on resistant and susceptible banana varieties. A low genetic structure of the P. fijiensis populations was detected in each country using 16 microsatellite markers. Cross‐inoculation experiments using isolates from susceptible and resistant cultivars were carried out, measuring a quantitative trait (the diseased leaf area) related to pathogen fitness on three varieties. A further analysis based on those data suggested the existence of a local pattern of adaptation to resistant cultivars in both of the study countries, due to the existence of specific (or genotype by genotype) host–pathogen interactions. However, neither cost nor benefit effects for adapted populations were found on the widely used “Cavendish” banana group. These results highlight the need to study specific host–pathogen interactions and pathogen adaptation on a wide range of quantitative resistance phenotypes in banana, in order to develop durable strategies for resistance deployment.

First Report of Banana Streak Virus Infecting Bananas (Musa spp.) in Georgia, U.S.A.

Banana streak virus (BSV) is a badnavirus containing a circular dsDNA genome of 7.4 kb that causes a viral leaf streak disease of banana (Musa spp.) worldwide (Dallot et al. 2001). On bananas, typical symptoms of BSV include broken or continuous chlorotic streaks or spindle-shaped patterns that are first chlorotic, become increasingly dark in color, and subsequently result in black streaking in older leaves (Dallot et al. 2001). In the summer of 2019, six symptomatic leaves from three different plants were collected from the University of Georgia Banana Research Plot, Tifton, GA. The cultivar is ‘Pisang Awak’, and it belongs to the tetraploid AABB genome group. Initial identification was performed by assessing disease symptoms including chlorotic streaks on leaves that became brown and black chlorotic streaks later, resembling those of banana streak disease (Lockhart 1986). BSV was verified via molecular and serological tests. Genomic DNA from leaf tissue of three different symptomatic plants and two healthy plants was extracted using a DNeasy Plant Mini Kit (Qiagen, Valencia, CA). Samples were tested for the presence of BSV by two separate PCR amplification methods. One was targeting the aspartic protease (AP) and reverse transcription (RT) regions of ORF3 using primer pair BSV 4673 (5′-GGAATGAAAGAGCAGGCC-3′) and BSV 5317 (5′-AGTCATTGGGTYCAACCTCTGTCCC-3′) with an amplicon size of 644 bp (Manoranjitham et al. 2012). Another PCR analysis was targeting the coat protein (CP) region of ORF3 with primer pair BSV 156 (5′-TTACCTCCAGCACAAAGTCG-3′) and BSV 962 (5′-TTCTCCACAGGCATAACACC-3′) designed in this study with a product size of 806 bp. Both PCR reactions for all six symptomatic samples produced the expected sizes of the fragments for BSV; however, two samples from the healthy plants did not produce any bands. The amplified products were then sequenced and subjected to BLAST analysis for further identification. Sequence analysis revealed that the obtained partial sequence of the AP and RT region (MN567071) shared 100% identity to corresponding sequences from BSV OL virus isolate BSOLV-IN2 (accession no. JQ409540). Furthermore, the obtained CP gene sequence (MN567072) also showed 100% identity with BSV isolate BSOLV-IN2. Samples were also tested for the presence of BSV by real-time PCR with primers BSV 1075 (5′-CACATTGACGGAAAGGACAACG-3′) and BSV 1198 (5′-TGTGAAATACCTCCTCCACTGC-3′) targeting the RNase H gene (Delanoy et al. 2003), and the results confirmed its identity as BSV. In addition to the molecular tests, a DAS-ELISA test was carried out on the remaining symptomatic leaf tissues for further confirmation of BSV according to the manufacturer’s protocol (Nano Diagnostics, Fayetteville, AR). All three samples tested by ELISA were positive for BSV. To the best of our knowledge, this is the first report of BSV infecting Musa spp. in Georgia. This virus could pose an imminent threat to the newly growing banana industry in this area if it spread in banana fields under conditions in Georgia. Our findings will be helpful for banana growers in Georgia by taking appropriate control strategies to combat this viral disease. Further research is needed to elucidate epidemiology, symptomatology, vector transmission, and crop losses due to BSV in Georgia and the United States.

Expansion of the cassava brown streak pandemic in Uganda revealed by annual field survey data for 2004 to 2017

Cassava brown streak disease (CBSD) is currently the most devastating cassava disease in eastern, central and southern Africa affecting a staple crop for over 700 million people on the continent. A major outbreak of CBSD in 2004 near Kampala rapidly spread across Uganda. In the following years, similar CBSD outbreaks were noted in countries across eastern and central Africa, and now the disease poses a threat to West Africa including Nigeria - the biggest cassava producer in the world. A comprehensive dataset with 7,627 locations, annually and consistently sampled between 2004 and 2017 was collated from historic paper and electronic records stored in Uganda. The survey comprises multiple variables including data for incidence and symptom severity of CBSD and abundance of the whitefly vector (Bemisia tabaci). This dataset provides a unique basis to characterize the epidemiology and dynamics of CBSD spread in order to inform disease surveillance and management. We also describe methods used to integrate and verify extensive field records for surveys typical of emerging epidemics in subsistence crops.

Yield and Fruit Quality Traits of Two Plantain Cultivars Grown at Two Locations in Puerto Rico under Black Leaf Streak Disease Pressure

Plantain (Musa balbisiana AAB) is a tropical rhizomatous perennial plant in the genus Musa spp., closely related to banana (Musa acuminata AAA). It is an important cash crop and staple for inhabitants in many parts of the world, including various ethnic groups in the United States. Black leaf streak disease (BLSD) or black sigatoka, caused by Pseudocercospora fijiensis (formerly Mycosphaerella fijiensis), is responsible for significant losses of this crop due to the high susceptibility of the most economically important cultivars. BLSD does not immediately kill plantain plants, but it causes severe leaf necrosis, which results in reduced photosynthetic area, thereby adversely impacting bunch weight and fruit production. Without cultural and chemical control, yields can be reduced by 20% to 80%, depending on severity. This study evaluated a BLSD-resistant cultivar, FHIA-21, against Maricongo, a standard commercial cultivar with no BLSD tolerance, at two locations in Puerto Rico on Ultisol (Corozal site) and Oxisol (Isabela site) soils. Total number of fruit and bunch yield were significantly higher at Isabela, with BLSD severity being significantly lower at this location. Average fruit production of ‘FHIA-21’ was significantly higher than that of ‘Maricongo’ at both locations, with fruit yields of 122,522 and 99,948 fruit/ha at Isabela and Corozal, respectively. Overall, fruit of ‘FHIA-21’ were significantly longer and had greater diameters than those of ‘Maricongo’. At Isabela, the mean bunch fruit weight was significantly higher for ‘FHIA-21’, but both cultivars exceeded the minimum local marketable fruit weight criterion of 270 g. At both locations, the numbers of functional leaves present at flowering and at harvest were significantly higher for ‘FHIA-21’ than for ‘Maricongo’, indicating more availability of photosynthetic area for ‘FHIA-21’ during the fruit-filling period. There were no significant differences between cultivars regarding the concentration of starch and soluble sugars for green fruit. Regarding ripe fruit, ‘FHIA-21’ had a significantly higher concentration of soluble sugars and less starch. In this study, ‘FHIA-21’ had good resistance against BLSD and, if accepted by consumers, is a viable alternative to current commercial cultivars. We also conclude from this study that the expression of the Banana streak virus (BSV) in planting material of this cultivar remains an unknown threat in yield decline of ‘FHIA-21’.

Historical Introgressions from a Wild Relative of Modern Cassava Improved Important Traits and May Be Under Balancing Selection.

Introgression of alleles from wild relatives has often been adaptive in plant breeding. However, the significance of historical hybridization events in modern breeding is often not clear. Cassava (Manihot esculenta) is among the most important staple foods in the world, sustaining hundreds of millions of people in the tropics, especially in sub-Saharan Africa. Widespread genotyping makes cassava a model for clonally propagated root and tuber crops in the developing world, and provides an opportunity to study the modern benefits and consequences of historical introgression. We detected large introgressed Manihot glaziovii genome-segments in a collection of 2742 modern cassava landraces and elite germplasm, the legacy of a 1930s era breeding to combat disease epidemics. African landraces and improved varieties were, on average, 3.8% (max 13.6%) introgressed. Introgressions accounted for a significant (mean 20%, max 56%) portion of the heritability of tested traits. M. glaziovii alleles on the distal 10 Mb of chr. 1 increased dry matter and root number. On chr. 4, introgressions in a 20 Mb region improved harvest index and brown streak disease tolerance. We observed the introgression frequency on chr. 1 double over three cycles of selection, and that later stage trials selectively excluded homozygotes from consideration as varieties. This indicates a heterozygous advantage of introgressions. However, we also found that maintaining large recombination-suppressed introgressions in the heterozygous state allowed the accumulation of deleterious mutations. We conclude that targeted recombination of introgressions would increase the efficiency of cassava breeding by allowing simultaneous fixation of beneficial alleles and purging of genetic load.

Alternative Approaches for Assessing Cassava Brown Streak Root Necrosis to Guide Resistance Breeding and Selection.

Cassava brown streak disease (CBSD) caused by the rapidly evolving cassava brown streak viruses (CBSVs), causes immense yield losses to the cassava value chain in eastern and southern Africa. Western Africa, another region that heavily depends on cassava is under eminent threat from CBSD. Resistance breeding is the best practical solution. However, complexities associated with CBSD resistance screening i.e., variable root sampling units, limit systematic attainment of genetic progress. Accordingly, we compared efficiency of five CBSD root necrosis assessment methods to guide selection: cassava brown streak disease root incidence (CBSDRi), cassava brown streak disease root severity (CBSDRs), cassava brown streak disease root severity computed as harmonic mean (CBSD-Harmonic), proportion-based root necrosis index (CBSD-proportion), and standardized root necrosis index (CBSD-standardized). The indexes (CBSD-proportion and CBSD-standardized) correct for variable sample size. We analyzed CBSD root necrosis data of 256 clones evaluated across 12 environments. Higher and variable standard errors were associated with root severity score 1 (no CBSD root necrosis). Lowest and highest plot-based heritability were respectively registered for CBSD-standardized (0.22) and CBSD-proportion (0.71). CBSDRs was only positively correlated with CBSDRi (r = 0.92) and CBSD-Harmonic (r = 0.97). Using best linear unbiased predictions (BLUPs), we ranked the top 15 CBSD resistant clones; only one clone (UG130014) featured in all the five assessment methods; two clones (UG130006 and UG120156) featured in four (CBSD-Harmonic, CBSDRi, CBSDRs, and CBSD-standardized); and five clones (UG120180, UG120063, UG130002, UG130033, and UG120183) featured in three methods (CBSD-Harmonic, CBSDRi, and CBSDRs). Influence of sample size was also quantified by sub-setting and analyzing CBSDRs data to have plots with at least 40 or 30 roots. Data stabilization was evident in plots with 30 roots. The significant influence of root sample sizes on overall ranking of clones, justifies the use of CBSD root necrosis indexes in early selection stages i.e., seedling and/or clonal trials, that are often characterized by high variations in roots assessed per plot. It is expected that this information will provide a foundation for harmonizing and/or optimizing on-going and future CBSD resistance breeding efforts.

Genome Resource of Barley Bacterial Blight and Leaf Streak Pathogen Xanthomonas translucens pv. translucens strain UPB886.

Xanthomonas translucens pv. translucens causes bacterial leaf streak and bacterial blight diseases of barley. This pathogen limits barley production globally but remains understudied, with limited genomic resources. To better understand the biology of this X. translucens subgroup, we sequenced the complete genome of the X. translucens pv. translucens strain UPB886.

Zinc binding proteome of a phytopathogen Xanthomonas translucens pv. undulosa.

Xanthomonas translucens pv. undulosa (Xtu) is a proteobacteria which causes bacterial leaf streak (BLS) or bacterial chaff disease in wheat and barley. The constant competition for zinc (Zn) metal nutrients contributes significantly in plant–pathogen interactions. In this study, we have employed a systematic in silico approach to study the Zn-binding proteins of Xtu. From the whole proteome of Xtu, we have identified approximately 7.9% of proteins having Zn-binding sequence and structural motifs. Further, 115 proteins were found homologous to plant–pathogen interaction database. Among these 115 proteins, 11 were predicted as putative secretory proteins. The functional diversity in Zn-binding proteins was revealed by functional domain, gene ontology and subcellular localization analysis. The roles of Zn-binding proteins were found to be varied in the range from metabolism, proteolysis, protein biosynthesis, transport, cell signalling, protein folding, transcription regulation, DNA repair, response to oxidative stress, RNA processing, antimicrobial resistance, DNA replication and DNA integration. This study provides preliminary information on putative Zn-binding proteins of Xtu which may further help in designing new metal-based antimicrobial agents for controlling BLS and bacterial chaff infections on staple crops.

Diversity and Phylogenetic Relationships of Full Genome Sequences of Cassava Brown Streak Viruses in Kenya

Cassava brown streak disease is caused by cassava brown streak virus (CBSV) and Uganda cassava brown streak virus (UCBSV). Many of the CBSV and UCBSV diversity studies utilize partial coat protein sequences due to the unavailability of representative full genome sequences. Hence, there is little information on the diversity of cassava brown streak viruses in the rest of the genomes of the two species that are present in the farmers’ fields. The aim of this study was to determine Kenyan full CBSV and UCBSV genomes, and their sequence diversity and phylogenetic relationships within various genome and genome segments. Twenty four CBSVs positive samples tested by RT PCR from major cassava producing regions in Kenya were sequenced using Illumina MiSeq. Quality assessment of the output reads was done using the CLC Genomics 5.5.1 software programs. Genome assembly was done by de novo and reference guided assembly. Nucleotide sequence similarity of CBSV and UCBSV was determined. Phylogenetic relationships between CBSV and UCBSV were determined by performing the neighbour-joining analysis using MEGA 6.0 software. Six CBSV and 9 UCBSV genomes were generated from this study. The coat protein of the CBSV sequences had nucleotide sequence similarity of 92-100% while P1 and P3 gene had 75-100% and 76-100%, respectively. The coat protein of the UCBSV sequences had nucleotide sequence similarity of 91-99%. P1 and P3 gene had 83-100% and 86-99%, respectively. The phylogenetic analysis of full genomes revealed two distinct clusters one for UCBSV and another cluster for CBSV. Individual gene segments phylogenetic tree resembled that of the whole genome by clustering the nucleotide sequences into two clusters, one belonging to UCBSV and the other CBSV. The study revealed an average genome nucleotide diversity of 21.5% and 15.8% in CBSV and UCBSV respectively. A vast genetic diversity observed in CBSV and UCBSV in this study portends a lot of challenges in developing molecular diagnostic techniques as well as control strategies against the viruses.