Cassava Brown Streak Disease Root Research Articles

Genetic analysis of cassava brown streak disease root necrosis using image analysis and genome-wide association studies.

Cassava brown streak disease (CBSD) poses a substantial threat to food security. To address this challenge, we used PlantCV to extract CBSD root necrosis image traits from 320 clones, with an aim of identifying genomic regions through genome-wide association studies (GWAS) and candidate genes. Results revealed strong correlations among certain root necrosis image traits, such as necrotic area fraction and necrotic width fraction, as well as between the convex hull area of root necrosis and the percentage of necrosis. Low correlations were observed between CBSD scores obtained from the 1-5 scoring method and all root necrosis traits. Broad-sense heritability estimates of root necrosis image traits ranged from low to moderate, with the highest estimate of 0.42 observed for the percentage of necrosis, while narrow-sense heritability consistently remained low, ranging from 0.03 to 0.22. Leveraging data from 30,750 SNPs obtained through DArT genotyping, eight SNPs on chromosomes 1, 7, and 11 were identified and associated with both the ellipse eccentricity of root necrosis and the percentage of necrosis through GWAS. Candidate gene analysis in the 172.2kb region on the chromosome 1 revealed 24 potential genes with diverse functions, including ubiquitin-protein ligase, DNA-binding transcription factors, and RNA metabolism protein, among others. Despite our initial expectation that image analysis objectivity would yield better heritability estimates and stronger genomic associations than the 1-5 scoring method, the results were unexpectedly lower. Further research is needed to comprehensively understand the genetic basis of these traits and their relevance to cassava breeding and disease management.

Epidemic Pressure of Cassava Mosaic and Brown Streak Diseases on Ten Exotic Cassava (Manihot esculenta Crantz) Cultivars in Kisangani, DRC

The crucial obstacle to cassava production in most of African countries is the diseases and pests. The present study assessed in field the epidemic pressure of Cassava mosaic disease (CMD) and Cassava brown streak disease (CBSD) on 10 exotic cassava genotypes in Kisangani. To assess the disease impact, trials were established in two sites in Kisangani, Tshopo Province in DRC. The experiment was laid out in randomized completed block design and thrice replicated. Sixty stem cuttings per variety were planted in a plot of 7 rows each measuring 25 m long. Results showed a relatively important CBSD pressure on all the ten exotic cassava genotypes tested (incidence close 60%, severity score 2 and 3.5 whiteflies/plant) and low CMD pressure (incidence 3.3%, severity score 2 and 3.5 whiteflies/plant). CMD remained relatively negligible depending on low symptom manifestation of the tested genotypes. Whitefly population varied according to the genotype and the crop age. The most abundant population was recorded on cultivar ‘Mayombe’ (17 whiteflies/plant). A negative relationship was statistically established between the abundance of whiteflies and the incidence and severity as well as for CBSD and for CMD. The production in terms of percentage of marketable tubers was (74.9%) for cultivar ‘Mayombe’, (70.3%) for ‘Obama 1’, (69.9%) for ‘Obama 2’ and (65.3%) for ‘Ngandajika’. CBSD resulted in variable yield loss on all cultivars tested. The cultivar ‘Butamu’ (85%) recorded the highest loss rate, followed by the cultivar ‘Mvuama’ (70.8%) and ‘Muzuri’ (64.3%). The yield in cassava tubers was destroyed (˂ 5 t/ha) by large necrotic spots of the brown streak in the pulp. This loss is due to the depressive of viral pandemia pressure on the output of ten exotic cassava cultivars studied in Kisangani. Our study highlighted that the best moment of harvesting cassava in Kisangani is 9 MAP, this moment would be ideal to minimize harvesting losses due to CBSD root necrosis.

Cassava Brown Streak Disease Response and Association With Agronomic Traits in Elite Nigerian Cassava Cultivars.

Cassava mosaic geminiviruses (CMGs) and cassava brown streak viruses (CBSVs) cause the highest yield losses in cassava production in Africa. In particular, cassava brown streak disease (CBSD) is and continues to be a significant constraint to optimal cassava production in Eastern and Southern Africa. While CBSD has not been reported in West Africa, its recent rapid spread and damage to cassava productivity in Eastern, and Southern Africa is alarming. The aim of this study was to evaluate Nigerian cassava genotypes in order to determine their responses to CBSD, in the event that it invades Nigeria, the world’s largest cassava producer. The study gathered information on whether useful CBSD resistance alleles are present in the elite Nigerian cassava accessions. A total of 1,980 full-sib cassava seedlings from 106 families were assessed in the field at the seedling stage for a year. A subset of 569 clones were selected and assessed for another year at the clonal stage in Namulonge, central Uganda, a known hotspot for CBSD screening. Results indicated that foliar and root incidences and severities varied significantly (p ≤ 0.01, p ≤ 0.001) except for CBSD foliar incidence at 6 months (CBSD6i). Highest and lowest plot-based heritability estimates for CBSD were registered for CBSD root severity (CBSDrs) (0.71) and CBSD6i (0.5). Positive and highly significant correlations were noted between CBSD root incidence (CBSDri) and CBSDrs (r = 0.90***). Significant positive correlations were also noted between CBSD foliar severity at 3 months (CBSD3s) and CBSD foliar incidence at 6 months (CBSD6i) (r = 0.77***), CBSD3s and CBSDrs (r = 0.35***). Fresh root weight (FreshRW) negatively correlated with CBSDri and CBSDrs, respectively (r = −0.21*** and r = −0.22***). Similarly, CBSD3s correlated negatively with cassava mosaic disease severity at 3 (CMD3s) and 6 months (CMD6s), respectively (r = −0.25*** and r = −0.21***). Fifteen clones were selected using a non-weighted summation selection index for further screening. In conclusion, results revealed that the elite Nigerian accessions exhibited significant susceptibility to CBSD within 2 years of evaluation period. It is expected that this information will aid future breeding decisions for the improvement of CBSD resistance among the Nigerian cassava varieties.

Outlook of Cassava Brown Streak Disease Assessment: Perspectives of the Screening Methods of Breeders and Pathologists.

Cassava production and productivity in Eastern, Central, and Southern Africa are ravaged by cassava brown streak disease (CBSD), causing yield losses of up to 100% when susceptible varieties are grown. Efforts to develop CBSD-resistant clones are underway. However, the methods for screening CBSD resistance currently vary between breeders and pathologists, with the limited empirical data to support their choices. In this study, we used the empirical CBSD foliar and root necrosis data from two breeding populations, termed cycle zero (C0) and cycle one (C1), to assess and compare the effectiveness of the CBSD screening methods of breeders vs. pathologists. On the one hand, the estimates of broad-sense heritability (H2) for the CBSD root necrosis assessment of breeder ranged from 0.15 to 0.87, while for the assessment method of pathologists, H2 varied from 0.00 to 0.71 in C0 clones. On the other hand, the marker-based heritability estimates (h2) for C0 ranged from 0.00 to 0.70 for the assessment method of breeders and from 0.00 to 0.63 for the assessment method of pathologists. For cycle one (C1) population, where both foliar and root necrosis data were analyzed for clones assessed at clonal evaluation trials (CETs) and advanced yield trials (AYTs), H2 varied from 0.10 to 0.59 for the assessment method of breeders, while the H2 values ranged from 0.09 to 0.35 for the CBSD computation method of pathologists. In general, higher correlations were recorded for foliar severity from the assessment method of breeders (r = 0.4, p ≤ 0.01 for CBSD3s and r = 0.37, p ≤ 0.01 for CBSD6s) in C1 clones evaluated at both clonal and advanced breeding stages than from the approach of pathologists. Ranking of top 10 C1 clones by their indexed best linear unbiased predictors (BLUPs) for CBSD foliar and root necrosis showed four overlapping clones between clonal and advanced selection stages for the method of breeders; meanwhile, only a clone featured in both clonal and advanced selection stages from the CBSD assessment method of pathologists. Overall, the CBSD assessment method of breeders was more effective than the assessment method of pathologists, and thus, it justifies its continued use in CBSD resistance breeding.

Genetic Gains for Yield and Virus Disease Resistance of Cassava Varieties Developed Over the Last Eight Decades in Uganda.

Achieving food security for an ever-increasing human population requires faster development of improved varieties. To this end, assessment of genetic gain for key traits is important to inform breeding processes. Despite the improvements made to increase production and productivity of cassava in Uganda at research level, there has been limited effort to quantify associated genetic gains. Accordingly, a study was conducted in Uganda to assess whether or not genetic improvement was evident in selected cassava traits using cassava varieties that were released from 1940 to 2019. Thirty-two varieties developed during this period, were evaluated simultaneously in three major cassava production zones; central (Namulonge), eastern (Serere), and northern (Loro). Best linear unbiased predictors (BLUPs) of the genotypic value for each clone were obtained across environments and regressed on order of release year to estimate annual genetic gains. We observed that genetic trends were mostly quadratic. On average, cassava mosaic disease (CMD) resistance increased by 1.9% per year, while annual genetic improvements in harvest index (0.0%) and fresh root yield (−5 kg per ha or −0.03% per ha) were non-substantial. For cassava brown streak disease (CBSD) resistance breeding which was only initiated in 2003, average annual genetic gains for CBSD foliar and CBSD root necrosis resistances were 2.3% and 1.5%, respectively. It’s evident that cassava breeding has largely focused on protecting yield against diseases. This underpins the need for simultaneous improvement of cassava for disease resistance and high yield for the crop to meet its current and futuristic demands for food and industry.

Evaluation of Newly Released Cassava Varieties for Yield Performance, Reactions to Cassava Diseases and Farmers’ Preference in Adjumani District of Uganda

Cassava viral diseases particularly cassava brown streak disease (CBSD) and cassava mosaic disease (CMD) have put pressure on cassava breeders to develop varieties that are resistant/tolerant to them. Several cassava varieties have been rolled out to farmers with the latest being NAROCASS series that are tolerant to these diseases. The yield performance of these new varieties have not been documented in some sub zones like Adjumani district that falls within a major West Nile agro-ecology of Uganda. Therefore this study sought to established yield performances of, reactions to major diseases, and farmers’ preference to these newly released cassava varieties in Adjumani. Results showed significant (P ≤ 0.05) differences among cassava varieties and experimental sites for all the parameters evaluated. Average yield performance by varieties were in the order of a local cassava—Alifasia (8.7 t/Ha) lowest, NAROCASS 2 (18.55 t/Ha), NASE 14 (33.97 t/Ha), NASE 19 (41.26 t/Ha), and NAROCASS 1 (41.71 t/Ha) highest. CMD foliar symptom was present at all sites on a local cassava—Alifasia, and on NAROCASS 1 in Ayiri parish, Ukusijoni sub-county. CBSD foliar symptoms were observed on off-types (TME 14) in the plot of NASE 14 in Miniki Parish only whereas CBSD root necrosis was observed at all sites on the local cassava—Alifasia, and on NASE 19 in Maaji parish, Ukusijoni sub-county. Cassava root rot disease was localised in Ukusijoni sub-county only. Farmers’ preferences to these newly released cassava varieties were in the order of NASE 19 (40.96%), NAROCASS 1 (24.86%), NAROCASS 2 (15.82.28%), NASE 14 (15.54%), and a Local cassava—Alifasia (2.83%). Result from this study strengthens the information gap in the breeding process towards developing a cassava variety with farmer-preferred attributes, and can also inform the utilisation of these improved cassava varieties in Adjumani district.

Adaptability and Phenotypic Stability of Resistance to Two Viral Diseases and Yield Traits in Cassava

Cassava productivity is hampered by pests and diseases including cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). The main objective of this study was to identify stable superior genotypes that combine disease resistance and high yield. Sixteen cassava genotypes were planted in a randomized complete block design with three replications for six planting seasons (years) at five sites in Tanzania. The genotypes were assessed using the additive main effect and multiplicative interaction (AMMI) analysis, and highly significant (P by-environment (G*E) interactions were observed for all traits studied. Percent sum of squares (SS) due to environment (12.66% - 85.23%) was the highest followed by G*E (14.12% - 39.56%) for CMD foliar symptoms, root weight and dry matter. On the other hand, % SS due to genotype (52.14% - 69.14%) was highest followed by G*E (26.14% - 35.91%) for CBSD foliar and root symptoms indicating that the environment and G*E greatly influenced trait expression. The most stable genotypes which combined disease resistance and high yield were NDL 2003/31 and NDL 2003/111. The findings of this study will give impetus for the release of new cassava varieties that are not only high yielding but are also dually resistant to both CMD and CBSD in different locations and sites.

Genetic analysis and QTL mapping for multiple biotic stress resistance in cassava.

In Sub-Saharan Africa cassava (Manihot esculenta Crantz) is one of the most important food crops where more than 40% of the population relies on it as their staple carbohydrate source. Biotic constraints such as viral diseases, mainly Cassava Mosaic Disease (CMD) and Cassava Brown Streak Disease (CBSD), and arthropod pests, particularly Cassava Green Mite (CGM), are major constraints to the realization of cassava’s full production potential in Africa. To address these problems, we aimed to map the quantitative trait loci (QTL) associated with resistance to CBSD foliar and root necrosis symptoms, foliar CMD and CGM symptoms in a full-sib mapping population derived from the genotypes AR40-6 and Albert. A high-density linkage map was constructed with 2,125 SNP markers using a genotyping-by-sequencing approach. For phenotyping, clonal evaluation trials were conducted with 120 F1 individuals for two consecutive field seasons using an alpha-lattice design at Chambezi and Naliendele, Tanzania. Previously identified QTL for resistance to CBSD foliar symptoms were corroborated, and a new putative QTL for CBSD root necrosis identified (qCBSDRNc14AR) from AR40-6. Two QTL were identified within the region of the previously recognized CMD2 locus from this population in which both parents are thought to possess the CMD2 locus. Interestingly, a minor but consistent QTL, qCGM18AR, for CGM resistance at 3 months after planting stage was also detected and co-localized with a previously identified SSR marker, NS346, linked with CGM resistance. Markers underlying these QTL may be used to increase efficiencies in cassava breeding programs.

Optimum Time for Harvesting Cassava Tubers to Reduce Losses Due to Cassava Brown Streak Disease in Northeastern DRC

The present study aimed to determine the appropriate time to harvest cassava tuberous root which minimize the losses due to cassava brown streak disease (CBSD) in the region of Yangambi, DRC. To achieve the aim of the study, 38 cassava cultivars were evaluated in Yangambi INERA’s Research Center for CBSD in the roots at harvest time between 9 and 13 months after planting (MAP). All the 38 cultivars tested showed CBSD root necrosis symptoms. Foliar symptoms occurred on 37.6% of the evaluated cultivars while CBSD root necrosis varied significantly among cultivars (7.0% to 82.5%) depending on susceptibility and the age of plant. This indicates the differential response of the cultivars to CBSD infection. 
 
 Whitefly population density decreased with age of cassava, it was of 3 whiteflies per plant (9 MAP) to 1 (10 MAP). We noticed that in older plants, whitefly population decreased from 1 at 11 MAP to none at 13 MAP. Although, some cultivars did not show CBSD symptoms up to 12 MAP, they were not necessarily less attractive to whitefly. Negative relationship (r = -0.08 and r = -0.25) has been found between whitefly number and foliar symptom severity or between whitefly and tuber necrosis severity. Beyond 12 MAP, CBSD necrosis (severity score 4) was present in the tubers of 3 cultivars (EUR/2011/0148, Yafelamonene and Ybi/2011/258). Our study shows that in order to mitigate the losses due to CBSD necrosis, the optimum harvesting time for cassava tubers in Yangambi is 9 MAP.

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.

Assessing the Degeneration of Cassava Under High-Virus Inoculum Conditions in Coastal Tanzania.

Cassava brown streak disease (CBSD), caused by cassava brown streak ipomoviruses (CBSIs), has become the most debilitating biotic stress to cassava production in East and Central Africa. Lack of CBSD-resistant varieties has necessitated the search for alternative control measures. Most smallholder farmers reuse stems from previous crops for planting in the new season. Recycling planting material in this way can lead to “degeneration” owing to the compounding effects of disease. In this study, degeneration was defined as the increase in CBSD incidence and reduction in marketable root yield over time. An experiment was established to study the rates of degeneration in selected cassava varieties Chereko, KBH2002_135, Kipusa, Kizimbani, and Mkuranga1 and cultivars Kiroba and Kikombe under high-CBSD inoculum conditions in Bagamoyo, Tanzania from 2013 to 2017. The experiment was replicated across two seasons: the first planted during the long rains (Masika) between March and June and the second planted during the short rains (Vuli) between October and December. Mean abundance of the whitefly vector (Bemisia tabaci) was much greater during the Vuli season (>19 insects per plant) than the Masika season (<2 insects per plant). CBSD shoot symptoms occurred naturally and were observed only on Kikombe, Kiroba, and Kipusa. New materials had overall lower CBSD shoot incidences (1.5%) compared with recycled materials (6.9%) in Masika, although no significant differences were obvious in Vuli. However, Masika (8.7%) had an overall lower CBSD shoot incidence than Vuli (16.5%) in the varieties that had shoot symptoms. CBSD root incidences were higher in Vuli (10.3%) thanMasika (4.4%), and root yields in Masika (29.4 t/ha) were significantly greater than those in Vuli (22.5 t/ha). The highest percentage of roots rendered unusable owing to CBSD was observed in Vuli. There was significantly higher unusable root incidence in recycled materials (3.7%) than in new materials (1.4%) in Masika but not in Vuli. Overall root yield was similar between recycled and new materials in either season. Significant reductions in root yield over the course of the experiment were observed both in Masika and Vuli, whereas changes in marketable yield were significant only in Masika. Differences in the response of varieties to degeneration led to the identification of four degeneration patterns, namely “strong,” “moderate,” “mild,” and “delayed” degeneration. The strongest effects of degeneration were most obvious in the susceptible cultivar (Kikombe), which also had the lowest marketable yield in either season. Seasonal differences were a key driver of degeneration, because its effects were much greater in Vuli than Masika. To the best of our knowledge, this work reports the first study of degeneration caused by cassava viruses.

Genetic Variation and Trait Correlations in an East African Cassava Breeding Population for Genomic Selection.

Cassava (Manihot esculenta Crantz) is a major source of dietary carbohydrates for >700 million people globally. However, its long breeding cycle has slowed the rate of genetic gain for target traits. This study aimed to asses genetic variation, the level of inbreeding, and trait correlations in genomic selection breeding cycles. We used phenotypic and genotypic data from the National Crops Resources Research Institute (NaCRRI) foundation population (Cycle 0, C0) and the progeny (Cycle 1, C1) derived from crosses of 100 selected C0 clones as progenitors, both to evaluate and optimize genomic selection. The highest broad-sense heritability (H2 = 0.95) and narrow-sense heritability (h2 = 0.81) were recorded for cassava mosaic disease severity and the lowest for root weight per plot (H2 = 0.06 and h2 = 0.00). We observed the highest genetic correlation (rg= 0.80) between cassava brown streak disease root incidence measured at seedling and clonal stages of evaluation, suggesting the usefulness of seedling data in predicting clonal performance for cassava brown streak root necrosis. Similarly, high genetic correlations were observed between cassava brown streak disease severity (rg= 0.83) scored at 3 and 6 mo after planting (MAP) and cassava mosaic disease, scored at 3 and 6 MAP (rg= 0.95), indicating that data obtained on these two diseases at 6 MAP would suffice. Population differentiation between C0 and C1 was not well defined, implying that the 100 selected progenitors of C1 captured the diversity in the C0. Overall, genetic gain for most traits were observed from C0 to C1.

Varietal response of cassava root yield components and root necrosis from cassava Brown streak disease to time of harvesting in Uganda

Cassava brown streak disease (CBSD) is the most important biotic constraint threatening cassava (Manihot esculenta Crantz) production in eastern and southern Africa, and the food and income security of millions of rural farmers. With no tangible solution in view, farmers cope with the disease by harvesting the crop early, a practice that also leads to yield losses owing to small root size. This study evaluated CBSD root necrosis (RN), the total fresh root yield (TFRY), percentage marketable fresh root yield (PMFRY) and dry matter content (DMC) of six cassava varieties (MM, 2006/90, MM, 2006/123, MM, 2006/128, MM, 2006/130, MM 96/4271, and TME14) at different times of harvesting after the recommended 12 months after planting (MAP). Trials were planted during April 2012 at Sendusu and Serere located in the Wakiso and Serere districts of Uganda, respectively. The two sites are distinct in climatic, soil and CBSD disease pressure conditions. A split-plot design was used with cassava varieties as the main plots and times of harvesting (12, 16, 20 and 24 MAP) as sub-plots. Highly significant differences (P ≤ 0.001) were detected between sites (S), varieties (V) and time of harvesting (T) for TFRY, PMFRY and RN, whereas only V effects were highly significant (P ≤ 0.001) for DMC. The V × S interactions were highly significant for TFRY, PMFRY and RN, while the V × T interactions were highly significant for PMFRY and significant (P ≤ 0.01) for TFRY and DMC. The PMFRY decreased by about 14–27% as the plants remained in the field after 12 MAP. There was a great difference among clones, depending on location. Variety MM 2006/128 performed the best, with virtually no root damage even at 24 MAP at both sites. The mean CBSD root necrosis severity score among the varieties at each site increased from 2.6 (at 12 MAP) to 3.1 (at 24 MAP) at Sendusu, and from 1.9 (at 12 MAP) to 2.4 (at 24 MAP) at Serere. However, for MM2006/128 which was the best performing variety, the root necrosis score remained about 1.0 at Sendusu and about 1.3 at Serere. Time of harvesting had no significant effect on DMC. This study showed it is possible to breed new cassava varieties that combine tolerance to CBSD with long periods of in-ground storability. Genotype and environment had a profound effect on all the traits analysed, suggesting that genotypes should be selected for specific environments and harvest times. The results indicate that some of the clones (MM, 2006/128, MM, 2006/123 and MM, 2006/130) investigated in this study will be useful in the fight against CBSD in the region especially for the mid-altitude areas, which have recently been seriously affected by the virus disease.

Training Population Optimization for Prediction of Cassava Brown Streak Disease Resistance in West African Clones.

Cassava production in the central, southern and eastern parts of Africa is under threat by cassava brown streak virus (CBSV). Yield losses of up to 100% occur in cases of severe infections of edible roots. Easy illegal movement of planting materials across African countries, and long-range movement of the virus vector (Bemisia tabaci) may facilitate spread of CBSV to West Africa. Thus, effort to pre-emptively breed for CBSD resistance in W. Africa is critical. Genomic selection (GS) has become the main approach for cassava breeding, as costs of genotyping per sample have declined. Using phenotypic and genotypic data (genotyping-by-sequencing), followed by imputation to whole genome sequence (WGS) for 922 clones from National Crops Resources Research Institute, Namulonge, Uganda as a training population (TP), we predicted CBSD symptoms for 35 genotyped W. African clones, evaluated in Uganda. The highest prediction accuracy (r = 0.44) was observed for cassava brown streak disease severity scored at three months (CBSD3s) in the W. African clones using WGS-imputed markers. Optimized TPs gave higher prediction accuracies for CBSD3s and CBSD6s than random TPs of the same size. Inclusion of CBSD QTL chromosome markers as kernels, increased prediction accuracies for CBSD3s and CBSD6s. Similarly, WGS imputation of markers increased prediction accuracies for CBSD3s and for cassava brown streak disease root severity (CBSDRs), but not for CBSD6s. Based on these results we recommend TP optimization, inclusion of CBSD QTL markers in genomic prediction models, and the use of high-density (WGS-imputed) markers for CBSD predictions across population.

Genome-wide association mapping and genomic prediction for CBSD resistance in Manihot esculenta

Cassava (Manihot esculenta Crantz) is an important security crop that faces severe yield loses due to cassava brown streak disease (CBSD). Motivated by the slow progress of conventional breeding, genetic improvement of cassava is undergoing rapid change due to the implementation of quantitative trait loci mapping, Genome-wide association mapping (GWAS), and genomic selection (GS). In this study, two breeding panels were genotyped for SNP markers using genotyping by sequencing and phenotyped for foliar and CBSD root symptoms at five locations in Uganda. Our GWAS study found two regions associated to CBSD, one on chromosome 4 which co-localizes with a Manihot glaziovii introgression segment and one on chromosome 11, which contains a cluster of nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes. We evaluated the potential of GS to improve CBSD resistance by assessing the accuracy of seven prediction models. Predictive accuracy values varied between CBSD foliar severity traits at 3 months after planting (MAP) (0.27–0.32), 6 MAP (0.40–0.42) and root severity (0.31–0.42). For all traits, Random Forest and reproducing kernel Hilbert spaces regression showed the highest predictive accuracies. Our results provide an insight into the genetics of CBSD resistance to guide CBSD marker-assisted breeding and highlight the potential of GS to improve cassava breeding.

QTL Mapping for Pest and Disease Resistance in Cassava and Coincidence of Some QTL with Introgression Regions Derived from Manihot glaziovii.

Genetic mapping of quantitative trait loci (QTL) for resistance to cassava brown streak disease (CBSD), cassava mosaic disease (CMD), and cassava green mite (CGM) was performed using an F1 cross developed between the Tanzanian landrace, Kiroba, and a breeding line, AR37-80. The population was evaluated for two consecutive years in two sites in Tanzania. A genetic linkage map was derived from 106 F1 progeny and 1,974 SNP markers and spanned 18 chromosomes covering a distance of 1,698 cM. Fifteen significant QTL were identified; two are associated with CBSD root necrosis only, and were detected on chromosomes V and XII, while seven were associated with CBSD foliar symptoms only and were detected on chromosomes IV, VI, XVII, and XVIII. QTL on chromosomes 11 and 15 were associated with both CBSD foliar and root necrosis symptoms. Two QTL were found to be associated with CMD and were detected on chromosomes XII and XIV, while two were associated with CGM and were identified on chromosomes V and X. There are large Manihot glaziovii introgression regions in Kiroba on chromosomes I, XVII, and XVIII. The introgression segments on chromosomes XVII and XVIII overlap with QTL associated with CBSD foliar symptoms. The introgression region on chromosome I is of a different haplotype to the characteristic “Amani haplotype” found in the landrace Namikonga and others, and unlike some other genotypes, Kiroba does not have a large introgression block on chromosome IV. Kiroba is closely related to a sampled Tanzanian “tree cassava.” This supports the observation that some of the QTL associated with CBSD resistance in Kiroba are different to those observed in another variety, Namikonga.

Interaction of genotype and environment effects on important traits of cassava (Manihot esculenta Crantz)

General and specific environmental adaptation of genotypes is the main goal of breeders. However, genotype-by-environment (G×E) interaction complicates the identification of genotypes for release. This study aimed at analyzing the effects of G×E interaction on the expression of important cassava traits using two multivariate analyses: additive main effects and multiplicative interaction (AMMI) and genotype stability index (GSI). Total carotene content (TCC), postharvest physiological deterioration (PPD), and reaction to viral diseases were significantly affected by G×E interaction effects. The low percent (%) variation due to genotype for cassava brown streak disease (CBSD) explained the influence of environment on CBSD expression. The % variation due to genotype for TCC was higher (96%) than variation due to environment (1.7%) and G×E interaction (2.4%) indicating a low interaction effect of environment on TCC accumulation. The % variation due to genotype was higher than % variation due to environment for all traits but CBSD root necrosis and CBSD on stems, indicating the influence of environment on the severity of the viral diseases. These findings indicate that screening for disease resistance requires multi-environment trials, whereas a single-environment trial suffices to screen for total carotene content.

Post-harvest impact of cassava brown streak disease in four countries in eastern Africa

Cassava brown streak disease (CBSD) is endemic to the coast of East Africa and the disease continues to spread to new areas in the Great Lakes region. In both these areas CBSD leaf symptoms occur at high incidences. However, it is the associated symptom of necrosis in the starch-bearing tissues that renders the root unfit for human consumption. Where root necrosis occurs, the economic viability of processing into flour is adversely affected. Surveys undertaken in Tanzania, Kenya, Uganda, and Malawi showed that CBSD leaf symptoms were present at high incidences but root necrosis incidence was lower than would be expected. It appears that a form of tolerance to CBSD occurs in which the plants are susceptible to infection by the virus but are less affected by the root symptom. Farmers practise selection for cassava varieties less prone to CBSD root necrosis leading to dependence on a decreasing number of varieties.

Genotype × environment interaction effects on early fresh storage root yield and related traits in cassava

Cassava (Manihot esculenta Crantz) is an important root crop worldwide. It exhibits substantial differential genotypic responses to varying environmental conditions, a phenomenon termed genotype×environment interaction (GEI). A significant GEI presents challenges in the selection of superior genotypes. The objective of this study was to examine the effect of genotype, environment and GEI on early fresh storage root yield (FSRY) and related traits in cassava. Accordingly, 12 cassava genotypes were evaluated in a randomised complete block design at three contrasting locations (Jinja, Nakasongola and Namulonge) in Uganda. Trials were harvested nine months after planting and the data collected were analysed using the additive main effects and multiplicative interaction (AMMI) model. The AMMI analysis of variance showed significant variation among genotypes for early FSRY and all other traits assessed. Locations were significantly different for all traits except for cassava brown streak disease root necrosis. The GEI effect was non-significant for early FSRY, but significant for other traits. For early FSRY, 48.5% of the treatment sum of squares was attributable to genotypes, 27.3% to environments, and 24.1% to GEI, indicating a predominance of genotypic variation for this trait. Predominance of genotypic variation was also observed for all the other traits. A majority of the genotypes (67%) had low interaction effects with locations for early FSRY, with Akena, CT2, CT4 and NASE14 being the most stable genotypes for the trait. Significant negative correlation was observed between cassava mosaic disease severity and early FSRY and storage root number, indicating significant negative effects of cassava mosaic disease on early FSRY and stability in cassava. The information generated will inform future selection initiatives for superior early-yielding cassava genotypes combining resistance to cassava mosaic and brown streak diseases in Uganda.

Cassava Pests and Diseases’ Prevalence and Performance as Revealed by Adaptive Trial Sites in North Western Agro-Ecological Zone of Uganda

Cassava adaptive trial was planted in ten sub counties across West Nile Agro-ecological Zone (WNAEZ) with six cassava varieties to test their performance and reactions to major pests and diseases present in the Zone. Th six cassava varieties comprised of improved (TME 14 and 204, NASE 13 and 14 and Akena – TMS I92/00067) and a local (Abiria) were selected based on their availability and preference in the region. The experiment was planted in RCBD design with three replicates. The experiment was planted in ten locations with the plot size was 6x6 metres. Results showed Cassava green mite (CGM), Cassava mosaic disease (CMD) and cassava bacterial blight (CBB) as major pest and diseases across all sites. Cassava Anthracnose (CA) and Cassava mealy bug (CM) were not present in the study sites. Cassava brown streak disease (CBSD) foliar symptoms was observed in three locations of Dranya s/c, Gimara s/c and Nyaravuru s/c on the three varieties of TME 204, TMS-I92/00067 and TME 14, whereas CBSD root necrosis was seen across all sites on TME 204, TMS-I92/00067, NASE 13, TME 14 and the Local except on NASE 14. In terms of yields, results showed that it was highest in TMS-I92/00067 (53.0 t/ha), TME 204 (46.0 t/ha), NASE 14 (39.4 t/ha), TME 14 (34.6 t/ha), NASE 13 (33.4 t/ha) and the local (22.7 t/ha) in that order. Farmers’ ranking of the studied cassava varieties in order of preference was in the order of NASE 14, TME 204, TMS-I92/00067, TME 14, NASE 13 and the Local. In conclusion, absence of both foliar and root symptoms on NASE 14 across all sites indicated that this variety is still tolerant to CBSD and can still be multiplied for production in West Nile Agro-ecological Zone.