Host range, purification, and genetic variability in Sweet potato chlorotic fleck virus

Sweet potato chlorotic fleck virus (SPCFV) has recently been classified as a putative new member of the genus Carlavirus (family Flexiviridae) on the basis of its molecular properties. In this study, SPCFV was characterized in terms of host range, physical and biological characteristics, and genetic variability. In addition to sweet potato, SPCFV infected some plant species in the families Convolvulaceae, Chenopodiaceae, and Solanaceae. Limited numbers of virus particles were observed in the assimilation parenchyma cells of infected plant tissues; some cells had a distorted and enlarged endoplasmic reticulum though without any cytoplasmic and amorphous inclusions. The normal length of SPCFV particles was determined to be approximately 800 nm. In enzyme-linked immunosorbent assays, polyclonal antibodies raised against purified SPCFV virions were able to detect the virus in infected sweet potato and indicator plant tissues. In immunoelectron microscopy, SPCFV particles were all strongly decorated when reacted with homologous antiserum. Comparison of the 3′ terminal part of the genome of a range of geographically diverse isolates revealed a high level of genetic diversity. The amino acid sequence identity in the coat protein and the nucleic acid binding protein ranged from 89 to 99.7% and from 75.9 to 99.2%, respectively. Phylogenetic analysis of both proteins showed a geographically associated clustering into two genogroups

Nematode distribution and damage to yam in central and eastern Uganda

Yams (Dioscorea spp.) are food crops of growing significance in sub Saharan Africa. Unfortunately, nematodes are major pests to their production. A study was undertaken in major yam growing areas of Uganda to investigate the association of plant parasitic nematodes with damage symptoms. Nematodes were assessed from tubers, roots and surrounding soil for seven cultivars belonging to Dioscorea alata, D. bulbisiana, D. burkilliana and D. cayenensis at harvest. Pratylenchus sudanensis was found in the greatest density and was followed byMeloidogyne spp. Higher densities of both nematodes were observed in the tubers rather than roots. Although symptoms of cracking and galling were relatively low, P. sudanensis incidence was strongly associated with cracking and Meloidogyne spp. with galling. Pratylenchus sudanensis and Meloidogyne spp. incidence their associated damage were, however, negatively correlated, suggesting inter-species competition. Principal components analysis of data suggested that differences in susceptibility to P. sudanensis occur between yam cultivars and species

DYNAMICS OF Cercospora zeina POPULATIONS IN MAIZE-BASED AGRO-ECOLOGIES OF UGANDA

Stability of pathogen populations characterised by slow temporal variation is important for durability of disease management systems in any agroecology. Temporal variation in population structure is attributed to factors related to ecology, biology and life history, and varies among organisms and ecosystems. The objective of this study was to investigate genetic variability of Cercospora zeina (previously called Cercospora zeae-maydis Type II) populations in maize ( Zea mays ) producing areas under Uganda conditions. Populations of the fungus were analysed for genetic variability using a fluorescent amplified fragment length polymorphism (AFLP) technique. Little or no genetic differentiation (\u3a6FST 0.05) was detected for populations sampled within the same year, within an agroecology. However, a weak to moderate population structure was detected between populations from different locations, within the same (\u3a6FST = 0.08) or different agroecologies (\u3a6FST = 0.09). Pair-wise comparisons using \u3a6FST gene diversity and genetic distance, showed a reduction in genetic diversity in younger populations, suggestive of minor effects of selection and genetic drift. Overall, the data suggest that during the 3 years of study the impact of selection and genetic drift on C. zeina populations in the two Ugandan agroecologies is slow, but progressive leading to homogenetity with agroecologies and differences between agroecologies.La stabilit\ue9 des populations d\u2019agents pathog\ue8nes caract\ue9ris\ue9e par une faible variation dans le temps, est importante pour la durabilit\ue9 dans les syst\ue8mes de gestion des pathologies des plantes dans n\u2019importe quelle zone agro-\ue9cologique. La variation dans le temps au sein d\u2019une population, est fonction de facteurs relatifs \ue0 l\u2019\ue9cologie, la biologie et l\u2019histoire de vie des pathog\ue8nes. Elle varie d\u2019un \ueatre vivant \ue0 un autre et d\u2019un \ue9cosyst\ue8me \ue0 un autre. L\u2019objectif de cette \ue9tude \ue9tait d\u2019\ue9valuer la variabilit\ue9 g\ue9n\ue9tique au sein des populations de Cercospora zeina (pr\ue9cedemment appel\ue9 Cercospora zeae-maydis Type II) dans les zones productrice de ma\uefs ( Zea mays ) en Ouganda. Les populations de ce champignon microscopique ont \ue9t\ue9 soumises \ue0 une \ue9tude de variabilit\ue9 g\ue9n\ue9tique gr\ue2ce \ue0 la technique du polymorphisme de longueur de fragments amplifi\ue9s (AFLP). Tr\ue8s peu ou aucune variation g\ue9n\ue9tique (\u3a6FST 0.05) n\u2019a \ue9t\ue9 observ\ue9e pour les populations \ue9chantillonn\ue9es au cours de la m\ueame ann\ue9e, dans une zone agro-\ue9cologique donn\ue9e. N\ue9anmoins, une structure populationnelle d\u2019envergure faible \ue0 mod\ue9r\ue9e a \ue9t\ue9 observ\ue9e entre les populations de diff\ue9rentes origines, (\u3a6FST = 0.08) \ue0 l\u2019int\ue9rieur d\u2019une m\ueame population ou (\u3a6FST = 0.09) entre les populations de diff\ue9rente zones agro \ue9cologique. La comparaison par paires utilisant \u3a6FST diversit\ue9 des g\ue8nes et distance g\ue9n\ue9tique, a montr\ue9 une r\ue9duction de diversit\ue9 g\ue9n\ue9tique dans les populations les plus jeunes, sugg\ue9rant ainsi un effet mineur de s\ue9lection et de d\ue9rive g\ue9n\ue9tique. Au total, les donn\ue9es collect\ue9es indiquent un faible impact de s\ue9lection et de d\ue9rive g\ue9n\ue9tique sur les populations de C. zeina dans les deux zones agro-\ue9cologiques Ougandaise durant les 3 ann\ue9es de l\u2019\ue9tude, mais cet impact est progressif et responsable de l\u2019homog\ue9n\ue9it\ue9 au sein des zones agro-\ue9cologiques et des diff\ue9rences entre les zones agro-\ue9cologiques

INHERITANCE OF ROOT DRY MATTER CONTENT IN SWEETPOTATO

There has been much emphasis on breeding for increased sweetpotato storage root yield, but less on dry matter yield, and its inheritance. High dry matter content (DMC) is associated with consumer preferences, and is important for the processing industry. This study was conducted to determine the type of gene action controlling DMC and to assess genotype by environment (G x E) interaction effect on DMC in sweetpotato. Five parental clones varying in DMC were hand-crossed in a half-diallel design to generate ten families. Ten genotypes of each family were planted in a trial at Namulonge (swamp and upland environments) and Serere in Uganda in 2009 and 2010. Highly significant (P<0.001) differences were found both between genotypes and between families for DMC. High significant general combining ability (GCA) (P<0.001) and specific combining ability (SCA) (P<0.01) were obtained, meaning that the differences among families for high DMC were due to both GCA and SCA. The relative importance of GCA and SCA was 0.59, indicating that additive gene action was slightly more predominant than non-additive gene action in predicting progeny performance for high DMC. Broad sense heritability (H) estimates for DMC were 0.70 and 0.73, respectively on genotype and family means across environments basis, suggesting that DMC was moderately influenced by the environment. Rapid selection for best genotypes would be possible, since progenies can be predicted from the phenotype of the parents. Parent SPK (GCA = 1.02) was the best combiner. The effect of location was less significant compared to seasons, suggesting the need to evaluate genotypes for several seasons, but in few locations to save resources.Plusieurs efforts ont \ue9t\ue9 fournis dans le cadre d\u2019augmenter le rendement de la patate douce, mais peu d\u2019efforts visant le rendement sec et son h\ue9ritabilit\ue9. La mati\ue8re s\ue8che est associ\ue9e aux pr\ue9f\ue9rences des consommateurs et elle est importante dans l\u2019industrie de transformation. Cette \ue9tude a \ue9t\ue9 men\ue9e dans le but de d\ue9terminer le type de l\u2019action g\ue9n\ue9tique contr\uf4lant la mati\ue8re s\ue8che, ainsi que d\u2019\ue9valuer l\u2019effet d\u2019interaction g\ue9notype x environnement sur la mati\ue8re s\ue8che sur la patate douce. Cinq diff\ue9rents parents en terme de mati\ue8re s\ue8che ont \ue9t\ue9 crois\ue9s en moiti\ue9 diall\ue8le et dix familles sont obtenues. Les semences sont plant\ue9es dans les boites en bois dans les serres \ue0 Namulonge, Uganda. Dix g\ue9notypes pour chacune des familles sont plant\ue9es dans l\u2019essai \ue0 Namulonge (environnement marrais et hautes terres) et Serere en bloques compl\ue8tement randomis\ue9es, avec deux r\ue9p\ue9titions, durant la p\ue9riode Octobre 2009-Mars 2010. Pour d\ue9terminer la mati\ue8re s\ue8che, une quantit\ue9 de 200 g pour chacune des g\ue9notypes a \ue9t\ue9 s\ue9ch\ue9e \ue0 650C jusqu\u2019\ue0 ce que le poids soit constant. Les donn\ue9es sont analys\ue9es en utilisant le logiciel Genstat. Aptitude g\ue9n\ue9rale \ue0 la combinaison (AGC) et aptitude sp\ue9cifique \ue0 la combinaison (ASC) sont calcul\ue9es selon Mod\ue8le I, M\ue9thode 4 selon la description de Griffing (1956). Hautes significative (P< 0,001) diff\ue9rences sont trouv\ue9es aussi bien entre g\ue9notypes que familles pour la mati\ue8re s\ue8che. Hautes significatives AGC (P<0,001) et ASC (P<0,01) sont trouv\ue9es, signifiant que les diff\ue9rences observ\ue9es entre les familles pour la mati\ue8re s\ue8che sont dues \ue0 la fois \ue0 AGC et ASC. L\u2019importance relative de l\u2019AGC et ASC \ue9tait 0,59, ce qui indique que l\u2019action g\ue9n\ue9tique additive \ue9tait un peu plus importante que l\u2019action g\ue9n\ue9tique non-additive en pr\ue9dicant la performance des prog\ue9nitures pour la mati\ue8re s\ue8che. L\u2019h\ue9ritabilit\ue9 en large sens (H) pour la mati\ue8re s\ue8che \ue9tait de 0,70 et 0,73 en se basant respectivement sur la moyenne du g\ue9notype et celle de la famille sur tous les environnements, sugg\ue9rant que la mati\ue8re s\ue8che \ue9tait mod\ue9r\ue9ment influenc\ue9e par l\u2019environnement. Ceci indique que la s\ue9lection rapide des g\ue9notypes serait possible, car les prog\ue9nitures peuvent \ueatre pr\ue9venues en se basant sur le ph\ue9notype des parents. Parent SPK (GCA=1,02) \ue9tait la meilleure combinant dans cette \ue9tude. L\u2019effet des locations \ue9tait moins significatif comparable aux saisons, sugg\ue9rant l\u2019importance d\u2019\ue9valuer les g\ue9notypes sur plusieurs saisons, mais dans les moins de locations dans le cadre d\u2019\ue9conomiser les ressources

Stability of sweet potato cultivars to Alternaria leaf and stem blight disease

Alternaria leaf petiole and stem blight is an economically important disease of sweet potato (Ipomoea batatus L.) in tropical and sub-tropical environments. Published research on cultivar resistance to the sweet potato disease is limited. To evaluate cultivar reaction and stability to the disease, multi-location and replicated experiments were established in 12 environments in Uganda. Disease severity (area under disease progress curves - AUDPC), and cultivar root yield were also assessed. Significant differences (P<0.001) in AUDPC were detected among cultivars. Mean AUDPC ranged from 46.3 (Araka Red) to 78.4 (New Kawogo) across locations and seasons and the genotypes Araka Red and Tanzania had the lowest disease values. The location and season effects accounted for 67.1% and 7.5% of the total variance of AUDPC recorded among cultivars. The ranking of cultivars based on predicted AUDPC from Additive Main Effect and Multiplicative Interactive model (AMMI) showed that the NASPOT 1, the susceptible check, and New Kawogo were most susceptible to the disease in 11 of the 12 environments. Low and stable disease was consistently recorded and predicted on NASPOT 3 and the landrace cultivars Tanzania, Dimbuca, and Araka Red across environments. These results suggest that landrace cultivars had relative stability to the disease and wide adaptation across environments. These results suggest that AMMI statistical model and other multivariate techniques can be utilized for prediction of Alternaria disease stability in these locations

Predicted land use and land cover outlook for semi-arid Lokere and Lokok catchments in Karamoja region, Uganda

The semi-arid Lokere and Lokok catchments in northeastern Uganda are experiencing land use and land cover (LULC) change driven by policies and actions aimed at pastoralist sedentarisation. While these efforts present a trajectory of a landscape dominated by farming, livestock herding or grazing persists. The objective of this study was to project medium, and long-term LULC for Lokere and Lokok catchments in Karamoja, Uganda. We applied automatic multi-perceptron neural network, built on Markov chain modeling method, along with multi-criteria evaluation strategies; all embedded in the IDRISI Land Change Modeler (LCM) to project the catchments\u2019 LULC to the year 2030 and 2050. The model was trained using 1994 and 2003 LULC, and validated with 2013 LULC. Results of three modelled policy scenarios; business as usual (BAU), pro-livestock and pro-farming; to the years 2030 and 2050 showed that small scale farming (SSF) would increase in all scenarios, even if policy shifts to promote livestock rearing. Pro-farming policies would, in both 2030 and 2050, result in reduction of grassland as SSF increases; doubling the 2003 land area by 2050. The results of this study facilitate assessment of potential impacts of the future LULC and policy evaluation in the catchments.Les bassins versants semi-arides de Lokere et de Lokok dans le nord-est de l\u2019Ouganda connaissent un changement d\u2019utilisation des terres et de couverture terrestre (UTCT) motiv\ue9 par des politiques et des actions visant la s\ue9dentarisation des pasteurs. Si ces efforts pr\ue9sentent une trajectoire d\u2019un paysage domin\ue9 par l\u2019agriculture, l\u2019\ue9levage ou le p\ue2turage persiste. L\u2019objectif de cette \ue9tude \ue9tait de projeter une UTCT \ue0 moyen et long terme pour les bassins versants de Lokere et Lokok \ue0 Karamoja, en Ouganda. Nous avons appliqu\ue9 un r\ue9seau neuronal multi-perception automatique, construit sur la m\ue9thode de mod\ue9lisation de cha\ueene de Markov, ainsi que des strat\ue9gies d\u2019\ue9valuation multicrit\ue8res; tous int\ue9gr\ue9s dans le mod\ue8le IDRISI Land Change Modeler (LCM) pour projeter le UTCT des bassins versants jusqu\u2019en 2030 et 2050. Le mod\ue8le a \ue9t\ue9 form\ue9 \ue0 l\u2019aide de 1994 et 2003 UTCT, et valid\ue9 avec UTCT de 2013. R\ue9sultats de trois sc\ue9narios de politique mod\ue9lis\ue9s; business as usual (BAU), pro-b\ue9tail et pro-agriculture; a montr\ue9 que l\u2019agriculture \ue0 petite \ue9chelle (SSF) augmenterait dans tous les sc\ue9narios, m\ueame si les politiques changeaient pour promouvoir l\u2019\ue9levage pour les ann\ue9es 2030 et 2050. Des politiques favorables \ue0 l\u2019agriculture entra\ueeneraient, en 2030 et 2050, une r\ue9duction des prairies \ue0 mesure que les champs de culture augmentent; doubler sa superficie de 2003 d\u2019ici 2050. Les r\ue9sultats de cette \ue9tude facilitent l\u2019\ue9valuation des impacts potentiels de UTCT future et l\u2019\ue9valuation des politiques dans les bassins versants

VEGETATION BIOMASS PREDICTION IN THE CATTLE CORRIDOR OF UGANDA

Pastoralists in Sub-Saharan Africa face complex problems notably frequent and severe droughts. This study was conducted in the cattle corridor of Uganda, a largely semiarid area to estimate the likely vegetative biomass production under the 2O71-2100 projected rainfall conditions. Spatio-temporal pattern of vegetative biomass production were determined by analysis of the seasonal variation of Normalised Difference Vegetation Index (NDVI) for 10 years from 2001-2010. A biomass relationship was established between the NDVI and the Standardised Precipitation Index (SPI); and used to project the period 2071-2100 NDVI using downscaled rainfall for the cattle corridor. A change trajectory performed on the annual means revealed the highest increase in vegetation in 2008 (0.031) and decrease in 2009 (-0.022). The SPI revealed two main droughts that were established to have occurred in the years of 2004 - 2005 and 2008-2009. The wettest year was 2003 and corresponded with the increase in NDVI. A strong positive correlation of rainfall and vegetation was established (r=0.99). Precipitation has influenced vegetative biomass in the cattle corridor as there is a positive correlation between precipitation and the vegetative biomass production. Secondly, vegetation is likely to be concentrated in areas that will have high precipitation in 2070-2100, such as Luwero and the districts south of it of the cattle corridor compared to those in the north of the cattle corridor of Uganda.Les \ue9leveurs en Afrique Sub-saharienne se confrontent aux probl\ue8mes complexes notamment les s\ue9cheresses fr\ue9quentes et plus graves. Cette \ue9tude a \ue9t\ue9 men\ue9e dans le corridor du b\ue9tail de l\u2019ouganda, une r\ue9gion largement semi-aride pour estimer la production susceptible de biomasse v\ue9g\ue9tale sous les conditions pluviom\ue9triques projet\ue9es en 2071-2100. Le mod\ue8le spatio-temporel de production de biomasse v\ue9g\ue9tale a \ue9t\ue9 d\ue9termin\ue9 par l\u2019analyse de la variation saisonni\ue8re de l\u2019Indice de V\ue9g\ue9tation par Diff\ue9rence Normalis\ue9e (NDVI) pendant 10 ans dans l\u2019intervalle de temps 2001-2010. Une relation de biomasse a \ue9t\ue9 \ue9tablie entre l\u2019indice de v\ue9g\ue9tation NDVI et l\u2019indice de pr\ue9cipitations normalis\ue9 (SPI), et elle est utilis\ue9e pour projeter le NDVI de la p\ue9riode 2071-2100 en utilisant les pr\ue9cipitations \ue0 \ue9chelle r\ue9duite pour le corridor du b\ue9tail. Une trajectoire de changement effectu\ue9e sur les moyennes annuelles a r\ue9v\ue9l\ue9 la plus forte augmentation de la v\ue9g\ue9tation en 2008 (0.031) et une diminution en 2009 (-0.022). Le SPI a r\ue9v\ue9l\ue9 deux principales s\ue9cheresses qui ont \ue9t\ue9 \ue9tablies pour avoir eu lieu dans les ann\ue9es 2004 - 2005 et 2008-2009. L\u2019ann\ue9e la plus humide \ue9tait 2OO3 et correspondait \ue0 une augmentation de l\u2019indice de v\ue9g\ue9tation NDVI. Une forte corr\ue9lation positive entre les pr\ue9cipitations et la v\ue9g\ue9tation a \ue9t\ue9 \ue9tablie (r = 0.99). Les pr\ue9cipitations ont influenc\ue9 la biomasse v\ue9g\ue9tale dans le corridor du b\ue9tail, car il existe une corr\ue9lation positive entre les pr\ue9cipitations et la production de la biomasse v\ue9g\ue9tale. Deuxi\ue8mement, la v\ue9g\ue9tation est susceptible d\u2019\ueatre concentr\ue9e dans les zones qui auront de fortes pr\ue9cipitations en 2070-2100, comme Luwero et les districts du Sud de celui-ci du corridor du b\ue9tail par rapport \ue0 ceux dans le nord du corridor du b\ue9tail de l\u2019ouganda

Root-hair endophyte stacking in finger millet creates a physicochemical barrier to trap the fungal pathogen Fusarium graminearum

The ancient African crop, finger millet, has broad resistance to pathogens including the toxigenic fungus Fusarium graminearum. Here, we report the discovery of a novel plant defence mechanism resulting from an unusual symbiosis between finger millet and a root-inhabiting bacterial endophyte, M6 (Enterobacter sp.). Seed-coated M6 swarms towards root-invading Fusarium and is associated with the growth of root hairs, which then bend parallel to the root axis, subsequently forming biofilm-mediated microcolonies, resulting in a remarkable, multilayer root-hair endophyte stack (RHESt). The RHESt results in a physical barrier that prevents entry and/or traps F. graminearum, which is then killed. M6 thus creates its own specialized killing microhabitat. Tn5-mutagenesis shows that M6 killing requires c-di-GMP-dependent signalling, diverse fungicides and resistance to a Fusarium-derived antibiotic. Further molecular evidence suggests long-term host-endophyte-pathogen co-evolution. The end result of this remarkable symbiosis is reduced deoxynivalenol mycotoxin, potentially benefiting millions of subsistence farmers and livestock. Further results suggest that the anti-Fusarium activity of M6 may be transferable to maize and wheat. RHESt demonstrates the value of exploring ancient, orphan crop microbiomes