Talks by Bonphace Collins Mangeni, PhD
Papers by Bonphace Collins Mangeni, PhD
International Journal of Genetics and Molecular Biology, 2020
Production of groundnuts (Arachis hypogaea L.) in Western Kenya is mainly constrained by groundnu... more Production of groundnuts (Arachis hypogaea L.) in Western Kenya is mainly constrained by groundnut rosette disease (GRD) which cause up to 100% yield loss. This disease expresses different symptoms as a result of variations in the groundnut rosette virus (GRV) associated satellite-ribonucleic acid (GRV Sat-RNA). Over the past 20 years, no work had been done to document the status of the disease in Kenya. Additionally, no sequences of any of the GRD associated viruses were available in the GeneBank from Kenya. This study determined the distribution of GRD and the genetic diversity of GRV Sat-RNA. Sampling was done in main groundnut growing areas of Western Kenya during the long and short rain seasons in 2016/2017. Total RNA was extracted from the leafy samples collected using RNeasy Mini Kit (Qiagen) according to the manufacturers’ protocol and used for double stranded cDNA synthesis using the SuperScript II kit. DNA libraries were sequenced on the Illumina MiSeq platform (Illumina). Reads were used for de novo assembly and contigs aligned to the viral genomes database using CLC Genomics Workbench 10.1.2. The assembled contigs were subjected to a BLASTn search against the GenBank database. Average GRD incidence was 53 and 41% in the short and long rain seasons, respectively. Chlorotic rosette was the dominant symptom followed by green rosette and mosaic. Nucleotide sequences of Sat-RNA revealed identities of 88 to 100% between the Kenyan isolates and those from Malawi, Nigeria and Ghana. All Kenya isolates clustered closest with green rosette variants of Malawi except one which clustered with chlorotic/yellow blotch variants. Rosette is widely distributed in Western Kenya and occurs wherever groundnuts are grown. The variations of GRD symptoms in Western Kenya could be due to the existence of different variants of Sat-RNA or other agents.
Virus Research, 2020
The complete genome sequences for two variant isolates of groundnut rosette assistor virus (GRAV)... more The complete genome sequences for two variant isolates of groundnut rosette assistor virus (GRAV) have been
determined from symptomatic groundnut plants in western Kenya. The sequences of the two GRAV isolates
(sc7.1 and sc7.2) are 84.2% identical at the nucleotide level and 98.5% identical at the coat protein level. The
variants sc7.1 and sc7.2 comprise 5850 and 5879 nucleotides respectively, and show similar genome organizations
with 7 predicted ORFs (P0, P1, P2, P3a, P3 (coat protein, CP), P4 (movement protein, MP) and P5 (coat
protein-readthrough protein, CP-RT). Currently, GRAV is an unassigned virus in the Luteoviridae family, due to
the fact that only the sequence of the coat protein was previously obtained. The presence of both ORF0 and ORF
4 within the genome sequence determined in the current work suggest that GRAV should be classified as a
member of the genus Polerovirus.
International Journal of Genetics and Genomics, 2019
The common bean (Phaseolus vulgaris), is a high protein crop and the main legume in the cropping ... more The common bean (Phaseolus vulgaris), is a high protein crop and the main legume in the cropping system of
western Kenya. Despite its importance, common bean yields are low (<1.0 t/ha) and declining. Bean Common mosaic virus (BCMV) and Bean common mosaic necrosis virus (BCMNV) are the most common and most destructive and can cause a yield loss as high as 100%. In Kenya, limited cultivars and exotic genotypes with resistance to BCMV and BCMNV strains have been reported. Reports indicate BCMNV being a widespread virus compared to BCMV in western Kenya. This study therefore, sought to screen popular cultivars for resistance to the virus. Sixteen popularly grown bean cultivars together with cowpea (Vigna unguiculata), soybean (Glycine max) and groundnut (Arachis hypogaea) were planted in a green house in a
completely randomized block design with three replicates. The plants were inoculated with BCMNV Enzyme Linked
Immunosorbent Assay (ELISA) positive isolate at 3-leaf stage. Data was taken weekly for 3 weeks on type of symptoms expressed and number of plants infected. Ten bean cultivars were susceptible, 4 tolerant and 2 resistant. For improved yields of common bean, farmers should be advised to plant certified seeds for all legumes in the cropping system.
International Journal of Genetics and Genomics, 2019
Bean common mosaic necrosis virus (BCMNV) is one of the most common and most destructive viruses ... more Bean common mosaic necrosis virus (BCMNV) is one of the most common and most destructive viruses of common bean and can cause a yield loss as high as 100%. The common bean (Phaseolus vulgaris L) is an important legume crop for food and cash in Kenya. In Kenya, there is inadequate documentation on the strains of the virus infecting common bean. This information is crucial in devising control measures. This study therefore, sought to characterize BCMNV isolates from western Kenya. Leafy samples showing virus-like symptoms were collected and analysed by Enzyme linked immunosorbent Assay (ELISA) and or next generation sequencing (NGS). Extraction of total RNA from ELISA positive samples was done using RNeasy Plant Mini Kit and NGS carried out following Illumina protocol to determine diversity of the virus. NGS data was trimmed and the sequence reads assembled into contigs, which were analyzed against virus sequence database. Phylogenetic analyses and comparisons were performed using MEGA7 program. The first complete genome sequence of Bean common mosaic virus (BCMNV) is reported from a Kenyan isolate. NGS technology revealed full-length sequence of BCMNV from an isolate BG 12 from Bungoma County with a genome of 9584 nt in length. Phylogenetic analysis of full-length sequences available through the Genbank clustered the isolate with the Tanzanian isolate strain TN-1 and two USA isolates, TN1a and NL-3K.
Common bean (Phaseolus vulgaris L) is an important food legume crop in Kenya as a major source of... more Common bean (Phaseolus vulgaris L) is an important food legume crop in Kenya as a major source of protein in human diet. The yield is 530 kg ha -1 and the country production is estimated at 529,265 tons. Bean production is declining in Kenya due to various abiotic and biotic factors. Virus diseases are a major yield reduction factor in bean production. Among the viruses infecting beans, Bean common mosaic virus (BCMV) and Bean common mosaic necrosis virus (BCMNV) are most wide spread. The current status of BCMV in western Kenya is not well documented. The main objective of this study was to carry out a diagnostic survey for Bean common mosaic disease (BCMD) in bean growing areas of western Kenya, characterize its causal agent and evaluate host resistance to BCMV and BCMNV. BCMD incidence varied across the AEZs being high in LM2 (17.90%) and lowest in LM3 (3.75%). Pathogenic characterization studies of isolates of BCMV and BCMNV on common bean collected from western Kenya revealed the presence of three pathogroups PG IV, PG VI and Pathogroup VII. Serological analysis of the samples revealed mixed infections of BCMV and BCMNV in common bean. Positive samples for BCMV and BCMNV detected by enzyme linked immunosobent assay, ELISA, were categorized into 3 isolates X, Y and Z. Two new pathogroups IV and VII belonging to BCMNV are shown to occur for the first time in the region. The presence of two SCAR DNA markers SW13 and SBD5 associated with the dominant I gene and recessive bc-1 2 resistance gene respectively to BCMV in twelve lines from the popular Andean Diversity Panel (ADP) from Kenya confirmed the presence of bc-1 2 gene in 75% of the lines whereas the I gene was present in only 3 (25%) of the lines
1. Introduction The common bean (Phaseolus vulgaris L) is an important food and cash crop particu... more 1. Introduction The common bean (Phaseolus vulgaris L) is an important food and cash crop particularly for the human dietary protein, vitamins, minerals and dietary fibre requirements (Arulbalachandrans and Mullainathan, 2009). In Kenya the crop is ranked the second most important staple diet after maize (Kiiya, 1997). According to FAO statistics P. vulgaris is globally grown on nearly 28 million hectares producing about 20 million tones of grains (FAOSTAT, 2008). In Eastern Africa region, Kenya leads in bean production with over 500,000 hectares of land under the crop which produces actual yield of approximately 250 kg ha-1 when intercropped and 700 kg ha-1 in pure stands under farmer management conditions (GOK, 1997). These yields are lower compared to world average estimated at over 7000 kg/ha and the researchers yield under experimental conditions in the country of as much as 3000 kg/ha (Abate and Ampofo, 1996). These differences in yield gap between the rest of the world including researchers and that of farmers in western Kenya could be attributed to several constraints such as low soil fertility, diseases and pests. Among the insect pests of common beans is A. fabae which is considered an important pest of beans limiting its production and accounting for yield losses ranging from 37 to 90% (Abate et al., 2000).
Cassava (Manihot esculenta Cranz) is an important food staple in Busia, Homabay, Siaya, Migori, K... more Cassava (Manihot esculenta Cranz) is an important food staple in Busia, Homabay, Siaya, Migori, Kwale, Kilifi and Marakwet Counties and is a secondary food crop for many Kenyans. The current yields of 3-4 tons/ha obtained in Western Kenya are far below world averages and this is largely attributed to pests and diseases. The usual practice of retaining some seed cuttings from the current ware crop or buying them from neighbours, leads to accumulation of viral diseases most important of which are caused by begomovirus infections. A survey for cassava mosaic disease (CMD) was carried out in main cassava growing areas of Western Kenya with a view to determine incidence and distribution of the causal viruses. A total of 33 cassava farms in seven sub-counties in Western Kenya were covered. Leaf samples were collected and analysed serologically and by molecular means. Cassava plants in most farms were severely affected by cassava mosaic disease. Disease incidence in farms ranged between 2% to 54%. Three cassava infecting begomoviruses, African Cassava Mosaic Virus (ACMV), East African Cassava Mosaic Virus (EACMV) and East African Cassava Mosaic Virus – Ugandan variant (EACMV-Ug) were found in the collected samples, with EACMV-Ug being most prevalent followed by EACMV. These are interesting findings given that in the past surveys, ACMV was the most abundant virus in the area. To increase cassava yields, it is recommended that cassava farmers be educated on cassava diseases and their control.
Common bean (Phaseolus vulgaris L.) is the most important legume and is second only to maize as a... more Common bean (Phaseolus vulgaris L.) is the most important legume and is second only to maize as a food crop in Kenya. Despite its importance, bean productivity is declining in western Kenya due to several biotic and abiotic constraints including several fungal diseases. Among these diseases, angular leaf spot (Phaeoisariopsis griseola (Sacc.) is one of the most damaging and widely distributed diseases of common bean, causing yield losses as high as 80%. Furthermore, the problem is compounded by limited information on pathogen distribution and variability in western Kenya hindering breeding for angular leaf spot (ALS) resistance. Therefore, this study was carried out to characterise the ALS pathogen (Phaeoisariopsis griseola) (Sacc.) into different pathotypes. Forty-two isolates of P. griseola were collected from different bean growing areas of western Kenya and characterized into six pathotypes (63:11, 30:26, 33:23, 63:7, 31:10 and 63:63) by use of 12 differential cultivars. Advanced lines and commercial varieties obtained from KALRO-Kakamega were separately inoculated with six pathotypes of P. griseola and evaluated for disease reaction in the screenhouse. A screening trial of Mesoamerican and Andean bean genotypes showed that two varieties were tolerant (disease scores 1 to 3), fourteen varieties were moderately resistant (scores 4 to 6) and four varieties were susceptible (7 to 9). The tolerant varieties were small-seeded, while the susceptible varieties were mostly large-seeded.
Common bean (Phaseolus vulgaris L.) is the most important legume and is second only to maize as a... more Common bean (Phaseolus vulgaris L.) is the most important legume and is second only to maize as a food crop in Kenya. Despite its importance, bean productivity is declining in western Kenya due to several biotic and abiotic constraints including several fungal diseases. Among these diseases, angular leaf spot (Phaeoisariopsis griseola (Sacc.) is one of the most damaging and widely distributed diseases of common bean, causing yield losses as high as 80%. Furthermore, the problem is compounded by limited information on pathogen distribution and variability in western Kenya hindering breeding for angular leaf spot (ALS) resistance. Therefore, this study was carried out to characterise the ALS pathogen (Phaeoisariopsis griseola) (Sacc.) into different pathotypes. Forty-two isolates of P. griseola were collected from different bean growing areas of western Kenya and characterized into six pathotypes (63:11, 30:26, 33:23, 63:7, 31:10 and 63:63) by use of 12 differential cultivars. Advanced lines and commercial varieties obtained from KALRO-Kakamega were separately inoculated with six pathotypes of P. griseola and evaluated for disease reaction in the screenhouse. A screening trial of Mesoamerican and Andean bean genotypes showed that two varieties were tolerant (disease scores 1 to 3), fourteen varieties were moderately resistant (scores 4 to 6) and four varieties were susceptible (7 to 9). The tolerant varieties were small-seeded, while the susceptible varieties were mostly large-seeded.
Cassava (Manihot esculenta Cranz) is an important food staple in Busia, Homabay, Siaya, Migori, K... more Cassava (Manihot esculenta Cranz) is an important food staple in Busia, Homabay, Siaya, Migori, Kwale, Kilifi and Marakwet Counties and is a secondary food crop for many Kenyans. The current yields of 3-4 tons/ha obtained in Western Kenya are far below world averages and this is largely attributed to pests and diseases. The usual practice of retaining some seed cuttings from the current ware crop or buying them from neighbours, leads to accumulation of viral diseases most important of which are caused by begomovirus infections. A survey for cassava mosaic disease (CMD) was carried out in main cassava growing areas of Western Kenya with a view to determine incidence and distribution of the causal viruses. A total of 33 cassava farms in seven sub-counties in Western Kenya were covered. Leaf samples were collected and analysed serologically and by molecular means. Cassava plants in most farms were severely affected by cassava mosaic disease. Disease incidence in farms ranged between 2% to 54%. Three cassava infecting begomoviruses, African Cassava Mosaic Virus (ACMV), East African Cassava Mosaic Virus (EACMV) and East African Cassava Mosaic Virus – Ugandan variant (EACMV-Ug) were found in the collected samples, with EACMV-Ug being most prevalent followed by EACMV. These are interesting findings given that in the past surveys, ACMV was the most abundant virus in the area. To increase cassava yields, it is recommended that cassava farmers be educated on cassava diseases and their control.
Common bean (Phaseolus vulgaris L) is an important food legume crop in Kenya as a major source of... more Common bean (Phaseolus vulgaris L) is an important food legume crop in Kenya as a major source of protein in human diet. The yield is 530 kg ha-1 and the country production is estimated at 529,265 tons. Bean production is declining in Kenya due to various abiotic and biotic factors. Virus diseases are a major yield reduction factor in bean production. Among the viruses infecting beans, Bean common mosaic virus (BCMV) and Bean common mosaic necrosis virus (BCMNV) are most wide spread. The current status of BCMV in western Kenya is not well documented. The main objective of this study was to carry out a diagnostic survey for Bean common mosaic disease (BCMD) in bean growing areas of western Kenya, characterize its causal agent and evaluate host resistance to BCMV and BCMNV. BCMD incidence varied across the AEZs being high in LM2 (17.90%) and lowest in LM3 (3.75%). Pathogenic characterization studies of isolates of BCMV and BCMNV on common bean collected from western Kenya revealed the presence of three pathogroups PG IV, PG VI and Pathogroup VII. Serological analysis of the samples revealed mixed infections of BCMV and BCMNV in common bean. Positive samples for BCMV and BCMNV detected by enzyme linked immunosobent assay, ELISA, were categorized into 3 isolates X, Y and Z. Two new pathogroups IV and VII belonging to BCMNV are shown to occur for the first time in the region. The presence of two SCAR DNA markers SW13 and SBD5 associated with the dominant I gene and recessive bc-12 resistance gene respectively to BCMV in twelve lines from the popular Andean Diversity Panel (ADP) from Kenya confirmed the presence of bc-12 gene in 75% of the lines whereas the I gene was present in only 3 (25%) of the lines
In western Kenya, groundnuts (Arachis hypogaea L.) is one of the major legumes where it is not on... more In western Kenya, groundnuts (Arachis hypogaea L.) is one of the major legumes where it is not only the principal source of protein but also a major source of small-holder cash income. However, groundnut production has continued to decline with farmers realizing less than 50% of the yield potential. Viral diseases play a great role in yield reduction. Cowpea mild mottle virus (CPMMV) has been reported to be one of the viruses infecting groundnuts but its status in western Kenya was not known. Therefore this study sought to establish whether the virus was already infecting groundnuts in this region. Two surveys were conducted in seven major groundnut growing Counties of western Kenya; Bungoma, Busia, Vihiga, Siaya, Migori, Nandi and Homabay, basing on various Agro-ecological zones (AEZs). Leafy samples were collected and tested by DAS-ELISA. Indicator plants were mechanically inoculated with CPMMV from positive samples and symptoms observed. The disease was found to be widespread in all the AEZs surveyed with high incidence at farm levels. Most farmers were found to use uncertified seed. ELISA tests confirmed the presence of CPMMV in the leafy samples collected from the farms. The virus induced varied symptoms on indicator plants tested. All the indicator plant used were major legumes grown in western Kenya and were found to be susceptible to CPMMV. This implies that CPMMV is a serious threat to legume production in western Kenya
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Talks by Bonphace Collins Mangeni, PhD
Papers by Bonphace Collins Mangeni, PhD
determined from symptomatic groundnut plants in western Kenya. The sequences of the two GRAV isolates
(sc7.1 and sc7.2) are 84.2% identical at the nucleotide level and 98.5% identical at the coat protein level. The
variants sc7.1 and sc7.2 comprise 5850 and 5879 nucleotides respectively, and show similar genome organizations
with 7 predicted ORFs (P0, P1, P2, P3a, P3 (coat protein, CP), P4 (movement protein, MP) and P5 (coat
protein-readthrough protein, CP-RT). Currently, GRAV is an unassigned virus in the Luteoviridae family, due to
the fact that only the sequence of the coat protein was previously obtained. The presence of both ORF0 and ORF
4 within the genome sequence determined in the current work suggest that GRAV should be classified as a
member of the genus Polerovirus.
western Kenya. Despite its importance, common bean yields are low (<1.0 t/ha) and declining. Bean Common mosaic virus (BCMV) and Bean common mosaic necrosis virus (BCMNV) are the most common and most destructive and can cause a yield loss as high as 100%. In Kenya, limited cultivars and exotic genotypes with resistance to BCMV and BCMNV strains have been reported. Reports indicate BCMNV being a widespread virus compared to BCMV in western Kenya. This study therefore, sought to screen popular cultivars for resistance to the virus. Sixteen popularly grown bean cultivars together with cowpea (Vigna unguiculata), soybean (Glycine max) and groundnut (Arachis hypogaea) were planted in a green house in a
completely randomized block design with three replicates. The plants were inoculated with BCMNV Enzyme Linked
Immunosorbent Assay (ELISA) positive isolate at 3-leaf stage. Data was taken weekly for 3 weeks on type of symptoms expressed and number of plants infected. Ten bean cultivars were susceptible, 4 tolerant and 2 resistant. For improved yields of common bean, farmers should be advised to plant certified seeds for all legumes in the cropping system.
determined from symptomatic groundnut plants in western Kenya. The sequences of the two GRAV isolates
(sc7.1 and sc7.2) are 84.2% identical at the nucleotide level and 98.5% identical at the coat protein level. The
variants sc7.1 and sc7.2 comprise 5850 and 5879 nucleotides respectively, and show similar genome organizations
with 7 predicted ORFs (P0, P1, P2, P3a, P3 (coat protein, CP), P4 (movement protein, MP) and P5 (coat
protein-readthrough protein, CP-RT). Currently, GRAV is an unassigned virus in the Luteoviridae family, due to
the fact that only the sequence of the coat protein was previously obtained. The presence of both ORF0 and ORF
4 within the genome sequence determined in the current work suggest that GRAV should be classified as a
member of the genus Polerovirus.
western Kenya. Despite its importance, common bean yields are low (<1.0 t/ha) and declining. Bean Common mosaic virus (BCMV) and Bean common mosaic necrosis virus (BCMNV) are the most common and most destructive and can cause a yield loss as high as 100%. In Kenya, limited cultivars and exotic genotypes with resistance to BCMV and BCMNV strains have been reported. Reports indicate BCMNV being a widespread virus compared to BCMV in western Kenya. This study therefore, sought to screen popular cultivars for resistance to the virus. Sixteen popularly grown bean cultivars together with cowpea (Vigna unguiculata), soybean (Glycine max) and groundnut (Arachis hypogaea) were planted in a green house in a
completely randomized block design with three replicates. The plants were inoculated with BCMNV Enzyme Linked
Immunosorbent Assay (ELISA) positive isolate at 3-leaf stage. Data was taken weekly for 3 weeks on type of symptoms expressed and number of plants infected. Ten bean cultivars were susceptible, 4 tolerant and 2 resistant. For improved yields of common bean, farmers should be advised to plant certified seeds for all legumes in the cropping system.