Browsing by Author "Tukamuhabwa, Phinehas"
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Item An Online Database of Sweetpotato Germplasm Collection in Uganda(HortScience, 2010-01-01) Yada, Benard; Tukamuhabwa, Phinehas; Alajo, Agnes; Mwanga, Robert O.M.Sweetpotato [Ipomoea batatas (L.) Lam], the world's seventh most important crop, is widely grown and consumed as a staple food crop in Uganda. Uganda is the third largest global producer after China and Nigeria (Food and Agricultural Organization, 2007). It lies within the East African region, which is considered a secondary center of diversity for the crop where the farmers grow and maintain large numbers of different cultivars and landraces (Mwanga et al., 2001; Villordon et al., 2006). Genetic erosion threatens this diversity as a result of sweetpotato virus disease (SPVD) caused by dual infection of Sweetpotato feathery mottle virus (Potyvirus; Potyviridae) and Sweetpotato chlorotic stunt virus (Crinivirus; Closteroviridae) (Gibson et al., 1998), Alternaria bataticola blight, and African sweetpotato weevils, Cylas puncticollis Boheman and Cylas brunneus Fabricius. Farmers are also known to abandon poor-performing traditional cultivars in favor of newly developed ones released by the national breeding program (Bashaasha et al., 1995; Mwanga et al., 2001). The National Sweetpotato Program based at the National Crops Resources Research Institute (NaCRRI), Namulonge, Uganda, undertook a rigorous germplasm collection, characterization, evaluation, and conservation program to mitigate sweetpotato genetic erosion and also to find superior germplasm for cultivar development in hybridization schemes. A total of 1303 accessions of sweetpotato germplasm were collected from 21 major sweetpotato-producing districts of Uganda from January to July 2005. Information about farmers' indigenous knowledge of the cultivars was also collected. These accessions were assembled at NaCRRI and morphologically characterized using 40 standard root, vine, leaf, and flower descriptors of sweetpotato [International Potato Center (CIP), Asian Vegetable Research and Development Center, and International Board for Plant Genetic Resources, 1991] scored 90 to 100 d after planting in the field. A total of 946 morphologically distinct accessions were identified after removal of duplicates. Field evaluations were also conducted for SPVD, Alternaria blight, and yield at three sites for two seasons. Subsequently, 192 superior genotypes were selected from the germplasm evaluation of which 190 were genetically distinct on molecular characterization using 10 fluorescent-labeled simple sequence repeat markers, IB-R16 (VIC), IB-R19 (PET), IBCIP-13 (NED), IB-R03 (PET), IBCIP-9 (6-FAM), IB-S09 (NED), IB-R08 (PET), IB-R12 (NED), IB-S07 (6-FAM), and IB-S07 (PET), obtained from CIP, Lima, Peru. The database for sweetpotato germplasm collection in Uganda referred to as the “Uganda Sweetpotato Germplasm Database” (USGDB) is described. To our knowledge, the USGDB is the most comprehensive description of collected sweetpotato germplasm in the region. USGDB has all 946 morphologically distinct accessions fully described, including passport (accession identifiers and information recorded by collectors) data, morphological characterization, and evaluation data. This database has been made available online for public use at: http://www.viazivitamu.org/ugasp_db/index.php. The database contains the names, accession number as assigned by collectors, geographical location (longitude and latitude), form of maintenance, and a total of 40 morphological descriptors. It further contains the total root yield, SPVD, and Alternaria bataticola blight disease resistance values for each accession. This online database is an important resource for enhancing the global exchange of sweetpotato germplasm. An online web-accessible database developed for the sweetpotato germplasm collection in Kenya called the “Viazivitamu database” is also available at http://www.viazivitamu.org (Villordon et al., 2007). The Ugandan and Kenyan databases will eventually be merged and expanded to produce a comprehensive regional database of sweetpotato germplasm resources that is representative of the entire East African region after checking for duplicates in the two collections. This USGDB collection is being maintained in the screenhouse and field at NaCRRI. Some 30 accessions are being maintained in vitro at the CIP gene bank at Lima, Peru. Request for this germplasm should be directed to the National Sweetpotato Program, NaCRRI, P.O. Box 7084, Kampala, Uganda.Item Assessment of Comparative Virulence and Resistance in Soybean Using Field Isolates of Soybean Rust(Canadian Center of Science and Education, 2013-04-15) Maphosa, Mcebisi; Talwana, Herbert; Tukamuhabwa, PhinehasA major impediment to breeding for resistance to Asian soybean rust (Phakopsora pachyrhizi) is the lack of stable sources of resistance, due to high variability in the pathogen. The objectives of this study were to assess comparative virulence of five diverse field isolates from major soybean producing areas in Uganda, and identify lines with resistance to isolates of soybean rust in seedling and adult plants under screen house and field conditions respectively. When inoculated with the five field isolates, all twelve lines evaluated showed diverse and mixed reactions, suggesting each location differed in soybean rust races and/or virulence. Experimental sites growing many diverse soybean lines yearly had the greatest diversity of soybean rust. The effectiveness of specific resistance genes was restricted to certain locations and gene Rpp2 previously resistant was ineffective producing a susceptible tan reaction at the seedling stage. A positive correlation between mean lesion density at the seedling stage and adult plant severity indicated that using field isolates to screen for seedling resistance can be a useful breeding approach to extrapolate resistance in adult plants. Overall, these results emphasise the relevance of using field isolates from the target areas to evaluate lines for soybean rust resistance.Item Characterization of Ugandan Sweetpotato Germplasm Using Fluorescent Labeled Simple Sequence Repeat Markers(HortScience, 2010-02-01) Yada, Benard; Tukamuhabwa, Phinehas; Wanjala, Bramwell; Alajo, Agnes; Mwanga, Robert O.M.The genetic relationships among 192 superior, high–yielding, and disease-resistant sweetpotato [Ipomoea batatas (L.) Lam] accessions from the Ugandan germplasm collection were analyzed using 10 fluorescent labeled simple sequence repeat (SSR) markers. Relatedness among the genotypes was estimated using the Nei and Li genetic distance coefficient, cluster analysis and principle component analysis methods of NTSYS-pc software. The polymorphic information content of the SSR markers used in this study ranged from 0.23 to 0.76 for loci IB-S07 and IB-R12, respectively, with a mean value of 0.62. The number of polymorphic alleles detected per locus ranged from two to six with a mean of four, a confirmation of the effectiveness of microsatellite detection on an automated ABI 3730 sequencer. The mean pairwise genetic distance among the 192 genotypes was 0.57, an indication of moderately high genetic diversity. Cluster analysis divided the accessions into four major groups with no relationship to the district of origin. Two sets of duplicates were identified through SSR genotyping in this study. Up to 190 distinct accessions for use as potential parental genotypes in hybridization schemes for cultivar development in the region were identified.Item Continuous Storage Root Formation and Bulking in Sweet potato(Gates Open Research, 2019) Bararyenya, Astere; Tukamuhabwa, Phinehas; Gibson, Paul; Grüneberg, Wolfgang; Ssali, Reuben; Low, Jan; Odong, Thomas; Ochwo-Ssemakula, Mildred; Talwana, Herbert; Mwila, Natasha; Mwanga, RobertSweetpotato (Ipomoea batatas (L.) Lam, family Convolvulaceae.) is one of the most important food crops worldwide, with approximately 106 million tons produced in almost 120 countries from an area of about 8 million ha and an average global yield of 11.1 tons/ha (FAO, 2016). Asia is the world’s largest sweetpotato producing continent, with 79 million tons, followed by Africa (FAOstat, 2016). About 75% of this global production is from China alone. A total of 21.3 million tons is produced in Africa, with 48% from the Great Lakes region. In East Africa, the crop is the second most important root crop after cassava and has played an important role as a famine-relief crop during its long history and has recently been reevaluated as a health-promoting food (Low et al., 2017). Uganda ranks as the fourth largest sweetpotato producer in the world after China, Nigeria and Tanzania, with a production of 2.1 million t. In Africa, Uganda is ranked third after Nigeria and Tanzania. Sweetpotato is one of the main staple crops in the food systems of Uganda, Rwanda, and Burundi with a per capita consumption of 50.9, 80.1 and 57.0 kg, respectivelyItem Evaluation of Cowpea Genotypes for Virus Resistance Under Natural Conditions in Uganda(Journal of Agricultural Science, 2014) Mbeyagala, Emmanuel K.; Mukasa, Blasio S.; Tukamuhabwa, Phinehas; Bisikwa, JenipherCowpea (Vigna unguiculata L. Walp) is an important grain legume in most parts of Sub Saharan Africa. However, viral diseases are a major limiting production factor causing significant yield losses. An experiment was conducted to evaluate the reaction of 105 different cowpea genotypes to viral infection in different agro-ecological zones of Uganda. The aim was to identify genotypes that could serve as sources of resistance to virus infection. Virus infection in these experiments occurred naturally through insect vectors. Results showed that there were significant differences in disease reaction among genotypes within and among agro-ecological zones in terms of Area Under Disease Progress Curve (AUDPC) and incidence. Interactions of genotype by season (GXS), genotype by location (GXL) and genotype by location by season (GXLXS) also significantly affected reaction to viral infection among genotypes. Introduced cowpea genotypes exhibited a more susceptible viral disease reaction compared to the landraces over the two seasons in the three locations. A number of landraces such as WC32, WC18, NE43, NE15, WC35B consistently showed resistance to virus infection in the three locations and therefore could be good sources of resistance. Low disease pressure (AUDPC) was also recorded on SECOW2W (released variety) as reported by previous studies. The landraces also gave consistently higher grain yield values compared to the introduced genotypes. Overall, data from this study showed that locally adapted cowpea genotypes offer resistance to virus infection and may be desirable germplasm for Ugandan cowpea breeding programs.Item Evaluation of Soybean Entries in the Pan-African Trials for Response to Coniothyrium glycines, the Cause of Red Leaf Blotch(Plant disease, 2022-02-05) Murithi, Harun M.; Obua, Tonny; Tukamuhabwa, Phinehas; Hartman, Glen L.Red leaf blotch (RLB), caused by the fungus Coniothyrium glycines, is an important disease of soybean known to cause yield losses across soybean-growing regions in Africa. Fungicides are one option to manage this disease, but utilization of host resistance may be a better option suited for smallholder soybean farmers in Africa. Fifty-nine soybean entries were evaluated for RLB severity in nine field locations in Ethiopia, Kenya, Uganda, and Zambia. Disease incidence was 100% and disease severity differed (P < 0.01) among entries at eight of the nine locations. Mean severity ratings ranged from 1.4 to 3.2 based on a 0-to-5 scale, with higher disease severities recorded in Ethiopia followed by Zambia. Eight of the 59 entries were common to all nine locations and had severity ratings ranging from 1.6 to 2.9. The cultivar SC Signal had the lowest RLB severity ratings in the combined analysis over locations. Based on correlations of weather variables to RLB severity, mean rainfall from planting to 30 days before assessment date had a positive correlation (r = 0.70; P = 0.035), as did mean morning maximum wind speed (r = 0.88; P = 0.016). Other variables, such as temperature and relative humidity, did not correlate to RLB severity. This is the most comprehensive report to date on the occurrence of RLB in the region, which for the first time demonstrates an association between rainfall and wind speed with RLB severity. It also represents the first extensive report evaluating soybean genotypes for resistance against RLB in multiple environments.Item Evaluation of soybean genotypes for resistance against the rust-causing fungus Phakopsora pachyrhizi in East Africa(Plant Pathology, 2021-01-16) Murithi, Harun Muthuri; Namara, Mercy; Tukamuhabwa, Phinehas; Mahuku, George; Thomma, Bart P. H. J.; Joosten, Matthieu H. A. J.Soybean rust, caused by the biotrophic fungus Phakopsora pachyrhizi, is the most important foliar disease of soybean (Glycine max) worldwide. Deployment of resistant soybean cultivars is the best option for managing this disease. Genes conferring resistance to P. pachyrhizi have been identified, but pathotypes of the rust fungus overcoming these resistance genes have also been found. To identify novel resistance genes, soybean genotypes from both local and international sources were screened at multiple locations in Tanzania and Uganda in 2016 and 2017. The results from this screening revealed that infection types, disease severities, and sporulation levels varied among the genotypes and locations. The majority of the genotypes had tan-coloured (TAN) lesions and developed moderate sporulation, implying susceptibility, while only seven of the 71 lines had reddish-brown (RB) lesions and showed low disease severities in all of the screening environments. We identified seven genotypes that were the most resistant to rust in the most locations over the two years. These genotypes will be useful for further studies and, ultimately, for rust management, as they show broad resistance to various pathotypes of the rust fungus.Item Evaluation of the American Yam Bean (Pachyrhizus spp.) for Storage Root Yield Across Varying Eco-geographic Conditions in Uganda(Journal of Agricultural Science, 2019) Andiku, Charles; Tukamuhabwa, Phinehas; Mukasa Ssebuliba, James; Talwana, Hebert; Tumwegamire, Silver; Grüneberg, Wolfgang J.The American yam bean (Pachyrhizus spp.) is a legume crop that is exclusively used for its storage roots. The seeds are inedible due to presence of toxic rotenone. It produces high storage root yields comparable of major root crops like cassava or sweetpotato. And flower pruning more than doubles its root yield performance. Using twenty five yam bean accessions, the current study aimed to determine root yield stability and adaptability, and presence of yam bean production mega environments in Uganda. Trials were planted at three stations, Namulonge, Serere, and Kachwekano during two consecutive seasons of 2011. Fresh storage root yields were significantly different (p < 0.05) across locations with the ideal location being Namulonge (fresh storage root yield of 10.1 t ha-1), followed by Serere (8.0 t ha-1), and Kachwekano (3.1 t ha-1). Results of AMMI analysis indicated the presence of genotype-by-environment interaction for fresh storage root yield. Through AMMI estimates and GGE visual assessment, genotype 209017 was the highest yielding with mean yield of 20.7 t ha-1. Genotype 209018 with mean yield of 15.5 t ha-1 was the most stable and adapted accession in the entire discriminating environment in Uganda. From the environmental focusing plot, the six environments were grouped into two putative mega environments for yam bean production.Item Evaluation of the performance of advanced generation soybean [Glycine max (L.) Merr.] genotypes using GGE biplot(Journal of plant breeding and crop science, 2020-09-30) Mukuze, Clever; Tukamuhabwa, Phinehas; Obua, Tonny; Kongai, Hellen; Rubaihayo, PatrickSoybean is an important food and cash crop in Uganda. Despite the importance of soybean in Uganda’s economy, its performance is highly affected by genotype × environment interaction making it difficult to select and recommend new superior soybean genotypes for diverse growing environments. The objectives of this study were to examine the nature of G × E interaction for soybean grain yield, to identify stable and high yielding soybean genotypes with desirable percentage protein and oil content for production in diverse environments and to determine ideal test location for future soybean breeding activities in Uganda. The experiment was conducted at six locations for two consecutive seasons of year 2018 (2018A and 2018B). Twenty-three newly advanced generation soybean lines and two commercial varieties were evaluated in a randomized complete block design replicated three times. Combined analysis of variance over locations and seasons was carried out for grain yield, protein and oil (%) content. The results for grain yield showed significant (p<0.05) differences for all the sources of variation except genotypes × season interaction. Percentage protein and oil content showed non-significant (p>0.05) for all the sources of variation except location. The genotype main effect plus G × E interaction biplot explained 65.74% of the total interaction sum of squares for grain yield and showed that the advanced generation soybean lines BSPS 48A-28; Mak 3N × 1N and NGDT 8.11×3N-2 were high yielding and stable and had other desirable agronomic traits. Nakabango was the most discriminating and representative test location.Item Genetic Diversity and Population Structure Analysis of Tropical Soybean (Glycine Max (L.) Merrill) using single Nucleotide Polymorphic Markers(Global Journal of Science Frontier Research, 2020) Obua, Tonny; Sserumaga, Julius P.; Opiyo, Stephen O.; Tukamuhabwa, Phinehas; Odong, Thomas L.; Mutuku, Josiah; Yao, NasserSoybean (Glycine max (L.) Merrill) is among the most important crops worldwide due to its numerous uses in feed, food, biofuel, and significant atmospheric nitrogen fixation capability. To understand the genetic diversity and population structure of tropical soybean germplasm, 89 genotypes from diverse sources were analyzed using 7,962 SNP markers. The AMOVA results showed low diversity among and high within the populations, while the polymorphism information content (PIC) was 0.27. Both phylogenetic and principal component analysis grouped the 89 soybean genotypes into three major clusters, while population structure grouped the soybean genotypes into two subpopulations. On the other, the average Roger genetic distances within the study population was 0.34. The low diversity reported in the studied soybean germplasm pool is particularly worrying, considering the new trends of climate change and the emergence of new pests and diseases of soybean. Therefore, in order to address these challenges and develop soybean varieties with desirable traits, there is a need to broaden the genetic base of tropical soybean through the importation of germplasm from other countries.Item Genetic Variability for Yield and Nutritional Quality in Yam Bean (Pachyrhizus sp.)(HortScience, 2016-09-01) Agaba, Rolland; Tukamuhabwa, Phinehas; Rubaihayo, Patrick; Tumwegamire, Silver; Ssenyonjo, Andrew; Mwanga, Robert O.M.; Gr€uneberg, Wolfgang J.The amount of genotypic and phenotypic variability that exists in a species is important for selection and initiating breeding programs. Yam bean is grown locally in tropical countries of the Americas and Asia for their tasty storage roots, which usually have low dry matter content. The crop was recently introduced in Uganda and other East and Central African countries to supplement iron (Fe) and protein content in diets. This study aimed to estimate genetic variability for root yield and quality traits among 26 yam bean accessions in Uganda. A randomized complete block design was used with two replications across two ecogeographical locations and two seasons during 2012 and 2013. Near-infrared reflectance spectroscopy (NIRS) was used to determine quality of storage root samples. Significant differences among genotypes were observed for all traits except root protein, zinc (Zn), and phosphorus contents. Genotypic variance components (Item Genetic variability of anti‑nutritional factors among soybean (Glycine max.) germplasm(Discover Agriculture, 2025-04-28) Palange, Norberto Jose; Obua, Tonny; Sserumaga, Julius Pyton; Wembabazi, Enoch; Ochwo‑Ssemakula, Mildred; Tukamuhabwa, PhinehasSoybean is a vital source of vegetable protein, carbohydrates, oil, and minerals. However, anti-nutritional factors (ANFs) can diminish its nutritional value for monogastric animals, including humans. This study assessed the variability of phytate and trypsin inhibitors in Ugandan soybean germplasm. A total of 308 soybean genotypes were analyzed for yield, phytate, and total trypsin inhibitors (TTI) using spectrophotometric methods. Significant variation was observed for yield, phytate, and TTI levels (p < 0.001). Phytate levels ranged from 14.8 mg kg⁻1(BSPS 48A-6–3) to 6928.8 mg kg⁻1(NGDT 2.15–7), while TTI varied from 14.7 mg kg⁻1(DN 16_N) to 1534.8 mg kg⁻1(Duiker). Using a weighted selection index, the best-performing genotypes, Ux 990–044, Ux 990–102, and S 6.22B, combined high yield with low ANF levels. Broad-sense heritability (H2) was 0.68 for phytate, 0.84 for TTI, and 0.08 for yield. The phenotypic coefficient of variation (PCV) for phytate (203.1%) was significantly higher than the genetic coefficient of variation (GCV) (137.6%), indicating substantial environmental influence, while moderate for TTI (PCV = 34.6%; GCV = 29.2%). Genetic advance (GA) values were 1667.6 mg kg⁻1 for phytate and 504.3 mg kg⁻1 for TTI, highlighting considerable genetic variability and heritability. These findings have practical implications for breeding programs; the identified genotypes that combine high yield and reduced ANFs can reduce processing costs for food and feed industries while enhancing nutritional security, especially in regions dependent on soybean as a protein source.Item Genetic variation and response to selection for storage root dry matter and associated traits in a population of yam bean (Pachyrhizus spp.) interspecies crosses(Euphytica, 2021-03-22) Agaba, Rolland; Rubaihayo, Patrick; Tukamuhabwa, Phinehas; Mwanga, Robert O. M.; Tumwegamire, Silver; Ndirigwe, Jean; Gru¨neberg, WolfgangThe goal of yam bean improvement in Africa is to develop superior high yielding and high dry matter cultivars that are preferred for adoption. In this study, the estimates of variance components, heritability and response to selection were studied in F3 yam bean families selected from interspecies crosses targeting improvement of storage root dry matter and associated traits. Breeding populations were generated using North Carolina II (NC II) mating design involving high dry matter P. tuberosus chuin cultivar, low dry matter P. ahipa and the high yielding P. erosus yam beans. The progenies were advanced through selfing from F1 to F2 population and then exposed to selection at 10% selection intensity to obtain 83 high dry matter lines. The selected lines were evaluated in an F3 trial using a randomized complete block design (RCBD) with three replications at the National Crops Resources Research Institute (NaCRRI) Namulonge, in Central Uganda. The results revealed significant (P < 0.001) genetic variation for storage root dry matter (RDM), storage root fresh yield (RFY), storage root dry yield (RDY), vine yield (VNY), fresh biomass yield (FBY), harvest index (HI), starch (STA) and protein (PRO) content. High genotypic coefficient of variation (GCV) and phenotypic coefficient of variation (PCV) were obtained for VNY, RDY, FBY, RFY, RDM and STA. Narrow sense heritability was higher than 0.5 and response to selection was 15.5 to 33.1 for RDM, RFY, RDY, VNY, FBY and STA, indicating rapid genetic progress is achievable and early generation selection would be effective to improve these traits. Significant (P < 0.01) positive genetic correlations were observed between RDM, RDY, RFY, VNY, FBY and STA ranging from 0.422 to 0.963 implying that simultaneous improvement of these traits is possible in the current yam bean populations.Item Genetic variation, Heritability estimates and GXE effects on yield traits of Mesoamerican common bean (Phaseolus vulgaris L) germplasm in Uganda(Plant Genetic Resources, 2018) Okii, Dennis; Mukankusi, Clare; Sebuliba, Sulaiman; Tukamuhabwa, Phinehas; Tusiime, Geoffrey; Talwana, Herbert; Odong, Thomas; Namayanja, Annet; Paparu, Pamela; Nkalubo, Stanley; Otim, Michael; Ugen, Michael; Buah, Stephen; Gepts, PaulGermplasm of common beans from the Mesoamerican gene pool races: Durango, Jalisco, Mesoamerica and Guatemala have highest genetic variation for the crop’s improvement. The objective was to assign 50 common bean germplasm in Uganda into its gene pool races based on analyses of population structure. Secondly, to estimate heritability and effects of genotype environment (GXE) interaction on common bean agronomic and yield traits in space and time. Sample genomic DNA was amplified in 2011 with 22 Simple sequence repeat markers (SSRs) and alleles separated using capillary electrophoresis. Field evaluations were conducted in 2010 and 2011 at NaCRRI and 2015 at CIAT – Kawanda. Multivariate analyses of SSRs data identified four subgroups within the germplasm: K4.1–K4.4, with corresponding Wrights fixation indices (FST) as 0.1829 for K4.1, 0.1585 for K4.4, 0.1579 for K4.2 and least for K4.3 at 0.0678. Gene pool race admixtures in the population (14%) were notable and attributed to gene flow. Four superior parents currently used in improving resistance to major diseases grouped as; Jalisco for MLB49-89A; Mesoamerica for MCM5001 and G2333; Durango for MEXICO 54. Heritability values for yield traits estimated using phenotypic data from above fixed parents, was above 0.81. Season and location had significant effect (P < 0.05) on numbers of: flower buds per inflorescence, pod formation and weight of 100 seeds. The findings will improve understanding of co-evolutionary relationships between bean hosts and pathogens for better disease management and will broaden the germplasm base for improving other tropical production constraints.Item Genome-Wide Association Analysis for Resistance to Coniothyrium glycines Causing Red Leaf Blotch Disease in Soybean(Genes, 2023-06-15) Lukanda, Musondolya Mathe; Dramadri, Isaac Onziga; Tukamuhabwa, Phinehas; Muthuri, Harun Murithi; Tusiime, GeoffreySoybean is a high oil and protein-rich legume with several production constraints. Globally, several fungi, viruses, nematodes, and bacteria cause significant yield losses in soybean. Coniothyrium glycines (CG), the causal pathogen for red leaf blotch disease, is the least researched and causes severe damage to soybean. The identification of resistant soybean genotypes and mapping of genomic regions associated with resistance to CG is critical for developing improved cultivars for sustainable soybean production. This study used single nucleotide polymorphism (SNP) markers generated from a Diversity Arrays Technology (DArT) platform to conduct a genome-wide association (GWAS) analysis of resistance to CG using 279 soybean genotypes grown in three environments. A total of 6395 SNPs was used to perform the GWAS applying a multilocus model Fixed and random model Circulating Probability Unification (FarmCPU) with correction of the population structure and a statistical test p-value threshold of 5%. A total of 19 significant marker–trait associations for resistance to CG were identified on chromosomes 1, 5, 6, 9, 10, 12, 13, 15, 16, 17, 19, and 20. Approximately 113 putative genes associated with significant markers for resistance to red leaf blotch disease were identified across soybean genome. Positional candidate genes associated with significant SNP loci-encoding proteins involved in plant defense responses and that could be associated with soybean defenses against CG infection were identified. The results of this study provide valuable insight for further dissection of the genetic architecture of resistance to CG in soybean. They also highlight SNP variants and genes useful for genomics-informed selection decisions in the breeding process for improving resistance traits in soybean.Item Genome-wide Association Mapping of Bruchid Resistance Loci in Soybean(PloS one, 2025-01-10) Mukuze, Clever; Obua, Tonny; Kweyu, Sharon V.; Kasule, Faizo; Tukamuhabwa, PhinehasSoybean is a globally important industrial, food, and cash crop. Despite its importance in present and future economies, its production is severely hampered by bruchids (Callosobruchus chinensis), a destructive storage insect pest, causing considerable yield losses. Therefore, the identification of genomic regions and candidate genes associated with bruchid resistance in soybean is crucial as it helps breeders to develop new soybean varieties with improved resistance and quality. In this study, 6 multi-locus methods of the mrMLM model for genome-wide association study were used to dissect the genetic architecture of bruchid resistance on 4traits: percentage adult bruchid emergence (PBE), percentage weight loss (PWL), median development period (MDP), and Dobie susceptibility index (DSI) on 100 diverse soybean genotypes, genotyped with 14,469 single-nucleotide polymorphism (SNP) markers. Using the best linear unbiased predictors (BLUPs), 13 quantitative trait nucleotides (QTNs) were identified by the mrMLM model, of which rs16_14976250 was associated with more than 1 bruchid resistance traits. As a result, the identified QTNs linked with resistance traits can be employed in marker-assisted breeding for the accurate and rapid screening of soybean genotypes for resistance to bruchids. Moreover, a gene search on the Phytozome soybean reference genome identified 27 potential candidate genes located within a window of 478.45 kb upstream and downstream of the most reliable QTNs. These candidate genes exhibit molecular and biological functionalities associated with various soybean resistance mechanisms and, therefore, could be incorporated into the farmers’ preferred soybean varieties that are susceptible to bruchids.Item Genome-wide association study identified candidate genes controlling continuous storage root formation and bulking in hexaploid sweetpotato(BMC plant biology, 2020) Bararyenya, Astère; Olukolu, Bode A.; Tukamuhabwa, Phinehas; Grüneberg, Wolfgang J.; Ekaya, Wellington; Low, Jan; Ochwo-Ssemakula, Mildred; Odong, Thomas L.; Talwana, Herbert; Badji, Arfang; Kyalo, Martina; Nasser, Yao; Gemenet, Dorcus; Kitavi, Mercy; Mwanga, Robert O. M.Continuous storage root formation and bulking (CSRFAB) in sweetpotato is an important trait from agronomic and biological perspectives. Information about the molecular mechanisms underlying CSRFAB traits is lacking. Results: Here, as a first step toward understanding the genetic basis of CSRFAB in sweetpotato, we performed a genome-wide association study (GWAS) using phenotypic data from four distinct developmental stages and 33,068 single nucleotide polymorphism (SNP) and insertion-deletion (indel) markers. Based on Bonferroni threshold (pvalue < 5 × 10− 7), we identified 34 unique SNPs that were significantly associated with the complex trait of CSRFAB at 150 days after planting (DAP) and seven unique SNPs associated with discontinuous storage root formation and bulking (DCSRFAB) at 90 DAP. Importantly, most of the loci associated with these identified SNPs were located within genomic regions (using Ipomoea trifida reference genome) previously reported for quantitative trait loci (QTL) controlling similar traits. Based on these trait-associated SNPs, 12 and seven candidate genes were respectively annotated for CSRFAB and DCSRFAB traits. Congruent with the contrasting and inverse relationship between discontinuous and continuous storage root formation and bulking, a DCSRFAB-associated candidate gene regulates redox signaling, involved in auxin-mediated lateral root formation, while CSRFAB is enriched for genes controlling growth and senescence. Conclusion: Candidate genes identified in this study have potential roles in cell wall remodeling, plant growth, senescence, stress, root development and redox signaling. These findings provide valuable insights into understanding the functional networks to develop strategies for sweetpotato yield improvement. The markers as well as candidate genes identified in this pioneering research for CSRFAB provide important genomic resources for sweetpotato and other root crops.Item Genome-wide Association study of Biological Nitrogen Fixation Traits in Mini-core Cowpea Germplasm(PLoS One, 2025-05-09) Nkurunziza, Gelase; Mbeyagala, Emmanuel K.; Tukamuhabwa, Phinehas; Ssemakula, Mildred Ochwo; Tumuhairwe, John Baptist; Odong, Thomas LapakaBiological Nitrogen Fixation (BNF) efficiency in legume crops such as cowpea (Vigna unguiculata L. Walp) has been less documented yet is key in improving yield performance and restoring soil fertility in sub-Saharan Africa. Nevertheless, little progress has been made in understanding the gene control of the BNF traits in cowpea to sustain the development of smart agriculture in this part of the world. This study aimed to identify cowpea genotypes and map genomic regions for BNF traits for developing high nitrogen-fixing cultivars. A total of 241 mini-core cowpea genotypes were inoculated with Bradyrhizobium spp in a screen house for two cycles. Phenotypic data collected on the number of nodules (NN) per plant, nodule efficiency (NE) in percentage, and nodule dry weight (NDW) per plant revealed significant differences implying high genetic variability in the mini-core population for nodulation capacity. Fifteen significant association signals were identified for BNF traits on nine chromosomes except Vu02 and Vu09 when two multi-locus models were considered. Markers accounting for over 15% variation for BNF traits included 2_31410 (2.32Mb) on Vu05 and 2_45545 (24.93Mb) on Vu06 for NN, 2_06530 (56.64Mb) and 2_27028 (34.31Mb) on Vu01 for NE and 2_50837 (10.07Mb) on Vu01 and 2_11699 (34.41Mb) on Vu07 for NDW, respectively. Additionally, positional candidate genes near the peak markers that encode genes associated with BNF in cowpea included Vigun06g121800, Vigun01g160600, Vigun10g014400, Vigun07g221500, Vigun07g221300 and Vigun11g096700. The genotype TVu-1477 was identified to have favorable alleles for both three studied traits. The significant markers identified in this study can be converted to Kompetitive Allele Specific-PCR (KASP) markers to accelerate the development of high-yielding cowpea varieties that also enhance soil fertility.Item Genotype by environment effects on promiscuous nodulation in soybean (Glycine max L. Merrill)(Agriculture & Food Security, 2017) Agoyi, Eric E.; Odong, Thomas L.; Tumuhairwe, John B.; Chigeza, Godfree; Diers, Brian W.; Tukamuhabwa, PhinehasUnderstanding factors influencing the expression of a trait is key in designing a breeding program. Genotype by environment interaction has great influence on most quantitative traits. Promiscuous nodulation is a trait of importance for soybean production in Africa, because of the soil bacteria Bradyrhizobium japonicum not being indigenous in most African soils. Most soybean cultivars require B. japonicum for nodulation leading to the need for seed inoculation before sowing soybean in Africa. Few cultivars have capability to nodulate with Bradyrhizobia spp. that are different from B. japonicum and native in African soils. Such cultivars are termed “promiscuous cultivars.” Field experiments were conducted in six locations in Uganda for two seasons, to investigate the extent of environmental influences on the nodulation ability of promiscuous soybean genotypes. Results: Additive main effect and multiplicative interaction effects showed highly significant environment and genotype by environment (G × E) interaction effects on all nodulation traits. G × E interaction contributed more to the total variation than genotypes. The genotypes Kabanyolo I and WonderSoya were the most stable for nodules’ dry weight (NDW), which is the nodulation trait the most correlated with grain yield. Genotype UG5 was the most stable for nodules’ number (NN), and Nam II for nodules’ effectiveness (NE). The genotype NamSoy 4M had the highest performance for NN, NFW, and NDW, but was less stable. WonderSoya had the highest NE. Genotype and genotype by environment analysis grouped environments into mega-environments (MEs), and four MEs were observed for NDW, with NamSoy 4M the winning genotype in the largest ME, and Kasese B the ideal environment for that nodulation trait. Conclusion: This study provides information that can guide breeding strategies. The low genetic effect that led to high environmental and G × E interaction effects raised the need for multi-environments testing before cultivar selection and recommendation. The study revealed genotypes that are stable and others that are high performing for nodulation traits, and which can be used as parental lines in breeding programs.Item Genotype by Environment Effects on Promiscuous Nodulation in Soybean (Glycine max L. Merrill)(Agric Food Secur, 2017-03-17) Agoyi, Eric E.; Odong, Thomas L.; Tumuhairwe, John B.; Chigeza, Godfree; Tukamuhabwa, PhinehasUnderstanding factors influencing the expression of a trait is key in designing a breeding program. Genotype by environment interaction has great influence on most quantitative traits. Promiscuous nodulation is a trait of importance for soybean production in Africa, because of the soil bacteria Bradyrhizobium japonicum not being indigenous in most African soils. Most soybean cultivars require B. japonicum for nodulation leading to the need for seed inoculation before sowing soybean in Africa. Few cultivars have capability to nodulate with Bradyrhizobia spp. that are different from B. japonicum and native in African soils. Such cultivars are termed “promiscuous cultivars.” Field experiments were conducted in six locations in Uganda for two seasons, to investigate the extent of environmental influences on the nodulation ability of promiscuous soybean genotypes. Additive main effect and multiplicative interaction effects showed highly significant environment and genotype by environment (G × E) interaction effects on all nodulation traits. G × E interaction contributed more to the total variation than genotypes. The genotypes Kabanyolo I and WonderSoya were the most stable for nodules’ dry weight (NDW), which is the nodulation trait the most correlated with grain yield. Genotype UG5 was the most stable for nodules’ number (NN), and Nam II for nodules’ effectiveness (NE). The genotype NamSoy 4M had the highest performance for NN, NFW, and NDW, but was less stable. WonderSoya had the highest NE. Genotype and genotype by environment analysis grouped environments into mega-environments (MEs), and four MEs were observed for NDW, with NamSoy 4M the winning genotype in the largest ME, and Kasese B the ideal environment for that nodulation trait. This study provides information that can guide breeding strategies. The low genetic effect that led to high environmental and G × E interaction effects raised the need for multi-environments testing before cultivar selection and recommendation. The study revealed genotypes that are stable and others that are high performing for nodulation traits, and which can be used as parental lines in breeding programs.