Browsing by Author "Muchugi, Alice"

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    Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome
    (GigaScience, 2019) Song, Bo; Song, Yue; Fu, Yuan; Balyejusa Kizito, Elizabeth; Ndagire Kamenya, Sandra; Nahamya Kabod, Pamela; Liu, Huan; Muthemba, Samuel; Kariba, Robert; Njuguna, Joyce; Maina, Solomon; Stomeo, Francesca; Djikeng, Appolinaire; Hendre, Prasad S.; Chen, Xiaoli; Chen, Wenbin; Li1, Xiuli; Sun, Wenjing; Wang, Sibo; Cheng, Shifeng; Muchugi, Alice; Jamnadass, Ramni; Shapiro, Howard-Yana; Van Deynze, Allen; Yang, Huanming; Wang, Jian; Xu, Xun; Achieng Odeny, Damaris; Liu, Xin
    The African eggplant (Solanum aethiopicum) is a nutritious traditional vegetable used in many African countries, including Uganda and Nigeria. It is thought to have been domesticated in Africa from its wild relative, Solanum anguivi. S. aethiopicum has been routinely used as a source of disease resistance genes for several Solanaceae crops, including Solanum melongena. A lack of genomic resources has meant that breeding of S. aethiopicum has lagged behind other vegetable crops. Results: We assembled a 1.02-Gb draft genome of S. aethiopicum, which contained predominantly repetitive sequences (78.9%). We annotated 37,681 gene models, including 34,906 protein-coding genes. Expansion of disease resistance genes was observed via 2 rounds of amplification of long terminal repeat retrotransposons, which may have occurred ∼1.25 and 3.5 million years ago, respectively. By resequencing 65 S. aethiopicum and S. anguivi genotypes, 18,614,838 single-nucleotide polymorphisms were identified, of which 34,171 were located within disease resistance genes. Analysis of domestication and demographic history revealed active selection for genes involved in drought tolerance in both “Gilo” and “Shum” groups. A pan-genome of S. aethiopicum was assembled, containing 51,351 protein-coding genes; 7,069 of these genes were missing from the reference genome. Conclusions: The genome sequence of S. aethiopicum enhances our understanding of its biotic and abiotic resistance. The single-nucleotide polymorphisms identified are immediately available for use by breeders. The information provided here will accelerate selection and breeding of the African eggplant, as well as other crops within the Solanaceae family.
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    Genetic Diversity in Shea Tree (Vitellaria Paradoxa Subspecies Nilotica) Ethno-Varieties in Uganda Assessed with Microsatellite Markers
    (Forests, Trees and Livelihoods, 2015) Gwali, Samson; Vaillant, Alexandre; Nakabonge, Grace; Okullo, John Bosco Lamoris; Eilu, Gerald; Muchugi, Alice; Bouvet, Jean-Marc
    Shea trees (Vitellariaparadoxa C. F. Gaertn.) are classified locally into several folk or ethno-varieties by farmers in Uganda. It is, however, not clear whether this folk classification is supported by genetic differentiation between ethno-varieties. Genetically linked traits from folk classification are useful in conservation and breeding programmes. A total of 118 individual shea trees constituting 28 ethno-varieties sampled from three farming systems of Uganda were analysed using microsatellite markers. The number of alleles amplified per microsatellite locus ranged from 6 to 13 with an average of 9.5, with a total of 106 alleles identified. Observed (Ho) and expected heterozygosity (He) per locus ranged from 0.366 to 0.934 and 0.580 to 0.840, respectively. Mean Ho and He values for all loci across all ethno-varieties were 0.633 and 0.727, respectively. Analysis of molecular variance indicated that most of the variation (86.28%) occurred within individual trees; 11.25% was found among individual trees within ethno-varieties while 2.47% was found among ethno-varieties. The in-breeding index (f = 0.130), fixation index (θP = 0.025), gene flow value (Nm = 6.56) and cluster analysis show that all shea tree ethno-varieties were a single out-crossing population with very low genetic differentiation and high gene flow. The low differentiation in shea tree ethno-varieties was most likely due to the utilization of non-genetic traits in folk classification. However, while ethno-variety genetic structure was very weak, overall spatial population structure indicated the presence of three populations (West Nile, Northern and Teso). The West Nile population was more distantly related to the other two most likely due to isolation barriers such as the Rift Valley, Lake Albert and River Nile.
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    Local knowledge, identification and selection of shea tree (Vitellaria paradoxa) ethnovarieties for pre-breeding in Uganda
    (The Journal of Agriculture and Natural Resources Sciences, 2020) Odoi, Juventine Boaz; Muchugi, Alice; Akias Okia, Clement; Gwali, Samson; Odong, Thomas L.
    Local knowledge is important in characterizing and selecting shea tree ethnovarieties since the local communities have lived with the species for quite so long. The communities have developed their classification methods based on specific phenotypic traits used to distinguish one ethnovariety from another. This has helped them select and conserve specific genotypes of their interest on farm. Variants of shea trees exist in different populations known by the local communities. This study aimed at identifying and selecting high oil yielding shea tree “ethnovarieties” in Katakwi; Otuke; Amuru; Moyo; Arua and Nakasongola districts of Uganda using local knowledge. The districts were selected because of their long historical association with shea trees which has become part of their socio-cultural and economic lifestyle, so they have broad local knowledge about shea tree variations within their areas. The study aimed at identifying and selecting superior individual shea tree ethnovarieties with high oil yield using local knowledge for seed collection to raise a half sib population. Data was collected in the months of November and December 2017 from 246 shea tree farmers through interviews, 8 focus group discussions conducted, and 6 Key informer interviews with opinion leaders, civic leaders and local leaders in the districts. List of fifteen shea butter tree ethnovarieties with their descriptive characteristics was generated per district. 53.4% of the people who were interviewed were women and 46.4% were men. Data analysis using Statistical Package for Social Sciences (SPSS 20v) was run using multivariate analysis and multiple regression analysis to test for any differences in local knowledge of shea tree ethnovarietis. Differences in local knowledge in the research districts was moderately significant with P = 0.043, df = 4 and X2 =9.837.
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    Variation in phenotypic traits of high oil yielding and early maturing shea trees (Vitellaria paradoxa) selected using local knowledge
    (The Journal of Agriculture and Natural Resources Sciences, 2020) Boaz Odoi, Juventine; Odong, Thomas L.; Akias Okia, Clement; Muchugi, Alice; Gwali, Samson
    Shea trees (vitellaria paradoxa) grow in West Nile, Teso, Lango and Acholi subregions of Uganda existing in different forms called enthnovarieties. Farmers from each of these subregions use phenotypic characteristics to differentiate one ethnovariety from the other. We conducted phenotypic characterization of shea trees identified by farmers as high oil yielding and early maturing and verified the farmers’ descriptors with standard phenotypic characterization. The study was conducted in the districts of Amuru, Arua, Katakwi, Moyo and Otuke between May and June 2017. One hundred eighty mature shea trees were purposively sampled from the five districts based on local knowledge. Descriptive statistics was then used to determine the variation among the different shea tree phenotypes characterized using standard descriptors. Twenty-seven ethnovarieties were recorded using farmers’ descriptors which were later on reduced to sixteen phenotypic traits using standard phenotypic descriptors related to fruit shapes, texture and kernel color. Variation in the kernel weights, fruit length and fruit width were significant (p < 0.05) and the shea fruit and seed width were highly correlated (78.6%) to their weights. We identified significant variation in shea trees within sites and fruit and seed weights between sites (p ≤ 0.001). Although variability within sites was significant, most parameters (height, diameter at breast height (dbh at 1.3 m), crown shape and height at first branching) were not. Shea fruit/kernel traits are important in characterizing varieties since they exhibit different forms across the sites since tree phenotypic attributes do not vary from location to location in Uganda. This lack of variability of ethnovarieties across the shea belt in Uganda is important in breeding for traits that can be acceptable by all the communities within the shea growing regions. The different shea ethnovarieties are therefore important in influencing policy decisions on their conservation.
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    Variation in Seedling Germination and Growth in Five Populations Of vitellariaparadoxa C.F. Gaertn.subsp. Nilotica: A Threatened useful fruit Tree Species in Uganda
    (Research Square, 2020) Boaz Odoi, Juventine; Odong, Thomas L.; Akias Okia, Clement; Lomoris Okullo, JohnBosco; Okao, Moses; Kabasindi, Harriet; Muchugi, Alice; Gwali, Samson
    We studied seedlings germination and growth performance in an economically and socially important fruit tree species of Vitellaria paradoxaC.F. Gaertn.subsp. nilotica (Kotschy) in Uganda. The study aimed at determining variability in germination of the five shea tree seed lots and seedlings growth performance based on their growth traits. Five populations were considered from four agroecological zones of Uganda and 180 candidates plus trees (16 ethnovarieties) selected as seed trees based on their traits for faster growth and high oil yield. A total of 1204 biological seeds were collected and sown in a general tree nursery at Ngetta Zonal Agricultural Research and Development Institute (NgeZARDI)during the month of June 2018 in a randomized incomplete block design with three replications. Results: Significant variation (χ = 526; p < 0.01) was observed in seedling phenotypic traits within and between populations. Regression equation for height growth and leaf size index were given asy = 0.3787 + 12.671x and y = 0.6483 + 15.413x respectively. Root collar diameter was more correlated to leaf size index (0.425) than to height growth (0.30). Clustering of shea tree seedlings based on phenotypic growth traits revealed one aggregated cluster indicating that most of the seedlings from the five populations were similar (Jaccard index 0.92, p < 0.01). However, clustering based on SNP markers revealed three different populations. We recorded higher growth (χ = 708; p< 0.001) in Arua shea population (19.69 cm)compared to the population average (19.04 cm). Red seeded; thin pulped and hairy fruited shea tree ethnovarieties assumed faster growth than the rest. Conclusions: The phenotypic analysis of shea tree seedlings revealed some fast-growing genotypes from the five studied populations. Thesegenotypes can be selected for faster growth for shea tree breeding in Uganda.