Browsing by Author "Djikeng, Appolinaire"

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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 and Population Structure of Brachiaria (syn. Urochloa) Ecotypes from Uganda
    (MDPI AG, 2020-08) Namazzi, Clementine; Sserumaga, Julius Pyton; Mugerwa, Swidiq; Kyalo, Martina; Mutai, Collins; Mwesigwa, Robert; Djikeng, Appolinaire; Ghimire, Sita
    Brachiaria (syn. Urochloa) grass is an important tropical forage of African origin that supports millions of livestock and wildlife in the tropics. Overgrazing, conversion of grasslands for crop production and non-agricultural uses, and the introduction of improved forages have threatened the natural diversity of Brachiaria grass in Uganda. This study established a national collection of Brachiaria ecotypes in Uganda and analyzed them for genetic diversity and population structure using 24 simple sequence repeats (SSR) markers. These markers had a high discriminating ability with an average polymorphism information content (PIC) of 0.89 and detected 584 alleles in 99 ecotypes. Analysis of molecular variance revealed a high within populations variance (98%) indicating a high gene exchange or low genetic differentiation (PhiPT = 00.016) among the ecotype populations. The Bayesian model based clustering algorithm showed three allelic pools in Ugandan ecotypes. The principal component analysis (PCA) of ecotypes, and Neighbor-joining (NJ) tree of ecotypes and six commercial cultivars showed three main groups with variable membership coefficients. About 95% of ecotype pairs had Rogers’ genetic distance above 0.75, suggesting most of them were distantly related. This study confirms the high value of these ecotypes in Brachiaria grass conservation and improvement programs in Uganda and elsewhere.