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Oryza Longistaminata) Populations in Tanzania Using Microsatellite Markers

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Oryza Longistaminata) Populations in Tanzania Using Microsatellite Markers Tanzania Journal of Science 46(3): 828-839, 2020 ISSN 0856-1761, e-ISSN 2507-7961 © College of Natural and Applied Sciences, University of Dar es Salaam, 2020 Assessment of Genetic Diversity of the Wild Rice (Oryza longistaminata) Populations in Tanzania Using Microsatellite Markers Hashim M. Mangosongo1, Emerald E. Mneney2, Jagger Harvey3 and Martina Kyallo3 1Department of Botany, University of Dar es Salaam, Tanzania, 2Mikocheni Agricultural Research Institute, Tanzania, 3Biosciences Eastern and Central Africa, Kenya. Corresponding author: [email protected] Received 8 Jan 2020, Revised 11 Oct 2020, Accepted 13 Oct 2020, Published Oct 2020 Abstract The genetic diversity of 132 samples of the perennial wild rice (Oryza longistaminata) populations from selected districts (Bagamoyo, Kibaha, Kilombero and Mbarali) in Tanzania was evaluated using twenty eight microsatellite markers. Genomic DNA was extracted using standard protocols. Polymerase Chain Reaction (PCR) was carried out in a total reaction volume of 10 µL, using Touchdown protocol. It was found that all 28 microsatellite markers generated polymorphic patterns, with average Polymorphic Information Content (PIC) value of 0.631. Moreover, a total of 243 alleles were detected by the 28 markers, with average of 8.68 alleles per marker. The percentages of genetic variations among and within populations were 10% and 90%, respectively, implying that there was more gene flow among populations than within populations. Furthermore, the O. longistaminata population from Kilombero had highest genetic diversity followed by population from Mbarali, while the lowest genetic diversity was recorded in the population from Kibaha. Generally the populations from Kilombero, Mbarali and Bagamoyo were found to have relatively high genetic diversity, hence have potential to be used in rice breeding. In situ conservation of this species is recommended, and it can be achieved by conserving all areas which harbour populations with high levels of genetic diversity. Keywords: Genetic diversity, Microsatellites, SSR Markers, Oryza longistaminata, Wild rice. Introduction longistaminata A. Chev. et Roehr, O. barthii Oryza longistaminata is the perennial, A. Chev., O. brachyantha A. Chev. et Roehr, rhizomatous wild rice species belonging to O. eichingeri A. Peter, and O. punctata genus Oryza, family Gramineae (Poaceae), Kotschy ex Steud. The O. longistaminata is which is one of the largest and most widely the most widely distributed wild rice species distributed families of flowering plants. The in Africa, and due to its extensive distribution genus Oryza consists of two cultivated in Africa it is sometimes referred to as species, namely Oryza sativa L. and Oryza African wild rice. The wide range of glaberrima Steud. In addition to the two distribution of O. longistaminata is caused by cultivated species, the genus also contains its perennial growth habit, dual regeneration about twenty two (22) wild species (Ukoskit ability (through seeds and rhizomes) and 2004) of which five are indigenous to Africa tolerance to biotic and abiotic stresses (Vaughan 1994). The five wild species which (Melaku et al. 2013). Inventory studies and are indigenous to Africa are O. herbarium materials show that Tanzania is a 828 http://journals.udsm.ac.tz/index.php/tjs www.ajol.info/index.php/tjs/ Tanz. J. Sci. Vol. 46(3), 2020 home to all the five wild rice species. Oryza which is one of the most important cereal longistaminata, which is the only cross- crops in the world, is the staple food to about pollinated wild rice species in Tanzania, a half of the global population (Song et al. belongs to AA genome (Gichuhi 2017). 2003). Similarly, rice is one of the most Moreover, this species is regarded as the wild important food crops in Tanzania, thus progenitor of the African cultivated rice improved rice productivity may contribute to called O. glaberrima (Kiambi et al. 2008). food security in the country. According to Oryza longistaminata is one of the most studies, effective conservation of genetic important wild rice species in agriculture as it resources from wild rice species as well as contains genes for bacterial blight resistance, selection and utilization of a wild rice high pollen production, long stigmas and genotype in rice breeding programs require drought tolerance (Khush et al. 1990, Kiambi knowledge or understanding on its genetic et al. 2005). These genes may be introgressed diversity (Govindaraj et al. 2015, into the cultivated rice through hybridization Mangosongo et al. 2019). Moreover, Dashab in order to improve the cultivated rice et al. (2011) asserted that success in breeding varieties or cultivars. In some countries, such programs depends on the amount of genetic as Ethiopia and Sudan, O. longistaminata is variation in the population, thus lack of used as famine food and as fodder for diversity limits success of any breeding livestock (Melaku et al. 2013). In Tanzania, program. O. longistaminata grows naturally in Genetic diversity is the amount of genetic wetlands and swampy areas, such as ponds, variability among individuals of a variety or rice fields, swamps, irrigation canals or population of a species (Brown 1983). It is a riverbeds in various regions, including Dar es measure of the magnitude of genetic Salaam, Coast, Morogoro, Iringa, Mbeya, variability within a population. Allele Kigoma, Mwanza and Shinyanga (Miezan frequency, heterozygosity, allelic richness and Second 1979, Katayama 1990, and percentage polymorphic loci are among Mangosongo et al. 2019). However, the measures of within-locus genetic fragmentation, loss and reduction of natural diversity. Genetic diversity results from many habitats of this species caused by human genetic differences between or among activities are among the main threats to the individuals and can be manifested in species genetic diversity. Habitat differences in DNA sequence, biochemical fragmentation and loss are believed to cause characteristics, physiological properties, or reduction or erosion of genetic diversity of O. morphological characters (Rao and Hodgkin longistaminata in different parts of the world 2002). Genetic diversity or variation is (Kiambi et al. 2008), thus a need for fundamental to evolution as it provides basic conservation. Application of in situ and/or ex materials on which adaptation and speciation situ conservation strategies would help to depend (Amos and Harwood 1998). Variation ensure effective conservation of this species. in genes is necessary for organisms to adapt Possession of agronomically important to ever changing environment. Therefore, genes makes the O. longistaminata an populations with high levels of genetic important reservoir of useful genes for diversity are regarded as healthy, thus tolerance to biotic and abiotic stresses that conferring ability to respond to threats such may be used in rice breeding programs (Song as diseases, parasites and environmental et al. 2005). Proper utilization of genetic changes. Conversely, low levels of genetic resources from wild rice species in rice variability limits the species ability to breeding may significantly improve respond to these threats in short and long cultivated rice cultivars and yield or terms. Genetic diversity may be gained productivity (Mangosongo et al. 2019). Rice, through mutation or through gene flow from 829 Mangosongo - Assessment of genetic diversity of the wild rice (Oryza longistaminata) ... neighbouring population and can be lost longistaminata in the study area was limited through genetic drift or through natural and inadequate. This study aimed to provide selection (Amos and Harwood 1998). knowledge on genetic diversity or variations This study evaluated the genetic diversity among and within O. longistaminata of O. longistaminata populations in four populations in the four districts. Such districts of Tanzania using microsatellite knowledge is essential for development of markers. The microsatellite markers, which proper conservation strategies and for are also known as Simple Sequence Repeats selection of genotypes to be used in rice (SSR) markers were preferred in this study breeding programs to ensure improved rice due to their technical simplicity, relatively quality and yield or productivity. low cost, high power of genetic resolution, co-dominance nature and high polymorphism Materials and Methods in plant species (Zhou et al. 2003, Semagn et The study area al. 2006, Melaku et al. 2013). Human This study was conducted in four selected activities, including cultivation observed in districts of Tanzania. The four districts were the study area are likely to cause habitat Bagmoyo, Kibaha, Kilombero and Mbarali fragmentation, hence affecting the genetic (Figure 1). In these districts O. diversity of the species. Prior to this study, longistaminata was sampled in swampy knowledge on the genetic diversity of O. areas, including in the rice fields. Figure 1: The map of Tanzania showing the location of study sites. Leaf sampling and DNA extraction individual plants in the four study sites Young leaf samples of O. longistaminata (districts). A total of 33 samples were were collected from 132 randomly selected collected from each site. Two to three newly 830 Tanz. J. Sci. Vol. 46(3), 2020 formed leaves were collected from each into the DNA analyser (ABI 3730) for plant. Collected leaf samples were preserved fragment analysis and the resulting fragments in a zip locked plastic bag containing silica were scored on the Genemapper Version
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