Sita R. Ghimire

Development of Microsatellite Markers and Analysis of Genetic Diversity and Population Structure of Colletotrichum gloeosporioides from Ethiopia.

Twenty three polymorphic microsatellite markers were developed for citrus plant pathogenic fungus, Colletotrichum gloeosporioides, and were used to analyze genetic diversity and population structure of 163 isolates from four different geographical regions of Ethiopia. These loci produced a total of 118 alleles with an average of 5.13 alleles per microsatellite marker. The polymorphic information content values ranged from 0.104 to 0.597 with an average of 0.371. The average observed heterozygosity across all loci varied from 0.046 to 0.058. The gene diversity among the loci ranged from 0.106 to 0.664. Unweighted Neighbor-joining and population structure analysis grouped these 163 isolates into three major groups. The clusters were not according to the geographic origin of the isolates. Analysis of molecular variance showed 85% of the total variation within populations and only 5% among populations. There was low genetic differentiation in the total populations (FST = 0.049) as evidenced by high level of gene flow estimate (Nm = 4.8 per generation) among populations. The results show that Ethiopian C. gloeosporioides populations are generally characterized by a low level of genetic diversity. The newly developed microsatellite markers were useful in analyzing the genetic diversity and population structure of the C. gloeosporioides populations. Information obtained from this study could be useful as a base to design strategies for better management of leaf and fruit spot disease of citrus in Ethiopia.

Homecoming of #Brachiaria#: Improved hybrids prove useful for African animal agriculture

ABSTRACT Species of the genus Brachiaria originate primarily from Africa, where they are constituents of natural grasslands. Due to their adaptation to acidic, low-fertility soils, millions of hectares of Brachiaria species have been sown as improved pastures in South and Central America, especially B. brizantha cv. Marandu and B. decumbens cv. Basilisk. Due to B. decumbens’ susceptibility to spittlebug insect pests in the Americas, CIAT in Colombia and EMBRAPA in Brazil initiated breeding programmes in the 1980s. First cultivars released from CIATs breeding programme – cvs. Mulato and Mulato-II – have also been investigated in African countries. They have been examined for integration in conservation agriculture systems (Madagascar), for drought and acidic soil tolerance (Rwanda) and for intercropping forages in dairy systems (Uganda, Madagascar), among others. Seed sales to African countries suggest that an area of at least 1,000 ha has been sown so far. The largest adoption of cv. Mulato-II is currently happening in eastern Africa, where it is used by over 20,000 farmers as a trap plant in the push-pull system for control of maize stem borers and parasitic Striga weed. Cv. Mulato-IIs particular advantage is its relatively high crude protein content due to greater leafiness and thinner stems than those of traditional Napier grass, resulting in higher nutritive quality. Yet new pest challenges have emerged, requiring further research attention. Diverse hybrids are in the pipeline for release, among them those that are suitable for cut-and-carry systems which are prevalent in eastern Africa. This paper reviews research, development and incipient adoption of new Brachiaria hybrids in African countries.

Brachiaria Grasses (Brachiaria spp.) harbor a diverse bacterial community with multiple attributes beneficial to plant growth and development

Endophytic and plant‐associated bacteria were isolated from plants and rhizoplane soil of naturally grown Brachiaria grasses at International Livestock Research Institute in Nairobi, Kenya. Eighty‐four bacterial strains were isolated from leaf tissues, root tissues, and rhizoplane soil on nutrient agar and 869 media. All bacterial strains were identified to the lowest possible taxonomic unit using 16S rDNA primers and were characterized for the production of Indole‐3‐acetic acid, hydrogen cyanide, and ACC deaminase; phosphate solubilization; siderophore production; antifungal properties; and plant biomass production. The 16S rDNA‐based identification grouped these 84 bacterial strains into 3 phyla, 5 classes, 8 orders, 12 families, 16 genera, and 50 unique taxa. The four most frequently isolated genera were Pseudomonas (23), Pantoea (17), Acinetobacter (9), and Enterobacter (8). The functional characterization of these strains revealed that 41 of 84 strains had a minimum of three plant beneficial properties. Inoculation of maize seedlings with Acinetobacter spp., Microbacterium spp., Pectobacterium spp., Pseudomonas spp., and Enterobacter spp. showed positive effects on seedling biomass production. The ability of Brachiaria grasses to host genetically diverse bacteria, many of them with multiple plant growth‐promoting attributes, might have contributed to high biomass production and adaptation of Brachiaria grasses to drought and low fertility soils.

The effect of different processing methods on nutrient and isoflavone content of soymilk obtained from six varieties of soybean grown in Rwanda

Abstract Soymilk is rich in nutrients and isoflavones, and could greatly promote nutrition and health. However, this product is not widely accepted due to an objectionable beany flavor. Several methods involving heat treatment and soaking in basic solutions prior to soymilk extraction have been reported to reduce the objectionable flavor. However, the effects of such treatments on the nutritional value and isoflavone content of soymilk, and the responses of different soybean varieties to nutrient extraction by these methods is not well studied. The aim of this study was to determine the effect of three processing methods on protein, fat, minerals, and isoflavone content in soymilk from six soybean varieties grown in Rwanda (Peka‐6, SB 24, Sc. Sequel, Sc, Squire, and a local variety) to find the best variety and processing method. The first method (M1) involved soaking soybeans in water for 12 hr prior to milk extraction, M2 involved blanching in NaHCO 3 prior to extraction and M3 involved soaking in NaHCO 3 solution for 16 hr and subsequent cooking prior to extraction. M1 resulted in significantly higher nutrient and isoflavone extraction than M2 and M3. Thus, M1 extracted more nutrients and can be recommended for soymilk production. However, where consumers prefer soymilk obtained by M2 or M3, Sc Squire and the local variety may be recommended. Sc. Squire has another advantage of higher isoflavone content than the other varieties. Further comprehensive studies on the sensory acceptability of products made from different varieties by different methods among different consumer categories will be necessary.

Genetic diversity and population structure of Urochloa grass accessions from Tanzania using simple sequence repeat (SSR) markers

Urochloa (syn.—Brachiaria s.s.) is one of the most important tropical forages that transformed livestock industries in Australia and South America. Farmers in Africa are increasingly interested in growing Urochloa to support the burgeoning livestock business, but the lack of cultivars adapted to African environments has been a major challenge. Therefore, this study examines genetic diversity of Tanzanian Urochloa accessions to provide essential information for establishing a Urochloa breeding program in Africa. A total of 36 historical Urochloa accessions initially collected from Tanzania in 1985 were analyzed for genetic variation using 24 SSR markers along with six South American commercial cultivars. These markers detected 407 alleles in the 36 Tanzania accessions and 6 commercial cultivars. Markers were highly informative with an average polymorphic information content of 0.79. The analysis of molecular variance revealed high genetic variation within individual accessions in a species (92%), fixation index of 0.05 and gene flow estimate of 4.77 showed a low genetic differentiation and a high level of gene flow among populations. An unweighted neighbor-joining tree grouped the 36 accessions and six commercial cultivars into three main clusters. The clustering of test accessions did not follow geographical origin. Similarly, population structure analysis grouped the 42 tested genotypes into three major gene pools. The results showed the Urochloa brizantha (A. Rich.) Stapf population has the highest genetic diversity (I = 0.94) with high utility in the Urochloa breeding and conservation program. As the Urochloa accessions analyzed in this study represented only 3 of 31 regions of Tanzania, further collection and characterization of materials from wider geographical areas are necessary to comprehend the whole Urochloa diversity in Tanzania.

Molecular Characterizations of Kenyan Brachiaria Grass Ecotypes with Microsatellite (SSR) Markers

Brachiaria grass is an emerging forage option for livestock production in Kenya. Kenya lies within the center of diversity for Brachiaria species, thus a high genetic variation in natural populations of Brachiaria is expected. Overgrazing and clearing of natural vegetation for crop production and nonagricultural uses and climate change continue to threaten the natural biodiversity. In this study, we collected 79 Brachiaria ecotypes from different parts of Kenya and examined them for genetic variations and their relatedness with 8 commercial varieties. A total of 120 different alleles were detected by 22 markers in the 79 ecotypes. Markers were highly informative in differentiating ecotypes with average diversity and polymorphic information content of 0.623 and 0.583, respectively. Five subpopulations: International Livestock Research Institute (ILRI), Kitui, Kisii, Alupe, and Kiminini differed in sample size, number of alleles, number of private alleles, diversity index, and percentage polymorphic loci. The contribution of within-the-individual difference to total genetic variation of Kenyan ecotype population was 81%, and the fixation index (FST = 0.021) and number of migrant per generation (Nm = 11.58) showed low genetic differentiation among the populations. The genetic distance was highest between Alupe and Kisii populations (0.510) and the lowest between ILRI and Kiminini populations (0.307). The unweighted neighbor-joining (NJ) tree showed test ecotypes grouped into three major clusters: ILRI ecotypes were present in all clusters; Kisii and Alupe ecotypes and improved varieties grouped in clusters I and II; and ecotypes from Kitui and Kiminini grouped in cluster I. This study confirms higher genetic diversity in Kenyan ecotypes than eight commercial varieties (Basilisk, Humidicola, Llanero, Marandú, MG4, Mulato II, Piatá and Xaraés) that represent three species and one three-way cross-hybrid Mulato II. There is a need for further collection of local ecotypes and their morphological, agronomical, and genetic characterizations to support Brachiaria grass breeding and conservation programs.