Assessment of Genetic Diversity of the Wild Rice (Oryza longistaminata) Populations in Tanzania Using Microsatellite Markers

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

Typology and characteristics of indigenous goats and production systems in different agro-ecological zones of Tanzania

Tanzania has a goat population of about 24.8 million most of which belong to the Small East African breed distributed in almost all agro-ecological zones. The different goat populations and the production system in which they are raised are not well characterized depriving animal breeders useful information in designing and running improvement and conservation programs. Therefore, the study was conducted in all agro-ecological zones in Tanzania to characterize the indigenous goats and the production system in which they are raised. Data on animals were collected from 688 randomly selected adult female goats and for production system description; 220 households were interviewed. Analysis of variance and discriminant analysis were used on quantitative data, while frequency analysis was used on qualitative data. Income generation and meat production were the primary goat rearing objectives. More than 55% of respondents grazed their animals freely in communal lands where natural pasture was the chief feed resource. Mating was mainly uncontrolled with apron and castration being used by goat keepers as mating control methods. Common diseases were contagious caprine pleural pneumonia and helminthiasis. Feed shortage, prevalence of diseases, and water scarcity were the major goat production constraints. There were morphological variations between and within these goat populations, and based on quantitative data, the goats were categorized into two groups. High twinning was observed in Ujiji and Lindi goats and low for Sukuma. The dominant coat color was plain white in Pare, Gogo, Maasai, and Tanga. Other coat color patterns were mixed black and white for Sukuma, reddish-brown for Lindi, black and reddish-brown for Ujiji, and white and reddish-brown for Pwani and Maasai. High within population variation is observed which is important as it can be used as a basis for genetic improvement through selection

Genetic and toxigenic variability within Aspergillus flavus population isolated from maize in two diverse environments in Kenya

Aspergillus flavus is the main producer of carcinogenic aflatoxins in agricultural commodities such as maize. This fungus occurs naturally on crops, and produces aflatoxins when environmental conditions are favorable. The aim of this study is to analyse the genetic variability among 109 A. flavus isolates previously recovered from maize sampled from a known aflatoxin-hotspot (Eastern region, Kenya) and the major maize-growing area in the Rift Valley (Kenya), and to determine their toxigenic potential. DNA analyses of internal transcribed spacer (ITS) regions of ribosomal DNA, partial beta-tubulin gene (benA) and calmodulin gene (CaM) sequences were used. The strains were further analyzed for the presence of four aflatoxin-biosynthesis genes in relation to their capability to produce aflatoxins and other metabolites, targeting the regulatory gene aflR and the structural genes aflP, aflD, and aflQ. In addition, the metabolic profile of the fungal strains was unraveled using state-of-the-art LC-MS/MS instrumentation. The three gene-sequence data grouped the isolates into two major clades, A. minisclerotigenes and A. flavus. A. minisclerotigenes was most prevalent in Eastern Kenya, while A. flavus was common in both regions. A. parasiticus was represented by a single isolate collected from Rift Valley. Diversity existed within the A. flavus population, which formed several subclades. An inconsistency in identification of some isolates using the three markers was observed. The calmodulin gene sequences showed wider variation of polymorphisms. The aflatoxin production pattern was not consistent with the presence of aflatoxigenic genes, suggesting an inability of the primers to always detect the genes or presence of genetic mutations. Significant variation was observed in toxin profiles of the isolates. This is the first time that a profound metabolic profiling of A. flavus isolates was done in Kenya. Positive associations were evident for some metabolites, while for others no associations were found and for a few metabolite-pairs negative associations were seen. Additionally, the growth medium influenced the mycotoxin metabolite production. These results confirm the wide variation that exists among the group A. flavus and the need for more insight in clustering the group

Marker-assisted selection complements phenotypic screening at seedling stage to identify cassava mosaic disease-resistant genotypes in African cassava populations

Abstract Cassava mosaic disease (CMD) is a serious threat to cassava production in sub-Saharan Africa. The use of genomic-assisted selection at the seedling trial stage would help to reduce the time for release, breeding cost, and resources used, hence increase selection efficiency in cassava breeding programs. Five cassava populations were screened for resistance to CMD during the seedling evaluation trial at 1, 3, and 5 months after planting using a scale of 1–5. The genotypes in the five populations were also screened using six molecular markers linked to the CMD2 gene. The correlation between the phenotypic and marker data was estimated. Based on Cassava Mosaic Disease Severity Score (CMDSS), between 53 and 82% of the progenies were resistant across the populations with an average of 70.5%. About 70% of the progenies were identified to be resistant to the disease across the populations with a range of 62–80% using the marker data. With both marker data and CMDSS combined, 40–60% of the progenies in each population, with an average of 52%, were identified to be resistant to CMD. There was a fairly significant correlation between the marker data and CMDSS in each cassava population with correlation coefficients ranging from 0.2024 to 0.3460 suggesting that novel genes not associated to the markers used might be involved in the resistance to CMD. The resistant genotypes identified in this study with potential for other desirable traits were selected for evaluation at the advanced trial stage thereby shortening the period required for the breeding program

Marker-assisted selection complements phenotypic screening at seedling stage to identify cassava mosaic disease-resistant genotypes in African cassava populations

Cassava mosaic disease (CMD) is a serious threat to cassava production in sub-Saharan Africa. The use of genomic-assisted selection at the seedling trial stage would help to reduce the time for release, breeding cost, and resources used, hence increase selection efficiency in cassava breeding programs. Five cassava populations were screened for resistance to CMD during the seedling evaluation trial at 1, 3, and 5 months after planting using a scale of 1–5. The genotypes in the five populations were also screened using six molecular markers linked to the CMD2 gene. The correlation between the phenotypic and marker data was estimated. Based on Cassava Mosaic Disease Severity Score (CMDSS), between 53 and 82% of the progenies were resistant across the populations with an average of 70.5%. About 70% of the progenies were identified to be resistant to the disease across the populations with a range of 62–80% using the marker data. With both marker data and CMDSS combined, 40–60% of the progenies in each population, with an average of 52%, were identified to be resistant to CMD. There was a fairly significant correlation between the marker data and CMDSS in each cassava population with correlation coefficients ranging from 0.2024 to 0.3460 suggesting that novel genes not associated to the markers used might be involved in the resistance to CMD. The resistant genotypes identified in this study with potential for other desirable traits were selected for evaluation at the advanced trial stage thereby shortening the period required for the breeding program

Mitochondrial DNA D-loop sequence analysis reveals high variation and multiple maternal origins of indigenous Tanzanian goat populations

The Small East African (SEA) goat are widely distributed in different agro-ecological zones of Tanzania. We report the genetic diversity, maternal origin, and phylogenetic relationship among the 12 Tanzanian indigenous goat populations, namely Fipa, Songwe, Tanga, Pwani, Iringa, Newala, Lindi, Gogo, Pare, Maasai, Sukuma, and Ujiji, based on the mitochondrial DNA (mtDNA) D-loop. High haplotype (H-d = 0.9619-0.9945) and nucleotide (pi = 0.0120-0.0162) diversities were observed from a total of 389 haplotypes. The majority of the haplotypes (n = 334) belonged to Haplogroup A which was consistent with the global scenario on the genetic pattern of maternal origin of all goat breeds in the world. Haplogroup G comprised of 45 haplotypes drawn from all populations except the Ujiji goat population while Haplogroup B with 10 haplotypes was dominated by Ujiji goats (41%). Tanzanian goats shared four haplotypes with the Kenyan goats and two with goats from South Africa, Namibia, and Mozambique. There was no sharing of haplotypes observed between individuals from Tanzanian goat populations with individuals from North or West Africa. The indigenous goats in Tanzania have high genetic diversity defined by 389 haplotypes and multiple maternal origins of haplogroup A, B, and G. There is a lot of intermixing and high genetic variation within populations which represent an abundant resource for selective breeding in the different agro-ecological regions of the country

Assessment of Genetic Diversity and Structure of Sudanese Sorghum Accessions using Simple Sequence Repeat (SSRs) Markers Assessment of Genetic Diversity and Structure of Sudanese Sorghum Accessions using Simple Sequence Repeat (SSRs) Markers

ABSTRACT 95 sorghum accessions (1,425 individuals) sampled represented most of crop-cultivated areas in Sudan. The genetic diversity and population structure was assessed using a panel of 39 SSRs marker, which covered the sorghum genome. Genotypic data was generated using the ABI 3730 genetic analyzer. The alleles were called and sized usin