Biology subjects

Tesfaye, K.

Publications and source records attributed to Tesfaye, K..

7 recordsLinked to original sources

bioRxiv2026

Genetic diversity and population structure of Ethiopian taro Colocasia esculenta (L.) Schott) as revealed by SSR markers

Abstract Taro (Colocasia esculenta (L.) Schott) is an important root and tuber crop that contributes to food security and livelihoods, but its genetic diversity remains poorly characterized in Ethiopia. This study assessed Ethiopian taro genetic diversity and population structure using simple sequence repeat (SSR) markers. We analyzed 119 accessions, 79 collected from farmers fields and 40 from the Ethiopian Biodiversity Institute (EBI), representing three regional populations: South Ethiopia Regional State (SERS), South West Ethiopia Peoples Regional State (SWEPRS), and Oromia. Fifteen polymorphic SSR markers produced 199 reproducible polymorphic loci, with 100% polymorphism. Polymorphism information content (PIC) ranged from 0.300 to 0.888 (mean 0.583). Diversity based on scored binary marker states was relatively low, with a mean effective number of alleles (Ne) of 1.077 and expected heterozygosity (He) of 0.066. Across populations, He ranged from 0.047 to 0.061, and the percentage of polymorphic loci ranged from 37.14% to 82.57%. Analysis of molecular variance showed that 98% of molecular variation occurred within populations and 2% among populations. Genetic differentiation ({Phi}PT, proportion of molecular variation among populations) was weak but significant ({Phi}PT = 0.016, P = 0.016). Principal coordinate analysis, neighbor-joining (NJ), and unweighted pair-group method with arithmetic mean (UPGMA) clustering showed extensive overlap among accessions and no clear geographic structuring. Bayesian clustering identified two groups as the strongest partition according to the {Delta}K criterion, but substantial admixture occurred, and groups did not correspond clearly to geographic populations. Despite relatively low diversity at individual scored loci, all 119 accessions had unique multilocus genotypes, indicating high multilocus genotypic diversity. Most molecular variation occurred within rather than among regional populations, potentially reflecting planting-material exchange and predominantly clonal propagation. These findings provide a basis for conserving, characterizing, and utilizing Ethiopian taro germplasm in crop improvement.

genetics↗

bioRxiv2026

What makes a banana false? How the genome of Ethiopian orphan staple Ensete ventricosum differs from the banana A and B sub-genomes

BackgroundEnsete ventricosum, also known as the "tree against hunger" plays a key role in Ethiopian food security and farming systems, feeding more than 20 million people. Since domestication via clonal selection in the south-west Ethiopian highlands, todays diverse enset landraces contribute multiple benefits including food, fibre by-product, animal bedding and cattle fodder to farmers and local communities. Improved genomic resources for this highly drought-tolerant plant are essential to supplement the conventional clonal selection-based breeding programme and pave the way towards targeted breeding. ResultsWe sequenced the genome of enset landrace Mazia, which is partially resistant/tolerant to Xanthomonas wilt and predicted 38,940 protein-coding genes. The Mazia assembly (540.14 Mb) is more complete than the previously published genome assembly of landrace Bedadeti (451.28 Mb) and displayed 1.41% heterozygosity and 64.64% repetitive DNA content. Comparative analyses with the Bedadeti assembly and chromosome-level genome sequences of the two main banana progenitors (Musa acuminata, AA genome; Musa balbisiana, BB genome) unexpectedly revealed [~]25% of the Mazia genome is unique to enset. Gene Ontology (GO) and sequence similarity search analysis of enset-specific protein-coding genes identified distinct functional signatures that underpin the lifestyle, adaptation, and corm productive quality of enset, including functions related to DNA integration, carbohydrate metabolism, disease resistance and transcriptional regulation. In contrast, Musa-specific genes showed enrichment for defence response, protein phosphorylation and fruit development pathways. Focusing on the classical nucleotide binding site leucine rich repeat (NLR) disease resistance genes, we identified and characterised NLRs in enset and Musa species genomes, revealing a considerable expansion in the Musa acuminata genome. We also identified unique genes in enset and banana genomes whose functional and evolutionary roles are yet to be determined. ConclusionsHere, we report a de novo genome assembly for the enset (Ensete ventricosum) landrace Mazia and provide a high-quality annotation of both Mazia and the previously published assembly of the landrace Bedadeti. Collectively, these genomic resources provide a valuable foundation for comparative genomics within the Musaceae family and open new opportunities for the development of marker-assisted breeding strategies to accelerate the improvement of agronomically important traits in enset.

bioinformatics↗

bioRxiv2025

Pan-genome analyses of 226 finger millet-infecting Magnaporthe oryzae strains from eastern Africa reveal two lineages that differ in their genetic make-up, virulence and effector gene content with gene loss driven by homologous recombination between Pot2 elements

Blast disease, caused by the filamentous ascomycete Magnaporthe oryzae, is the main biotic constraint to finger millet production in eastern Africa. M. oryzae is a pathogen on many grass species, but the high host-specificity of blast isolates underscores the need to study pathogen diversity and virulence at the host level. Here, we fill a void on knowledge on finger millet-infecting strains of M. oryzae by sequencing 226 isolates pure-cultured from infected tissues, mainly peduncles and panicles, sampled from field-grown finger millet accessions across Ethiopia, Kenya, Tanzania and Uganda. Phylogenetic analysis showed that eastern African isolates are genetically distinct from Asian isolates, and differentiated into two groups potentially driven by climate variables. One group was dominated by isolates from Kenya and Uganda (KU group), and the other by isolates from Ethiopia and Tanzania (ET group). Analysis of the portfolio of 887 predicted effector genes showed that the KU group had significantly fewer effectors, concomitant with higher virulence levels on the two finger millet accessions tested. We demonstrate that homologous recombination between transposable elements, leading to genomic deletions, plays a key role in gene removal. Transcript profiling of fungal genes in compatible and incompatible interactions revealed upregulation in the incompatible interaction as a characteristic of an estimated 30% of effector genes, including seven of the eight homologs of known avirulence genes from rice-infecting M. oryzae identified in our study. Prioritization of these effectors for functional validation will pave the way for identifying cognate resistance genes and improving finger millet for resistance to blast disease.

plant biology↗

bioRxiv2024

Genetic Diversity of Zymoseptoria tritici Populations in Central and South-eastern Ethiopia

Septoria tritici blotch (STB), caused by the hemibiotrophic fungus Zymoseptoria tritici, is a serious threat to global wheat production, and a major bottleneck to wheat production in Ethiopia. Accurate identification and analysis of the pathogens genetic structure helps inform robust STB management. This study analyzed the molecular identity and genetic structure of 200 Z. tritici isolates retrieved from diseased crops in central and south-eastern regions of Ethiopia. Allelic diversity at 12 simple sequence repeat (SSR) loci was examined for all 200 isolates, and 165 isolates were identified by Sanger sequencing of the internal transcribed spacer (ITS) region of nuclear DNA (rDNA) region. The microsatellites were highly polymorphic, with mean number of alleles (Na) = 6.23, effective alleles (Ne) =2.90, Neis gene diversity (H) =0.57, and polymorphic information content (PIC) =0.59, and an analysis of molecular variance confirmed the presence of low population differentiation (Fixation Index (FST) = 0.02, Gene Flow (Nm) = 14.7), with 95% of the total genetic variation residing within populations, and only 5% residing between populations. The highest genetic diversity (Number of allele (Na) = 9.33, Effective number of allele (Ne) = 3.41 and Neis gene diversity (H) = 0.68) was observed in the Oromia special zone surrounding Finfinnee (OSZ) Z. tritici populations, followed by Arsi and North Shewa populations, indicating that these areas are ideal for multi-location germplasm resistance screening, and also pathogen genetic and genomic analyses. Cluster analyses did not clearly divide the populations into genetically separate clusters according to their geographic sampling areas, probably because of high gene flow. All individual samples showed genetic admixture, and shared genomic backgrounds from two subgroups (K=2). Overall, the SSR markers proved to be highly informative and effective genetic tools for unlocking the pathogens genetic structure. The Z. tritici populations of central and southeast Ethiopia exhibit high genetic diversity, indicating the need to deploy durable and diverse disease management strategies. North Shewa, OSZ, Arsi and West Arsi administrative zones represent hotspots for genetic and genomic analyses of Z. tritici. Moreover, these areas would be excellent locations for host-pathogen interaction studies, and wheat germplasm screening for STB resistance.

plant biology↗

bioRxiv2024

Plant Development Drives Dynamic Shifts in the Root Compartment Microbiomes of Wild and Domesticated Finger Millet Cultivars

BackgroundPlant-microbe interactions in two root compartments - the rhizosphere and endosphere - play vital roles in maintaining plant health and ecosystem dynamics. The microbial communities in these niches are shaped in complex ways by factors including the plants developmental stage and cultivar, and the compartment where the interactions occur. Different plant cultivars provide distinct nutritional and ecological niches and may selectively enrich specific microbial populations through the secretion of root exudates. This gives rise to complex and dynamic plant-microbe interactions; some cultivars promote the recruitment of beneficial symbionts while others may deter pathogens. To clarify these processes, this work investigated the structure of the endosphere and rhizosphere microbial communities of wild type finger millet and five domesticated cultivars across two plant developmental stages. ResultsOur results showed that the plant developmental stage, compartment, and cultivar have varying degrees of impact on root-associated microbiomes. The dominant bacterial phyla in all samples were Proteobacteria, Actinobacteria, and Bacteroidetes, while the dominant fungal phyla were Ascomycota and Basidiomycota. All of these phyla exhibited pronounced variations in abundance. In general, an increased abundance of Actinobacteria in the endosphere was accompanied by a reduced abundance of Proteobacteria. The most pronounced changes in microbial community structure were observed in the rhizosphere during the flowering stage. Changes in the microbiome patterns of the rhizosphere were driven predominantly by the genus Pseudomonas. Moreover, the host plants developmental stage strongly influenced the microbial communities, suggesting that plants can recruit specific taxa based on their need for particular soil consortia. ConclusionsOur results show that both host developmental stage and domestication strongly affect the assembly and structure of the plant microbiome. Moreover, plant root compartments can selectively recruit specific taxa from associated core microbial communities to fulfill their needs in a manner that depends on both the plants developmental stage and the specific root compartment that is involved. These findings show that deterministic selection pressures exerted by plants during their growth and development can significantly affect their microbial communities and have important implications for efforts to create tools for manipulating the microbiome to sustainably improve primary productivity.

microbiology↗

bioRxiv2020

The genotypic and genetic diversity of enset (Ensete ventricosum) landraces used in traditional medicine is similar to the diversity found in starchy landraces

BackgroundEnset (Ensete ventricosum) is a multipurpose crop extensively cultivated in southern and southwestern Ethiopia for human food, animal feed and fiber. It contributes to the food security and rural livelihoods of 20 million people. Several distinct enset landraces are cultivated for their uses in traditional medicine. Socio-economic changes and the loss of indigenous knowledge might lead to the decline of important medicinal landraces and their associated genetic diversity. However, it is currently unknown whether medicinal landraces are genetically differentiated from other landraces. Here, we characterize the genetic diversity of medicinal enset landraces to support effective conservation and utilization of their diversity ResultsWe evaluated the genetic diversity of 51 enset landraces of which 38 have reported medicinal value. A total of 38 alleles were detected across the 15 SSR loci. AMOVA revealed that 97.6% of the total genetic variation is among individual with an FST of 0.024 between medicinal and non-medicinal landraces. A neighbor-joining tree showed four separate clusters with no correlation to the use values of the landraces. Principal coordinate analysis also confirmed the absence of distinct clustering between the groups, showing low differentiation among landraces used in traditional medicine and those having other use values. ConclusionWe found that enset landraces were clustered irrespective of their use value, showing no evidence for genetic differentiation between enset grown for medicinal uses and non-medicinal landraces. This suggests that enset medicinal properties may be restricted to a more limited number of genotypes, a product of interaction with the environment or management practice, or partly misreported. The study provide baseline information that promotes further investigations in exploiting the medicinal value of these specific landraces

genetics↗

bioRxiv2019

Affordable and robust phenotyping framework to analyse root system architecture of soil-grown plants

The analysis of root system growth, root phenotyping, is important to inform efforts to enhance plant resource acquisition from soils. However, root phenotyping remains challenging due to soil opacity and requires systems that optimize root visibility and image acquisition. Previously reported systems require costly and bespoke materials not available in most countries, where breeders need tools to select varieties best adapted to local soils and field conditions. Here, we present an affordable soil-based growth container (rhizobox) and imaging system to phenotype root development in greenhouses or shelters. All components of the system are made from commodity components, locally available worldwide to facilitate the adoption of this affordable technology in low-income countries. The rhizobox is large enough (~6000 cm2 visible soil) to not restrict vertical root system growth for at least seven weeks after sowing, yet light enough (~21 kg) to be routinely moved manually. Support structures and an imaging station, with five cameras covering the whole soil surface, complement the rhizoboxes. Images are acquired via the Phenotiki sensor interface, collected, stitched and analysed. Root system architecture (RSA) parameters are quantified without intervention. RSA of a dicot (chickpea, Cicer arietinum L.) and a monocot (barley, Hordeum vulgare L.) species, which exhibit contrasting root systems, were analysed. The affordable system is relevant for efforts in Ethiopia and elsewhere to enhance yields and climate resilience of chickpea and other crops for improved food security.\n\nSignificance StatementAn affordable system to characterize root system architecture of soil-grown plants was developed. Using commodity components, this will enable local efforts world-wide to breed for enhanced root systems.

plant biology↗