Biology subjects

Negawo, A. T.

Publications and source records attributed to Negawo, A. T..

4 recordsLinked to original sources

bioRxiv2025

Genetic Diversity and Phylogenetic Relationships of Cultivated and Wild Urochloa Species Conserved in the ILRI Forage Genebank

Understanding the genetic diversity and evolutionary relationships within the genus Urochloa is essential for effective germplasm conservation and the development of improved forage cultivars. In this study, we assessed the genetic diversity, population structure, and phylogenetic relationships of 545 accessions representing 17 Urochloa species conserved in the ILRI Forage Genebank for the last four decades at its Zway field site in Ethiopia. Large numbers of genome-wide SNP and SilicoDArT markers were generated by the GBS based Diversity Arrays Technology (DArT)seq platform, providing valuable resources for genetic analysis in Urochloa spp. From these, we filtered a subset of high-quality SNP and SilicoDArT markers suitable for cross-species analysis, which was then used to characterize species differentiation and to detect admixture patterns across wild and cultivated species. Hierarchical clustering grouped all 545 accessions into two major groups, clearly separating the brizantha complex (U. brizantha, U. decumbens, and U. ruziziensis) from the rest of the species, which were primarily wild and less domesticated relatives. The analysis further identified four well-defined phylogenetic clades, largely consistent with previously reported evolutionary relationships within the genus. The three clades, primarily composed of wild species, exhibited clear genetic separation, high diversity, and strong geographic structuring with limited admixture, reflecting reproductive isolation (their apomictic nature) and differing ploidy levels that have driven local adaptation. In contrast, the brizantha complex exhibited extensive admixture and comparatively lower genetic variation, consistent with their historical polyploidization events, shared ancestry, and domestication (particularly in the key forage species U. brizantha and U. decumbens). Population structure analysis using the admixture model revealed multiple genetically distinct clusters and populations across clades, including species-specific clusters, mixed-species groups, and within-species populations, highlighting substantial genetic variation within and among species shaped by historical gene flow (particularly among diploid and sexual types), differences in ploidy levels, and adaptive divergence. The identification of genetically differentiated populations in wild species underscores their potential as reservoirs of unique adaptive traits such as drought tolerance, waterlogging and disease resistances, and nutrient-use efficiency. Meanwhile, the genetically diverse cultivated gene pool provides valuable resources for improving biomass productivity, nutritional quality, and resilience to environmental stress. Our findings provide a comprehensive genetic overview of one of the most important tropical forage genera and offer strategic insights for the conservation and utilization of Urochloa genetic resources.

plant biology↗

bioRxiv2025

Genome-wide association mapping for grain and forage quality traits in a subtropical oat germplasm collection adapted to highland regions of Eastern Africa

Oat (Avena sativa L.) is a globally important cereal cultivated for both livestock feed and human nutrition. However, its productivity is increasingly constrained by both biotic and abiotic stresses, exacerbated by rapid climate change. To support the development of dual-usage, stress-resilient and high-yielding cultivars adapted to subtropical agroecologies, we evaluated the genetic structure and agronomic performance of a 169-member oat association panel. This panel was phenotyped for key vegetative, forage feed quality and grain related traits across three subtropical locations in Sub-Saharan Africa (SSA) over two growing seasons and genotyped using Genotyping-by-Sequencing (GBS). Diversity analysis, based on filtered SNPs, showed moderate genetic diversity (He = 0.39 and PIC = 0.3), and population structure analysis identified two main sub-groups with varying degrees of admixture, suggesting gene flow among different groups. Genome-wide association analysis uncovered 42 SNPs significantly associated with sixteen traits (false discovery rate, FDR, <0.05), along with 46 candidate genes located near these loci. Notably, candidate genes associated with seed traits included a homolog of rice OsAK3, encoding adenylate kinase, and a UDP-glucosyltransferase homologous to rice GSA1, both previously shown to regulate grain size. These genes were located near QTL linked to seed length, width, and thousand-grain weight. Another key candidate, encoding a subunit of the ESCRT-II complex (VPS25), was identified near a separate QTL and is implicated in intracellular trafficking, endosperm development, and overall seed quality. By illuminating the genetic architecture of economically important traits and identifying molecular markers linked to yield, quality and resilience, this study provides valuable genomic resources to support genomics-based breeding aimed at developing climate-resilient, productive oats varieties adapted to sub-tropical agro-ecologies.

genomics↗

bioRxiv2024

Whole genome resequencing of a global collection of Napier grass (Cenchrus purpureus) to explore global population structure and QTL governing yield and feed quality traits

Napier grass (Cenchrus purpureus) is a C4 perennial grass species native to Sub-Saharan Africa (SSA), primarily used to feed cattle in SSA. In this study, we sequenced the genomes of 450 Napier grass individuals, sourced from 20 different countries. More than 170 million DNA variants (SNPs and Indels) were detected, of which [~]1% informative SNPs were used to assess genetic diversity in the collection. Our resequencing study provided valuable insights into the genetic diversity across a global Napier grass collection. Furthermore, a genome-wide association study on two independent populations, identified multiple quantitative trait loci (QTL) that were significantly associated with desirable agronomic traits, such as biomass yield, nitrogen and cellulose content. Therefore, our results will serve as a valuable resource in safeguarding and unravelling the patterns of Napier grass genetic diversity, in the face of climate change, and spearhead genomics-based breeding programs to develop high-yielding and drought-tolerant varieties suitable for forage and biofuel production.

plant biology↗

bioRxiv2021

Insights into the genetic architecture of complex traits in Napier grass (Cenchrus purpureus) and QTL regions governing forage biomass yield, water use efficiency and feed quality traits

Napier grass is the most important perennial tropical grass native to Sub-Saharan Africa and widely grown in tropical and subtropical regions around the world, primarily as a forage crop for animal feed, but with potential as an energy crop and in a wide range of other areas. Genomic resources have recently been developed for Napier grass that need to be deployed for genetic improvement and molecular dissection of important agro-morphological and feed quality traits. From a diverse set of Napier grass genotypes assembled from two independent collections, a subset of 84 genotypes that best represents the genetic diversity of the collections were selected and evaluated for two years in dry (DS) and wet (WS) seasons under three soil moisture conditions: moderate water stress in DS (DS-MWS); severe water stress in DS (DS-SWS) and, under rainfed (RF) conditions in WS (WS-RF). Data for agro-morphological and feed quality traits, adjusted for the spatial heterogeneity in the experimental blocks, were collected over a two-year period from 2018 to 2020. A total of 135,706 molecular markers were filtered, after removing markers with missing values > 10% and a minor allele frequency (MAF) < 5 %, from the high-density genome-wide markers generated previously using the genotyping by sequencing (GBS) method of the DArTseq platform. A genome-wide association study (GWAS), using two different mixed linear model algorithms, identified more than 58 QTL regions and markers associated with agronomic, morphological and water-use efficiency traits. QTL regions governing purple pigmentation and feed quality traits were also identified. The identified markers will be useful in the genetic improvement of Napier grass through the application of marker-assisted selection and for further characterization and map-based cloning of the QTLs.

genetics↗