The eastern Africa region, Ethiopia and its surroundings, is considered as the center of origin and diversity for sorghum, and has contributed to global sorghum genetic improvement. The germplasm from this region harbors enormous genetic variation for various traits but little is known regarding the genetic architecture of most traits. Here, 1425 Ethiopian landrace accessions were phenotyped under field conditions for presence or absence of awns, panicle compactness and shape, panicle exsertion, pericarp color, glume cover, plant height and smut resistance under diverse environmental conditions in Ethiopia. In addition, F1 hybrids obtained from a subset of 1341 accessions crossed to an A1 cytoplasmic male sterile line, ATx623, were scored for fertility/sterility reactions. Subsequently, genotyping-by-sequencing generated a total of 879,407 SNPs from which 72,190 robust SNP markers were selected after stringent quality control (QC). Pairwise distance-based hierarchical clustering identified 11 distinct groups. Of the genotypes assigned to either one of the 11 sub-populations, 65% had high ancestry membership coefficient with the likelihood of more than 0.60 and the remaining 35% represented highly admixed accessions. A genome-wide association study (GWAS) identified loci and SNPs associated with aforementioned traits. GWAS based on compressed mixed linear model (CMLM) identified SNPs with significant association (FDR ≤ 0.05) to the different traits studied. The percentage of total phenotypic variation explained with significant SNPs across traits ranged from 2 to 43%. Candidate genes showing significant association with different traits were identified. The sorghum bHLH transcription factor, ABORTED MICROSPORES was identified as a strong candidate gene conditioning male fertility. Notably, sorghum CLAVATA1 receptor like kinase, known for regulation of plant growth, and the ETHYLENE RESPONSIVE TRANSCRIPTION FACTOR gene RAP2-7, known to suppress transition to flowering, were significantly associated with plant height. In addition, the YELLOW SEED1 like MYB transcription factor and TANNIN1 showed strong association with pericarp color validating previous observations. Overall, the genetic architecture of natural variation representing the complex Ethiopian sorghum germplasm was established. The study contributes to the characterization of genes and alleles controlling agronomic traits, and will serve as a source of markers for molecular breeding.
Finger millet (Eleusine coracana (L.) Gaertn) is a highly nutritious crop, predominantly grown in the semi-arid tropics of the world. Finger millet has a niche market opportunity due to its human health benefits and being rich in calcium, iron and dietary fiber and gluten-free. Ethiopia is the center of the genetic diversity of the crop. However, the productivity of finger millet in the country is low (<2.4 tons ha−1) compared with its potential yield (6 tons ha−1). The yield gap in Ethiopia is due to a range of biotic and abiotic stresses and socio-economic constraints that are yet to be systemically documented and prioritized to guide future production and improved variety development and release. The objective of this study was to document finger millet production opportunities, constraints and farmer-preferred traits in Ethiopia as a guide to variety design in improvement programs. A participatory rural appraisal (PRA) study was undertaken in six selected districts of the Southern Nation Nationalities People Region (SNNPR) and Oromia Region in Ethiopia. Data were collected from 240 and 180 participant farmers through a semi-structured questionnaire and focus group discussion, respectively. Finger millet was the most important crop in the study areas grown mainly for a combination of uses, including for food, feed and cash (reported by 38.8% of respondent farmers), food and feed (14.5%), food and cash (13.7%), food (11.5%) and food, cash, feed and construction material (9.7%). Hand weeding was used by 59.2% of the respondent farmers, followed by hand weeding and chemical herbicides (40.8%). Finger millet was mainly planted as a sole crop (reported by 97.0% respondents), mixed (1.7%) and sole and mixed (1.3%). About 75.6% of respondent farmers only practiced finger millet rotation with other crops. Respondent farmers indicated their source of fresh seed was from the Bureau of Agriculture (49.1%), farmer-to-farmer seed exchange (22.1%), own saved seed (7.5%), local producers (7.5%), research institutions (5.8%), unknown sources (4.1%), local market (3.5%) and cooperatives (0.42%). The total cost of finger millet production per hectare was calculated at 1249 USD with a total income of 2139 USD/ha, making a benefit to cost ratio of 1.71:1.00 and indicating the relatively low yield gains using the currently grown varieties. The main constraints to finger millet production in the study areas were drought stress (reported by 41.3% respondents), lack of improved varieties (12.9%), lack of financial resources (11.3%), small land holdings (10.8%), limited access to seed (10.0%), a shortage of fertilizers (5.4%), poor soil fertility (4.6%), shortage of draught power (1.3%), labour shortages (1.3%) and high labour costs (1.3%). The most important farmer-preferred traits in a finger millet variety were high grain yield, compact head shape, ‘enjera’-making quality, high marketability and early maturity, resolved through principal component analysis. The above-mentioned production constraints and farmer-preferred traits are strategic drivers to enhance finger millet productivity and need to be incorporated into Ethiopia’s finger millet breeding and technology development.
A total of 123 drug-resistant and drug-sensitive Shigella flexneri types 1-6, and their Escherichia coli K12 transconjugants were used for plasmid profile analysis by agarose gel electrophoresis. Resistance factors (R-factors) were further characterized by incompatibility testing. The overall distribution of small plasmids in S. flexneri showed that a cryptic plasmid of about 4.6 Kb was found in all serotypes, and a plasmid of about 4.2 Kb was found in serotypes 1-4. Shigella flexneri types 2, 4 and 6 showed a 6.5 Kb plasmid which correlated with SSu-resistance. All S. flexneri serotypes harboured large plasmids of about 217 Kb. Plasmid profile analysis of S. flexneri in Ethiopia showed a high degree of uniformity within individual serotypes. However, there was a limited variability which, at times, could be useful for epidemiological investigation. Shigella flexneri serotypes 1-6 harboured resistance plasmids with diverse molecular weights but mostly belonging to incompatibility groups N and X.
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