Genome-wide association study reveals genomic loci influencing agronomic traits in Ethiopian sorghum (Sorghum bicolor (L.) Moench) landraces.

Uncovering the genetic basis of agronomic traits in sorghum landraces that have adapted to various agro-climatic conditions would contribute to sorghum improvement efforts around the world. To identify quantitative trait nucleotides (QTNs) associated with nine agronomic traits in a panel of 304 sorghum accessions collected from diverse environments across Ethiopia (considered to be the center of origin and diversity), multi-locus genome-wide association studies (ML-GWAS) were performed using 79,754 high quality single nucleotide polymorphism (SNP) markers. Association analyses using six ML-GWAS models identified a set of 338 significantly (LOD ≥ 3)-associated QTNs for nine agronomic traits of sorghum accessions evaluated in two environments (E1 and E2) and their combined dataset (Em). Of these, 121 reliable QTNs, including 13 for flowering time (DF), 13 for plant height (PH), 9 for tiller number (TN), 15 for panicle weight (PWT), 30 for grain yield per panicle (GYP), 12 for structural panicle mass (SPM), 13 for hundred seed weight (HSW), 6 for grain number per panicle (GNP), and 10 for panicle exertion (PE) were consistently detected by at least three ML-GWAS methods and/or in two different environments. Notably, Ethylene responsive transcription factor gene AP2/ERF, known for regulation of plant growth, and the sorghum Terminal flower1/TF1 gene, which functions in the control of floral architecture, were identified as strong candidate genes associated with PH and HSW, respectively. This study provides an entry point for further validation studies to elucidate complex mechanisms controlling important agronomic traits in sorghum. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01381-5.

Genetic diversity, population structure, and selection signature in Ethiopian sorghum [Sorghum bicolor L. (Moench)] germplasm.

Ethiopia, the probable center of origin and diversity for sorghum [Sorghum bicolor L. (Moench)] and with unique ecogeographic features, possesses a large number of sorghum landraces that have not been well studied. Increased knowledge of this diverse germplasm through large-scale genomic characterization may contribute for understanding of evolutionary biology, and adequate use of these valuable resources from the center of origin. In this study, we characterized genetic diversity, population structure and selection signature in 304 sorghum accessions collected from diverse sorghum growing regions of Ethiopia using genotyping-by-sequencing. We identified a total of 108,107 high-quality single-nucleotide polymorphism (SNPs) markers that were evenly distributed across the sorghum genome. The average gene diversity among accessions was high (He = 0.29). We detected a relatively low frequency of rare alleles (26%), highlighting the potential of this germplasm for subsequent allele mining studies through genome-wide association studies. Although we found no evidence of genetic differentiation among administrative regions (FST = 0.02, P = 0.12), population structure and cluster analyses showed clear differentiation among six Ethiopian sorghum populations (FST = 0.28, P = 0.01) adapting to different environments. Analysis of SNP differentiation between the identified genetic groups revealed a total of 40 genomic regions carrying signatures of selection. These regions harbored candidate genes potentially involved in a variety of biological processes, including abiotic stress tolerance, pathogen defense and reproduction. Overall, a high level of untapped diversity for sorghum improvement remains available in Ethiopia, with patterns of diversity consistent with divergent selection on a range of adaptive characteristics.

Carriage, Risk Factors, and Antimicrobial Resistance Patterns of Salmonella Isolates from Raw Beef in Jimma, Southwestern Ethiopia.

PURPOSE: Consumption of raw beef infected with multidrug-resistant Salmonella is pertinent to the world public health risk of antimicrobial resistance. Henceforth, this study aimed to investigate the carriage, antimicrobial resistance (AR) patterns, and the revealing risk factors of Salmonella-contaminating beef in abattoirs and butcher shops in Jimma town. METHODS: A cross-sectional study was conducted to investigate the carriage and AR patterns and to reveal the risk factors of beef contaminated by Salmonella spp. Three hundred and forty-eight swab samples were collected from abattoirs (n=210) and butcher shops (n=138) and the conventional cultural methods were employed for identification of Salmonella. Isolates were subjected to 12 antimicrobials using the Kirby-Bauer disk diffusion method for AR patterns. RESULTS: The occurrence of Salmonella isolates from the abattoir samples was 11.4%, whereas about 6.52% of isolates were recovered from butcher shops. Educational status (abattoir: odds ratio (OR)=8.40, confidence interval (CI)=1.186-59.493; butcher shops: OR=9.17, CI=1.15-73.239), job related training (abattoir: OR=5.50, CI=1.065-28.416), contamination risk perception (abattoir: OR=5.31, CI=1.256-22.489), neatness of knives (abattoir: OR=7.6, CI=0.892-65.376), source of contamination (abattoir: OR=8.44, CI=1.682-42.39), wearing of protective cloth (butcher shops: OR=8.44, CI=1.682-42.39), manner of hand washing (butcher shops: OR=7.25, CI=1.210-43.442), and money handling (butcher shops: OR= 9.69, CI=1.578-59.474) were among the potential risk factors significantly associated with Salmonella carcass contamination in the abattoir and butcher shops. Of the 33 Salmonella isolates, 14 (58.3%) and six (66.7%) of the abattoir and butcher shops isolates, correspondingly, were resistant to two or more antibiotics. CONCLUSION: The finding of this investigation exhibited extensive multidrug-resistant Salmonella isolates in the study setting. Hence, establishing standard meat safety requirements and provision of training for meat handlers and prudent use of antimicrobials are recommended.