SUMMARY: The phenotypic analysis of root system growth is important to inform efforts to enhance plant resource acquisition from soils; however, root phenotyping remains challenging because of the opacity of soil, requiring systems that facilitate root system visibility and image acquisition. Previously reported systems require costly or bespoke materials not available in most countries, where breeders need tools to select varieties best adapted to local soils and field conditions. Here, we report an affordable soil‐based growth (rhizobox) and imaging system to phenotype root development in glasshouses or shelters. All components of the system are made from locally available commodity components, facilitating the adoption of this affordable technology in low‐income countries. The rhizobox is large enough (approximately 6000 cm² of visible soil) to avoid restricting vertical root system growth for most if not all of the life cycle, yet light enough (approximately 21 kg when filled with soil) for routine handling. 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. The RSAs of a dicot species (Cicer arietinum, chickpea) and a monocot species (Hordeum vulgare, barley), exhibiting contrasting root systems, were analysed. Insights into root system dynamics during vegetative and reproductive stages of the chickpea life cycle were obtained. This affordable system is relevant for efforts in Ethiopia and other low‐ and middle‐income countries to enhance crop yields and climate resilience sustainably.

Eleusine coracana, finger millet, is a multipurpose crop cultivated in arid and semi-arid regions of Africa and Asia. RNA sequencing (RNA-seq) was used in this study to obtain valuable genomic resources and identify genes differentially expressed between Al-tolerant and Al-susceptible genotypes. Two groups of finger millet genotypes were used: Al-tolerant (215836, 215845, and 229722) and Al-susceptible (212462, 215804 and 238323). The analysis of the RNA-seq data resulted in 198,546 unigenes, 56.5% of which were annotated with significant hits in one or more of the following six databases: NR (48.8%), GO (29.7%), KEGG (45%), PlantTFDB (19.0%), Uniprot (49.2%), and NT (46.2%). It is noteworthy that only 220 unigenes in the NR database had significant hits against finger millet sequences suggesting that finger millet’s genomic resources are scarce. The gene expression analysis revealed that 322 genes were significantly differentially expressed between the Al-tolerant and Al-susceptible genotypes, of which 40.7% were upregulated while 59.3% were downregulated in Al-tolerant genotypes. Among the significant DEGs, 54.7% were annotated in the GO database with the top hits being ATP binding (GO:0005524) and DNA binding (GO:0003677) in the molecular function, DNA integration (GO:0015074) and cell redox homeostasis in the biological process, as well as cellular anatomical entity and intracellular component in the cellular component GO classes. Several of the annotated DEGs were significantly enriched for their corresponding GO terms. The KEGG pathway analysis resulted in 60 DEGs that were annotated with different pathway classes, of which carbohydrate metabolism and signal transduction were the most prominent. The homologs of a number of significant DEGs have been previously reported as being associated with Al or other abiotic stress responses in various crops, including carboxypeptidase SOL1, HMA3, AP2, bZIP, C3H, and WRKY TF genes. A more detailed investigation of these and other DEGs will enable genomic-led breeding for Al tolerance in finger millet. RNA-seq data analysis also yielded 119,073 SNP markers, the majority of which had PIC values above 0.3, indicating that they are highly informative. Additionally, 3,553 single-copy SSR markers were identified, of which trinucleotide SSRs were the most prevalent. These genomic resources contribute substantially to the enrichment of genomic databases for finger millet, and facilitate future research on this crop.

Finger millet (Eleusine coracana (L.) Geartn.) is a self-pollinating amphidiploid crop cultivated with minimal input for food and feed, as well as a source of income for small-scale farmers. To efficiently assess its genetic diversity for conservation and use in breeding programs, polymorphic DNA markers that represent its complex tetraploid genome have to be developed and used. In this study, 13 new expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were developed based on publicly available finger millet ESTs. Using 10 polymorphic SSR markers (3 genomic and 7 novel EST-derived), the genetic diversity of 55 landrace accessions and 5 cultivars of finger millet representing its major growing areas in Ethiopia was assessed. In total, 26 alleles were detected across the 10 loci, and the average observed number of alleles per locus was 5.6. The polymorphic information content (PIC) of the loci ranged from 0.045 (Elco-48) to 0.71 (UGEP-66). The level of genetic diversity did not differ much between the accessions with the mean gene diversity estimates ranging only from 0.44 (accession 216054) to 0.68 (accession 237443). Similarly, a narrow range of variation was recorded at the level of regional states ranging from 0.54 (Oromia) to 0.59 (Amhara and Tigray). Interestingly, the average gene diversity of the landrace accessions (0.57) was similar to that of the cultivars (0.58). The analysis of molecular variance (AMOVA) revealed significant genetic variation both within and among accessions. The variation among the accessions accounted for 18.8% of the total variation (F_ST = 0.19; P < 0.001). Similarly, significant genetic variation was obtained among the geographic regions, accounting for 6.9% of the total variation (P < 0.001). The results of the cluster, principal coordinate, and population structure analyses suggest a poor correlation between the genetic makeups of finger millet landrace populations and their geographic regions of origin, which in turn suggests strong gene flow between populations within and across geographic regions. This study contributed novel EST-SSR markers for their various applications, and those that were monomorphic should be tested in more diverse finger millet genetic resources.

Aluminum (Al) toxicity is a major abiotic stress that negatively impacts plant growth and crop productivity. Al ions are released into soil solutions as a function of soil pH, which is in turn determined by a combination of factors, including local geology, historic vegetation and land-use patterns. Selection and use of Al-tolerant crops is a preferred method to address the problem of Al toxicity. The present study evaluated a combination of modern cultivars, advanced breeding lines and a local landrace for Al tolerance using a seedling-based hydroponic assay. Two sequential experiments were conducted to score root and shoot traits in the presence of aluminum. Initially, six Al concentrations (0, 50, 100, 120, 150 and 200 µM) were tested on six chickpea genotypes to identify the single Al concentration that best discriminates among genotypes. Subsequently, 31 chickpea genotypes were evaluated at 0 and 120 µM Al. Progressive declines in trait values were observed in all genotypes with increasing Al, although the degree of sensitivity varied significantly among genotypes. Genotypes were evaluated both for total root length under 120 µM Al and for relative root growth compared to a 0 µM Al control treatment. Considering both parameters, we identified four tolerant chickpea genotypes (DZ-2012-CK-0237, Wollega LV, DZ-2012-CK-0233 and Natoli) and two sensitive genotypes (Akaki and Fetenech). Wollega LV is a local landrace obtained from acidic soil regions of Western Ethiopia, presenting the possibility that historical selection during cultivation on acidic soils might underlie its unusual tolerance. The aluminum tolerance traits identified here are candidates for introgression breeding of new Ethiopian chickpea varieties with potential to increase yield and expand the area of cultivation.

Background: Plectranthus edulis(Vatke) Agnew (Lamiaceae), locally known as Ethiopian potatosyno.Ethiopian dinich, is one of the native Ethiopian edible tuber crops that has been significantly contributing to household food security for millions of subsistence farmers. However, its current production is declining to the extent of total extinction from several administrative regions where it used to be widely cultivated. It is one of the less researched crops regardless of being indigenous and its contribution to food security during time of scarcity. Therefore, we intended to assess the level of genetic diversity in 67 accessions, representing nine populations that were collected from diverse agro-ecologies in the country, using ISSR markers and hence, to generate a baseline information that assists marker assisted breeding, conservation and germplasm management efforts.Results: In the present study, ten polymorphic ISSR markers were screened and optimized, that generated an average of 7.4 scorable bands per marker and revealed high overall percent polymorphism (95%), Nei’s gene diversity (h = 0.40) and Shannon index (I = 0.62) suggesting ISSR’s effectiveness in detecting high levels of genetic diversity. A considerably high overall populations gene diversity (Nei’s) (h = 0.32) and Shannon index (I = 0.47) were observed, revealing high potential of the populations for further breeding and conservation efforts particularly for population from Gurage administrative zone, which showed the highest values. Similarly, estimation of pairwise genetic distance revealed the importance of cross breeding population from Awi administrative zone to the rest populations. Analysis of hierarchical molecular variance (AMOVA) showed higher levels of genetic differentiation within populations (92%), and collection regions (94%) suggesting that either clonal mode of propagation in the crop or farmers selection pressure for important agronomic traits or both maintained the original heterozygosity in the crop. UPGMA phylogenetic analysis did not strictly group the populations based on their geographic region of origin, which could be attributed to the widely practiced tuber exchange and hence continuous human mediated exchange of genetic material and sharing of the same genetic base among the geographic regions.Conclusions: The ISSR markers used in the present study were effective in revealing extent and patterns of genetic diversity inP. edulispopulations. However, it is important to couple them with agro-morphological traits or codominant molecular markers to get more reliable information for use in breeding and conservation. Several of the potential administrative zones we covered are useful forP. edulisdiversification and conservation. However, the crop is currently highly marginalized and this led to rapid decline in population size and loss of valuable agronomic traits. To address this challenge, there is an urgent need to take counteractive measures.