Novel Expressed Sequence Tag-Derived and Other Genomic Simple Sequence Repeat Markers Revealed Genetic Diversity in Ethiopian Finger Millet Landrace Populations and Cultivars

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 (FST = 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

Suitability of existing Musa morphological descriptors to characterize East African highland ‘matooke’ bananas

Article purchased; Published online: 18 Sept 2017Morphological traits are commonly used for characterizing plant genetic resources. Germplasm characterization should be based on distinctly identifiable, stable and heritable traits that are expressed consistently and are easy to distinguish by the human eye. Characterization and documentation of a representative sample of East African highland bananas (Lujugira–Mutika subgroup) was carried out following an internationally accepted standard protocol for bananas. Eleven cultivars were characterized using an existing set of minimum descriptors (31 qualitative and quantitative traits) with the aim of determining stable descriptors and the ability of these descriptors to distinguish among East African highland banana cultivars. There was variation in stability of these descriptors within cultivars and across the 11 cultivars. Only 10 (32%) out of 31 descriptors studied were stable in the 11 cultivars. However, they had similar scores and therefore are not suitable to distinguish between cultivars within this group. Nonetheless, these 10 descriptors may be useful for distinguishing the East African highland bananas as a group from other groups of bananas. A few descriptors were unique to the cultivar ‘Tereza’ and may be used to distinguish this cultivar from other ‘matooke’ cultivars. None of the quantitative descriptors were stable

Genotype by environment interaction and grain yield stability of Ethiopian black seeded finger millet genotypes

Finger millet ( Eleusine coracana \ua0(L.) Gaertn) is an important cereal widely produced in Ethiopia across diverse agro-ecologies. It is valued by local farmers for its ability to grow in adverse agro-climatic conditions, where other cereals fail. The yield potential of this crop is in the range of 4-5 tonnes/ha, but the current national average grain yield is far below the potential (2.1 tonnes). Lack of improve varieties which are stable, high yielder and stress tolerant is a major limiting factor to production of this crop in Ethiopia. A field experiment was conducted using twelve black seeded finger millet (Eleusine coracana subsp. coracana) genotypes, including local and standard checks (Degu) at two locations (Bako and Gute) in Ethiopia for three years (2014 - 2016). The objective of this study was to identify stable and high yielding genotypes for grain yield and other agronomic traits among the black seeded finger millet genotypes of Ethiopia. The additive main effect and multiplicative interaction (AMMI) model analysis of variance revealed highly significant (P&lt;0.01) differences between environments, genotype, and Interaction Principal Component Analysis (IPCA-I), but significant variations (P&lt;0.05) for G x E interactions. This indicates that the genotypes performed differently over environments and that the test environments are highly variable. Only the first IPCA-I showed high significance (P&lt;0.01) and contributed 48.39% of the total genotype by environment interaction (G x E). Genotypes BKFM0020, BKFM0006 and BKFM0010, which had high grain yield, but with IPCA value close to zero, indicated the wide adaptability/stability. Similarly, analysis using Eberhart and Russell model revealed that these genotypes were within the relatively acceptable range of regression coefficients (bi), approaching to one (0.742, 0.8176 and 1.0578), and deviation from regression closer to zero (s2di) (0.0385, -0.0661 and -0.0248), respectively. This implied that pipeline genotypes were stable, widely adaptable and high yielders than the other genotypes. Genotype and genotype by environment (GGE bi-plot) analysis also revealed that these candidate genotypes were stable and high yielder. Besides, these genotypes showed resistance to blast disease, which is a threat to finger millet production in the study areas. Therefore, these genotypes were selected as potential candidates for possible release in western Oromia and similar agro-ecologies of the country.Le petit mil ( Eleusine coracana (L.) Gaertn) est une c\ue9r\ue9ale importante largement produite en \uc9thiopie dans les diff\ue9rents zones agro-\ue9cologiques. Il est appr\ue9ci\ue9 par les agriculteurs locaux pour sa capacit\ue9 de grandir dans des conditions agro-climatiques d\ue9favorables, o\uf9 les autres c\ue9r\ue9ales \ue9chouent. Le potentiel du rendement en grain de cette culture de mil se situe entre 4 \ue0 5 t ha-1, mais le rendement moyen national actuel est tr\ue8s inf\ue9rieur au potentiel (2,1 tonnes). Le manque de vari\ue9t\ue9s am\ue9lior\ue9es, stables, \ue0 rendement en grain \ue9lev\ue9 et tol\ue9rantes au stress est un t facteur majeur limitant la production de cette culture de mil en \uc9thiopie. Une exp\ue9rience au champs a \ue9t\ue9 conduite avec douze g\ue9notypes des grains noir de mil (Eleusine coracana subsp. Coracana), y compris des contr\uf4les locaux et standard (Degu) \ue0 deux locations (Bako et Gute) en \uc9thiopie pendant trois ans (2014 - 2016). L\u2019objectif de cette \ue9tude \ue9tait d\u2019identifier des g\ue9notypes stables et de rendement tr\ue8s\ua0\ue9lev\ue9 pour le rendement en grain de mil et d\u2019autres caract\ue9ristiques agronomiques parmi les genotypes des grains noir de mil en \uc9thiopie. L\u2019analyse de variance du methode avec effet principal additif et interaction multiplicative (AIM) a r\ue9v\ue9l\ue9 des diff\ue9rences tr\ue8s significatives (P &lt;0,01) entre les locations, le g\ue9notype et l\u2019analyse en composantes principales de l\u2019interaction (IPCA-I), mais des variations significatives (P &lt;0,05) pour G x E interactions. Cela indique que les g\ue9notypes se sont comport\ue9s diff\ue9remment selon les locations et que les locations de test sont tr\ue8s variables. Seule la premi\ue8re IPCA-I a montr\ue9 une signification \ue9lev\ue9e (P &lt;0,01) et a contribu\ue9 pour 48,39% du total des interactions g\ue9notype par la location (G x E). G\ue9notypes BKFM0020, BKFM0006 et BKFM0010, qui avait un rendement en grain \ue9lev\ue9, mais avec une valeur IPCA proche de z\ue9ro, a indiqu\ue9 la grande adaptabilit\ue9 / stabilit\ue9. De m\ueame, une analyse utilisant les m\ue9thodes\ua0d\u2019Eberhart et Russell a r\ue9v\ue9l\ue9 que ces g\ue9notypes se situaient dans la plage relativement acceptable des coefficients de r\ue9gression (bi), se rapprochant de un (0,742, 0,8176 et 1,0578) et de l\u2019\ue9cart par rapport \ue0 la r\ue9gression proche de z\ue9ro (s2di) (0,0385, 0,0661 et -0,0248), respectivement. Cela impliquait que les g\ue9notypes de pipeline \ue9taient stables, largement adaptables et ont eu le rendement tr\ue8s\ua0\ue9lev\ue9 que les autres g\ue9notypes. Les analyses de g\ue9notype et g\ue9notype par la location (bi-parcelle GGE) ont \ue9galement r\ue9v\ue9l\ue9 que ces g\ue9notypes candidats \ue9taient stables et avaient une bonne rentabilit\ue9. En outre, ces g\ue9notypes ont montr\ue9 une r\ue9sistance \ue0 la maladie fongique qui constitue une menace pour la production de mil dans les zones d\u2018 \ue9tude. Par cons\ue9quent, ces g\ue9notypes ont \ue9t\ue9 s\ue9lectionn\ue9s comme candidats potentiels pour une lib\ue9ration \ue9ventuelle dans l\u2019ouest d\u2019Oromia et des zones agro-\ue9cologiques similaires du pays

Prevalence of depression and anxiety symptoms and their determinant factors among patients with cancer in southern Ethiopia: a cross-sectional study

ObjectiveThe study was aimed to assess the prevalence of depression and anxiety symptoms and their determinant factors among patients with cancer attending follow-up at Hawassa University Comprehensive Specialized Hospital cancer treatment centre, Ethiopia.DesignInstitution-based cross-sectional study design was implemented.SettingPatients with cancer at Hawassa University Comprehensive Specialized Hospital cancer treatment centre from October 2019 to December 2019.ParticipantsRandomly selected 415 patients with cancer who had follow-up at cancer treatment centre.Main outcome measuresAnxiety and depression symptoms were assessed using Hospital Anxiety and Depression Scale.ResultThe prevalence rates of depression and anxiety symptoms were found to be 244 (58.8%) and 249 (60.0%), respectively. Older age (&gt;50 years) (AOR (adjusted OR)=2.24, 95% CI=1.14 to 4.40), being unemployed (AOR=1.96, 95% CI=1.08 to 3.56), advanced stage of cancer such as stage III (AOR=5.37, 95% CI=1.34 to 21.45) and stage IV (AOR=4.55, 95% CI=1.12 to 18.44), comorbid psychotic symptoms (AOR=1.67, 95% CI=1.07 to 2.61) and eating problem in the past 2 weeks (AOR=6.16, 95% CI=1.98 to 19.11) were independent factors significantly associated with depressive symptoms. In addition, cancer stage such as stage II (AOR=3.92, 95% CI=1.07 to 14.36) and stage IV (AOR=5.04, 95% CI=1.44 to 17.59) and comorbid psychotic symptoms (AOR=1.73, 95% CI=1.12 to 2.66) were significantly associated with anxiety symptoms.ConclusionDepression and anxiety symptoms among patients with cancer were considerably high. Age, occupation, cancer stage, comorbid psychotic symptoms and eating problem were determinant factors of depressive symptoms among patients with cancer. Moreover, cancer stage and comorbid psychosis were determinants of anxiety symptoms. Healthcare professionals working in the oncology unity need to conduct routine screening and treatment of depression and anxiety symptoms for patients with cancer.</jats:sec

Crossbreeding east African highland bananas: lessons learnt relevant to the botany of the crop after 21 years of genetic enhancement

Open Access JournalEast African highland bananas (EAHB) were regarded as sterile. Their screening for female fertility with “Calcutta 4” as male parent revealed that 37 EAHB were fertile. This was the foundation for the establishment of the EAHB crossbreeding programs by the International Institute of Tropical Agriculture (IITA) and the National Agricultural Research Organization (NARO) in Uganda in the mid-1990s. The aim of this study was to assess the progress and efficiency of the EAHB breeding program at IITA, Sendusu in Uganda. Data on pollinations, seeds generated and germinated, plus hybrids selected between 1995 and 2015 were analyzed. Pollination success and seed germination percentages for different cross combinations were calculated. The month of pollination did not result in significantly different (P = 0.501) pollination success. Musa acuminata subsp. malaccensis accession 250 had the highest pollination success (66.8%), followed by the cultivar “Rose” (66.6%) among the diploid males. Twenty-five EAHB out of 41 studied for female fertility produced up to 305 seeds per pollinated bunch, and were therefore deemed fertile. The percentage of seed germination varied among crosses: 26% for 2x × 4x, 23% for 2x × 2x, 11% for 3x × 2x, and 7% for 4x × 2x. Twenty-seven NARITA hybrids (mostly secondary triploids ensuing from the 4x × 2x) were selected for further evaluation in the East African region. One so far –“NARITA 7”– was officially released to farmers in Uganda. Although pollination of EAHB can be conducted throughout the year, the seed set and germination is low. Thus, further research on pollination conditions and optimization of embryo culture protocols should be done to boost seed set and embryo germination, respectively. More research in floral biology and seed germination as well as other breeding strategies are required to increase the efficiency of the EAHB breeding program

Significant progressive heterobeltiosis in banana crossbreeding

Open Access Journal; Published online: 27 Oct 2020Background Heterobeltiosis is the phenomenon when the hybrid’s performance is superior to its best performing parent. Banana (Musa spp. AAA) breeding is a tedious, time-consuming process, taking up to two decades to develop a consumer acceptable hybrid. Exploiting heterobeltiosis in banana breeding will help to select breeding material with high complementarity, thus increasing banana breeding efficiency. The aim of this study was therefore to determine and document the level of heterobeltiosis of bunch weight and plant stature in the East African highland bananas, in order to identify potential parents that can be used to produce offspring with desired bunch weight and stature after a few crosses. Results This research found significant progressive heterobeltiosis in cross-bred ‘Matooke’ (highland cooking) banana hybrids, also known as NARITAs, when grown together across years with their parents and grandparents in Uganda. Most (all except 4) NARITAs exhibited positive heterobeltiosis for bunch weight, whereas slightly more than half of them had negative heterobeltiosis for stature. The secondary triploid NARITA 17 had the highest heterobeltiosis for bunch weight: 249% versus its ‘Matooke’ grandparent and 136% against its primary tetraploid parent. Broad sense heritability (across three cropping cycles) for yield potential and bunch weight were high (0.84 and 0.76 respectively), while that of plant stature was very low (0.0035). There was a positive significant correlation (P < 0.05) between grandparent heterobeltiosis for bunch weight and genetic distance between parents (r = 0.39, P = 0.036), bunch weight (r = 0.7, P < 0.001), plant stature (r = 0.38, P = 0.033) and yield potential (r = 0.59, P < 0.001). Grandparent heterobeltiosis for plant stature was significantly, but negatively, correlated to the genetic distance between parents (r = − 0.6, P < 0.001). Conclusions Such significant heterobeltiosis exhibited for bunch weight is to our knowledge the largest among main food crops. Since bananas are vegetatively propagated, the effect of heterobeltiosis is easily fixed in the hybrids and will not be lost over time after the release and further commercialization of these hybrids

Finger millet RNA-seq reveals differential gene expression associated with tolerance to aluminum toxicity and provides novel genomic resources

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

Polymerase delta-interacting protein 38 (PDIP38) modulates the stability and activity of the mitochondrial AAA+ protease CLPXP

Over a decade ago Polymerase δ interacting protein of 38 kDa (PDIP38) was proposed to play a role in DNA repair. Since this time, both the physiological function and subcellular location of PDIP38 has remained ambiguous and our present understanding of PDIP38 function has been hampered by a lack of detailed biochemical and structural studies. Here we show, that human PDIP38 is directed to the mitochondrion in a membrane potential dependent manner, where it resides in the matrix compartment, together with its partner protein CLPX. Our structural analysis revealed that PDIP38 is composed of two conserved domains separated by an α/β linker region. The N-terminal (YccV-like) domain of PDIP38 forms an SH3-like β-barrel, which interacts specifically with CLPX, via the adaptor docking loop within the N-terminal Zinc binding domain of CLPX. In contrast, the C-terminal (DUF525) domain forms an immunoglobin-like β-sandwich fold, which contains a highly conserved putative substrate binding pocket. Importantly, PDIP38 modulates the substrate specificity of CLPX and protects CLPX from LONM-mediated degradation, which stabilises the cellular levels of CLPX. Collectively, our findings shed new light on the mechanism and function of mitochondrial PDIP38, demonstrating that PDIP38 is a bona fide adaptor protein for the mitochondrial protease, CLPXP

Children with Moderate Acute Malnutrition with No Access to Supplementary Feeding Programmes Experience High Rates of Deterioration and No Improvement: Results from a Prospective Cohort Study in Rural Ethiopia

Background: Children with moderate acute malnutrition (MAM) have an increased risk of mortality, infections and impaired physical and cognitive development compared to well-nourished children. In parts of Ethiopia not considered chronically food insecure there are no supplementary feeding programmes (SFPs) for treating MAM. The short-term outcomes of children who have MAM in such areas are not currently described, and there remains an urgent need for evidence-based policy recommendations. Methods: We defined MAM as mid-upper arm circumference (MUAC) of ≥11.0cm and <12.5cm with no bilateral pitting oedema to include Ethiopian government and World Health Organisation cut-offs. We prospectively surveyed 884 children aged 6–59 months living with MAM in a rural area of Ethiopia not eligible for a supplementary feeding programme. Weekly home visits were made for seven months (28 weeks), covering the end of peak malnutrition through to the post-harvest period (the most food secure window), collecting anthropometric, socio-demographic and food security data. Results: By the end of the study follow up, 32.5% (287/884) remained with MAM, 9.3% (82/884) experienced at least one episode of SAM (MUAC <11cm and/or bilateral pitting oedema), and 0.9% (8/884) died. Only 54.2% of the children recovered with no episode of SAM by the end of the study. Of those who developed SAM half still had MAM at the end of the follow up period. The median (interquartile range) time to recovery was 9 (4–15) weeks. Children with the lowest MUAC at enrolment had a significantly higher risk of remaining with MAM and a lower chance of recovering. Conclusions: Children with MAM during the post-harvest season in an area not eligible for SFP experience an extremely high incidence of SAM and a low recovery rate. Not having a targeted nutrition-specific intervention to address MAM in this context places children with MAM at excessive risk of adverse outcomes. Further preventive and curative approaches should urgently be considered