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.

Early infant diagnosis of HIV infection using DNA-PCR at a referral center: an 8 years retrospective analysis.

BACKGROUND: Over the last decade, Ethiopia adopted different strategies of prevention of mother to child transmission of HIV (PMTCT). Prior to implementation of Option A in 2011, there was no provision of prophylaxis for PMTCT. With 'Option A', PMTCT interventions relied on maternal CD4 count. In early 2013, ''Option B+'' has been started; with this option, antiretroviral therapy is started and continued for life to any HIV positive pregnant mother irrespective of CD4 count with an enhanced treatment for the baby. Though there are a number of studies which evaluated the effectiveness of PMTCT interventions, the current study assessed the real-world effectiveness of PMTCT options in a setting where there is limitation of resources. OBJECTIVE: This study tried to address three questions: what proportion of babies tested by DNA-PCR are HIV infected in the first 2 months of life? How does the type of PMTCT intervention affect presence of HIV infection at this age? What are the factors affecting HIV transmission, after controlling for type of PMCT-HIV intervention? METHODS: We assessed records of 624 registered HIV exposed infants and 412 mothers who were delivered at Bishoftu Hospital from May 2006 to August 2014. Presence of HIV infection at 6-8 weeks of age was assessed from the records. Maternal and infant risk factors for infection at this age were analyzed. Data were collected using standard data abstraction format and were analyzed using SPSS version 20. RESULTS: Among all the infants who were delivered at the hospital during the study period, 624/936 (66.7 %) had undergone early infant diagnosis at 6-8 weeks. Twenty-seven (4.3 %) were positive for HIV DNA PCR at the age of 6-8 weeks. None of the infants who received ''Option B+'' had a positive HIV DNA PCR result. HIV infection rate was highest among those who took either no prophylaxis or single dose Nevirapine (11.5 and 11.1 % respectively). Those who took single dose Nevirapine and Zidovudine had HIV positivity rate of 3.9 %. Many of the covariates which were shown to be predictors on bivariate analysis were found not to be independent predictors on multivariate analysis. CONCLUSION: PMTCT ''Option B+'' resulted in zero HIV infection rates among the included infants. There was a high loss to follow up rate at 6-8 weeks of age. The authors recommend that a better strategy of linkage to care and treatment should be devised for HIV exposed infants.

Exploring adaptation responses of maize to climate change scenarios in southern central Rift Valley of Ethiopia.

In this study, we assessed responses of adaptation options to possible climate change scenarios on maize growth and yield by using projections of 20 coupled ensemble climate models under two representative concentration pathways (RCPs) 4.5 and 8.5 by means of a DSSAT model. Growth and yield simulations were made across present and future climate conditions using the hybrid maize variety (Shone). Subsequently, simulated yields were compared with farmer' average and on-farm trial yields. Results showed that on-farm trial yield (5.1-7.3 t ha-1) lay in between farmers' average yield (2.9-5 t ha-1) and water-limited potential yield (6.3-10.6 t ha-1). Maize yields achieved in farmers' fields are projected to decline towards mid-century and further towards the end of the century regardless of the adaptation options compared with baseline in low potential clusters. Results of a combination of adaptation options including February planting, use of 64 kg ha-1 N and conservation tillage provided yield advantage of 5.8% over the 30 cm till under medium GHGs emission scenario during mid-century period at Shamana. Mulching with 5 t ha-1 was projected to produce a 4-5% yield advantage in the Hawassa cluster during the mid-century period regardless of changes in tillage or planting window. Under a high GHGs emission scenario, over 13.4% yield advantage was projected in the Bilate cluster due to conservation tillage and June planting during the mid-century period. In the Dilla cluster, the use of 10 t ha-1 mulch, conservation tillage and early planting (February) would result in a 1.8% yield advantage compared with the control either in medium or high GHGs emission scenarios. Thus, the most promising and least risky practices among simulated strategies were the use of nitrogen and mulching in combination with tillage or planting date adjustment. However, adaptation options remained least promising and highly risky if not integrated with mulching or nitrogen use. Hence, the negative impacts of future climate change and subsequent yield gaps would be reduced by optimizing the application of nitrogen, mulch and their interaction with planting date and tillage in high and low potential areas of maize production.

Ethiopia's wheat production pathways to self-sufficiency through land area expansion, irrigation advance, and yield gap closure.

Ethiopia is the second largest wheat producer in Africa. Though wheat production has been increasing steadily in the past decades, the demand for the crop outstripped domestic supply and forced the country to cover about 30 % of the deficit through commercial imports and food aid. The utilization of wheat is rising at 9 % annually while the production is increasing at 7.8 %, showing a continued widening between consumption and production. With a growing demand due to bourgeoning population, increase in income, and preference toward wheat-based products, the country has a long journey to achieve wheat self-sufficiency and save the scarce foreign currency reserve spent on import. The government of Ethiopia is committed to self-sufficiency through initiatives such as wheat area expansion, irrigation development and yield gap closure. In this review, we explored wheat production trends and the roles of the recent government initiatives toward wheat self-sufficiency. The review indicated that wheat production and productivity have increased in Ethiopia, but the wheat self-sufficiency of the country has declined from 99 % in the 1960s to 70 % at present. The future land area expansion in traditionally wheat-producing areas is limited, and wheat land suitability and yield potential is likely to reduce under climate change. Thus, the options to transform the wheat sector while reducing greenhouse gas emissions is through yield gap closure through intensification on existing cropland and judicious temporal and spatial expansion of irrigated wheat areas. The yield gap closure requires higher and more efficient input supply and utilization, investments in modern technologies, as well as supportive agricultural policies. To improve the productivity of small landholder farmers and increase intensity of production through irrigation investment on irrigation structures and facilities is required. Finally, we recommend further studies on yield gap analysis, the role of government initiatives, and wheat land suitability under current and future climate change scenarios at the local level.

Genotype by environment interaction and yield stability of cowpea (Vigna unguiculata (L.) Walp.) genotypes in moisture limited areas of Southern Ethiopia.

Genotype by environment interaction (GEI) markedly influences the success of breeding strategies in a versatile crop such as cowpea (Vigna unguiculata (L.) Walp.). Twenty cowpea genotypes were tested in a randomized complete block design with three replications at Gofa, Kucha, and Humbo in Meher seasons of 2016 and 2017 (E1 to E6) and Belg seasons of 2017 and 2018 (E7 to E12) to quantify and evaluate the effects of genotypes, environments and their interactions for grain yield of cowpea genotypes and to identify stable and/or high-yielding genotypes. The environment, genotype, and GEI effects were highly significant (p < 0.001), with the contribution of 42.3%, 23.0%, and 34.7%, respectively to the TSS. Additive main effect and multiplicative interaction (AMMI), genotype main effects plus genotype-environment interaction (GGE), ASV (AMMI stability value), and Genotype stability index (GSI) were used to identify stable genotypes. The GGE-biplot model showed that the twelve environments used for the study clustered under three mega-environments. Our results showed that IT96D-604(G12), IT-89KD (G16), IT93K-293-2-2 (G14), 93K-619-1(G13), IT97K-569-9(G20), and IT99K-1060(G15) scored the highest grain yield (1.67, 1.62, 1.55, 1.51, 1.51, and 1.45 t ha-1), respectively, over environments. AMMI and GGE biplots analyses identified G16 (IT-89KD) and G14 (IT93K-293-2-2) as stable and high-yielding genotypes across environments and can be further tested in variety verification and later on released as varieties and can also be used for different breeding purposes in all cowpea growing areas in southern Ethiopia. The four high-yielding genotypes IT96D-604, 93K-619-1, IT97K-569-9, and IT99K-1060 could be recommended to be included in breeding or variety verification trials for release. Moreover, our results denoted the effectiveness of AMMI and GGE biplot techniques for selecting stable genotypes, high yielding, and responsive.

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.