Ukama Ustawi (UU)- Annual Project report CGIAR Initiative on Diversification in East and Southern Africa 2024 in Ethiopia

12 page

Genomic prediction powered by multi-omics data

Genomic selection (GS) has transformed plant breeding by enabling early and accurate prediction of complex traits. However, its predictive performance is often constrained by the limited information captured through genomic markers alone, especially for traits influenced by intricate biological pathways. To address this, the integration of complementary omics layers—such as transcriptomics and metabolomics—has emerged as a promising strategy to enhance prediction accuracy by providing a more comprehensive view of the molecular mechanisms underlying phenotypic variation. We used three datasets, each collected under a single-environment condition, which allowed us to isolate the effects of omics integration without the confounding influence of genotype-by-environment interaction. We assessed 24 integration strategies combining three omics layers: genomics, transcriptomics, and metabolomics. These strategies encompassed both early data fusion (concatenation) and model-based integration techniques capable of capturing non-additive, nonlinear, and hierarchical interactions across omics layers. The evaluation was conducted using three real-world datasets from maize and rice, which varied in population size, trait complexity, and omics dimensionality. Our results indicate that specific integration methods—particularly those leveraging model-based fusion—consistently improve predictive accuracy over genomic-only models, especially for complex traits. Conversely, several commonly used concatenation approaches did not yield consistent benefits and, in some cases, underperformed. These findings underscore the importance of selecting appropriate integration strategies and suggest that more sophisticated modeling frameworks are necessary to fully exploit the potential of multi-omics data. Overall, this work highlights both the value and limitations of multi-omics integration for genomic prediction and offers practical insights into the design of omics-informed selection strategies for accelerating genetic gain in plant breeding programs

Smallholder farmers’ preferences for agroecology policies in Zimbabwe

5 page

Alternating tillage with conservation agricultural practices in intensive rice (Oryza sativa L.)-based cropping systems can improve soil health and increase crop and systems productivity in the Eastern Indo-Gangetic Plains

Available ariable land for agriculture in South Asia's Eastern Indo-Gangetic Plains (EIGP) is decreasing while the population and the demand for food is increasing. Despite this pressure to intensify land use, large tracts of land still remain fallow during the dry season. Making productive use of these lands is essential to increasing farm output while safeguarding food security. One potential part of the solution to this challenge lies in improved land management practices. Conservation agriculture with no or reduced tillage (CA), or alternating tillage where monsoon rice is established with full tillage and dry season crops with reduced or zero tillage (AT), can potentially facilitate improved crop establishment, increase yield, and improve soil health and the resilience of cropping systems. This study was undertaken to evaluate CA, AT and conventional tillage (CT) under double- or triple cropping sequences on loamy soil in a (sub) tropical environment in the EIGP northern Bangladesh. The experiment included six cropping systems (CS) over three consecutive years: CS1, Aman rice (Oryza sativa L.) – Boro or winter rice (Oryza sativa L.) (R-R); CS2, Aman rice – Wheat (Triticum aestivum L.) (R-W); CS3, Aman rice – Maize (Zea mays L.)(R-M); CS4, Aman rice - Mung bean (Vigna radiata L.) (R-M); CS5, Aman rice – Wheat – Mung bean (R-W-MB); and CS6, Aman rice – Maize – Mung bean (R-M-MB). In CS5 and CS6, mung bean replaced land fallowing after the predominant dry season crop. Maize, but not rice, yields were higher in AT or CA than CT. The R-W-MB and R-M systems had the highest system-level rice equivalent yield. Soil chemical properties, except SOM, total N, and Mn, in the 0–15 cm portion of the soil profile also differed significantly among the systems. Cropping systems had a significant effect on soil penetration resistance up to 30 cm soil depth. The buffering capacity of the soil under these treatments against diurnal temperature variation was also higher under CA followed by AT. These results suggest that AT with CA-based management practices can improve cropping systems level yields and soil properties. These practices can also be be adapted to rice-based farming systems where they can support improved land management and increase systems productivity and soil health. Long-term studies are required across soil types, climates, and socio-economic conditions to extrapolate findings to larger areas of the EGP

Unveiling native mycorrhizal fungi diversity: insights into growth performance, nutrient uptake, and root system robustness in caper-bush (Capparis spinosa L.) seedlings

This study investigates the role of native arbuscular mycorrhizal fungi (AMF) in enhancing the growth performance, nutrient uptake, and root system robustness of caper bushes (Capparis spinosa L.), a key species for rehabilitating marginal lands in the Mediterranean region. The primary aim is to identify AMF communities in the rhizosphere soils of caper bushes and evaluate their effects on seedling growth and nutrition. Greenhouse experiments were conducted over two years in Morocco's Safi region, using two seedling groups: one inoculated with a newly identified native AMF complex, and another uninoculated (control) group. Numerous AMF morphotypes were discovered in the rhizospheric soils under mature caper-bush plants, predominantly from the Glomus genus. Soil analysis revealed a sandy loam texture and high alkalinity. Results showed that AMF inoculation significantly enhanced plant biomass (similar to 135 %), root length (similar to 58 %), and the number of secondary roots (similar to 141 %) compared to controls. Mycorrhizal dependency was approximately 58 %. Furthermore, inoculated plants showed substantial improvements in mineral nutrient levels: potassium (K+), calcium (Ca2+), phosphorus (P), magnesium (Mg2+), iron (Fe2+), and zinc (Zn2+), with increases ranging from similar to 1.5 to similar to 3 times that of non-inoculated plants. The fresh and dry weights of mycorrhizal plants also increased by similar to 87 % and similar to 135 %, respectively. Additionally, the specific absorption rates for these nutrients were enhanced, with increases ranging from similar to 7 % to similar to 170 %. These results highlight pre-transplant AMF inoculation as a promising strategy to enhance caper-bush growth and nutrition in challenging environments. Future research should focus on optimizing AMF inoculation for caper-bush cultivation and exploring its potential for land restoration

Risk-return trade-offs in diversified cropping systems under conservation agriculture: Evidence from a 14-year long-term field experiment in north-western India

Conservation agriculture practices are promoted to increase productivity, profitability, and sustainability across diverse cropping systems. Many studies have used these goals in decision support frameworks to identify the most effective treatment among those examined. While this approach is valuable, it lacks actionable guidance for farmers regarding maximizing return, while minimizing risk. It does not provide specific recommendations on how to allocate land across various cropping systems and tillage practices to achieve such objectives. This would require another long-term experiment exploring various combinations of treatments. To address this challenge, we propose the application of modern portfolio theory, specifically leveraging mean-variance and conditional value at risk optimization models. Using these models has enabled us to identify the optimal cropping system combinations with different tillage practices that maximized yield and net returns with minimal associated risk. The proposed approach allows for recommendations involving combinations of treatments that may not have been previously tested in a geography. In a 14-year long-term conservation agriculture study involving twelve combination of tillage and cropping systems, we showed how different combination of treatments differ in risk-return profile using mean-variance and conditional value-at-risk models that trace out a frontier of options—combinations of treatments that give highest returns at minimal risk. For example, we find that across risk neutral (most profitable) and most risk averse (lowest risk) farmers, the optimal treatments on the frontier encompass of maize-mustard-mungbean (MMuMb) under zero tillage and maize-wheat-mungbean (MWMb) under bed planting (which offer high returns and associated risk), maize-maize-Sesbania (MMS) under zero tillage (providing a balance of moderate returns and risk), and MMS under conventional tillage (yielding lower returns and risk). Additionally, risk-averse farmers stand to gain by diversifying their land allocation. For instance, they could allocate 54 % of their land to MMuMb under zero tillage and 46 % to MWMb under bed planting to target net returns of INR 1,32,000, with downside risk of INR 56,000, otherwise they can allocate 44 % and 56 % of their land to MMS under zero tillage and MWMb under bed planting, respectively, with a targeted net return of INR 1,22,000 and downside risk of INR 43,540. This highlights the nuanced trade-off between risk and return in maize based diversified cropping systems under different tillage practices. Leveraging mean-variance and conditional value at risk optimization models in the analysis of long-term experiments can yield novel treatment combinations that hold promise and can be recommended to farmers for implementation

Minimización de las pérdidas poscosecha de granos: Resultados de las plataformas poscosecha en México 2017-2022

En este libro se presentan los resultados del CIMMYT y de la red de colaboradores en México sobre la implementación de plataformas poscosecha en diferentes agroecologías de sistemas agroalimentarios de autoconsumo y en transición hacia el mercado. El objetivo de esta publicación es compartir los resultados de investigación realizada entre 2017 y 2022, así como las recomendaciones derivadas de estas plataformas y los temas que aún requieren investigación. Este libro está dirigido a agricultores, técnicos, agentes de cambio y representantes gubernamentales.200 page

Mitigating micro-nutrient deficiencies in the diets of rural farm households on the south-central coast of Bangladesh: What roles do the markets and homestead play?

This study explores the roles of market access and on-farm production in ensuring adequate micronutrient consumption among households in coastal Bangladesh. First, the study employed a 7-day weighed food record method, where respondents documented all food items consumed daily at the household level. These food items were then converted into their corresponding nutritional values to estimate the intake of key nutrients, including protein, crude fiber, fat, calcium, potassium, iron, magnesium, phosphorus, zinc, vitamin A, vitamin C, niacin, riboflavin, thiamin, and folate. Household nutritional requirements were calculated based on the Bangladesh Recommended Dietary Allowances (RDAs), accounting for the age and sex of household members. Nutrient adequacy was assessed by comparing actual nutrient intake against these RDA benchmarks. Second, the study analyzed the determinants of nutrient adequacy using truncated regression models, incorporating relevant socioeconomic and demographic variables. The findings reveal a stark contrast: households meeting RDAs predominantly source their nutrients from markets, highlighting the significance of market accessibility and financial capacity. In contrast, households failing to meet RDAs depend heavily on homesteads, which often lacks dietary diversity and nutrient density. Moreover, the food sources vary depending on the micronutrients in question. Additionally, the study identifies key socio-economic vulnerabilities: younger household heads, often prioritizing crop sales, require greater nutritional awareness; female-headed households face unique barriers to adequate nutrient intake; and households burdened by credit constraints experience reduced consumption of critical nutrients like folate and crude fiber. To address these challenges, the study advocates target group differentiated policy approaches, promoting nutrient-dense crop production, subsidized food safety nets, market-based interventions, credit restructuring, and homestead gardening programs that can attain and long-term nutritional resilience in coastal Bangladesh

Physiological and biochemical responses to cold stress in sesame (Sesamum indicum L.) during the early growth stage

Cold stress significantly impacts sesame during its early growth stages, with varying responses observed among different genotypes. Ten genotypes were evaluated for phenotypic response to various temperatures during germination. Cold stress at 10, 12, 14, and 16 °C inhibited germination, with zero germination at 10 °C. At 14 °C, genotypes showed significant germination variation, and it was selected as the threshold temperature for assessing cold tolerance in sesame. Four genotypes were grouped into two, and each group with extreme germination responses (high and low) were selected for further biochemical and physiological studies. Genotypes V5 and V7 exhibited higher cold tolerance, better germination percentage, and seedling parameters under low temperatures, while V8 and V9 showed significant reductions, indicating cold sensitivity. Biochemical analyses revealed that cold-tolerant genotypes had enhanced activities of antioxidant enzymes, including catalase, superoxide dismutase, and peroxidase, as well as higher proline accumulation compared to sensitive genotypes. These antioxidants played a crucial role in mitigating the oxidative stress induced by cold, as evidenced by lower levels of hydrogen peroxide and malondialdehyde in the tolerant genotypes. Cold-tolerant genotypes also accumulated higher soluble sugars and protein levels, contributing to osmotic regulation and membrane stability. The findings highlight the importance of enzymatic and non-enzymatic antioxidants in cold stress tolerance, suggesting these biochemical markers could be used to identify and develop cold-resistant sesame cultivars. The results offer valuable insights into the mechanisms underlying cold tolerance and provide a foundation for breeding efforts to improve sesame cold resistance.293-30

Molecular diversity studies in sweet corn inbred lines using Single Nucleotide Polymorphic markers

Sweet corn (Zea mays L. saccharata) is an important specialty maize, valued for its sweetness and nutritional quality with high consumer demand. The development of superior hybrids relies on genetically diverse inbred lines. Advances in genotyping technologies have transformed the way breeding programs manage their genetic resources. The identification of Single Nucleotide Polymorphisms (SNPs) can improve understanding of the molecular diversity of sweet corn inbred lines and their classification into heterotic groups, which is useful in determining certain crosses to obtain hybrids with higher yield performance. To evaluate molecular diversity, 23 sweet corn inbred lines were genotyped using 97 genome-wide single nucleotide polymorphism (SNP) markers through Kompetitive Allele-Specific PCR (KASP) during 2024-25 at the University of Agricultural Sciences, Raichur, Karnataka. After quality filtering, 56.04% of markers were polymorphic, with polymorphism information content (PIC) values ranging from 0 to 0.375 (mean = 0.39), indicating moderate genetic variability. Cluster analysis using the unweighted pair group method with arithmetic mean (UPGMA) grouped the lines into three major clusters, with most inbreds concentrated in Cluster I, while Clusters II and III contained divergent sweet corn inbred lines (SC-40, SC-9, SC-34 and SC-16), highlighting their potential as valuable sweet corn inbred lines. Principal component analysis (PCA) corroborated the clustering, identifying SC-34, SC-40 and SC-16 as distinct from the core group. The results demonstrate that SNP-based genotyping effectively reveals genetic structure and diversity in sweet corn, further providing a robust framework for heterotic grouping and informed parental selection in hybrid breeding programs.977-98