International Crops Research Institute for the Semi-Arid Tropics
ICRISAT Open Access RepositoryNot a member yet
12134 research outputs found
Sort by
Molecular Characterization and Resistance Profiling of Groundnut Genotypes to Leaf Spot Disease Using SSR Markers
Get PDFLate Leaf Spot (LLS), caused by Nothopassalora personata, is a major fungal disease that significantly reduces peanut (Arachis hypogaea L.) production, particularly in Sub-Saharan Africa, including Uganda. This disease lowers the quality of the produce and leads to severe yield losses. Despite control measures, genetic resistance in local peanut cultivars remains limited, and effective management strategies are not well established. Therefore, genetic improvement using LLS resistance is crucial for enhancing peanut productivity. This study aimed to characterize and profile resistance of 25 ICRISAT peanut genotypes, introduced from Malawi and evaluated under Ugandan environmental conditions, using Simple Sequence Repeat (SSR) markers. Genomic DNA was extracted from leaf samples using an optimized Cetyltrimethylammonium Bromide (CTAB) protocol, quantified via spectrophotometry, and amplified by Polymerase Chain Reaction (PCR). Eight SSR markers previously associated with LLS resistance were used to assess their ability to differentiate resistant genotypes. Results revealed that five markers (PM375, PMc588, pPGPseq2B10, pPGPseq2F5, pPGseq17F6) were strongly correlated with LLS resistance, while one marker (pPGseq13A7) was monomorphic. Nine genotypes (36%) carried at least one resistance allele, with five genotypes (20%) classified as resistant, containing four or more resistance alleles, including ICGV-SM 16605, ICGV-SM 16615, ICGV-SM 16602, ICGV-SM 16613, and ICGV-SM 16637. Multivariate analyses, including scatter plots, Unweighted Pair Group Method with Arithmetic Mean (UPGMA) phylogeny, and heat-map clustering, clearly separated genotypes into resistant, tolerant, and susceptible groups. This study highlights the potential of Marker-Assisted Selection (MAS) in identifying and utilizing resistant genotypes for breeding LLS-resistant peanut cultivars in Uganda. Identifying these resistant genotypes offers a valuable resource for improving disease resistance and enhancing sustainable peanut farming production in Uganda and other regions of Sub-Saharan Africa
Annotated 3D Point Cloud Dataset of Broad-Leaf Legumes Captured by High-Throughput Phenotyping Platform
Get PDFThis data descriptor presents novel, annotated 3D point cloud plant scans generated by a high-throughput phenotyping platform (LeasyScan, ICRISAT, India). It focuses on broad-leaf legume species (mungbean, common bean, cowpea, and lima bean). The dataset, generated by PlantEye(R) F600 technology, captures multispectral 3D scans of plant canopies. It includes 223 scans, providing detailed organ-level segmentation annotations for embryonic leaves, leaves, petioles, stems, and whole plants. The dataset fills a critical gap in plant phenomics research by offering a base of annotated data to support AI model development efforts in 3D computer vision. Data preprocessing, annotation procedures, and potential applications in crop research disciplines are further discussed. The dataset, preprocessing code, annotations, and a MIAPPE-compliant data sheet are also presented via the GitHub repository for further updates and expansion
Combining complementary multiplex extraction chemistries enhances proteome coverage and analytical insights in tiny insects: A study on sweet potato whitefly Bemisia tabaci
No full textAdvancements in protein extraction methodologies are essential for enhancing insect proteomics, especially in sap-feeding small insects, where high lipid content and limited tissue volume impede efficient protein recovery. This study systematically assessed seven extraction chemistries, lysis buffer (LB), dissolution buffer (DB), TRIzol®, trifluoroacetic acid (TFA), trichloroacetic acid (TCA), TCA-phenol, and phenol— under varying pH conditions to determine the most effective workflow for comprehensive proteomic profiling of Bemisia tabaci. Qualitative two-dimensional electrophoresis (2-DE) analysis indicated that phenol and TCA-phenol methods maintained protein integrity across a wide molecular weight range, while acidic conditions enhanced the resolution of low-abundance proteins. Quantitative liquid chromatography-tandem mass spectrometry (LC–MS/MS) analyses demonstrated that the TCA-phenol method yielded the highest protein recovery and reproducibility (coefficient of variation = 12.6 %), identifying 1010 proteins with balanced representation of soluble and membrane fractions. Principal component and overlap analyses confirmed distinct, method-specific proteomic signatures, with TCA-phenol and TFA achieving the most extensive proteome coverage. Functional annotation revealed that DB and LB enriched primary metabolic and biosynthetic processes, whereas the TCA-phenol method provided the broadest functional spectrum, capturing detoxification, energy metabolism, and stress-related proteins. Overall, this research illustrates that no single extraction chemistry is universally optimal; rather, combining complementary methods enhances proteome coverage. These findings establish a standardized comparative framework for small-insect proteomics and offer valuable methodological insights to advance research in insect physiology, stress adaptation, and ecological interactions
National Stakeholder Engagement Workshop for Sustainable Agricultural Planning and Climate Adaptation in Malawi
Get PDFThe International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Malawi successfully convened a one-day stakeholder engagement workshop on 1st October 2025 at Lingadzi Inn in Lilongwe as part of its Sustainable Farming Program. The primary objective of the workshop was to bring together key actors and stakeholders across Malawi’s agriculture sector to collaboratively develop a practical and actionable sustainable farming systems plan. This plan is intended to enhance climate adaptation and build resilience among vulnerable farming communities, promoting long-term sustainability in agricultural practices. The workshop was attended by a total of 23 participants, comprising 19 males and 4 females, who represented a diverse range of institutional stakeholders actively involved in the program’s implementation. Among the attendees were representatives from the Department of Agricultural Research Services (DARS), District-level Department of Agricultural Extension Services from Mzimba, Kasungu, Balaka, and Zomba, the Lilongwe University of Agriculture and Natural Resources (LUANAR), the Department of Land Resources and Conservation, the Department of Crop Development, ICRISAT as well as regional partners including the International Institute of Tropical Agriculture (IITA) Malawi and CIAT Malawi. The technical sessions commenced with an introductory remark from the Country Representative of ICRISAT Malawi, setting the stage for the day’s discussions. This was followed by a series of insightful presentations beginning with Dr. Martin Moyo, who provided a comprehensive overview and recap of the Sustainable Farming Science Program. Subsequent presentations were delivered by experts including Dr. Botoman from ICRISAT, Dr. Pungulani representing DARS, Dr. Phiri from LUANAR, and representatives from districts identified as key climate risk areas. The workshop concluded with plenary discussions, allowing participants to exchange ideas, raise concerns, and collectively contribute to refining the strategies for Sustainable Agricultural Planning and Climate Adaptation in Malawi. “By bringing all stakeholders to the same table, Malawi can turn climate risks into opportunities, shaping agricultural systems that protect our soils, nourish our people, and safeguard the future for generations to come.
Monitoring, evaluation, and learning tracking report: Site specific fertilizer advisory in the mixed highland farming systems in Ethiopia
Get PDFThe site-specific fertilizer advisory tool was developed to provide farmers with precise, landscape-driven nutrient management recommendations to produce teff, wheat, sorghum, and maize. Its main objective is to optimize fertilizer use efficiency, enhance crop productivity, and improve economic returns under Ethiopia’s diverse agroecological conditions. Field events and training sessions were organized collaboratively by ICRISAT (36%) and the Ministry of Agriculture through the local extension services (64%). These sessions targeted smallholder farmers and included piloting and scaling of the advisory tool in farmer field conditions. This multi-actor engagement strengthened the quality, reach, and sustainability of the piloting and scaling activities, ensuring that both technical and local perspectives were integrated into the process.
During the piloting and scaling phases of the site-specific fertilizer advisory service, partners organized three primary types of awareness and capacity-building activities: training sessions, field days, and demonstrations. These events were used to gather feedback on the performances of the site-specific fertilizer innovations through focus group discussions (FGD) and a telephone survey. About 1455 (218 female and 1237 male) samples of innovation users were participated in the MELIA feedback survey, constituting 284 in the training, 470 in the field day events and 700 in the field demonstrations over the three years. The percentage distribution of event types organized by the implementing partners reflects a balanced mix of engagement approaches designed to effectively reach farmers. Field demonstrations made up the largest share of events, underscoring their importance in practically showcasing the performance of the site-specific fertilizer advisory tool under real field conditions. Field days and experience-sharing sessions formed the next major category, providing opportunities for stakeholders to discuss implementation progress, share lessons, and provide feedback on the advisory service. In addition, field day events provided practical, on-farm demonstrations where participants observed the performance of site-specific nutrient recommendations under real farming conditions. These demonstrations reinforced learning by visually illustrating the differences in crop response across treatments and landscape positions. During the field days, the experience-sharing provided opportunities for stakeholders to discuss emerging lessons, challenges, and adoption trends
Targeting Aflatoxin Resistance in Groundnut: Gene Discovery and CRISPRCas9-based Validation
No full textAflatoxin contamination, primarily caused by Aspergillus flavus, significantly threatens food safety and human health. Despite extensive research, the molecular and biochemical mechanisms underlying resistance remain only partially understood. Various strategies have been explored, including genetic analyses, cellular defense responses such as secondary cell wall reinforcement, biocontrol agents, and identifying resistance- and susceptibility-associated genes. While these studies have identified potential targets for precision breeding in groundnut, the complexity of resistance mechanisms during Aspergillus infection remains challenging. This study employed an integrative metabolomics and proteomics approach to investigate resistance mechanisms in two contrasting peanut genotypes: transgenic 4RNAi-expressing groundnut (resistant) and WT-ICGV 91114 (susceptible). We identified key regulatory events influencing enzyme activity, post-translational modifications, and gene expression during Aspergillus infection. Notably, proteomic changes preceded metabolite alterations, underscoring the significance of protein-level regulation in resistance. Integrating metabolomics and proteomics revealed metabolic and protein profiles linked to
phenylpropanoid, flavonoid, and fatty acid biosynthesis, pathways crucial for suppressing aflatoxin production. Furthermore, we investigated putative susceptibility-associated genes, providing insights into potential targets for precise breeding interventions. To explore genetic
modification strategies, we developed a proof-of-concept CRISPR/Cas9 system in groundnut via Agrobacterium-mediated transformation, achieving a transformation efficiency of 20% and an editing efficiency of 6% by targeting the phytoene desaturase (PDS) gene. Building on this system, we used CRISPR-Cas9 to manipulate susceptibility genes involved in host-pathogen interactions. This enabled us to study how groundnut recognizes fungal pathogens, triggers defense responses, and regulates metabolic pathways to counteract aflatoxin biosynthesis. Understanding these molecular interactions provides a foundation for breeding aflatoxin-resistant groundnut varieties. This comprehensive study advances knowledge of resistance mechanisms against Aspergillus infection and aflatoxin contamination, laying the groundwork for sustainable agricultural strategies to enhance food safety
Multi-locus Genome-Wide Association Study Uncovers Candidate Genes for Early Leaf Spot and Rust Resistance in Groundnut
No full textEarly leaf spot (ELS) and rust, caused by Cercospora arachidicola and Puccinia arachidis respectively, are major fungal diseases limiting global groundnut (Arachis hypogaea L.) production. Mini-core set was evaluated for ELS at 3 locations Senegal, Malawi and Mali and for rust at Dharwad for three seasons using the modified 9-point scale. High-density genotyping was performed using whole genome resequencing data to identify genomic regions associated
with early leaf spot and rust resistance. After quality filtering, 561,009 high-confidence SNPs were obtained. To dissect the genetic architecture of resistance to these diseases, genome-wide association study (GWAS) was conducted on 184 diverse groundnut mini-core lines which revealed four marker trait associations (MTAs) significantly associated with ELS resistance and twelve MTAs associated with rust resistance, collectively explaining 10–59% of the phenotypic variance. The most significant SNPs were Ah01_48511619 and Ah17_133493906 for rust resistance, which were clearly differentiating the resistant and susceptible minicore lines and also validated in other diverse populations. These SNPs encode sterol c4-methyl oxidase 1-2 and MYB transcription factor. Sterol c4-methyl oxidase 1-2 is involved in
brassinosteroids biosynthesis which inturn has a role in salicylic acid pathway and MYB transcription factor involved in activation of WRKY disease resistance genes to combat against fungal pathogens. For ELS resistance, the most significant SNP (Ah14_140021024) is associated with MYB transcription factor explaining phenotypic variance of 59%. The validated markers and the predicted candidate genes can be useful in integrating favorable alleles into elite cultivars through marker-assisted selection (MAS) for the development of cultivars with improved disease resistance. The ELS markers can be utilized in the breeding programs upon further validation
Advancing Groundnut Breeding for Semi-Arid Tropics through HighThroughput Phenotyping for Early Vigour Traits
No full textEarly vigour is a vital trait in groundnut (Arachis hypogaea L.) that enhances adaptation to soil moisture stress in semi-arid tropics, where early rainfall cessation often limits crop productivity. Its importance in improving yield potential under such conditions has been increasingly recognized. However, the lack of efficient high-throughput phenotyping tools has restricted the rapid and precise identification of early vigour lines in breeding programs. This study addresses this gap by evaluating a groundnut mini-core set (184 accessions), 5 checks, and 3 elite breeding selections from the field testing using the high-throughput phenotyping platform “LeasyScan.” LeasyScan employs 3D point cloud technology and AI to measure canopy and transpiration dynamics in a 6-week assay. The experiment was conducted in an alpha-lattice design with three replications. Key recorded traits included digital biomass, leaf area index, number of primary branches, projected leaf area, light penetration depth, plant height, and 3D leaf area. A 3- to 6-fold genetic variation was observed for various adaptation traits. Plant height, 3D leaf area, and digital biomass emerged as robust indicators growth rate
and used for identifying early vigour lines. Five high-vigour genotypes - ICG4670, ICG13491, ICG332, ICG7190, and ICG15309 and five low-vigour genotypes - ICG6402, ICG532,
ICG2925, ICG11855, and ICG9037 were identified. Future research involving whole-genome re-sequencing and GWAS analysis aims to uncover candidate genes linked to early vigour traits, enabling the development of markers for effective selection in regions without highthroughput
phenotyping facilities. This study underscores the transformative potential of highthroughput phenotyping in accelerating the development of drought-resilient, high-yielding groundnut varieties, contributing significantly to global food security efforts
Agroforestry: A Climate Resilient and Sustainable Land Use
No full textAgroforestry (AF) means combining shrubs, trees, crops, and livestock to manage rural land resources. It generates economic, environmental, and social benefits. Traditionally, agroforestry systems have been mixed farming systems. In India, agroforestry has been around for generations as a way of life. Approximately 10% of all agricultural land worldwide is believed to be covered by agroforestry. Nearly half of the needs for firewood, small timber (65%), wood for plywood (70–80%), the base material for paper pulp (60%), and nutritious green food for animals (9–11%) are met by it. Agroforestry has become of greater significance in tackling numerous challenges as well as offering a broad range of socioeconomic and environmentally friendly advantages, especially in the wake of the Kyoto Protocol to the United Nations Framework Convention on Climate Change (UNFCCC). When combined with field crops, trees have the ability to significantly boost the economy by diversifying the land, generating sustainable income, and enhancing the security of food, fuel, and fodder. Because agroforestry simultaneously reduces the amount of greenhouse gases produced from the soil by storing carbon in topsoil and biomass from trees, it increases the likelihood of minimizing and adapting to the effects of changing the climate. By 2030, India aims to reduce the amount of greenhouse gases, it emits by 33–35% from 2005 levels. India has launched a landmark National Agroforestry Policy 2014 that promotes agroforestry. Also outlined is a recommendation to upscale and promote agroforestry research at the national level through institutional mechanisms. The policy aims to foster collaboration across numerous projects, plans, and organizations that incorporate agroforestry features to improve the livelihoods, revenue, and productivity of small-scale landowners. The policy also seeks to increase awareness about agroforestry and its benefits among farmers, stakeholders, and the public. It also encourages the use of agroforestry practices for sustainable land management. Lastly, the policy seeks to create an enabling environment for agroforestry development
The Ameliorative Effects of Lime and Vermicompost on Yield and Yield Components of Barley (Hordeum vulgar L.) and Soil Properties in Acidic Soil of Northwestern Ethiopia
Get PDFSoil acidity and fertility depletion are the major challenges to crop production in the northwestern highlands of Ethiopia. In response to this problem, this study was conducted on acidic soils of Banja district of northwestern Ethiopia to evaluate the main and interaction effects of different rates of lime and vermicompost application on soil properties, and yield and yield components of barley during 2020 main cropping season. The factorial combinations of four rates of lime (0, 50, 100, and 150%) or (0, 0.93, 1.86, and 2.79 t/ha-1) with three rates of vermicompost (0, 2.5 and 5 t ha-1) were laid out in randomized complete block design with three replications. Soil samples were taken at a depth of 0-15 cm before the application of treatments and after harvesting. The results revealed that the interaction effects of lime (2.79 t ha-1) with VC (5 t ha-1) significantly increased soil pH (5.55), exchangeable calcium (14.36%), and exchangeable sodium (0.58%). Similarly organic carbon (3.17%), and exchangeable magnesium (1.49%) increased at the application of lime (1.86 t ha-1) with vermicompost (5 t ha-1). The main effects also increased total nitrogen, available phosphorus, cation exchangeable capacity, and potassium, whereas significantly decreased exchangeable acidity and aluminum. The main and interaction effects of lime and vermicompost significantly improved yield and yield components of barley. The highest grain yield of 5097 kg ha-1 was recorded from the combined application of lime 1.86 t ha-1 and vermicompost 5 t ha-1. Whereas, the lowest grain yield of 3635 kg ha-1 was recorded from the control. Overall, the combined application of organic fertilizer and lime amendments could be recommended to amend soil acidity and improve the availability of nutrients and crop yield. However, further research is needed to evaluate the long-term effects of both organic and lime amendments