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Recent Submissions
- Socioeconomic Impact and Policy Assessments of the Red Palm Weevil in UAE, Egypt, and Morocco: Informed Consent Information Sheet: Key Informants Interviews (KII’s) InstrumentDate: 2025-12-31Type: Working PaperStatus: Open accessDeveloped under C4RPWC Work Package 1 (Socioeconomics and Policy), this document is an informed-consent sheet and Key Informant Interview (KII) instrument for assessing RPW’s socioeconomic and policy impacts in the UAE and Egypt. It targets experts and policymakers, capturing data on infestation trends, production losses, control costs, and the effectiveness of policies and quarantine measures. The tool supports evidence-based recommendations to strengthen RPW management.
- الآثار الاجتماعية والاقتصادية وتقييم السياسات المتعلقة بسوسة النخيل الحمراء في الإمارات العربية المتحدة ومصر والمغرب : ورقة معلومات الموافقة المستنيرة أداة مقابلات الأشخاص المرجعيينDate: 2025-12-31Type: Working PaperStatus: Open accessThis is the Arabic version of the informed-consent sheet and Key Informant Interview (KII) instrument for assessing RPW’s socioeconomic and policy impacts in Morocco.
- Identification of key genes in chickpea transcriptomics and the development of ChickpeaOmicsR as a comprehensive resource to advance breeding and genomic studiesAuthor(s): Alsamman, Alsamman M.; Mousa, Khaled H.; Abd El-Hak, Asmaa E.; Korkar, Doaa A.; Saedwi, Anas M.; Khaled, Sandy; Al-Soudy, Al-Sayed; El Allali, Achraf; Kehel, Zakaria; Mokhtar, Morad M. (Frontiers Media SA, 2026-03-10)Date: 2026-03-10Type: Journal ArticleStatus: Open accessIntroduction: Chickpea (Cicer arietinum L.) is a key legume crop and a major source of dietary protein in developing countries, yet its productivity is constrained by multiple biotic and abiotic stresses. Advances in RNA-seq and whole-genome sequencing enable detailed exploration of stress-responsive gene expression, but existing resources lack integrated, user-friendly tools for multi-omics analysis in chickpea. Methods: This study analyzed transcriptomic responses to six stress conditions—drought, heat, cold, salinity, Fusarium infection, and developmental stages—using publicly available RNA-seq datasets. We identified differentially expressed genes (DEGs), enriched gene ontology (GO) terms, and protein–protein interaction (PPI) networks. Critically, we developed Chickpea OmicsR, the first comprehensive R package that automates the integration of transcriptomic, genomic, and proteomic data and standardizes fragmented chickpea gene nomenclature; enables breeders without bioinformatics expertise to perform complex analyses (e.g., DEG identification, PPI visualization, GWAS integration) in minutes; and provides pre-validated datasets and analytical workflows unavailable in existing tools. Results: Each stress triggered distinct molecular pathways. Drought and heat stress affected cell wall organization and defense responses, while cold stress influenced circadian rhythm genes. Fusarium stress involved pathways related to innate immunity and secondary metabolism. Developmental stages showed the highest transcriptome variability among the conditions tested. Discussion: The development of Chickpea OmicsR addresses critical gaps in chickpea research infrastructure. By providing an integrated and accessible tool that enables complex analyses for breeders without bioinformatics expertise, it accelerates the discovery of stress-resilient genes and the development of improved chickpea varieties.
- An integrated phenotypic and molecular approach to identify salinity-tolerant lentil (Lens culinaris Medik) genotypesAuthor(s): Yadav, Ashutosh; Devate, Narayana; Barpete, Surendra; Singh, Vijayata; Basarahalli, Srilekha; Das, Arpita; Gebregziabher, Berhane Sibhatu; Patidar, Jitendra; Namdeo, Rohit; Agrawal, Shiv Kumar (Frontiers Media, 2026-06-22)Date: 2026-06-22Type: Journal ArticleStatus: Open accessSalinity in soil and irrigation water has emerged as a serious challenge to global agricultural productivity. Lentil (Lens culinaris Medik.) is highly sensitive to salinity, particularly during early seedling establishment, which adversely affects growth and development. Systematic screening at the seedling stage can therefore serve as an effective strategy to identify novel sources of salt-tolerant donors. In this study, 50 elite breeding genotypes from ICARDA breeding program were evaluated for seedling-stage salinity tolerance under salt stress (electrical conductivity of 8 dS m−1) and control conditions through pot culture. Important morpho-physiological traits, including shoot and root length and their biomass were recorded at 30 days after sowing, revealing substantial genetic variability. Based on the cumulative salt tolerance index (CSTI), 35 genotypes were classified as salt sensitive, eight as moderately tolerant, and seven as salt tolerant, with “X2018-482-S5” as the most tolerant and “FLIP2014-083L-S9” as the most sensitive. Selected tolerant genotypes were further evaluated under saline field conditions, where X2018-482-S5, ILL7547, X2011S-89-23-S1, X2011S-91-77-2-S1, and ILL6819/ILL6207-S2 exhibited stable growth and yield performance comparable to the tolerant checks PSL9 and PDL1. Gene expression analysis revealed coordinated upregulation of the High-Affinity Potassium Transporter (HKT) and NAC domain-containing protein-72 in tolerant genotypes, with significantly higher transcript levels compared to sensitive check FLIP2014-083L-S9 at 6 and 12 h post treatment with 100 mM NaCl treatment, indicating enhanced ion homeostasis and stress-responsive regulation. Overall, the integration of seedling-stage phenotyping, field validation, and molecular analysis provides robust evidence for identifying promising salinity tolerant lentil genotypes for breeding programs targeting salt-affected environments.
- Genetic diversity, population structure and enhancing selection efficiency in wheat pre-breeding using the CGIAR mid-density DArTag panelAuthor(s): Amounane, Fatima; Backhaus, Anna Elisabeth; Amri, Ahmed; Belquadi, Loubna; Alsamman, Alsamman M.; Kehel, Zakaria (Cambridge University Press (CUP): STM Journals - No Cambridge Open)Date: 2026-04-24Type: Journal ArticleStatus: Open accessBread wheat (Triticum aestivum L.) is a vital crop with production demand increasing due to population growth. However, bread wheat is facing challenges, including the emergence of pests and diseases, reduced genetic diversity and climate change. To meet food security, pre-breeding can help to develop varieties by incorporating desirable traits from wild relatives and landraces. Although pre-breeding is crucial, it does not often take full advantage of recent genotyping technologies. The DArTag mid-density wheat panel, developed by CIMMYT as part of the CGIAR initiative, offers a low-cost genotyping solution, but its applicability in pre-breeding programs has not been widely evaluated. This study aims to assess population structure, genetic diversity and genomic selection in a set of 484 pre-breeding bread wheat lines derived from crosses with wild relatives, using the DArTag mid-density wheat panel to investigate the ability of this genotyping approach to validate pedigrees, identify specific trait subsets and detect potential introgressions for targeted selection. Our results demonstrate that the panel captured genetic diversity in the pre-breeding population, identifying seven subpopulations with different genetic compositions; analysis confirmed the existence of private alleles associated with important agronomic traits, highlighting the role of wild relatives, especially Aegilops bicornis and Aegilops ovata, in genetic variation. In addition, the genotyping also facilitates pedigree validation and generates trait-specific sub-populations for phenotyping. The sub-populations and markers found in this work are useful resources that can be effectively used to accelerate wheat improvement, offering new insights into the contribution of wild relatives and landraces to wheat diversity.