Agricultural Research Knowledge
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- ICARDA 2024 Financial StatementAuthor(s): (ICARDA), International Center for Agricultural Research in the Dry Areas (International Center for Agricultural Research in the Dry Areas (ICARDA), 2024-12-31)Date: 2024-12-31Type: ReportStatus: Open accessICARDA's Financial Report offers a meticulous examination of our financial achievements, underscoring our unwavering commitment to transparency, effectiveness, and responsible fiscal stewardship. The report provides invaluable perspectives on income origins, expenditure distribution, investment tactics, and critical financial benchmarks. As we persist in propelling agricultural research and pioneering breakthroughs in arid regions, this report serves as a testament to our unwavering dedication to sound financial strategies, bolstering our mission to enrich livelihoods and foster sustainable development.
- Differences in Manioc Diversity Among Five Ethnic Groups of the Colombian AmazonAuthor(s): Peña-Venegas, Clara; Stomph, Tjeerd; Verschoor, Gerard; Becerra, Augusto; Struik, Paul C. (MDPI, 2014-12-09)Date: 2014-12-09Type: Journal ArticleStatus: Open accessManioc is an important root crop in the tropics and the most important staple food in the Amazon. Manioc is diverse but its diversity has not yet been clearly associated with environmental or social factors. Our study evaluates how variation in edaphic environments and in social factors influences manioc diversity among five ethnic groups of the Amazon region of Colombia. Inventories of landraces, genetic analysis of manioc diversity, visits to farmers’ swiddens and interviews with farmers were carried out during two years of field work. Morphotypic and genotypic diversity of manioc were large. The different ethnic groups of our study cultivate different sweet and bitter manioc landraces which they select and maintain in accordance with their ancestral rules and norms. Differences in available environments among indigenous communities (such as the presence of different soils) did not markedly affect manioc morphotypic or genotypic diversity, while social factors considerably influenced observed manioc diversity. Manioc diversity was explained by two parallel processes of manioc diversification: volunteer seedling selection and manioc seed exchange. We argue that, for a full understanding of manioc diversity, indigenous knowledge, as well as morphological and genetic variation should be taken into account.
- Identification of genes that have undergone adaptive evolution in cassava (Manihot esculenta) and that may confer resistance to cassava brown streak diseaseAuthor(s): Ferguson, Morag; Koga, T.M.; Johnson, D.A.; Koga, K.A.; Hirsch, G.N.; Becerra, Augusto; Messier, W. (Academic Journals, 2015-01-14)Date: 2015-01-14Type: Journal ArticleStatus: Open accessCassava (Manihot esculenta) is a vital food security crop and staple in Africa, yet cassava brown streak disease (CBSD) and cassava mosaic disease result in substantial yield losses. The aim of this study was to identify genes that have undergone positive selection during adaptive evolution, from CBSD resistant, tolerant and susceptible M. esculenta varieties and inter-specific hybrids, as well as a wild cassava species. Transcriptomes of 13 genotypes were sequenced and three genes with strong positive selection were detected (designated as EG2771, EG964 and EG5651). Sequence variation for candidate genes in 18 different cassava genotypes was examined in relation to known response to CBSD and whitefly infection. Although, we cannot ascribe a selection pressure that was responsible for the observed positive selection with complete certainty at this stage, given the congruence of the pattern of particular alleles of our positively selected genes and the pattern of disease resistance of the cassava varieties we examined, it is likely that some protein variants coded by alleles of EG2771 and EG964 may be associated with CBSD and whitefly resistance responses. This warrants further investigation. Other alleles of our positively selected genes were likely influenced by domestication or some other unknown selective pressure.
- A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genesAuthor(s): Soto, Johana Carolina; Ortiz, Juan Felipe; Perlaza-Jiménez, Laura; Vásquez, Andrea Ximena; Becerra, Augusto; Mathew, Boby; Leon, Jens; Bernal, Adriana; Ballvora, Agim; Lopez, Camilo (BioMed Central, 2015-03-16)Date: 2015-03-16Type: Journal ArticleStatus: Open accessBackground Cassava, Manihot esculenta Crantz, is one of the most important crops world-wide representing the staple security for more than one billion of people. The development of dense genetic and physical maps, as the basis for implementing genetic and molecular approaches to accelerate the rate of genetic gains in breeding program represents a significant challenge. A reference genome sequence for cassava has been made recently available and community efforts are underway for improving its quality. Cassava is threatened by several pathogens, but the mechanisms of defense are far from being understood. Besides, there has been a lack of information about the number of genes related to immunity as well as their distribution and genomic organization in the cassava genome. Results A high dense genetic map of cassava containing 2,141 SNPs has been constructed. Eighteen linkage groups were resolved with an overall size of 2,571 cM and an average distance of 1.26 cM between markers. More than half of mapped SNPs (57.4%) are located in coding sequences. Physical mapping of scaffolds of cassava whole genome sequence draft using the mapped markers as anchors resulted in the orientation of 687 scaffolds covering 45.6% of the genome. One hundred eighty nine new scaffolds are anchored to the genetic cassava map leading to an extension of the present cassava physical map with 30.7 Mb. Comparative analysis using anchor markers showed strong co-linearity to previously reported cassava genetic and physical maps. In silico based searching for conserved domains allowed the annotation of a repertory of 1,061 cassava genes coding for immunity-related proteins (IRPs). Based on physical map of the corresponding sequencing scaffolds, unambiguous genetic localization was possible for 569 IRPs. Conclusions This is the first study reported so far of an integrated high density genetic map using SNPs with integrated genetic and physical localization of newly annotated immunity related genes in cassava. These data build a solid basis for future studies to map and associate markers with single loci or quantitative trait loci for agronomical important traits. The enrichment of the physical map with novel scaffolds is in line with the efforts of the cassava genome sequencing consortium.
- Assessment of cassava (Manihot esculenta Crantz) diversity, loss of landraces and farmers preference criteria in southern Benin using farmers’ participatory approachAuthor(s): Agre, Angelot; Bhattacharjee, Ranjana; Dansi, Alexandre; Becerra, Augusto; Dansi, M.; Sanni, Ambaliou (Springer (part of Springer Nature) (Springer Open Choice Hybrid Journals), 2017-02-01)Date: 2015-12-11Type: Journal ArticleStatus: Timeless limited accessCassava (Manihot esculenta Crantz) is one of the highly produced and consumed food crops in Benin Republic. Through the application of participatory research appraisal tools and techniques, such as direct observations, group discussions and field visit, cassava production constraints, the diversity at the community level and farmers’ varieties preference criteria were assessed in southern Benin. Base on national statistic cassava production fifty five (55) villages were selected and surveyed in the southern Benin. Descriptive statistics were used to analyse the data collected. About 11 constraints were listed by farmers, and the most important were low productivity, low post-maturity underground storage capacity of the roots of some cultivars, viral disease (cassava mosaic disease), susceptibility to high soil moisture, and lack of early maturing cultivars, which together accounted for 68.02 % of the total responses. Additionally, a total of 125 existing landraces were recorded. The distribution and extent pattern revealed 59 elites cultivars (cultivated by many households and on large areas) that were further grouped into 23 categories based on their agronomic, technological and culinary characteristics. In most of the villages, the farmers’ perception of cultivar loss was based on abandonment of some cultivars due to their poor agronomic (69.12 % of responses) and culinary and/or technological attributes (30.88 % of responses). Within the existing diversity, cultivar choice or preferences are based on 22 culinary, technological, agronomic and economic criteria and their importance vary across the different department. Among these criteria, the most important were high productivity, good quality of the gari, early maturity and good friability accounted together for 48.12 % of the total responses. The presence of duplicates or synonyms was also observed and it is suggested that both morphological and molecular characterization and classification be carried out for better identification of cultivars.
- Rhynchophorus palmarum in Disguise: Undescribed Polymorphism in the “Black” Palm WeevilDate: 2015-12-18Type: Journal ArticleStatus: Open accessDuring studies to adapt pheromone trapping of Rhynchophorus palmarum to the special coconut growing conditions at the Colombian Pacific coast, 152 atypically-colored specimens were captured in a total collection of 53,802 of the normally completely black weevil. Five specimens had the typical coloration of Rhynchophorus ferrugineus, an invasive species recently introduced to Aruba and Curação. A regional expansion of this invasion to the South American continent was feared and all atypical specimens were submitted to taxonomic analysis. Both conventional and molecular methods were employed. Conventional taxonomics confirmed the samples as belonging to R. palmarum but registered undescribed and species-atypical morphological variability in the subgular suture (wide vs. narrow), the ratio between intraocular distance and width of antennal scrobes (>0.35 vs. < 0.29) and the indentation of the mandibles (up to three mandibular teeth vs. bilobed). Molecular analysis placed all samples inspected, black and reddish alike, firmly within the R. palmarum group and the hypothesis of having inter-specific hybrids was rejected using co-dominant single sequence repeat markers with allelic specificity for both species.
- Cassava traits and end-user preference: relating traits to consumer liking, sensory perception, and geneticsAuthor(s): Bechoff, Aurelie; Tomlins, Keith; Genevieve, Fliedel; Becerra, Augusto; Westby, Andrew; Hershey, Clair; Dufour, Dominique (Taylor & Francis)Date: 2017-07-19Type: Journal ArticleStatus: Timeless limited accessBreeding efforts have focused on improving agronomic traits of the cassava plant however little research has been done to enhance the crop palatability. This review investigates the links between cassava traits and end-user preference in relation with sensory characteristics. The main trait is starch and its composition related to the textural properties of the food. Pectin degradation during cooking resulted in increased mealiness. Nutritional components such as carotenoids made the cassava yellow but also altered sweetness and softness; however, yellow cassava was more appreciated by consumers than traditional (white) varieties. Components formed during processing such as organic acids gave fermented cassava products an acidic taste that was appreciated but the fermented smell was not always liked. Anti-nutritional compounds such as cyanogenic glucosides were mostly related to bitter taste. Post-harvest Physiological Deterioration (PPD) affected the overall sensory characteristics and acceptability. Genes responsible for some of these traits were also investigated. Diversity in cassava food products can provide a challenge to identifying acceptance criteria. Socio-economic factors such as gender may also be critical. This review leads to questions in relation to the adaptation of cassava breeding to meet consumer needs and preference in order to maximize income, health and food security.
- Conservation dynamics of roots and tuber crops under on-farm management.Author(s): De Haan, Stef; De Maria Rodriguez Garcia, Flor; Becerra, Augusto; Polreich, Severin; Scurrah, Maria; Nuñez Coronado, Jorge Humberto; Juarez, Henry; Plasencia Amaya, Franklin; Luz, Bernardo; Meza, Katherin (Indian Society of Plant Genetic Resources, 2016-12-14)Date: 2016-12-14Type: Journal ArticleStatus: Timeless limited accessConservation dynamics of roots and tuber crops under on-farm management
- Fungal endophytes in germinated seeds of the common bean, Phaseolus vulgarisAuthor(s): Parsa, Soroush; García-Lemos, Adriana M.; Castillo, Katherine; Ortiz, Viviana; Becerra, Augusto; Braun, Jerome; E. Vega, Fernando (Elsevier (12 months), 2016-05-01)Date: 2016-02-06Type: Journal ArticleStatus: Open accessWe conducted a survey of fungal endophytes in 582 germinated seeds belonging to 11 Colombian cultivars of the common bean (Phaseolus vulgaris). The survey yielded 394 endophytic isolates belonging to 42 taxa, as identified by sequence analysis of the ribosomal DNA internal transcribed spacer (ITS) region. Aureobasidium pullulans was the dominant endophyte, isolated from 46.7 % of the samples. Also common were Fusarium oxysporum, Xylaria sp., and Cladosporium cladosporioides, but found in only 13.4 %, 11.7 %, and 7.6 % of seedlings, respectively. Endophytic colonization differed significantly among common bean cultivars and seedling parts, with the highest colonization occurring in the first true leaves of the seedlings
- Genetic diversity of Enterolobium cyclocarpum in Colombian seasonally dry tropical forest: implications for conservation and restorationAuthor(s): Thomas, Evert; Gil-Tobón, Carlos; P. Gutiérrez, Janneth; Alcázar-Caicedo, Carolina; Moscoso-Higuita, Luis Gonzalo; Becerra, Augusto; Loo, Judy; González, Mailyn Adriana (Springer (part of Springer Nature), 2017-04-01)Date: 2016-12-19Type: Journal ArticleStatus: Timeless limited accessEnterolobium cyclocarpum is a characteristic legume tree species of seasonally dry tropical forests (SDTFs) of Mesoamerica and northern South America typically used in silvopastoral and agroforestry systems. Remaining populations of E. cyclocarpum in Colombia are severely fragmented owing to the highly degraded state of SDTF in the country, posing threats to both their in situ persistence and their usefulness as seed sources for future planting efforts. We genotyped E. cyclocarpum populations at nine sampling sites across a latitudinal gradient of SDTF in Colombia by means of eight nSSR markers to elucidate the species diversity distribution in the country. Our data suggest that a deep divide seems to have existed between Caribbean and Andean populations of E. cyclocarpum in Colombian SDTF that may date back to the last glacial maximum (~21,000 BP), or longer. However, we only found evidence of genetic differentiation between trees from the southern Cauca River valley and populations at more northern locations. All the latter populations showed signs of admixture which may be the result of human-influenced movement of germplasm, particularly after the introduction of cattle by European settlers. Most of the sampled sites showed heterozygosity scores close to Hardy–Weinberg expectations. Only the three southern-most populations displayed significantly positive values of inbreeding coefficient, potentially affecting their in situ maintenance and their use as seed sources. Based on our findings we identify priority areas for the in situ conservation of remaining E. cyclocarpum populations, and propose a strategy for sourcing of appropriate planting material for use in future tree planting efforts.
- Cost-Effective Cassava Processing: Case Study of Small-Scale Flash-Dryer ReengineeringAuthor(s): Tran, Thierry; Abass, Adebayo; Taborda, Luis; Chapuis, Arnaud; Precoppe, Marcelo; Adinsi, Laurent; Bouniol, Alexandre; Ojide, Makuachukwu; Suraju Adeyemi, Adegbite; Lukombo, Simon; Sartas, Murat; Teeken, Bela; Fotso Kuate, Apollin; Ndjouenkeu, Robert; Moreno-Santander, Martín Alonso; Belalcazar, John; Becerra, Augusto; Dufour, Dominique (Springer, 2022-04-07)Date: 2022-04-07Type: Book ChapterStatus: Open accessThe development and scaling out of flash-dryer innovations for more efficient, small-scale production of high-quality cassava flour (HQCF) and starch is described. The diagnoses of cassava-processing SMEs (small and medium enterprises) revealed their energy expenditures for drying were considerably higher than those of large-scale industrial companies, which was mostly due to suboptimal design of flash-drying systems. As a result, small-scale production of cassava starch and HQCF often incurs high production costs, incompatible with market prices of final products. Taking stock of this situation, RTB scientists have developed several innovations to optimize energy efficiency and costs, including a longer drying pipe, reengineered heat exchanger, larger blower for higher air velocity, and a higher product/air ratio. This was based on numerical modelling to determine the key design features of energy-efficient flash dryers, followed by construction and demonstration of a pilot-scale prototype. As a result, improved small-scale flash dryers are now being scaled out to the private sector in various countries, using the Scaling Readiness framework and achieving 10–15% gains in productivity and incomes. A method for diagnosis of process efficiency is also described, to identify technical bottlenecks and to document and measure the outcomes and impacts during the implementation of scaling-out projects.
- Agriculture Water Management, Food Security, and Sustainable Agriculture in the People’s Republic of China and India under Climate ChangeAuthor(s): Prakash Aryal, Jeetendra; Bahadur Rahut, Dil; Becerra, Augusto; Sonobe, Tetsushi (Asian Development Bank Institute, 2024-07-15)Date: 2024-07-15Type: Working PaperStatus: Open accessWater shortage is one of the major environmental challenges in emerging Asian economies such as India and the People’s Republic of China (PRC), presenting significant threats to livelihood and food security in coming decades. The growing population, increasing demand for food, rapid urbanization, and climate-induced water stress will make water an increasingly scarce and critical resource in these nations. Agriculture, as the largest water-consuming sector, accounts for 64% of water use in the PRC and 80% in India. Understanding both the demand and supply sides of water management in agriculture is crucial to addressing future water and food security in these countries. While there are significant differences between the PRC and India in agricultural water management, both countries have predominantly focused on supply-side measures, emphasizing sustainable production practices such as “more crop per drop.” To manage agricultural water resources effectively and ensure long-term sustainability, it is essential to adopt a broader perspective that integrates a comprehensive food system and natural resource management approach. This holistic view will help in developing strategies that balance both the supply and demand sides of water management, addressing the complex challenges of water scarcity in India and the PRC.
- AMMI and GGE biplot analysis for barley genotype yield performance and stability under multi environment condition in southern EthiopiaAuthor(s): Derbew, Shegaw; Firew, Mekbib; Lakew, Berhane; Bekele, Agdew; Bishaw, Zewdie (Wiley (24 months - No Online Open), 2024-09-10)Date: 2024-09-10Type: Journal ArticleStatus: Open accessBarley (Hordeum vulgare L.) is a major grain crop farmed in Ethiopia throughout the long rainy season (Meher) and the short rainy season (Belg) of the year. Barley genotypes were subjected to multi-environment experiments in six different settings to identify stable genotypes and estimate the impact of genotype × environment interaction (GEI) on grain production. In each area, the field experiment was conducted from mid-July to January during the primary cropping season of 2021. Three replications of a randomized complete block design were used to set up the trials. According to the additive main effects and multiplicative interaction (AMMI) study, genotype (18.19%), GEI (22.98%), and environment (58.83%) all had an impact on the major treatment sum of squares. The more variance attributed to the environments is a sign of environmental diversity. Given that the two interaction principal component analysis (IPCAs) accounted for 76.94% of the interaction sum of squares, they were sufficient for cross-validation of the grain yield variance explained by GEI. In contrast to the GGE biplot approaches, which indicated genotypes G12, G3, and G9 as stable and high-yielding genotypes throughout the environments, the AMMI stability value identified genotypes G3, G12, and G9 as high yielding with stable performance across environments. In general, the GGE biplot and AMMI analysis models demonstrated that genotypes G12, G3, and G9 were stable and yielded well, making G3 acceptable for cultivation in a wider range of environments and G12 and G9 suitable for release.
- Assessment of genetic structure and trait associations of Watkins wheat landraces under Egyptian field conditionsAuthor(s): Elkot, Ahmed Fawzy; Nassar, Ahmed E.; Elmassry, Elsayed L.; Forner-Martínez, Macarena; Awal, Rajani; Wingen, Luzie U.; Griffiths, Simon; Alsamman, Alsamman M.; Kehel, Zakaria (Frontiers, 2024-12-01)Date: 2024-12-01Type: Journal ArticleStatus: Open accessBackground: Wheat landraces represent a reservoir of genetic diversity that can support wheat improvement through breeding. A core panel of 300 Watkins wheat landraces, as well as 16 non-Watkins landraces and elite wheat cultivars, was grown during the 2020–2021 and 2021–2022 seasons at four Agricultural Research Stations in Egypt, Gemmiza, Nubaria, Sakha, and Sids, to evaluate the core panel for agromorphological and yield-related traits. The genetic population structure within these genotypes were assessed using 35,143 single nucleotide polymorphisms (SNPs). Results: Cluster analyses using Discriminant Analysis of Principal Components (DAPC) and k-means revealed three clusters with moderate genetic differentiation and population structure, possibly due to wheat breeding systems and geographical isolation. The best ancestry was k = 4, but k = 2 and k = 3 were also significant. A genome-wide association study (GWAS) identified clustered marker trait associations (MTAs) linked to thousand kernel weight on chromosome 5A, plant height on chromosomes 3B and 1D, days to heading on chromosomes 2A, 4B, 5B and 1D, and plant maturity on chromosomes 3A, 2B, and 6B. In the future, these MTAs can be used to accelerate the incorporation of beneficial alleles into locally adapted germplasm through marker-assisted selection. Gene enrichment analysis identified key genes within these loci, including Reduced height-1 (Rht-A1) and stress-related genes. Conclusion: These findings underscore significant genetic connections and the involvement of crucial biological pathways.
- Genomic analysis association of tolerance to heat stress in subtropical Egyptian goats Raised in hot dry environmentAuthor(s): Aboul Naga, Adel Mahmoud; Alsamman, Alsamman M.; Melak, Sherif Awad Aziz; Nassar, Ahmed E.; Abdelsabour, Taha H; Mohamed, Layaly G.; Adly, Monica; Elshafie, M.H. (BioMed Central)Date: 2025-06-11Type: Journal ArticleStatus: Open accessThe study investigated subtropical Egyptian goat populations (382 does) from different hot dry ecological zones (Upper Egypt, Coastal Zone of Western Desert, and New Valley Desert Oasis) to identify genes associated with tolerance to heat stress. Animals were encouraged to walk for 7 km under direct solar radiation from 12:00 to 14:00 pm in July and August (imitating summer grazing on poor pasture under hot dry conditions). Temperature Humidity Index (THI) ranged from 98.6 to 109.3, indicating that the animals were under severe heat stress. Physiological parameters were measured at rest (7:00 am) and after exposure to heat stress (14.00 pm). Animal heat tolerant index (AHTI) was estimated from their response in the four main physiological parameters ranged from (0: high tolerant to 4: low tolerant). The GWAS analysis revealed 90 marker SNPs associated with heat stress in 108 genotypes of Egyptian goat. Ninety markers are found in forty-seven distinct genes distributed across the genome. In terms of the markers (SNPs) that have direct effect on these traits via homozygous alleles, twenty-eight SNPs are connected to heat stress. The snpeff approach revealed that KDM6A, TRPM3, USP54, GLTSCR2, NAALADL2, GATAD2A, CTNNA2, LOC102175876, ZBTB8A, ETNPPL, LRRC43, SNTB1, RPS6KA5, and ARHGAP26 genes influence tolerance to heat stress. These genes offer crucial insights into the biological mechanisms that enhance resilience to elevated temperature conditions. The studied subtropical Egyptian goat breeds showed a high ability to tolerate heat stress and identifying these genomic loci can be utilized to monitor and control tolerance of subtropical goat to heat stress, while maintaining their production performance.
- Towards the establishment of genetic reserves for key crop wild relatives in Lebanon: Analysis of strategies across diverse ecogeographical landscapesAuthor(s): Sayde, Eliane; Yazbek, Mariana; Zucchini, Cecilia; Chalak, Lamis; Negri, Valeria; Raggi, Lorenzo (Elsevier (12 months), 2025-04-01)Date: 2025-01-09Type: Journal ArticleStatus: Open accessThis study aims to identify best areas for the establishment of a genetic reserves network in Lebanon to achieve the in situ conservation of 35 targeted CWR taxa belonging to Aegilops L., Triticum L., Avena L., Hordeum L., Cicer L., Lens Mill. and Pisum L. CWR occurrence were analysed taking advantage of the CAPFITOGEN3 toolbox. A generalist Ecogeographical Land Characterization map (ELC-map) was generated the combination of CWR taxon populations with each defined ELC category (namely “CWR-Eco unit”) was then identified and considered as main conservation target. Two different complementarity analyses were performed to identify the minimum number of sites required to conserve the maximum number of CWR-Eco units inside and outside protected areas. The gap existing in ex situ conservation of the target CWR diversity was estimated by comparing the unique CWR-Eco units conserved in genebanks with those occurring in the wild. A total of 24 ELC categories were defined for Lebanon harboring 253 different CWR-Eco units from a total of 1460 CWR populations. According to complementary analysis results, 22.2 % of the considered protected areas harbor populations of 18 target CWR taxa (51.4 % of the total). A network of 79 cells (5 × 5 km each) is required for the conservation of the whole predicted diversity of taxa not included in the 6 identified protected areas. A total of 215 CWR-Eco units (85.0 % of the total) are covered by ex situ conserved material.
- Genome-wide identification, characterization, and expression analysis of the MADS-box gene family in grass pea (Lathyrus sativus) under salt stress conditionsAuthor(s): Abdelsattar, Mohamed; Nassar, Ahmed E.; Mousa, Khaled H.; Ahmed, Ahmed; El-Baghdady, Manal M. S.; Radwan, Khaled; Ibrahim, Manar S.; El Allali, Achraf; Hamwieh, Aladdin; Alsamman, Alsamman M.; Kehel, Zakaria (BioMed Central)Date: 2025-05-21Type: Journal ArticleStatus: Open accessBackground The MADS-box gene family possesses significant potential to improve crop production under harsh conditions by regulating growth, development, and the expression of floral organs. The grass pea (Lathyrus sativus), a crop grown predominantly in arid and semi-arid regions, could benefit greatly from the functions of MADS-box genes, which are not yet well characterized in this promising plant. Results In this study, a comprehensive analysis of all MADS-box genes in grass pea was performed at both the genomic and transcriptomic levels. A total of 46 genes were identified and classified based on their MADS-box domains. A comparative phylogenetic analysis with apple, Arabidopsis, and rice categorized the grass pea genes into 31 type I genes (M , M , M ) and 15 type II genes (MIKCc, MIKC*). Annotation analysis revealed variations in the intron-exon structures of the genes, with most type I genes being intronless. Ten distinct conserved motifs were identified across the genes. Structural analysis revealed the presence of MEF2-like and SRF-TF domains in the grass pea proteins. Protein-protein interaction analysis revealed extensive interactions among type II MADS-box genes, while enrichment analysis showed their involvement in various aspects of plant life, particularly floral organ development. Examination of the cis-elements in the promoter regions of the genes revealed up to 76 potential cis-elements, which were categorized into four groups based on their putative role in transcriptional regulation. RNA-seq was used to profile gene expression under different conditions to gain insights into their potential functional significance. Quantitative PCR (qPCR) analysis validated the expression levels of eight selected genes (LSMADS_D1, LSMADS_R5, LSMADS_R7, LSMADS_R9, LSMADS_D11, LSMADS_D13, LSMADS_R13, and LSMADS_D29) under salt stress conditions and confirmed their involvement in stress responses. Conclusion This study represents the first genome-wide exploration of the MADS-box gene family in grass pea. Our results provide valuable insights that could improve our understanding of the plant’s genomics, contribute to strengthening its resilience to challenging conditions, and help position it as an important crop in arid regions.
- Gene expression and genome-wide association analyses identify suitable targets for salinity tolerance in chickpeaAuthor(s): Awaly, Sara; Abdellatif, Randa; Radwan, Khaled; Abdelsattar, Mohamed; Alsamman, Alsamman M.; H. Osman, Neama (Elsevier (12 months), 2025-05-01)Date: 2025-03-22Type: Journal ArticleStatus: Timeless limited accessChickpea is an important source of protein for developing countries, but it is highly susceptible to salt stress, which significantly affects its growth and yield. This study investigates the genetic and molecular mechanisms of salt tolerance in chickpea by integrating genome-wide association studies (GWAS) and gene expression analyses. Gene expression data were analyzed from three chickpea datasets to identify genes associated with salt stress. A total of 97 differentially expressed genes (DEGs) were identified (FDR < 0.05), including key genes involved in abscisic acid signaling, the dehydration response and cell wall modification, such as TPS2, NCED1, CDF1, DHN3 and NAC7. A GWAS analysis utilizing SNP genotyping data from 679 chickpea accessions and 11 agronomic traits revealed significant associations (p < 0.001) between SNPs within the DEGs identified in the previous analysis and key agronomic traits, including days to maturity, plant height, and seed weight. Among them, 13 DEGs were specifically associated with traits such as yield and flowering time. Finally, qPCR analysis confirmed the differential expression of eight genes in root tissues under different salinity conditions. Patatin-1-Kuras 2-like had the highest expression levels, with a 20–24-fold increase in response to salinity. Other genes such as NCED1 and CDF1 were upregulated at lower salt concentrations (50 mM NaCl), while TPS3 and drKD showed reduced expression at higher concentrations (150 mM NaCl). In conclusion, this study provides a comprehensive understanding of the genetic and molecular basis of salt tolerance in chickpea and highlights key genes and pathways that may serve as valuable targets for the development of salt-resistant cultivars and ultimately contribute to improved crop productivity and food security in salt-stressed regions.
- Identification of novel proteomic biomarkers for hypertension: a targeted approach for precision medicineAuthor(s): Aldisi, Rana S.; Alsamman, Alsamman M.; Krawitz, Peter; Maj, Carlo; Zayed, Hatem (BioMed Central)Date: 2025-02-12Type: Journal ArticleStatus: Open accessBackground Hypertension is a critical public health issue worldwide. The identification of specific proteomic biomarkers in the Qatari population aims to advance personalized treatment strategies. Methods We conducted proteomic profiling on 778 Qatari individuals using an aptamer-based SOMAscan platform to analyze 1,305 biomarkers. Statistical analysis involved two-way ANOVA and association analyses with FDR correction, alongside pathway and gene-set enrichment analyses using Reactome and DisGeNET databases. Results The study identified 26 significant protein biomarkers associated with hypertension. Notably, QORL1 and BMP1 were identified as novel protein biomarkers. Enrichment analysis linked these biomarkers to critical pathways involved in vascular biology, immune system responses, and pathologies like arteriosclerosis and coronary artery disease. Correlation analyses highlighted robust interactions, particularly between QORL1 and various Apolipoprotein E isoforms, suggesting these biomarkers play pivotal roles in the molecular mechanisms underlying hypertension.
- Leveraging Synergies from Integrative Land-Biodiversity-Climate Action through Ecosystem Restoration in Central AsiaAuthor(s): (ELD), The Economics of Land Degradation (Economics of Land Degradation Initiative (ELD))Date: 2025-07-07Type: BriefStatus: Open accessA concise policy brief summarizing the Central Asia case study. It outlines regional investment needs, projected benefits (2.1:1 return), and identifies land restoration targets per country. The brief emphasizes the necessity of overcoming fragmentation through integrated action and provides tabulated LDN, NDC, and NBSAP targets for each Central Asian country.