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Durum Wheat cv. Svevo Reference Genome Rel.2.0:A Comprehensive Tool for Wheat Genomics
Author(s): Mazzucotelli, Elisabetta; Forestan, Cristian; Zastrow-Hayes, Gina; Swarbreck, David; Lev-Mirom, Yael; Cavalet-Giorsa, Emile; Bozzoli, Matteo; Mastrangelo, Anna Maria; Marone, Daniela; Ranwez, Vincent; Girodolle, Johanna; Llaca, Victor; Fengler, Kevin; Harris, Charlotte; Toegelová, Helena; Navrátilová, Pavla; Faccioli, Primetta; Desiderio, Francesca; Valladares, Ana Paola; Kaithakottil, Gemy; L. Rusholme-Pilcher, Rachel; Spannagl, Manuel; Gundlach, Heidrun; Mayer, Klaus; C. Blake, Victoria; Faris, Justin; Xu, Steven; Z. Sen, Taner; Yao, Eric; Sanchez, Julio Isidro y; Liu, Chunyi; Farooq, Muhammad; Stefanelli, Sandra; Cappucci, Chiara; Oren, Leah; Eilam, Tamar; Giorgioni, Mario; Stella, Alessandra; Lazzari, Barbara; Lauria, Massimiliano; Ceriotti, Aldo; Pirona, Raul; Tavakol, Elahe; Klymiuk, Valentyna; Ens, Jennifer; Chawla, Harmeet Singh; Walkowiak, Sean; Pecchioni, Nicola; Bassi, Filippo; Sanchez-Garcia, Miguel; Sonnante, Gabriella; L. Curci, Pasquale; Giuliano, Giovanni; Aprea, Giuseppe; Pasha, Asher; Gadaleta, Agata; Marcotuli, Ilaria; Masci, Stefania; Sestili, Francesco; palombieri, Samuela; Scaglione, Davide; Morgante, Michele; Simkova, Hana; J. Provart, Nicholas; Krattinger, Simon G.; Pozniak, Curtis; Chantret, Nathalie; Hall, Anthony E.; Distelfeld, Assaf; Tuberosa, Roberto; Maccaferri, Marco; Cattivelli, Luigi (Wiley Open Access, 2026-10-01)
Date: 2026-07-13
Type: Journal Article
Status: Open access
Advancements in plant genome sequencing and assembly have enabled the production of increasingly accurate and contiguous genome sequences. Here, we present the chromosome-level assembly of the durum wheat (Triticum turgidum L. ssp. durum, cv. Svevo) reference genome produced using accurate long-reads, optical mapping and Hi-C. The new assembly (Svevo Rel.2.0) comprises 263 hybrid scaffolds with an N50 value of 112.3 Mb, arranged into 14 contiguous pseudomolecules spanning 10.4 Gb. The Svevo Rel.2.0 genome assembly was annotated using extensive short- and long-read RNA sequencing data obtained from 60 tissue/treatment combinations. The resulting annotation comprises 68 154 high-confidence protein-coding genes, which have been integrated into a comprehensive transcriptome atlas accessible through an eFP browser. Annotation was manually curated for storage protein gene families and for Leucine-Rich Repeat-Containing Receptor genes yielding 3763 LRR-CR loci. The genome assembly's accuracy and completeness were demonstrated by the correct reconstruction of the physical map of Tg1-B (Tenacious glumes 1), a locus controlling the free threshing trait located on chromosome 2B that was not assembled in the previous genome release (Svevo Rel.1.0). A wealth of 6621 QTLs/MTAs from the literature were mapped onto Svevo Rel.2.0 to identify QTL hotspots and trait-specific candidate genes. The ancestry of the durum genome to representative wild emmer populations from North-Eastern and Southern-Levant Fertile Crescent assessed by tracing haplotype transmission patterns revealed a clear mosaic pattern. This new durum reference genome, enhanced with advanced annotation and an expression atlas linked to QTLome data, is the most comprehensive tool available for durum wheat genomics.
The climate-biodiversity-livestock nexus in Mediterranean mixed agroecosystems: Modeling crop yields adaptation using a system-GMM approach
Author(s): Benmehaia, Mohamed Amine; Mezerdi, Farid; Mokhtari, Sakher; Frija, Aymen (Springer Heidelberg)
Date: 2026-06-15
Type: Journal Article
Status: Timeless limited access
Across the semi-arid landscapes of Mediterranean Agroecosystems, crop productivity is increasingly threatened by rising temperatures, erratic rainfall, and evolving land-use pressures. While crop diversification and livestock integration are widely promoted as adaptive strategies, their combined effectiveness remains underexplored in data-scarce contexts like North Africa. This study investigates the dynamic interactions between climate stressors, crop diversity, and livestock integration, with a specific focus on understanding how these components jointly shape crop productivity across diverse agroecological settings. Using a System-GMM estimation approach, the analysis addresses endogeneity, persistence, and interactions effects. By endogenizing livestock integration, the model empirically accounting for feedback loops between livestock dynamics and cropping systems diversification, particularly under variable climate conditions. Machine-learning techniques are used for optimal model selection. Interaction and marginal effects analysis are conducted to uncover synergistic effects. Findings reveal that crop yield responds non-monotonically to temperature anomalies, rainfall deficits, and diversification indices. The impact of crop diversification is strongly conditioned by livestock presence and type. Sheep grazing, when combined with diversified cropping systems, enhances yield resilience to heat stress but exacerbates vulnerability to rainfall deficits. Several double and triple interaction terms are statistically significant, confirming the presence of context-specific synergies and trade-offs. This study contributes by endogenizing livestock integration within a dynamic GMM framework, and by generating stress-specific insights that can guide more targeted and resilient adaptation strategies for North African agroecosystems. The results offer generalizable implications for mixed farming systems operating under climate uncertainty.
Compost as a sustainable tool for greenhouse horticultural productivity: benefits, limitations, and state of the art
Author(s): Lhaj, Majda Oueld; Moussadek, Rachid; Mouhir, Latifa; Sanad, Hatim; Zouahri, Abdelmjid; Spaccini, Riccardo; Paradiso, Roberta (Frontiers Media SA, 2026-06-10)
Date: 2026-06-10
Type: Journal Article
Status: Open access
Greenhouse horticulture plays a vital role in modern agriculture, offering a controlled environment for the cultivation of high-value crops while mitigating the adverse effects of climate variability. However, its intensive nature requires sustainable soil management strategies to maintain productivity and long-term fertility. This review, conducted following a PRISMA-based systematic methodology and synthesizing peer-reviewed studies published between 2015 and 2025, evaluates the role of compost as a sustainable soil amendment in greenhouse systems. Quantitative evidence indicates that compost application can enhance crop yield (up to 20–40%), improve soil health, and increase nutrient availability. In addition to these benefits, compost contributes to circular economy principles through organic waste valorization and reduced reliance on synthetic inputs. Nevertheless, limitations such as variability in composition, salinity risks, and nutrient imbalances are critically discussed, highlighting the need for optimized management strategies. Particular emphasis is placed on application rate, compost maturity, and incorporation methods to maximize agronomic benefits while minimizing environmental risks. Overall, compost represents a promising pathway for sustainable intensification in greenhouse horticulture, with strong global relevance for food security under climate change and resource constrained conditions.
Starting points of agroecological transitions in Africa: Why and how farm structure matter
Author(s): Girard, Pierre; Mercandalli, Sara; Berre, David; Andrieu, Nadine; Bezner Kerr, Rachel; Coe, Richard; Dedieu, Benoît; Madsen, Sidney; Scopel, Eric; Asnake, Woinishet; Mekuria, Wolde; Dembele, Catherine; Frija, Aymen; Haule, Yohana; Magaju, Christine; Kassahun Mengistu, Dejene; Orounladji, Boko Michel; Raharimalala, Sitrakiniana (Elsevier)
Date: 2026-06-16
Type: Journal Article
Status: Open access
In sub-Saharan Africa, dominant agricultural models such as the Green Revolution have shown limitations, and agroecology is emerging as an alternative. Yet, empirical evidence remains scarce on who adopts agroecological practices and on what types of farms. A widely accepted narrative suggests that smallholders are more rooted in agroecological systems, while larger, better-endowed farms follow “conventional” models. This paper challenges that dualistic view by providing evidence of a wider set of relationship between farm structure and the diversity of agroecological practices across multiple African contexts. For this purpose it informs the diversity of existing patterns of farms structure and starting points of agroecological transition (AET) – defined as current state of agroecological principles implemented by farms along their trajectories. By situating these starting points within the socio-technical context of national and regional AET, we gain valuable insights into which farm structures support different agroecological principles, how socio-technical regime influence these dynamics, and what policy options emerge to foster AET. Using harmonized data from 2721 farms across nine study areas in six African countries, the article shows that starting points of agroecological transitions are highly diverse and influenced by farm structure. Three patterns emerge: smallest farms mostly combine autonomy and income diversification while larger farms tend to combine conventional intensification with crop-livestock integration. Other small to medium scale farms are characterized by more land allocated to legume contributing to soil health. Future agricultural policies should consider this diversity of patterns in providing locally-relevant support to promote sustainable transitions.
Livestock roles in agroecological transitions in mixed crop-livestock systems of Tunisia
Author(s): Alary, Veronique; Frija, Aymen; Jones, Sarah; Ouerghemmi, Hassen; Shiri, Zahra; Idoudi, Zied; M'hamed, Hatem Cheikh (ELSEVIER SCI LTD)
Date: 2026-08-03
Type: Journal Article
Status: Open access
CONTEXT Despite the well-recognized role of livestock in providing goods and ecosystem services, agronomy research over the past decades has predominantly focused on plots and crops, often underestimating the contribution of animals to economic diversification within mixed farming systems. While integrated livestock-crop practices remain among the most frequently cited examples of agroecology in action, few studies assess the extent to which livestock contribute to the agroecological transition, particularly in integrated crop-livestock systems. Most of them focus on the use or non-use of these practices, particularly in mixed livestock systems. OBJECTIVE The objectives of this study are to 1) develop a method for characterizing the agroecological transition stage of crop-livestock farming systems and 2) analyze how integrating livestock into crop farming systems can promote agroecological transitions. The analysis compares farms at different stages of agroecological transition, assessed using indicators corresponding to FAO's ten elements and HLPE's thirteen principles of agroecology, across farms with contrasting levels of livestock integration. METHODS This study used data collected from a survey administered to 692 households in northwest Tunisia. Factor and cluster analyses were used to analyze the data and identify defining characteristics of crop-livestock farms at different stages of agroecological transitions, and to distill the relative importance of livestock contributions to agroecological performance, in line with agroecological principles. RESULTS AND CONCLUSION The results show that livestock play a crucial role in the agroecological transitions of Tunisian mixed farming systems. Increasing livestock numbers on mixed farms is associated with enhanced synergies among crops, trees, and animals, particularly through nutrient recycling and the utilization of residues as livestock feed. However, challenges persist regarding knowledge co-creation, recycling and connectivity, and land and resource governance in landscapes with mixed farming systems. SIGNIFICANCE The study addresses the discrepancy between global frameworks and on-the-ground realities by integrating localized analyses of farming and livestock systems with broader principles of agroecology. While integrating livestock into farming systems in dryland areas can be considered a transformative pathway toward sustainable agriculture, the findings underscore the significance of social networks and connectivity between producers and consumers, governance, and knowledge sharing in promoting agroecological practices.