Understanding greenhouse gas fluxes in semi-arid ecosystems is critical for improving our understanding of biogeochemical cycles, particularly in underrepresented regions like the African Sahel. In these landscapes, greenhouse gas exchange arises from ground, trees, and water ponds, and is further shaped by environmental conditions and grazing. The carbon dioxide, methane, and nitrous oxide fluxes were quantified from these components in a Sahelian savanna in Senegal, while also assessing grazing impacts and environmental drivers (soil water content, temperature, vapor pressure deficit, photosynthetically active radiation). The ground was a net carbon dioxide sink during the rainy season but shifted toward neutrality or weak emission in the dry season, consistently acted as a methane sink, and was a year-round nitrous oxide source. Seasonal ponds were strong methane and nitrous oxide emission hotspots, with methane emissions being high enough to offset the sink of the overall savanna landscape. Trees contributed to carbon dioxide and methane uptake via branches, whereas stems were net methane and carbon dioxide emitters. Both stems and branches emitted nitrous oxide, and the presence of trees enhanced carbon dioxide, methane and nitrous oxide fluxes from soils beneath their canopies. Grazing enhanced ground gross primary production, reduced methane uptake, while no effect was seen on nitrous oxide fluxes. Temporal variability of carbon dioxide and nitrous oxide fluxes was strongly linked to soil water content and temperature, whereas methane fluxes showed no correlations with any of the measured drivers. These results demonstrate that tree- and pond-mediated fluxes, together with grazing, substantially alter the greenhouse gas fluxes of savanna ecosystems and incorporating these effects is essential for accurately representing semi-arid savannas in global greenhouse gas budgets.
Although the green revolution adapted a handful of crops to homogeneous and high-input industrialized agriculture, much of the global population still relies on the local production of variable crop cultivars by low-input smallholder farms. This diversity of unhomogenized crops1, like that of the grain and bioenergy crop sorghum2-5, offers raw materials for genetic gain and cultivar improvement. However, breeding efforts can be constrained by highly specialized traits and breeding targets6. Here, to bridge this diversity, we constructed a 33-member pangenome reference and a diversity panel across 1,984 cultivars and landraces. We leveraged these resources to explore the complex interplay among historical contingency, ongoing adaptation and previously uncharacterized structural diversity. Specifically, our analyses conclusively demonstrated multiple nested and deeply diverged structural variants in the domestication gene SHATTERING1, which distinguish the previously established multicentric origin of sorghum. We then applied landscape genomics to reveal how gene flow and secondary contact created the complex genetic mosaic in contemporary breeding networks. As proof of concept for pangenome-accelerated trait discovery, we connected biosynthetic gene cluster structural variation to phenotypic leaf concentration of the cyanogenic glucoside dhurrin. Combined, these approaches will accelerate breeding and trait discovery and provide a framework for similar applications in other crops.
Genotype × environment (G × E) interactions present a critical challenge for sorghum breeding in the Sahel, where high climatic and edaphic variability strongly affects crop performance under rainfed conditions. This study develops a quantitative framework to define and characterize target population environments (TPE) for sorghum cultivation in Senegal by integrating climate variability, soil properties, and process-based crop modeling. We combined the SAMARA crop model with 50 years of daily historical climate data (1974–2024) and spatially explicit soil information to simulate rainfed sorghum grain yield and water stress patterns across Senegal. TPE were delineated through multivariate classification incorporating simulated yield distributions, phenology-specific water stress indices for early and late developmental stages, and interannual yield stability metrics. We quantified yield sensitivity to water stress at different developmental stages using linear regression and assessed genotype × TPE interactions through joint regression analysis (Finlay–Wilkinson). Five distinct TPE were identified. Northern environments (TPE 1–2) exhibited low simulated yield potential (< 1.0 t ha⁻1), high interannual variability, and severe terminal water stress, defining marginal zones for rainfed sorghum. Central and southern environments (TPE 3–5) showed moderate to high yield potential (more than 2.5 t ha⁻1) but differed markedly in stress regimes. Terminal drought emerged as the dominant constraint, causing simulated yield reductions exceeding 40
Pod size is a key agronomic trait in peanut (Arachis hypogaea) that underwent strong selection during domestication. In a previous study, we fine-mapped a quantitative trait locus (QTL) for pod and seed size to a 168.37 kb region on chromosome A07. Here, we integrated structural variation analysis, gene sequence comparison, and transcriptomic profiling to refine candidate genes and uncover molecular mechanisms underlying domestication-related differences in pod size. Comparative genomic analyses among Arachis duranensis, A. monticola, and four cultivated varieties (Fleur11, Tifrunner, Shitouqi, Fuhuasheng) revealed multiple structural variations in the QTL interval, including a 25 kb inversion between the wild species (A. duranensis and A. monticola) and all cultivated genotypes. This inversion altered the orientation of a candidate gene, Aradu.DN3DB/Arahy.5EZV1I (SAP), which also carried a non-synonymous SNP distinguishing wild and cultivated lines. RNA-Seq profiling of two parental lines (Fleur11 and 12CS_091) and two near-isogenic lines (NILs) at 20 and 40 days after flowering (DAF20, DAF40) identified two differentially expressed genes in the QTL region: Aradu.SFU0J/Arahy.VEUG4Z (phytochromobilin synthase) and gene.15763 (mitochondrial ribosomal protein), both showing higher expression in large-pod genotypes. GO enrichment analysis revealed contrasting strategies between pod size groups: small-pod genotypes emphasized early maturation and storage metabolism, while large-pod genotypes maintained prolonged growth through hormonal signaling and cell division, supporting greater pod expansion. This study identifies three promising candidate genes for seed and pod size variation during peanut domestication: Aradu.DN3DB/Arahy.5EZV1I, gene.15763, and Aradu.SFU0J/Arahy.VEUG4Z. The 25 kb inversion affecting Aradu.DN3DB/Arahy.5EZV1I and the expression differences in Aradu.SFU0J/Arahy.VEUG4Z between large- and small-pod genotypes suggest structural and transcriptional mechanisms contribute to phenotypic variation. These findings advance understanding of domestication-related traits in peanut and provide a foundation for functional validation, which could guide breeding strategies to optimize pod and seed size.
In this study, the concentrations of heavy metals Fe, As, Mn, Cr, Ni, Zn, Ti, and Cu were measured in soil samples from an agricultural site located near a cement plant that has been operating in the area for several decades. The results of the analyses showed the following decreasing ranking of average concentrations : Fe > Ti > Cr > Ni > As > Mn > Zn > Cu. The maximum concentrations of As (54.79 mg/kg) and Cr (148.86 mg/kg) exceeded the limits set by the World Health Organization and the Food and Agriculture Organization of the United Nations (FAO). The analysis of correlations between the concentrations of the different heavy metals studied indicated anthropogenic origins for the metallic elements As, Zn, and Cr. The agricultural field showed moderate enrichment by Ni, significant enrichment by Cr, and very high enrichment by As, with enrichment factors of 4.725, 8.315, and 20.599, respectively. Approximately 33.33% of the study area had an As concentration exceeding the permitted limit. The individual pollution index (PI) indicated moderate As pollution of the agricultural field. The overall Nemerow pollution index (P N ) placed the study site within the precautionary range for the trace metal Cr. Regarding As, the site was in the area of severe pollution, with a P N of 3.097. However, the potential ecological risks were low.
