A sorghum pangenome reference improves global crop trait discovery

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 sorghum2,3,4,5, 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

Labile Pool-I and Labile Pool-II Carbon: Two-Step Acid Hydrolysis

Labile carbon pools, comprising rapidly and moderately degradable fractions of soil organic carbon, are key indicators of soil quality and carbon dynamics, extracted through sequential acid hydrolysis to assess short- and long-term nutrient cycling. Assessing these pools offers valuable insights into carbon dynamics, soil quality, and resilience in agricultural systems

Distribution, conservation, and indigenous knowledge of finger millet germplasm in different agroecologies in Uganda

Introduction: Crop improvement is crucial in addressing food and nutritional security, as it requires a wide range of genetic diversity to serve as germplasm during breeding. Finger millet is an underutilized yet climate-resilient crop with valuable genetic variation that can be leveraged to enhance food security and improve nutritional quality. Methods: This study examines varietal diversity, farmers’ preferred attributes, varietal distribution, production environments, and traditional conservation practices of finger millet germplasm across six agroecological regions (Mid-Northern, Northern, West Nile farmlands; Southern dryland and highlands, Western highlands, and Karamoja drylands) in Uganda. Data was collected between June 2020 and February 2021 through household surveys, key informant interviews, and field observations. Results: Most agroecologies were highly to moderately suitable for finger millet production, and farmers utilized traditional knowledge to select and conserve millet germplasm for present and future purposes. Over 90% of the varieties collected were landraces exhibiting wide variability, providing desirable traits necessary for improving finger millet. A total of 460 landrace accessions were collected, and 198 distinct local names were documented across ethnic groups, depending on morphology, maturity, and cultural significance. Farmer selection and conservation of finger millet focused on taste (38.6%), drought tolerance (31.9%), pest and disease tolerance (14.1%), and early maturity (12.4%), confirming the role of preferential traits in addressing food and nutrition security. Conservation practices include sharing seeds with neighbors or relatives, replanting stored seeds, and selecting and storing seeds in designated areas, such as farm stores or rooftops. Over 72.1% of the seed was from farmer-saved sources, underscoring the important role of farmers in maintaining varietal diversity. Correlation analysis showed significant associations between soil characteristics, agroecology, seed sources, and farmer preference. PCA grouped varietal adoption drivers into environment factors, market/consumption attributes, and seed system/conservation practices. However, threats such as labor demands, drought, pests, diseases, aging farmers, and the replacement of millet with maize and rice pose a risk of genetic erosion. Conclusion: The abundance of landraces presents a rich genetic pool for breeding and conservation. Integrating both in situ and ex situ conservation strategies is recommended to safeguard finger millet diversity to support food and nutrition security

Regenerative rice farming for sustaining productivity, reducing energy demand, and methane emissions in India: A comprehensive review

Rice is cultivated on approximately 165 million hectares in over 100 countries, serving as a staple food for >3 billion people. Asia accounts for ∼90% of global rice production, while rice contributes around 40% of India's food grain production. Traditional rice cultivation relies heavily on water resources (between 1000 and 2000 mm), consumes high labour and energy, and emits substantial amounts of methane gases. As estimated, the annual mean atmospheric concentration of methane (CH4) ranged from 1889 to 2017 ppb (2020 annual mean across India), which is critical and demands an alternative, sustainable solution. Thus, the regenerative rice system stands out as a viable option to address these environmental challenges and can contribute to sustainable agricultural development while also reducing energy demands. This method employs direct seeding in non-puddled fields. It creates an aerobic soil environment, promoting strong rice roots and a median water reduction of 52.5% (IQR: 45–60%; n = 16 studies), thriving on 600–700 mm. Similarly, based on field experiments, an average decrease in energy consumption of 24.5% (IQR: 6.4–42.5%; n = 9 studies) and a 56% reduction in methane emissions (IQR: 34–78%; n = 9 studies) were observed. Regenerative rice contributes to Sustainable Development Goals 2 (Zero Hunger), 12 (Responsible Production and Consumption), 13 (Climate Action), and 15 (Life on Land), while reducing environmental impact compared to a puddled rice system. To evaluate its potential for scaling, this review examines existing research on regenerative rice production systems and proposes directions for future research, extension, and policy advocacy

Tapping wild Cicer species for enhancing variability in the cultivated genepool for chickpea breeding

Wild relatives represent valuable reservoirs of novel genes and alleles that can be harnessed to enhance climate resilience in cultivated crops. In chickpea, the use of wild Cicer species has opened new avenues for broadening the genetic base of elite cultivars. In the present study, Cicer reticulatum (ICC 17264) and Cicer echinospermum (IG 69978) were used as donor parents. At the same time, the ‘desi’ landrace ICC 4958 served as the recurrent parent to develop a pre-breeding population with enhanced genetic variability. A set of 300 BC₂F₄ introgression lines (ILs) derived from this population was evaluated during the 2018-19 post-rainy season at ICRISAT, Patancheru. The experiment was conducted in an augmented design with four checks: ICC 4958, JG 14, JG 130, and ICCV 10. The objectives were to identify high-yielding introgression lines and to assess the extent of genetic variability and inheritance patterns for yield and associated traits. Significant variation was observed among the ILs across all traits studied, indicating successful introgression of useful variation from wild donors. Ten superior ILs, along with several trait-specific promising lines, were identified as potential resources for future chickpea improvement programmes. Selection was primarily based on seed yield per plant, pod weight per plant, biological yield, number of seeds per plant, and number of effective pods per plant. Most of the traits exhibited significant positive correlations with seed yield per plant. In contrast, days to 50% flowering, days to flowering, and days to maturity were not significantly associated with yield. Cluster analysis grouped the ILs into three distinct clusters, with the ten superior ILs and the best-performing check, ICC 4958, grouped in Cluster I. Principal component analysis further revealed that pods per plant, pod weight per plant, seeds per plant, and biological yield were strongly associated with seed yield per plant and contributed substantially to variation in the first principal component (PC1). These results suggest that seed yield per plant can serve as a reliable indicator for selecting yield-contributing traits in the chickpea breeding programme

Sewage water and sludge co-implementation effects on soil properties and green chili in Typic Haplustalf of southern India

Sewage water and sludge provide a viable option to meet crop water and nutrient demands in the face of rising climatic stress. Thus, a 2-year field study (2018 and 2019) was conducted to evaluate the effect of sewage water and sludge on soil properties and the growth response of green chili. The experiment comprised nine treatment combinations involving three types of irrigation water: normal water (I1), treated sewage water (I2), untreated sewage water (I3) along with three soil amendments: farmyard manure (FYM) at 25 t ha−1 (SA1), sewage sludge at 25 t ha−1 (SA2), and a mix of sewage sludge at 12.5 t ha−1 + FYM at 12.5 t ha−1 (SA3). Soil-available nutrient status of N, P, and K increased by ˜10%–15%, ˜14%–20%, and ˜13%–18%, respectively, in I3 and SA2. Sewage water and sludge application further improved soil microbial populations, which included actinomycetes, fungi, and bacteria. Concurrently, multivariate analysis of variance (MANOVA) demonstrated a positive influence of irrigation and soil amendments on soil properties. Across both study years, I3 and SA2 recorded a higher mean green chili yield, with an improvement of approximately 25% over I1 and SA1. Hence, the findings reveal the feasibility of harnessing sewage water resources as sustainable inputs, advancing both resource efficiency and short-term agricultural sustainability in the region

Candidate Gene Discovery for Rust Resistance Through Multi-Locus Genome-Wide Association Study in Groundnut

Rust, caused by Puccinia arachidis, is one among the most destructive fungal diseases constraining global groundnut (Arachis hypogaea L.) production. While the development of disease-resistant varieties stands as the most effective approach to preventing substantial yield losses, the genetic mechanisms underlying resistance to rust is not yet well understood, emphasizing the necessity for further detailed research. In this study, 184 accessions from the ICRISAT groundnut mini-core collection were evaluated for rust resistance at Dharwad, India, across multiple seasons, as well as in Vietnam for one season. Whole-genome resequencing-based genome-wide association study (GWAS) identified five highly significant marker trait associations (MTAs) for rust resistance (p = 5.22 × 10-13 to 7.21 × 10-08). Among these, two robust rust-associated kompetitive allele specific PCR (KASP) markers, snpAH00607 at chromosome Ah01 and snpAH00609 at chromosome Ah17, were validated across diverse set of breeding and pre-breeding lines. These markers were linked to candidate genes encoding sterol C4-methyl oxidase 1-2, implicated in brassinosteroid-mediated salicylic acid signalling, and MYB transcription factor known to be associated with defense responses. The identified SNPs, validated markers, and candidate genes will serve as important resources for marker-assisted breeding of rust disease resistant groundnut varieties

A New Remote Sensing-Derived High Resolution Eco-Physiological Land Use Land Cover (HR Eco-P LULC) Product in Support of Regional Climate Modeling over the Indian Landscape

Multiple global land use and land cover (LULC) datasets have been produced by different scientific organizations, but their classification schemes often do not align with the specific requirements of land surface models (LSMs) embedded within Regional Climate Models (RCMs). These datasets frequently miss regional variability and typically lack sufficient detail on the biophysical and ecological characteristics of vegetation. This issue is particularly significant in ecologically diverse regions like the Indian subcontinent, where distinct Plant Functional Types (PFTs) influence land-atmosphere-soil interactions. This study addresses these limitations by developing a ‘High Resolution Eco-Physiological LULC (HR Eco-P LULC)’ product at 50m spatial resolution to better represent the ecological, physiological, and morphological characteristics of the Indian land surface types. The dataset is generated through synthesis of six distinct and well established Remote Sensing products such as the Advanced Wide Field Sensor (AWiFS) LULC 250K, LULC 50K, Wasteland Map 50K, crop type maps, vegetation type, and elevation data, resulting in HR Eco-P LULC with an overall accuracy of 91.15% and a kappa coefficient of 0.89. To ensure compatibility with LSMs and facilitate direct comparison, HR Eco-P LULC was configured to represent sub-grid land surface heterogeneity using fractional layers, following the format used in the LSMs, where the ESA Climate Change Initiative (CCI) LULC has been traditionally employed. When evaluated against CCI LULC, HR Eco-P fractional layers revealed substantial spatial mismatches in the representation of PFTs and non-vegetation categories such as urban areas and bare soil, highlighting its improved ecological specificity and relevance for regional applications. The performance of the new dataset was evaluated using the high-resolution Delhi Model with Chemistry and aerosol framework (DM-Chem) over Delhi and Bhubaneswar, showing improved simulation of near-surface weather parameters with comparatively lower RMSE, particularly over Bhubaneswar. This versatility makes the product suitable for diverse applications such as agro-ecosystem modeling, land degradation assessment, climate projections, weather forecasting, and disaster management. It provides a valuable tool for researchers and policymakers to better understand land dynamics and support informed decision-making

Farmer-Developed Varieties as Innovations – The Case of Kunjukunju Rice Cultivar from Kerala

Farmers have been continuously contributing to evolving crop varieties that fit specific locations and changing conditions. There are different possibilities for recognizing farm innovations in India. The Biological Diversity Act ensures equitable sharing of benefits to the conservers of biological resources, their by-products, creators or holders of traditional knowledge, innovations and practices associated with such resources. The National Innovation Foundation scouts and supports grassroots innovations that have been developed without any help from a formal sector. The country also has the Protection of Plant Varieties and Farmers’ Rights Act, which offers legal protection to its Plant Genetic Resources for Food and Agriculture. This sui-generis legislation for plant variety protection has a unique component: Farmer’s Rights, which facilitates the recognition of crop varieties conserved and developed by farmers or farming communities, along with other provisions. This article examines the opportunities and challenges of these legislations, taking the case of Kunjukunju, a rice cultivar from Kerala that is claimed to have been ‘developed’ by a farmer innovator 50+ years ago and which lacks evident and documented information. The methodology adopted for this case analysis could be a promising one for inquiring about and resolving such concerns regarding the rights over Plant Genetic Resources

Determination of Total Soil Organic Carbon (Dry Combustion Method)

The Walkley–Black method, a widely used technique for estimating soil organic carbon, offers rapid and cost-effective analysis despite incomplete oxidation, typically recovering 60–86% of SOC and requiring a correction factor for accuracy. Despite these drawbacks, the method continues to be a standard in soil testing laboratories for rapid SOC assessment. The dry combustion method, conducted at high temperatures, determines the total carbon content of soils using a CHN analyzer