International Crops Research Institute for the Semi-Arid Tropics
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Controls on soil organic matter stability and composition of neutral-to-alkaline topsoil and subsoil across Indo-Gangetic plains
No full textElusive controls over soil organic carbon (SOC) in neutral-to-alkaline soils limit long-term carbon dynamic predictions across vast agricultural areas such as Indo-Gangetic Plain (IGP). We studied the causes of low SOC content in neutral-to-alkaline topsoil and subsoil under tropical to subtropical climates by identifying factors controlling soil organic matter (SOM) fractions, SOC pools, and SOM molecular composition. We investigated topsoil and subsoil from six paired forest and agricultural fields within 12 sites across IGP, using SOM fractionation, 196-day soil incubation, and pyrolysis-GC/MS. A three-pool kinetic model estimated labile, intermediate, and stable SOC pools from respiration curves, with non-hydrolyzable SOC as the stable pool. Measured soil properties include pH, exchangeable cations, CEC, inorganic/organic C, texture, oxalate-extractable Al/Fe (active Al/Fe), and dithionite-extractable Al/Fe. SOC turnover over decades is regulated by the intermediate SOC pool, which is closely associated with mineral-associated SOM. Active Al/Fe, rather than exchangeable Ca2+, clay, or agricultural activity, controlled the stability of intermediate pool in both topsoil and subsoil. In topsoil, agricultural activity reduced light fraction carbon by 38 % and intermediate pool size by 34 %, but had no significant effect in subsoil or on more stable fractions/pools. Active Al/Fe had a stronger effect on stabilizing carbon in less carbon-saturated subsoil. SOM degradation was intense (e.g., high abundance of N-containing compounds) and was attributed to low active Al/Fe levels under drier conditions, and to elevated microbial activity driven by neutral-to-alkaline soil pH. Cultivation had a non-significant influence on SOM composition. In conclusion, the low SOC in neutral-to-alkaline IGP soils is primarily due to drying and elevated pH, which limits active Al/Fe formation, thereby reducing SOC stability and intensifying SOM degradation. Cultivation further exacerbates SOC loss in topsoil. This highlights the need for understanding and targeted management of these SOM regulating factors to enhance ecological and agricultural sustainability in neutral-to-alkaline soils
Molecular and pathotype diversity of Magnaporthe oryzae isolates in NEH region of India and its implications on rice resistance breeding
Full text linkRice blast, caused by filamentous pathogen Magnaporthe oryzae, is a major peril to rice production, particularly in the North Eastern Hill (NEH) region of India. The dynamics of 24 M. oryzae isolates collected from different geographical locations within the NEH region using 43 SSR markers and pathotyping 17 rice monogenic lines revealed significant genetic diversity. The highest polymorphic information content value of 0.90 was observed for marker mgm285. Five distinct groups were identified with isolate LB 3 collected from upland field in Meghalaya distinct from the rest of the isolates. Significant genetic distinction between isolates from upland and lowland fields, as well as differentiation of tissue infection were observed suggesting the adaptive nature of pathogen and the involvement of specific virulence factors. The highest dissimilarity (0.90) was found between NB 1 and NoB 1 isolates. The virulence frequency varied in the range of 35–76%. The pathotyping of isolates using monogenic lines identified 8 pathotypes, of which pathotype 1 (LB 5 and LB 11) from lowland (Meghalaya) was the most virulent, while pathotype 8 (LB 1) from Nagaland was the least virulent. The data revealed that lowland isolates were more heterogeneous than upland isolates, which had intermediate virulence. In order to prevent future disease outbreaks and to strategically and sustainably breed blast-resistant rice cultivars for NEH region, the profiling M. oryzae isolates is needed along with additional research to unravel the mechanism of host-pathogen interaction via inclusive molecular approaches
Oligo-dT Anchored cDNA SCoT: An Innovative Approach for Deciphering Fusarium Wilt Resistance-Related Differential Gene Expression in Chickpea
No full textThe cDNA start codon targeted marker (cDNA-SCoT) methodology is a unique, simple, quick, and efficient method for investigating differential gene expression. The differentially expressed fragments (DEFs) in resistant and susceptible cultivars were identified using cDNA-SCoT profiling. Sanger sequencing and the nBLAST homology search program were used to characterize the functional properties of DEFs. As a result, this methodology is innovative and would be utilized in future studies to identify potential functional genes, which can then be used in marker creation, marker-assisted selection, and uncovering the regulatory role of the relevant genes
Enhancing Farming Systems in Vulnerable Regions of Maharashtra, India: Evaluating Innovation Bundles for Sustainable Intensification
Full text linkThis study examines the design and evaluation of socio-technical innovation bundles for rainfed mixed farming systems in Latur district, Maharashtra. The region faces severe challenges including water scarcity, land degradation, low soil organic carbon, and limited access to technologies and markets. Using an integrated assessment approach combining Land Resource Inventory, hydrological assessment, and Multi-dimensional Sustainability Assessment Tool (MSAT), we developed contextualized intervention bundles at both landscape and household levels. Results show significant improvements across multiple dimensions: crop yields increased by 25-45%, groundwater levels rose by 4 meters, and household net returns improved by 14-40% depending on farm type. The interventions enhanced agro-biodiversity, reduced women's drudgery, improved food security, and increased milk production by 10-25%. The study demonstrates that water deficit challenges can be addressed by shifting from sugarcane to soybean-chickpea systems or sapota with micro-irrigation. This systems science approach provides a framework for large-scale transformation of dryland farming systems in vulnerable regions
Effects of nutrient omission and landscape positions on grain sorghum production in northern Ethiopia
Full text linkLowsoil fertility, inappropriate fertilizer application, and lowinput use are prominent factors contributing to low agricultural productivity in Ethiopia, where soil fertility
status varies significantly across the landscape. Applying the correct rate, type, timing, and placement of fertilizers is essential for maximizing agricultural benefits and ensuring sustainable productivity. Addressing these issues is critical for promoting sustainable agricultural practices and improving food security. Therefore, the objective of the experiment was to identify the major yield-limiting soil nutrients for sorghum yield in northern Ethiopia. A randomized complete block design with three replicationswas used at each landscape positions. The nutrients evaluated in the study were nitrogen (N), phosphorus (P), sulfur (S), zinc (Zn), boron (B), and potassium (K). The treatment applied included control, recommended NP (RNP), NPSZnB,
NPKSZnB, NPZnB, NPSB, NPSZn, 150% NPKSZnB, and 50% NPKSZnB. These treatments were implemented across each landscape position. The research findings indicated that the application of 150% All + K nutrients resulted in the highest grain and biomass yields across all landscape positions. When compared with the RNP treatment, there was no significant difference in yield at all slopes. Omitting S, Zn, B, and K did not significantly affect the grain and biomass yields, suggesting that these nutrients are not yield limiting for sorghum in the study area. These findings
suggest that prioritizing N- and P-containing nutrients is essential for maximizing sorghum yield, thus contributing to sustainable agricultural practices and improved food security in the region
Drought-Induced Cyanogenesis in Sorghum (Sorghum bicolor L.): Genotypic Variation in Dhurrin Biosynthesis and Stress Response
Full text linkThe accumulation of the livestock-harming cyanogenic glucoside dhurrin in the vegetative tissues limits the use of sorghum as a major pasture crop. This study integrates transcriptomics and metabolomics data from the ICSV 93046, CSH 24-MF and ICSR 14001 genotypes, which differ in drought tolerance and cyanide potential (HCNp), to understand the molecular processes of cyanogenesis under drought stress conditions. While ICSV 93046 showed drought adaptation and reduced HCNp, ICSR 14001 and CSH 24-MF exhibited decreased drought stress tolerance with HCN accumulation. The differentially expressed gene (DEG) data showed drought-related genes were significantly upregulated in ICSV 93046 but downregulated in ICSR 14001. KEGG pathway analysis revealed enriched dhurrin biosynthesis and cyanoamino acid metabolism genes, with higher expression in ICSR 14001 than in ICSV 93046. WGCNA analysis revealed that hub genes are involved in drought-induced signalling components, such as phospholipases (PLPs) and lipoxygenases (LOXs), which are implicated in membrane protection. In drought-sensitive genotypes, stress-induced membrane damages lead to the release of dhurrin into the cytoplasm, thus elevating HCN content and activating defence responses. Conversely, the drought-adapted genotype could mitigate HCN production by averting membrane injury, thereby effectively modulating the oxidative stress and preventing the release of dhurrin into the cytoplasm
Leaf reflectance and physiological attributes monitoring differentiate rice cultivars under drought-stress and non-stress conditions
Full text linkRice production in Africa is unambiguously hampered by drought. This study aimed to monitor the efficiency of physiological traits (stomatal conductance (gsw), transpiration rate (E)), and leaf-reflectance (NDVI and RDVI) at vegetative (VS) and reproductive (RS) stages for selection of drought-tolerant genotypes. To achieve these objectives, we screened 14 rice genotypes under drought-stress and non-stress conditions in the greenhouse. At VS-drought-stress, the relative-gsw and relative-E consistently showed efficiency in differentiating drought-tolerant genotypes APO and UPLR-17 from the drought-sensitive ones at 11-, 18- and 27-days during VS-drought-stress, while NDVI, CRI1 and CRI2 at 18- and 27-days. At RS-drought-stress, genotypes APO and UPLR-17 were selected as drought-tolerant genotypes based on the multi-trait-genotype-ideotype-distance-index (MGIDI) confirming the selection at 11-, 18- and 27-days during VS-drought-stress. This consistency in selecting APO and UPLR-17 as drought-tolerant genotypes at both VS and RS proved the efficiency of gsw, E, NDVI, RDVI, CRI1 and CRI2 in selecting for drought-tolerant varieties at VS. Genotypes UPLR-17 and APO consistently showed homozygosity status for the favorable alleles G, A, G and C for drought-tolerant QTLs DTY1.1 (snpOS00400), DTY1.1 (snpOS00402), DTY1.1 (snpOS00408) and DTY12.1 (snpOS00483), respectively, confirming their drought tolerance status. At RS, with GYP recorded positive and significant correlation with RDVI, while regression analysis revealed that 34% of the variability in GYP is explained by RDVI. The regression analysis coupled with correlation analysis between LDS, DTF, RDVI and GYP implied that these traits can be used as predictors of GYP at RS-drought-stress. While gsw, E and NDVI are recommended for monitoring during VS-drought-stress screening
Aflatoxin exposure is associated with an increased risk of gallbladder cancer
No full textGall bladder cancer (GBC) is common among the socioeconomically deprived populations of certain geographical regions. Aflatoxin is a genotoxic hepatocarcinogen, which is recognized to have a role in the pathogenesis of hepatocellular carcinoma. However, the role of aflatoxin in the pathogenesis of GBC is largely unknown. We determined serum AFB1-Lys albumin adduct (AAA) levels as a marker of aflatoxin exposure in the patients with GBC and compared to those without GBC. The relationship of AAA levels to cytogenetic (TP53mutation&HER2/neu amplification) and radiological characteristics of the tumor was assessed. We included GBC cases (n = 51) and non-GBC controls (n = 100). Mean serum AAA levels were higher in the GBC group (n = 51) than those without GBC (n = 100) (26.1 ± 12.2 vs. 13.1 ± 11.9 ng/mL; p 50 years) (odds ratio [OR] = 3.2 [CI: 1.3–8.2]; p = .013), positive Helicobacter pylori serology (OR = 5.1 [CI: 1.4–17.8]; p = .012), presence of GS (OR = 5 [CI: 1.5–16.9]; p = .009) and detectable AAA levels (OR = 6.8 [CI: 1.3–35.7]; p = .024) were independent risk factors for the presence of the GBC among all study subjects. Among patients harboring GS, older age (age >50 years) (OR = 4.5 [CI: 1.3–14.9]; p = .015), female gender (OR = 3.8 [CI: 1.2–12.5]; p = .027), presence of multiple GS (OR = 21.9 [CI: 4.8–100.4]; p 50 years (OR = 2.6 [CI: 1.3–5.2]; p = .010) and frequent peanut consumption (OR = 2.3 [CI: 1.1–4.9]; p = .030) were independent risk factors for high serum AAA levels. The current study has implications for the prevention of GBC through the reduction of dietary aflatoxin exposure
Development of a Multiplex TaqMan Assay for Rapid Detection of Groundnut Bud Necrosis Virus: A Quarantine Pathogen in the USA
Full text linkGroundnut bud necrosis orthotospovirus (GBNV), a tripartite single-stranded RNA virus, poses a significant threat to United States agriculture. GBNV is a quarantine pathogen, and its introduction could lead to severe damage to economically important crops, such as groundnuts, tomatoes, potatoes, peas, and soybeans. For the rapid and accurate detection of GBNV at points of entry, TaqMan reverse transcriptase–quantitative polymerase chain reaction (RT-qPCR) assays were developed and the results validated using conventional reverse transcriptase–polymerase chain reaction (RT-PCR) followed by Sanger sequencing. These assays target highly conserved regions of the nucleocapsid (NP) and movement (MP) proteins within the viral genome. Multiplex GBNV detection assays targeting the NP and MP genes, as well as an internal control plant gene, ACT11, showed efficiency rates between 90% and 100% and R2 values of 0.98 to 0.99, indicating high accuracy and precision. Moreover, there was no significant difference in sensitivity between multiplex and singleplex assays, ensuring reliable detection across various plant tissues. This rapid, sensitive, and specific diagnostic assay will provide a valuable tool at ports of entry to prevent the entry of GBNV into the United States
Genetic structure of Ethiopian finger millet landraces and genome-wide association mapping for agronomic and nutritional traits
Full text linkFinger millet (Eleusine coracana subsp. coracana) (2n = 4x = 36) remains one of the most important millets in East Africa (EA), where it was most likely domesticated along the highlands of Ethiopia and Uganda. The goal of the current study was to understand the population structure of the Ethiopian finger millet landraces and identify quantitative trait nucleotides (QTNs) and haplotypes associated with agronomic and nutritional traits. In a field evaluation across three environments, 448 genotypes were assessed for days to flowering (DTF), days to maturity (DTM), thousand seed weight (TSW), grain yield (GY), stay-green score (STG), and drought score (DrtSc). The harvested grain was analyzed for Fe and Zn contents. A subset of 391 genotypes was skim-sequenced, generating 24,112 high-quality SNPs that were employed for population structure, association mapping, and haplotype analysis. Seventy marker-trait associations were detected including 15 major QTNs with more than 30% phenotypic variance explained (PVE) for all traits except STG and GY. Pleiotropic major QTNs were identified for DTM/DTF and Fe/Zn on chromosomes 9B and 2B, respectively. Haplotype analysis of major QTNs identified 54 significant haplotype blocks and 2 additional haplotypes for a multidrug ABC transporter gene family like protein on chromosome 4A that was associated with PTH. Favorable haplotypes from pleiotropic DTM/DTF and Fe/Zn QTNs were present in 13 and 12 genotypes respectively, majority from Tigray region. Two genotypes from Tigray and one from Amhara harbored favorable haplotypes for DTM/DTF and Fe/Zn. These findings provide invaluable insights for targeted breeding to enhance finger millet resilience, nutritional profile, and yield