International Crops Research Institute for the Semi-Arid Tropics
ICRISAT Open Access RepositoryNot a member yet
12134 research outputs found
Sort by
Agroinfiltration-mediated transient assay for rapid evaluation of constructs in pigeonpea
Get PDFThe process of generating stable transformants is time-consuming, labor-intensive, and genotype-dependent. In contrast, transient gene expression techniques, such as agroinfiltration, offer a rapid assessment of gene function and expression. Agroinfiltration, widely employed for studying gene function, has been extensively applied in leaf tissues of Nicotiana benthamiana and various other plant species. Despite its broad utility in various plants, to our knowledge, no prior investigation has been reported in pigeonpea. In this study, we developed an agroinfiltration method for transiently expressing a green fluorescent protein (mGFP5) reporter gene in four pigeonpea genotypes using syringe infiltration at the seedling stage under greenhouse conditions. The expression of the reporter gene mGFP5 was assessed at 72-, 96-, and 120 h post-infiltration (hpi). Additionally, we assessed the effect of morphogenic genes, specifically growth-regulating factor 4 (GRF4) and GRF-interacting factor 1 (GIF1), from both rice and pigeonpea on the expression of mGFP5 in four pigeonpea genotypes. Our findings demonstrate that OsGRF4-GIF1 led to enhanced mGFP5 expression compared to CcGRF4-GIF1 in four diverse pigeonpea genotypes. Fluorescence could be detected till 120 hpi. Furthermore, PCR, RT-PCR, and fluorescence quantification confirmed the presence and expression of mGFP5 at 72 hpi. Our results highlight the efficacy of agroinfiltration in quickly evaluating candidate genes in four genetically diverse pigeonpea genotypes, thereby reducing the time required for the initial assessment of constructs suitable for diverse molecular biology analyses
Developing pangenomes for large and complex plant genomes and their representation formats
Get PDFBackground
The development of pangenomes has revolutionized genomic studies by capturing the complete genetic diversity within a species. Pangenome assembly integrates data from multiple individuals to construct a comprehensive genomic landscape, revealing both core and accessory genomic elements. This approach enables the identification of novel genes, structural variations, and gene presence-absence variations, providing insights into species evolution, adaptation, and trait variation. Representing pangenomes requires innovative visualization formats that effectively convey the complex genomic structures and variations.
Aim
This review delves into contemporary methodologies and recent advancements in constructing pangenomes, particularly in plant genomes. It examines the structure of pangenome representation, including format comparison, conversion, visualization techniques, and their implications for enhancing crop improvement strategies.
Key scientific concepts of review
Earlier comparative studies have illuminated novel gene sequences, copy number variations, and presence-absence variations across diverse crop species. The concept of a pan-genome, which captures multiple genetic variations from a broad spectrum of genotypes, offers a holistic perspective of a species’ genetic makeup. However, constructing a pan-genome for plants with larger genomes poses challenges, including managing vast genome sequence data and comprehending the genetic variations within the germplasm. To address these challenges, researchers have explored cost-effective alternatives to encapsulate species diversity in a single assembly known as a pangenome. This involves reducing the volume of genome sequences while focusing on genetic variations. With the growing prominence of the pan-genome concept in plant genomics, several software tools have emerged to facilitate pangenome construction.
This review sheds light on developing and utilizing software tools tailored for constructing pan-genomes in plants. It also discusses representation formats suitable for downstream analyses, offering valuable insights into the genetic landscape and evolutionary dynamics of plant species. In summary, this review underscores the significance of pan-genome construction and representation formats in resolving the genetic architecture of plants, particularly those with complex genomes. It provides a comprehensive overview of recent advancements, aiding in exploring and understanding plant genetic diversity
Lower vicine content reduces the reproductive yield performance in faba bean (Vicia faba L.)
Get PDFFaba bean is a nutritionally and medicinally rich popular legume crop. However, vicine-convicine remain as potential threats for “favism” in human beings. In this study, 189 diverse faba bean accessions have been evaluated for yield component traits and vicine content in seeds followed by a correlation study. Combined genetic variability analysis shows that traits like days to pod initiation (DPI), pod length (PL), test weight (TW) and grain yield have minimally been influenced by the environment. PCA revealed that TW, PL and PW were the primary indicators for deciding yield performance. LC–MS/MS confirms that vicine concentration varied in between 3.489 and 10.025 g/kg and a significant positive correlation (0.40***) was observed between vicine conc. and grain yield of faba bean. Thus, present study demonstrated that the faba bean genotypes containing lower vicine were mostly poor yielding, which might be regulated by vicine in faba bean. Therefore, complete elimination of vicine or development of near-zero vicine faba bean could drastically reduce the yield potential of the crop, hence one has to be very cautious and follow efficient selection strategies while optimizing lower concentration of vicine for development of low vicine varieties. This study shows that faba bean genotypes containing 4.0–5.5 g/kg vicine were fairly productive and also have considerably lower vicine
Introgression and Mapping of Cotton Leaf Curl Disease Resistance from Wild Gossypium armourianum Kearney into Upland Cotton (G. hirsutum)
No full textCotton leaf curl disease (CLCuD), caused by the whitefly transmitted geminivirus complex (cotton leaf curl virus [CLCuV] and their satellite molecules), is a serious threat to successful upland cotton production in northwest India and Pakistan. The disease causes significant losses in fiber yield and the quality of cotton. Owing to the regular emergence of resistance-breaking strains of CLCuV, all the previously available CLCuD-resistant germplasms of upland cotton have become compromised, and none of the extant upland cotton cultivars is resistant to this disease. Therefore, alternate sources of CLCuD resistance need to be explored, as genetic resistance is the only pragmatic and tenable management strategy to combat this malady. Here, we report for the first time the introgression and mapping of CLCuD resistance from a related nonprogenitor wild diploid D-genome cotton species, Gossypium armourianum, into upland cotton. A backcross population (G. hirsutum/G. armourianum/G. hirsutum) was developed for this purpose. A single major QTL was found to be associated with resistance to CLCuD and was located on chromosome D01 through the genotyping-by-sequencing technique
Characterization of Nothopassalora personata Causing Late Leaf Spot Disease in Peanut Across Major Peanut-Growing Regions of India
No full textPeanut (Arachis hypogaea L.), also known as groundnut, is an important legume crop globally, serving as a key food and edible oil source for millions of people. Late leaf spot (LLS), caused by Nothopassalora personata (Berk. & M.A. Curtis) (syn. Cercosporidium personatum [Berk. & M.A. Curtis] Deighton), is the most destructive foliar fungal disease affecting peanuts, resulting in severe defoliation and yield losses of 40 to 90%. As a highly adaptable and evolving pathogen, N. personata rapidly develops new pathotypes, posing an ongoing threat to peanut crop. Monitoring the prevalence and genetic diversity of this pathogen in various agroecologies is requisite for tracking its spread and identifying areas of high risk. This study aimed to evaluate the disease severity and genetic diversity of N. personata across major peanut-growing regions in India. The survey revealed that disease severity (DS) ranged from 36.75 to 91.70%, with high humidity and moderate temperatures fostering disease progression. During the survey, the characteristic symptoms were observed, including dark brown lesions surrounded by chlorotic halos, advancing to necrosis and defoliation in severe cases. Forty isolates of N. personata were collected and identified through microscopic and molecular analysis using LSU-specific primers. Of these, five isolates (OD-8, KA-6, GJ-12, AP-3, and AP-4) exhibited high virulence in detached leaf assay. These results provide critical insights into the epidemiology of LLS, contributing to the development of effective disease forecasting models, which in turn guide targeted control measures. Further, whole-genome sequencing of N. personata isolates with different virulence patterns could identify key pathogenicity-related genes, paving the way for innovative control measures and the development of peanut varieties with enhanced resistance
Unveiling the efficiency and effectiveness of two distinct mutagens in early mutant generations of sodic tolerant finger millet [Eleusine coracana (L.) Gaertn] genotype
Get PDFFinger millet is an essential small millet that has gained attention for its high calcium content and C4 physiology. The self-pollination nature of the crop paves the way for the deliberate advent of candid variability, for which induced mutagenesis would be a suitable breeding method for the quick de- velopment of improved cultivars. In the present indagation, the sodic tolerant variety TRY1 finger millet was subjected to gamma rays and EMS to obtain early maturing genotypes. A preliminary experiment was conducted to investigate the LD50 value biological damages incurred by different mutagen doses, and mutagenic efficiency, effectiveness was estimated. Doses of gam- ma rays were used in the range of 100–500Gy. The EMS concentrations were 10 mM–50 mM. The LD50 values derived were 326.53 Gy of gamma rays and 15.36 mM EMS. Reduction in various quantitative traits became colinear with increased dose, irrespective of the mutagens. In the M2 generation, the chlorophyll mutants such as albino, xantha, chlorina, viridis, albomaculata and xantha viridis were noticed. The highest noted chlorophyll mutant was chlorina (1.906 %–Gamma ray and 2.748 %–EMS), and viridis (0.701 %–gamma ray and 0.451 %–EMS) was with the least frequency. Mutagenic effectiveness was high in lower doses of the mutagen (1.65–250 Gy and 5.20–10 mM). The mutagenic efficiency was higher in lower doses of both the mutagens, con- cerning the mutagenic frequency and lethality (0.116-250 Gy, 0.085-10 mM) injury (0.336–250 Gy, 0.176–15 mM) and sterility (0.205–250 Gy, 0.206–10 mM). Thus, gamma ray and EMS at their minimum dose proved efficient in inducing variations
Effects of land management practices on runoff and soil and nutrient losses in the rainfed agroecosystem of the Beles River Basin, Ethiopia
Get PDFThe Beles River Basin is facing severe soil erosion driven by human-induced activities, leading to significant losses of soil organic carbon (SOC) and nutrients (nitrogen (N) and phosphorus (P)). Effective land management practices (LMPs), including mechanical, biological, and agronomic techniques, are potential strategies for mitigating this degradation, but their effectiveness depends on site-specific and agroecological conditions. However, limited information is available on this aspect of the study area. The objective of the current study was to evaluate the effects of LMPs in the warm subhumid lowlands of the Beles River Basin on runoff, soil loss, and sediment-associated losses of SOC, N, and P from agricultural land. Four LMPs (vetiver grass strips (VGS), conservation agriculture (CA), soil bunds (SB), and fanya juu (FJ)) were evaluated via runoff plots arranged in a randomized complete block design (RCBD) with three replicates. Farmer practices were used as a control (C). The experiments, which were performed over three years (2021–2023), generated runoff, soil loss, and nutrient loss data. The three-year mean annual runoff ranged from 58.5 to 407.5 mm, and the soil loss ranged from 4.3 to 45.4 t/ha, whereas the annual rainfall varied between 1,402 mm in 2021, 1,254 mm in 2022, and 1,261 mm in 2023. On average, runoff was reduced by 36%–85%, and soil loss was reduced by 53%–91% in the LMP-treated plots. Additionally, sediment-associated losses of SOC, N, and P were reduced by 55%–90%, 52%–90%, and 28%–72%, respectively. The results revealed significant differences (p < 0.05) among the treatments in terms of reducing runoff, soil loss, and sediment-associated losses of SOC, N, and P. The mean annual runoff and soil loss rates during the study were 407.5, 230.3, 136.3, 59.6, and 58.5 mm and 45.4, 21.5, 11.1, 4.5, and 4.3 t/ha under the control, VGS, CA, SB, and FJ practices, respectively. The highest rates of runoff and soil loss were observed under the control conditions (407.4 mm and 45.4 t/ha). Runoff, soil loss, SOC, and nutrient (N and P) losses were significantly lower (p < 0.05) in the plots treated with FJ and SB than in the other plots. However, CA and VGS also significantly varied (p < 0.05) in reducing runoff, soil, SOC, and nutrient losses over the years. These results highlight the key role of LMPs in warm subhumid lowland rainfed agroecosystems as effective land management techniques for controlling soil and nutrient loss
Synergistic effects of aquatic weed biochar and inorganic fertilizer on soil properties, maize yield, and nitrogen use efficiency on Nitisols of Northwestern Ethiopian Highlands
Get PDFSoil acidity and poor fertility limit crop production in Ethiopia. Biochar from organic wastes, such as water hyacinth (Eichhornia crassipes), offers a potential solution. This study investigated the effects of co-applying water hyacinth biochar (WHB) with inorganic fertilizers on soil characteristics, maize yield, and nitrogen (N) use efficiency under field conditions. Four rates of WHB (0, 5, 10, and 20 t ha−1) were combined with two levels of recommended inorganic fertilizers (half and full rates of 180/138 kg N/P2O5 ha−1), plus a control (no biochar/fertilizer), during the 2022 and 2023 growing seasons. Results indicated that WHB significantly improved soil physicochemical properties (p < 0.05), across fertilizer rates, demonstrating both additive and independent effects. Consequently, WHB application reduced bulk density, increased porosity, and soil pH, and decreased exchangeable acidity and exchangeable Al3+, with the 20 t ha−1 WHB rate eliminating exchangeable Al3+. Moreover, available phosphorus, organic carbon, total nitrogen, cation exchange capacity, and exchangeable potassium were significantly improved (p < 0.05). Co-applying WHB with half and full rates of chemical fertilizers enhanced maize grain yield by 33.6 % and 30.8 %, respectively, compared to sole half and full fertilizer rates (non-biochar), with yield increases of up to 10 % in the second year compared to the first. Maize total biomass and 1000-grain weight also showed significant improvements. Nitrogen use efficiency significantly improved, especially when WHB was used with half the fertilizer level. These findings demonstrate the potential of combining WHB with inorganic fertilizers to improve soil fertility and enhance crop production in acidic soils
Patent Examination Process through AI and its Challenges in India, EU and the US
Get PDFThe role of Artificial Intelligence (AI) in the patent examination for the United States Patent and Trademark Office (USPTO), European Patent Office (EPO), and Indian Patent Office (IPO) is under development. Traditional patent examination systems currently encounter increasing difficulties in managing rising worldwide patent applications. The combination of machine learning (ML) technology with natural language processing (NLP) simplifies prior art research while improving patent classification methods and claims examination, thus enhancing patent examination effectiveness and precision. The USPTO uses similarity search as an AI tool and EPO utilises AI-PreSearch for automated classification and prior art identification tasks. The integration of AI in India focuses on modern process implementation to handle increasing numbers of patent applications and corresponding examination delays. The article shows how AI can reinvent global patent
examination through specific recommendations for its future development
Integrating carbon sequestration and yield optimization in Indian cropping systems
Get PDFAgriculture contributes significantly to greenhouse gas (GHG) emissions but also holds strong potential for mitigation – particularly through soil organic carbon (SOC) sequestration. This study evaluates the impact of integrated management practices—such as biochar application, optimized irrigation, and fertilizer management on yield improvement and SOC sequestration in semi-arid regions of Maharashtra, India. Using APSIM simulations across five districts and diverse cropping systems, it compares these practices with conventional farming. Results indicate that integrated practices consistently improve yields, SOC levels, and economic viability. For instance, maize yields under integrated practices increased by over 30 %, with substantial SOC gains. A cost-benefit analysis reveals high benefit-cost ratios, making these practices economically viable for smallholder farmers. This study highlights the transformative potential of integrated practices in addressing food security and environmental sustainability, especially in semi-arid regions. Policy recommendations include subsidizing biochar, promoting precision irrigation technologies, and integrating SOC sequestration strategies into national climate action plans. These findings provide actionable insights for scaling sustainable agricultural practices in resource-constrained settings