International Crops Research Institute for the Semi-Arid Tropics
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Identification of candidate genes associated with resistance to aflatoxin production in peanut through genetic mapping and transcriptome analysis
Full text linkPeanut (Arachis hypogaea L.) is a globally significant oil and economic crop, serving as a primary source of edible oil and protein. Aflatoxin contamination is a main risk factor for peanut food safety and industry development worldwide. The most cost-economic and effective control strategy entails the exploration and utilization of natural resistance in peanut, alongside the development of resistant varieties. However, the underlying mechanism of resistance to aflatoxin production (AP) in peanuts remains elusive. In this study, a RIL population derived from a cross between Zhonghua 10 (susceptible) and ICG 12625 (resistant), was used to identify quantitative trait loci (QTLs) for AP resistance. Overall, seven QTLs associated with AP resistance were mapped on five chromosomes, explaining 6.83–17.86% of phenotypic variance (PVE). Notably, only two major QTLs, namely qAftA07and qAftB06.2, were consistently detected across different environments with 6.83–16.52% PVE. To predict the candidate genes for AP resistance in qAftA07and qAftB06.2, the transcriptome analysis of seeds from parental lines inoculated with Aspergillus flavus were conducted. A total of 175 and 238 candidate genes were respectively identified in qAftA07 and qAftB06.2, encompassing genes with non-synonymous genomic variations as well as differentially expressed genes. Combined with the weighted gene co-expression network analysis, 10 and 11 genes in qAftA07 and qAftB06.2 were characterized showing a high correlation with aflatoxin content, thereby representing the most promising candidate genes within these two QTLs. These results provide valuable insights for future map-based cloning studies targeting candidate genes associated with AP resistance in peanut
Data-driven strategies to improve nitrogen use efficiency of rice farming in South Asia
Full text linkIncreasing nitrogen use efficiency (NUE) in agricultural production mitigates climate change, limits water pollution and reduces fertilizer subsidy costs. Nevertheless, strategies for increasing NUE without jeopardizing food security are uncertain in globally important cropping systems. Here we analyse a novel dataset of more than 31,000 farmer fields spanning the Terai of Nepal, Bangladesh’s floodplains and four major rice-producing regions of India. Results indicate that 55% of rice farmers overuse nitrogen fertilizer, and hence the region could save 18 kg of nitrogen per hectare without compromising rice yield. Disincentivizing this excess nitrogen application presents the most impactful pathway for increasing NUE. Addressing yield constraints unrelated to crop nutrition can also improve NUE, most promisingly through earlier transplanting and improving water management, and this secondary pathway was overlooked in the IPCC’s 2022 report on climate change mitigation. Combining nitrogen input reduction with changes to agronomic management could increase rice production in South Asia by 8% while reducing environmental pollution from nitrogen fertilizer, measured as nitrogen surplus, by 36%. Even so, opportunities to improve NUE vary within South Asia, which necessitates sub-regional strategies for sustainable nitrogen management
Links between protein-source diversity, household behavior, and protein consumption inadequacy in the Indian rural semi-arid tropics
Full text linkOur study analyzes the determinants, sources, and levels of protein consumption among 785 households across nine districts in six Indian states in the semi-arid tropics. We found that 80% of these households consumed less protein than recommended and relied on cereals for 60–75% of their protein intake. Notably, even when protein-rich foods are accessible to households, they still consume them insufficiently. We found that their protein intake deficiency is driven by a lack of diversity of protein sources (in particular, legumes, millets, and livestock), as well as by a dearth of women's education and role in household decision-making and low incomes and assets. We advocate for initiatives to raise nutrition awareness, empower women, and adopt a nutrition-centric farming approach
Understanding Heat Tolerance Mechanism in Groundnut (Arachis hypogaea L.)
No full textHeat stress is a critical constraint to groundnut productivity, causing significant yield losses. In order to dissect the genetic mechanism of heat tolerance in groundnut, a mapping population (JL 24 × 55-437) was developed at ICRISAT. A genetic map was constructed using genotyping by-sequencing, comprising 478 SNP loci spanning 1,961.39 cM. Quantitative trait locus (QTL) analysis identified 45 major QTLs for 21 traits, with three QTL clusters (Cluster-1-Ah03, Cluster-2-Ah12, Cluster-3-Ah20) harbouring 66.6% of these QTLs. These clusters explained
phenotypic variance ranging from 10.4% to 49.5%. Candidate genes in these clusters included arahy.J0Y6Y5 (DHHC-type zinc finger family protein), arahy.8ZMT0C (peptide transporter 1), and arahy.92ZGJC (post-illumination chlorophyll fluorescence increase), indicating roles in stress response and signal transduction. To further explore heat tolerance, bulked segregant RNA sequencing (BSR-seq) was performed using 11 heat-tolerant (HT) and 10 heat-sensitive (HS) genotypes derived from the mapping population. Plants were subjected to heat stress (45°C) in a controlled environment, and DEGs were identified in flower (155 DEGs: 84 upregulated, 71 downregulated) and pod tissues (1,097 DEGs: 726 upregulated, 371 downregulated). Gene ontology analysis revealed functional enrichment of iron ion binding proteins in flowers and hydrolase activity genes in pods. In silico analysis of significant DEGs highlighted Phosphatidate cytidyltransferase (PCT) as a key candidate gene, showing an exceptionally high fold change (815.11) between tolerant and sensitive genotypes. PCT plays a potential role in signal transduction and stress response mechanisms. In leaves, HSP17 expression increased many fold increased in tolerant genotypes as compared to sensitive
genotypes. Understanding heat tolerance mechanism is the key to developing heat tolerant groundnut cultivars that can thrive well in harsh environments
A Systems Approach to Agricultural Sustainability: Building Resilience through Landscape Management and Genetic Advances
No full textSustainable crop production in India is under severe stress, with nearly 120 million hectares affected by soil degradation, water scarcity, and climate variability. Climate projections indicate significant shifts in rainfall patterns, leading to prolonged growing periods and heightened crop water stress, particularly in semi-arid regions. By 2050, India will need to produce 550 million tonnes of food grains to sustain its growing population. Meanwhile, per capita water availability is expected to decline sharply, intensifying pressure on agricultural
systems. While advances in genomics and biotechnology have led to stress-tolerant crop varieties, their effectiveness is linked to broader landscape conditions. A systems approach integrating landscape management with genetic advancements is essential to strengthen agricultural resilience. Addressing these challenges requires a holistic approach that considers the complex interactions between land, water, crops and climate. By aligning innovation with
sustainable resource management, agricultural systems can be transformed to withstand future environmental stresses, securing food and water availability for generations to come
High Throughput Phenotyping (HTP) Improves Selection Intensity in Groundnut Breeding Pipeline at ICRISAT
No full textGroundnut (Arachis hypogaea L., 2n = 4x = 40) is mainly grown in semi-arid agro-ecologies of Africa and Asia where a combination of abiotic and biotic stresses compromises its yield and quality. Optimizing the breeding scheme for selection intensity enables breeding programs to realise higher rate of genetic gain for targeted traits as well as optimizes time and resources. Selection intensity can be increased by increasing the number of ‘selection candidates’ (that decreases the proportion (p) of candidates selected). High throughput phenotyping (HTP) and genomic tools can be used to exercise selection on many ‘selection candidates.’ At ICRISAT, a two-step selection approach is being deployed to improve drought tolerance that involves a HTP platform, LeasyScan to select early vigour followed by screening in a Managed Stress Environment (MSE). The digital biomass, leaf area index and plant height are used as selection criteria for early vigour. Accordingly, the populations of groundnut breeding pipeline were advanced from F2 to F4 using single seed descent (SSD) method. The selected single plants in
F4 generation were raised as F5 progeny rows and harvested as F6 progeny bulks. During Rainy 2024, a total of 1645 F6 progeny bulks were screened simultaneously in LeasyScan and in artificial foliar fungal disease (FDR) screening nursery (<5 in a 0 to 9 scoring scale at 75 days after planting). A total of 322 F6 progeny bulks from 104 families were selected and advanced to MSE testing. ICGV 171044, one of the parents in the 12 selected families was identified as
a potential genotype contributing to early vigour. The mid-density genotyping panel containing 2500 SNP markers distributed across 20 groundnut chromosomes from 263 cultivated accessions is being used to genotype all the lines advanced to Stage I multi-environment testing. The 1645 progeny bulks are genotyped using 5K mid-density array used in developing Genomic Selection models for early vigor and late leaf spot disease resistance. These progenies
will be categorized into training set and testing set for GS model development and crossvalidation studies
Unraveling Genetic Susceptibility: Targeting GR-RBP Genes to Combat Aflatoxin Contamination in Groundnut
No full textAflatoxins, toxic secondary metabolites produced by Aspergillus fungi, pose a major threat to groundnut by increasing susceptibility to infection and reducing quality. Despite extensive breeding efforts, achieving durable resistance in groundnut germplasm remains challenging. A
promising approach involves targeting genes linked to susceptibility to Aspergillus infection. Glycine-rich RNA-binding protein (GR-RBP)-coding genes, known to influence plant hypersensitivity and susceptibility to A. flavus, have been well-studied in model plants, but their role in groundnut remains unclear. This study identified 23 Arachis hypogaea GR-RBP (Ah.GR-RBP) genes, and their chromosomal distribution, subcellular localization, and regulatory elements in putative promoter regions were analyzed. Expression analysis revealed that Ah.GR-RBP.1, Ah.GR-RBP.12, Ah.GR-RBP.3, and Ah.GR-RBP.15 was highly expressed in
susceptible genotypes. Additionally, a gene-editing-based vector system was developed and validated using the PDS gene in groundnut. These identified Ah.GR-RBP genes will undergo
further validation through knockout experiments using this vector system. This research provides valuable insights into potential candidate genes for precision breeding strategies
aimed at reducing aflatoxin contamination in groundnut
Breeding Climate-Resilient Pigeonpea in Climate Change Era: Current Breeding Strategies and Prospects
No full textPigeonpea [Cajanus cajan (L.) Millspaugh] is a prominent pulse crop of low-input agriculture and serves as a prime protein source in the traditional cereal-based diet to fill the nutritional gap in tropical and subtropical regions. However, the production potential of pigeonpea has not been harnessed completely owing to its susceptibility to numerous biotic and abiotic stresses and cultivation in marginal lands. In the era of climate change, the pigeonpea is exposed to unforeseen weather calamities and the resurgence of various pests and diseases resulting in up to cent per cent yield losses depending on the crop growth stage and vulnerability to the stress. Thus, there is a pressing need to develop climate-smart crop varieties to meet the food demand of an ever-growing population. Though conventional breeding approaches successfully developed high-yielding cultivars, the success rate was poor owing to a narrow genetic base, difficulty in identifying genes tolerant to biotic and abiotic stresses and poorly developed genetic resources. With refinements and advancements in DNA sequencing technologies, a huge quantity of genomic data is available in the public domain, providing novel insights into the crop evolution and breeding history. Integrating conventional and genomic-assisted breeding (GAB) approaches with high-throughput phenotyping platforms could effectively accelerate the production potential and provide a better understanding of the trait genetics to accelerate the rate of genetic gain. Novel technologies, viz. genome-wide association studies, genome editing, etc., delivered promising results for improving the stress resilience. This chapter provides an insight into the breeding strategies for pigeonpea resilience in the current context of climate change, emerging pests and diseases
Response of maize to different nutrient sources under different landscape positions in cereal mixed farming systems of tropical agroecosystems
Full text linkNutrient omission trials were conducted on farmers’ fields in 2020 and 2022. The experiment included nine treatments: three treatments with nitrogen (N), phosphorus (P), potassium (K), sulfur (S), zinc (Zn), and boron (B) as individual, blended, and compound fertilizer; four treatments with the omission of K, S, Zn, or B; NP-only; and control without any nutrient. Treatments were arranged in a randomized complete block design with three replications under foot slope (FS), mid-slope (MS), and hillslope (HS) positions. Results showed that soil properties and maize yield significantly varied among landscape positions, with substantial soil fertility and yield increasing trends from HS to FS position. The highest grain yield (6.18 t ha−1) was recorded at the FS position, with the respective yield increments of 14% and 16% compared to the MS and HS positions. Applying all nutrients in blended form resulted in the highest grain yield (6.52 t ha−1), but it was not significantly different from yields of compound and individual fertilizer forms. Applying all nutrients in blended form increased grain yield by 7.4% and 264.2% compared to the NP-only and the control, respectively, indicating the non-significant effects of K, S, Zn, and B on yield. Overall, N and P are the most yield-limiting nutrients for maize production, and site-specific NP fertilizer recommendations targeting landscape position are required to enhance nutrient use efficiency and sustainably intensify maize yield. Developing site-specific fertilizer recommendations advisory will enhance nutrient use efficiency, increase and sustain yield, and benefit farmers while improving soil and environmental quality
Rapid Generation Advancement (RGA) in Groundnut (Arachis hypogaea L.): Challenges and Opportunities
No full textDeveloping new crop cultivars requires production of homozygous lines following selffertilization for 4-5 generations after hybridization. Rapid Generation Advancement (RGA) or speed breeding reduces the breeding cycle time by faster seed-to-seed time, thus enhancing the
rate of genetic gain. At ICRISAT, RGA protocol is standardized, optimized, and deployed in groundnut breeding to generate the homozygous lines; it used harvest of immature pods, drying at room temperature for five days, followed by excising the kernels from the pods and taking
them for the next cycle of planting. The seed-to-seed time is reduced to 65-70 days in short duration (100-105 days) and about 75-80 days in medium-duration (~120 days) varieties. Optimization is done in planting trays (with rectangular cup size of 7.5 cm width at the top, 8.0
cm depth and 5.0 cm width at the bottom) filled with autoclaved (at 120 °C for 50 minutes) growing medium (red alluvial soil: sand; cocopeat; and vermicompost in 3:3:2:1 ratio) to which basal fertilisers of N, P2O5, and K2O were mixed. The RGA protocol at ICRISAT-Hyderabad (17.5178° N, 78.2790° E) conditions is standardized in a semi-controlled poly-house which is equipped with incandescent light bulb with tungsten filament that are used in December and
January in the morning and evening to increase the light intensity (>600 μmol/m²/s), and water coolers that are used in April and May to bring down the temperature by 50C to 35-370C. The RGA protocol is successfully deployed in groundnut breeding at ICRISAT to turn around 10% of the populations from F2 to F3 and F3 to F4. However, the key challenge with the current protocol is scalability as it requires careful excision of kernels from immature pods. So, to facilitate easy excision of the kernels, the harvest must be delayed thus increasing the seed-to-seed time by 15-20 days. Experiments are ongoing to reduce the pod filling duration with different photoperiod lengths (10-18 hours) and light intensity levels (600 and 800 μmol/m²/s). RGA is amenable to the single-seed descent (SSD) method of breeding used in groundnut breeding and when combined with Genomic Selection (GS), it will be valuable in strengthening genetic gain by faster recycling of the parents and optimizing the resources