International Crops Research Institute for the Semi-Arid Tropics
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Dissecting genomic regions and underlying candidate genes in groundnut MAGIC population for drought tolerance
Get PDFBackground
Groundnut is mainly grown in the semi-arid tropic (SAT) regions worldwide, where abiotic stress like drought is persistent. However, a major research gap exists regarding exploring the genetic and genomic underpinnings of tolerance to drought. In this study, a multi-parent advanced generation inter-cross (MAGIC) population was developed and evaluated for five seasons at two locations for three consecutive years (2018–19, 2019–20 and 2020–21) under drought stress and normal environments.
Results
Phenotyping data of drought tolerance related traits, combined with the high-quality 10,556 polymorphic SNPs, were used to perform multi-locus model genome-wide association study (GWAS) analysis. We identified 37 significant marker-trait associations (MTAs) (Bonferroni-corrected) accounting, 0.91- 9.82% of the phenotypic variance. Intriguingly, 26 significant MTAs overlap on four chromosomes (Ah03, Ah07, Ah10 and Ah18) (harboring 70% of MTAs), indicating genomic hotspot regions governing drought tolerance traits. Furthermore, important candidate genes associated with leaf senescence (NAC transcription factor), flowering (B3 domain-containing transcription factor, Ulp1 protease family, and Ankyrin repeat-containing protein), involved in chlorophyll biosynthesis (FAR1 DNA-binding domain protein), stomatal regulation (Rop guanine nucleotide exchange factor; Galacturonosyltransferases), and associated with yield traits (Fasciclin-like arabinogalactan protein 11 and Fasciclin-like arabinogalactan protein 21) were found in the vicinity of significant MTAs genomic regions.
Conclusion
The findings of our investigation have the potential to provide a basis for significant MTAs validation, gene discovery and development of functional markers, which could be employed in genomics-assisted breeding to develop climate-resilient groundnut varieties
Diversity in the population of Fusarium oxysporum f. sp. ricini causing castor wilt disease in India
No full textA major constraint on castor crop productivity is wilt disease caused by Fusarium oxysporum f. sp. ricini (For). In this study, morphological, pathogenic and molecular features of F. oxysporum f. sp. ricini isolates collected from different castor-growing agro-climatic zones of India were analyzed. Eighty-nine F. oxysporum f. sp. ricini isolates were obtained from wilt-infected root samples of castor plants from different states of India viz., Andhra Pradesh, Bihar, Gujarat, Haryana, Karnataka, Madhya Pradesh, Maharashtra, Odisha, Rajasthan, Telangana and Tamil Nadu. Morphology assessment in terms of variability in radial growth, size of micro and macroconidia and number of septa, grouped the isolates into 5 clusters in biplot analysis. A genotype-by-isolates bi-plot analysis ranked genotypes for pathogen susceptibility, with JI-35 being closest to the ideal and most susceptible, and DCS-9, and Kranthi being less susceptible. In contrast, 48–1 and JI-258 showed resistance, while Haritha and VP-1 exhibited intermediate susceptibility levels. K-means cluster analysis found 5 groups for pathogenic variability studies of isolates. The six isolates viz., For-12-5 (61.8 %), For-12-10 (50.5 %), For-13-47 (51.4 %), For-113 (86.1 %), For-13-33 (77.9 %) and For-53 (62.2 %) recorded as highly virulent isolates against wilt disease which showed >50 % average wilt incidence mean value across cultivars. Out of 40 ISSR primers tested, 11 primers gave polymorphic bands and analysis of genetic variability among 36 F. oxysporum f. sp. ricini isolates showed polymorphism with PIC, heterogygosity index, effective multiplex ratio, Marker index, and Shannon Diversity Index which ranged (in %) between 0.22 and 0.69, 0.19–0.44, 11.09–27.9, 6.14–8.98, and 0.78–3.04 respectively. The dendrogram analysis revealed 53 % similarity among the isolates studied and these isolates grouped broadly into 6 clusters. Variability among isolates was significant in morphological, pathogenic and molecular characters of F. oxysporum f. sp. ricini
Indians Demanding More Plant-Based Protein, but Farmers’ Profits Drop: Empirical Evidence to Understand the Dilemma
Get PDFThis study estimates changes in productivity and profitability and their respective components for two major Indian sse crops, pigeon peas and chickpeas. Results show that average profitability declined during the period under consideration (2009–2014) for both pulse crops. Lower profits are driven by increases in input prices and decreases in total factor productivity, output growth,
and output (constant) prices. The reduction in total factor productivity is primarily due to a slow increase in output. Finally, the technical efficiency estimates are lower than for cereal crops like rice and wheat: 72% for chickpeas and 71% for pigeon peas
Celebrating Professor Rajeev K. Varshney's transformative research odyssey from genomics to the field on his induction as Fellow of the Royal Society
Get PDFProfessor Rajeev K. Varshney's transformative impact on crop genomics, genetics, and agriculture is the result of his passion, dedication, and unyielding commitment to harnessing the potential of genomics to address the most pressing challenges faced by the global agricultural community. Starting from a small town in India and reaching the global stage, Professor Varshney's academic and professional trajectory has inspired many scientists active in research today. His ground-breaking work, especially his effort to list orphan tropical crops to genomic resource-rich entities, has been transformative. Beyond his scientific achievements, Professor Varshney is recognized by his colleagues as an exemplary mentor, fostering the growth of future researchers, building institutional capacity, and strengthening scientific capability. His focus on translational genomics and strengthening seed system in developing countries for the improvement of agriculture has made a tangible impact on farmers' lives. His skills have been best utilized in roles at leading research centres where he has applied his expertise to deliver a new vision for crop improvement. These efforts have now been recognized by the Royal Society with the award of the Fellowship (FRS). As we mark this significant milestone in his career, we not only celebrate Professor Varshney's accomplishments but also his wider contributions that continue to transform the agricultural landscape
Identification of Donors for Fresh Seed Dormancy and Marker Validation in a Diverse Groundnut Mini-Core Collection
Get PDFDomestication and extensive selection in the development of modern, high-yielding commercial groundnut cultivars have resulted in the selection of an undesirable trait known as in situ germination, which is also referred to as the pre-harvest sprouting of seeds. This is particularly prevalent in regions where humid weather coincides with the harvest season. Delayed harvesting and pre-sprouting can cause production losses and increase the chances of aflatoxin contamination, thereby impeding the quality and kernel yield. Breeding early maturing groundnut cultivars with 2–3 weeks of fresh seed dormancy, particularly in Spanish-type cultivars, enhances the sustainability of agriculture. In this context, we conducted a comprehensive evaluation of a groundnut mini-core collection, a major resource for genetic diversity, for fresh seed dormancy using an in vitro germination assay for two seasons, viz., rainy 2022 and post-rainy 2022–2023 at ICRISAT (Hyderabad). To enhance the effectiveness and accuracy of traditional breeding methods via the use of markers for marker-assisted selection, we performed molecular screening of the mini-core accessions using two allele-specific markers. The GMFSD1 marker was successfully validated by effectively differentiating dormant and non-dormant genotypes. By employing phenotypic and marker data, we identified a set of accessions, viz., ICG 5827 (Virginia Runner), ICG 11457 (Virginia Runner), ICG 7000 (Virginia Bunch), and ICG 11322 (Virginia Bunch) of sub spp. hypogaea var. hypogaea and ICG 9809 (Spanish Bunch) of sub spp. fastigiata var. vulgaris that exhibited a fresh seed dormancy period ranging from 2 to 3 weeks. These identified accessions hold potential as donors in breeding programs that are designed to address the groundnut production needs in various cropping systems across different countries. The validated marker, particularly GMFSD1, demonstrated considerable potential for facilitating faster breeding of groundnut cultivars with the desired dormancy using marker-assisted selection. This research provides a foundation to expediting groundnut breeding programs and offers opportunities to mitigate pre-harvest sprouting, ultimately improving seed quality and productivity in groundnut-producing regions
Soil property and crop yield responses to variation in land use and topographic position: Case study from southern highland of Ethiopia
Get PDFUnderstanding soil property and crop yield responses to variations in land use and topographic gradient is vital for designing targeted soil and agronomic management practices. This study investigated the interrelationships between land use, topographic position, soil properties, and crop yield. Three replicates of three land use types - enset agroforestry, cropland (annual crop), and grazing land - were selected along a toposequence (upper, middle and lower) for the study. A total of 54 composite soil samples were collected and analyzed. Grain yield and above ground biomass were also gathered from the cropland and analyzed. Soil profile descriptions revealed notable variations in soil physical properties, including soil texture, bulk density, color, horizons, and depth among the pedons of the three topographic positions. Clay and silt fractions exhibited significant differences between land uses and topographic positions, while the sand fraction was influenced by topographic position alone. Crop and grazing lands displayed higher clay content compared to the enset field. A decreasing trend in clay fraction was observed from upper to lower topographic positions. The enset field had significantly higher soil pH, OC, TN, and K+ contents than crop field. A significantly higher available P of 16.61 mg kg−1 was measured from lower slope position followed by 14.08 mg kg−1 in middle slope. The upper slope position had the highest exchangeable acidity of 3.09 cmol(+) kg−1), followed by middle slope with 2.77 cmol(+) kg−1), 2.45 cmol(+) kg−1) in the lower slope position. Grain yield and above ground biomass decreased from lower slope to middle slope and upper slope positions. These observed variations in soil properties and crop yield among land uses and topographic positions underscore the necessity for tailored soil management strategies and agronomic practices specific to land use types and the specific localized topographic conditions to optimize agricultural productivity
Editorial: Sustainable intensification of smallholder farming systems in Sub-Saharan Africa and South Asia
Get PDFAgricultural production in sub-Saharan Africa (SSA) and South Asia (SA) is mainly rainfall-dependent and dominated by smallholder farming systems. These smallholder farming systems with landholdings <5 ha produce about 80% of the food consumed in these regions (Chauvin et al., 2012; Jayne et al., 2014). Despite the contribution of the smallholder farmers to food production in these regions especially in SSA, productivity from their farms is low due to several factors such as low and declining soil fertility, limited use of external inputs, unfavorable policy, market and institutional arrangements, pests, and diseases, as well as the effects of climate change. The low productivity of agriculture among smallholder farmers exacerbates poverty levels since it is the main source of livelihood for more than 50% of the workforce in these regions (Odusola, 2021)
Good fences make good neighbors? Exploring potential transformative impacts of local governance towards livestock fence-in rights in Malawi
Get PDFMalawi's export earnings are dominated by tobacco, accounting for over 60% of export earnings. The demand for an alternative export commodity, pigeon pea, has been rising over the past decade, especially from India. In addition to their export potential, pigeon pea is an effective cover crop to protect soil heath and productivity in the dry season. They are mostly grown in southern region on very small farms, however, there are opportunities for expansion into central region given the existence of larger farms and agroecological suitability for the crop. Currently, social norms in the central region constrain this expansion. Livestock, and goats in particular, are left to roam free in the dry season by over two-thirds of farmers, relative to only one-third in the south. This leads to significant damage to pigeon pea crops and discourages farmers from growing them and taking advantage of the increased export demand. Much land is left bare and the few farmers that do grow crops during the dry season are forced to put up fences. This study assesses ex-ante implications, especially on agroecological transformation and economic growth, of shifting local governance arrangements among farmers around keeping livestock towards controlled systems. These externalities have been understudied in the development programming, yet their impacts are substantial, especially in lower-income countries. The policy solution under study is for the local government and non-state actors to support local governance arrangements through indirect payments to agroecosystem services. These can include information campaigns on benefits of controlled livestock systems, training and subsidizing modern goat house construction and feed preservation, and contract farming and product certification for adhering to acceptable community norms. Medium-term policy interventions include varietal development of adaptable short duration pigeon pea, initiating a review of the appropriate laws, and instituting more studies to understand these community norms
Strategies for enhancing productivity, resilience, nutritional quality, and consumption of pearl millet [Pennisetum glaucum (L.) R. Br.] for food and nutritional security in India
Get PDFPearl millet [Pennisetum glaucum (L.) R. Br.] is an important component of agri-food system in areas experiencing drought and high temperature and for increasing the resilience to climatic stresses and addressing malnutrition. The purpose of this review is to examine strategies for improving productivity, stress resilience, and nutritional quality of pearl millet and to understand its consumption pattern. Genetic diversification of hybrid parental lines remains strategically important to breed diverse, disease-resistant and drought-tolerant hybrids. Resistance to diseases, tolerance to drought, and high temperature and greater contents of iron and zinc are targeted in improving hybrid parental lines. Lodging resistance, compact panicles, panicle exertion, and improved seed set are universal traits, whereas duration, tillering ability, seed color, and seed size have a strong regional preference. The strategy of developing high-yielding and disease-resistant hybrids with adaptation to challenged agro-ecologies has led to increase in yield from 303 to 1219 kg/ha between 1960 and 2020. Yield and stress resilience are to be increased further using conventional breeding and new tools like genomic selection, speed breeding, genome editing, and precision phenotyping. Mainstreaming grain nutritional traits, viz., iron and zinc contents in genetic improvement are essential to develop high-yielding and nutrient-rich pearl millet. There is need to enhance the consumption of pearl millet by strengthening existing value-chain, providing consumer a choice of diverse range of food products, creating awareness about its health benefits and promotion through government schemes
Dryland cropping in different Land uses of Senegal using Sentinel-2 and hybrid ML method
Get PDFIn rainfed and dryland agricultural areas with smallholder farms (less than 2 ha), crop diversity is high due to farmers' decisions and local climatic conditions, leading to a complex spatial–temporal distribution of crops. Monitoring and mapping crops is crucial for food security and implementing agricultural support programs. This study aims to map crop types across Senegal using Sentinel-2 satellite imagery and the limited ground reference data available, which has been increasing recently. The study compares conventional supervised classification algorithms to unsupervised classification algorithms using high-resolution satellite imagery. Crop type classification for 2020 in Senegal employed supervised machine learning algorithms, including Classification and Regression Trees (CART), Random Forest (RF), and Support Vector Machine (SVM) on the Google Earth Engine (GEE) cloud platform, and the unsupervised Iso-clustering classification algorithm with Spectral Matching Techniques (SMTs). Due to limited ground data, supervised classifiers achieved 45-55% accuracy, whereas the unsupervised semi-automatic approach achieved over 75% accuracy. The study indicates that supervised classifiers' performance depends on ground data quantity, while SMT shows good performance even with limited ground data. This SMT approach is valuable for classifying crop types in dryland areas with smallholder farms and diverse cropping patterns