International Crops Research Institute for the Semi-Arid Tropics
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Global Status of Genetic, Genomic, and Bioinformatics Resources for Pulse Crop Improvement
No full textPulses are a powerhouse of protein and hold an immense potential for food security and sustainable agriculture. However, exploiting their full potential centers on harnessing genetic, genomic, and bioinformatics resources still needs a great fillip. Efforts have been made globally to collect, preserve, and characterize their germplasm, facilitating the identification of desirable traits for breeding programs. Such collections can serve as a rich reservoir for genetic studies, enabling the development of improved varieties with enhanced yield, nutritional content, and resistance to biotic and abiotic stresses. Pulse genome sequencing has accelerated during the last 10 years, and most pulse crops now have high-quality reference genomes, transcriptomes, and genetic maps accessible. Moreover, genomic tools enable the detection of key genes responsible for important agronomic traits, disease resistance, and stress tolerance, paving the way for precision breeding approaches. Dedicated databases to curate genetic and phenotypic information and tools utilized for genome assembly, annotation, and variation analysis are constantly evolving. Pulses could see a revolutionary leap in genetic improvement through the synergy of cutting-edge genomic and phenomic tools with accelerating techniques such as genomic selection and speed breeding. The fusion of artificial intelligence (AI) and machine learning (ML) technologies with genomic science heralds a new era in crop breeding and genetic harvest in pulses. These tools offer exciting possibilities for boosting productivity, enhancing nutritional quality, and ensuring resilience to environmental stresses. As these tools become increasingly accessible and their applications more widespread, the potential for transformative impacts on global pulse scenarios continues to grow
Utilizing X-ray radiography for non-destructive assessment of paddy rice grain quality traits
Full text linkBackground
Agricultural systems are under extreme pressure to meet the global food demand, hence necessitating faster crop improvement. Rapid evaluation of the crops using novel imaging technologies coupled with robust image analysis could accelerate crops research and improvement. This proof-of-concept study investigated the feasibility of using X-ray imaging for non-destructive evaluation of rice grain traits. By analyzing 2D X-ray images of paddy grains, we aimed to approximate their key physical Traits (T) important for rice production and breeding: (1) T1 chaffiness, (2) T2 chalky rice kernel percentage (CRK%), and (3) T3 head rice recovery percentage (HRR%). In the future, the integration of X-ray imaging and data analysis into the rice research and breeding process could accelerate the improvement of global agricultural productivity.
Results
The study indicated, computer-vision based methods (X-ray image segmentation, features-based multi-linear models and thresholding) can predict the physical rice traits (chaffiness, CRK%, HRR%). We showed the feasibility to predict all three traits with reasonable accuracy (chaffiness: R2 = 0.9987, RMSE = 1.302; CRK%: R2 = 0.9397, RMSE = 8.91; HRR%: R2 = 0.7613, RMSE = 6.83) using X-ray radiography and image-based analytics via PCA based prediction models on individual grains.
Conclusions
Our study demonstrated the feasibility to predict multiple key physical grain traits important in rice research and breeding (such as chaffiness, CRK%, and HRR%) from single 2D X-ray images of whole paddy grains. Such a non-destructive rice grain trait inference is expected to improve the robustness of paddy rice evaluation, as well as to reduce time and possibly costs for rice grain trait analysis. Furthermore, the described approach can also be transferred and adapted to other grain crops
Enhancing Irrigation Water Management and Malt Barley Practices for Smallholder Farmers at Barneb Irrigation Scheme, Legambo District, Ethiopia
Full text linkA pre-scale-up study was conducted at the Barneb small-scale irrigation scheme to promote improved irrigation technologies for malt barley, aiming to enhance water use efficiency, farm productivity, and the economic benefits of smallholder farmers. Traditional flooding methods were found to be inefficient due to water wastage, soil erosion, and waterlogging. To address these issues, a Farmer Research Group (FRG) consisting of 30 farmers (26 male and 4 female household heads) was established. The improved irrigation practice involved double row raised bed furrow irrigation with a 40 cm bed width, 20 cm furrow width, and 20 cm row spacing, along with recommended fertilizer rates (100 kg ha⁻¹ Urea and 100 kg ha⁻¹ NPS). Net irrigation depths were 19 mm during the initial stage and 44.3 mm during the mid-season stage, with irrigation applied at 30-day intervals. Results showed that improved seed combined with improved irrigation and agronomic practices yielded 4,250 kg ha⁻¹, a 25% increase over the 3,400 kg ha⁻¹ yield from local seed under traditional practices. Water productivity also improved significantly, with the improved method achieving 4.7 kg m⁻³, nearly double that of the farmer's practice (2.4 kg m⁻³). The net benefit from improved practices was 133,300 ETB ha⁻¹, which is 55.14% higher (47,375 ETB ha⁻¹ more) than the 85,925 ETB ha⁻¹ achieved through traditional methods. In conclusion, the study recommends scaling up the improved technologies through collaborative efforts between the Ministry of Agriculture, NGOs, and private sectors via integrated irrigation extension programs
Integrated Soil Fertility Management Strategies for Resilient Soils in Ethiopia
Full text linkSoil fertility depletion and nutrient mining are critical challenges to sustainable crop production in Sub-Saharan Africa (SSA). Addressing these issues requires a multifaceted approach, including improved soil management practices, the use of organic fertilizers, and the adoption of sustainable agronomic practices. Integrated soil fertility management (ISFM) is one of the approaches to improving the yields of crops while preserving sustainable and long-term soil health and fertility through the combined application of fertilizers, recycling of organic resources, use of responsive crop varieties, and improved agronomic practices, which minimize nutrient losses and improve the nutrient-use efficiency of crops (Agegnehu and Amede, 2017; Vanlauwe et al., 2015). The fertility status of steep-slope cultivated lands has been depleted due to the loss of soil organic matter and nutrient reserves. The response of such soils to the application of nutrients is low, unless their fertility is restored through the adoption of an integrated soil-crop system for improved crop-nutrient response and yield (Minh et al., 2023)
Exploring rancidity in pearl millet flour: A lipidomic and biochemical approach
No full textPearl millet is a nutritious and climate-resilient cereal extensively grown in the arid and semi-arid regions of South Asia and Sub-Saharan Africa. Despite its exceptional nutritional qualities, pearl millet suffers from limited acceptance, partly due to the short shelf life of its milled flour. The stored flour quickly becomes rancid after 7–10 days due to the rancidity of fatty acids and oils caused by various factors, including enzymes and metal ions. In this study, we examined high iron (biofortified [ICMH-1202 (BF5) and Dhanashakti (BF6)] and regular [PA-9285 (NBF2) and MP-7872 (NBF4)] millet grain-based stored flour. Hydrolysis of triacylglycerols led to the accumulation of free fatty acids. Data on acid value, peroxide value, and enzymatic activities showed that high iron lines exhibit a higher rate of lipid oxidation and peroxidation after 45 days of storage. The biochemical profiling of these lines indicated that the high-iron and low-iron lines are comparable regarding rancidity-linked traits until 14 days after grinding for most surrogate traits. These findings suggest that iron-rich flour is likely more susceptible to rancidity than low-iron lines after 45 days of storage. The results indicate that high-iron varieties would not affect the general Indian practices of using flour within 14 days, but they may require post-harvest stabilization to enhance shelf life beyond two weeks. However, it is crucial to emphasize that iron-rich varieties are vital in addressing hunger and malnutrition. These exploratory results suggest that heat treatment could help improve the shelf life of iron-rich pearl millet grains on a smaller scale, but a better solution is still needed for large-scale commercialization and to monitor this key trait in released varieties without compromising their nutritional content
Current Agriculture Practices: Baseline Survey Report: Central Highlands Ecoregion Foodscape (CHEF)
Get PDFThe Nature Conservancy (TNC) Central Highlands Ecoregion Foodscapes (CHEF) Use Case targets eleven counties in the central highland region of Kenya that transition from water towers, smallholder transition zone, semiarid production zone, to rangelands. The mission of the Use Case is to improve and sustain the health, diversity, and productivity of the croplands and rangelands to meet the needs of the present and future communities. The interaction of land use systems and agrifood systems in the region is the driver of production decline and depletion of ecosystem services and biodiversity. The CHEF Use Case embeds a foodscapes-scale approach along the transitions to design, validate, and action that are sensitized to local contexts. The approach fosters bridging traditional knowledge and scalable nature-based interventions to drive and achieve an inclusive and sustainable food systems transformation and to accelerate system-wide change. The Use Case aims to catalyze the implementation of regenerative practices and innovations across the transition zones, representing the diversity of geographic and food production archetypes
Developing pangenomes for large and complex plant genomes and their representation formats
Full text linkBackground
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.)
Full text linkFaba 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
Targeting nutrient sources and forms to identify yield-limiting nutrients for wheat under contrasting rainfall regimes and landscape positions in mixed-farming systems
Full text linkWheat yield gap in Ethiopia is high due to low nutrient availability, soil heterogeneity, undulating landscape, and climate. A study was conducted to identify yield-limiting nutrients for wheat yield under varying landscape positions and rainfall regimes. The treatments included all nutrients in blended (All-Blend), compound (All-Comp), and individual (All-Ind) forms containing N, P, K, S, Zn, and B, while K, S, Zn, and B omitted treatments were (All-Blend)-K, (All-Blend)-S, (All-Blend)-Zn, and (All-Blend)-B. Besides, NP only, 50 and 150% of the rate of all nutrients in the blended form (All-Blend), and a control without any nutrients were included. Results showed that the highest yield was obtained from the application of 150% of All-Blend across landscape positions and rainfall regimes, with grain yield improvement of 109.5% (2.54 t ha−1) by applying 150% of All-Blend under the foot slope position and high rainfall regime compared to the control and yield improvement of 72.5% under the low rainfall regime. With the control treatment grain yield was lower by 27–70% across landscape positions and rainfall regimes. The grain yield penalties due to K, S, Zn, and B omission were 0.54–9% over landscape positions and rainfall regimes compared to applying All-Blend, implying that the omission of K, S, Zn, and B were not yield-limiting nutrients for wheat production in the study areas. Thus, it will be crucial to consider landscape strata and rainfall regimes to optimize NP rates. Further study is also suggested as nutrient applications in blended, compound, or individual forms are inadequate to conclude
Tree integration in conservation agriculture: A case study of teak (Tectona grandis) + bael (Aegle marmelos) based agroforestry in the Bundelkhand region
Full text linkThe present study was carried out during the winter (rabi) seasons of 2021–22 and 2022–23 at ICAR-Central Agroforestry Research Institute, Jhansi, Uttar Pradesh to study the impact of conservation agriculture practices within a teak (Tectona grandis L.)+ bael (Aegle marmelos L.)-based agroforestry system on growth rate and yield parameters of tree and crop component, as well as on soil properties. It examined the effect of tillage methods and residue retention on the growth and yield of chickpea (Cicer arietinum L.) and linseed (Linum usitatissimum L.) as well as soil properties. The experiment was laid out in a randomized block design (RBD), with three replications having eight treatments of comprising combinations, viz. Tillage methods (conventional and minimum); Cropping systems (sorghum-chickpea and maize-linseed); and Residue management practices (residue retention and no retention). Results indicated that residue retention under conventional tillage significantly enhanced plant height and dry matter accumulation in both linseed and chickpea. Crop yields were comparable under conventional and minimum tillage, although residue retention significantly boosted the yields of both crops. Conservation agricultural practices contributed to higher productivity in the teak+ bael-based agroforestry system. Residue retention improved soil organic carbon content by 24–39% compared to no residue retention. Additionally, nutrient availability (N, P, K, S, Zn, Fe, Mn, and Cu) was enhanced through minimum tillage combined with residue retention