International Crops Research Institute for the Semi-Arid Tropics
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Genome assembly, comparative genomics, and identification of genes/pathways underlying plant growth-promoting traits of an actinobacterial strain, Amycolatopsis sp. (BCA-696)
Get PDFThe draft genome sequence of an agriculturally important actinobacterial species Amycolatopsis sp. BCA-696 was developed and characterized in this study. Amycolatopsis BCA-696 is known for its biocontrol properties against charcoal rot and also for plant growth-promotion (PGP) in several crop species. The next-generation sequencing (NGS)-based draft genome of Amycolatopsis sp. BCA-696 comprised of ~ 9.05 Mb linear chromosome with 68.75% GC content. In total, 8716 protein-coding sequences and 61 RNA-coding sequences were predicted in the genome. This newly developed genome sequence has been also characterized for biosynthetic gene clusters (BGCs) and biosynthetic pathways. Furthermore, we have also reported that the Amycolatopsis sp. BCA-696 produces the glycopeptide antibiotic vancomycin that inhibits the growth of pathogenic gram-positive bacteria. A comparative analysis of the BCA-696 genome with publicly available closely related genomes of 14 strains of Amycolatopsis has also been conducted. The comparative analysis has identified a total of 4733 core and 466 unique orthologous genes present in the BCA-696 genome The unique genes present in BCA-696 was enriched with antibiotic biosynthesis and resistance functions. Genome assembly of the BCA-696 has also provided genes involved in key pathways related to PGP and biocontrol traits such as siderophores, chitinase, and cellulase production
Mapping Quantitative Trait Loci (QTLs) for Reproductive Stage Salinity Tolerance in Rice
Get PDFSalinity is one of the major abiotic stresses that abate the yield of several crop species including rice. Several studies were conducted to identify quantitative trait loci (QTLs) for traits associated with salinity tolerance, mostly at the seedling stage of crop growth. However, the reproductive stage of development is highly sensitive to salt stress, and hence, better QTLs must be developed. QTLs have been identified in the present study for salt tolerance of the reproductive stage in rice using recombinant inbred lines (RILs). Thirty-day-old rice seedlings of 184 RILs derived from a cross between a salt sensitive RP Bio226 (indica), and a salt-tolerant Jarava (indica), were used to identify QTLs linked to salinity tolerance in moderate (field) and severe (pot) stress conditions. One hundred polymorphic simple sequence repeat (SSR) markers were used to construct a genetic linkage map that covered a 1349.4 cm genome with an average distance of 13.5 cm between loci. Eighteen new QTLs [logarithm of odds (LOD) 2.5 and above] were identified on chromosomes 1, 2, 6, 10, 11, and 12 using composite interval mapping with the phenotypic variation explained by QTL (PVE) as high as >42% with an LOD value of 5.2. qYLSt-12 with an LOD of 2.8 and a phenotypic variance (PV) of 6.4%, flanked by RM27940-RM27971, was identified for yield in moderate stress conditions. The qSTR-2 detected for salinity tolerance on chromosome 2 with 8.9% of the PV is the most significant finding of the present research. No QTL for salinity component traits has been reported in the region of RM110-RM423. The other salinity trait QTLs identified are qSN-11, qSN-12 for Na+ concentration with a total PVE% of 13.9 and qSNK-12.1, qSNK-12.2 for the Na+/K+ ratio showing a total of 26.7% of the PV. The QTLs for yield component traits viz. plant height, panicle number, panicle length, and biomass were also identified in the present study. Previous studies reported QTLs for salinity tolerance in rice on chromosome 1 but none of the QTLs in our study were on qSaltol or nearby position; therefore, Jarava conferred salinity tolerance in RILs due to novel QTLs. Fine mapping of these novel QTLs is suggested and could be helpful to enhance the level of tolerance through marker-assisted selection for the pyramiding of different QTLs in one background
Future Staples for Nutrition Security and Sustainability
No full textClimate change and environmental degradation have spurred a critical need for more sustainable farming methods, together with more resilient crops and systems that can adapt to and mitigate climate change and be less taxing on natural resources. In addition, the need to improve diets to tackle the alarming and increasing levels of undernutrition, micronutrient deficiency and related non-communicable diseases has drawn attention to sustainable solutions that are central to the health of people and the planet while also being viable and building the resilience of farmers. Given that staples dominate farming systems and diets, solutions to diversify them with smarter foods like millets (including sorghum) are what can have a resounding impact. Millets are being recognised for contributing to some of the biggest nutrition and health needs. They are also acknowledged as being highly resilient and are able to survive under high temperatures and in highly marginalised land. Millets require fewer pesticides, fertilisers and less water to survive. Market predictions are also showing these ancient grains are making a comeback, increasing in popularity and demand
CRISPR edited floriculture crops: A revolutionary technique to increase flower production, their color and longevity
No full textFloriculture has become one of the noticeable commercial trade markets in the agriculture sector. By applying modern breeding approaches, novel traits have been modified that are related to fragrance, floral color, morphology, vase life, aroma, and resistance against both abiotic and biotic stresses. There is very much scope in the modern breeding process compared to classical breeding. Its application through plant tissue culture, development of transgenics by genetic modification in pathways, development of locus-specific markers by marker-assisted selection (MAS), and genomics study to get novel varieties that appeal to customers. Genome editing, enhanced its potential in editing key genes attributing to the different traits that were modified or mutated in plants. However, CRISPR-Cas technology is becoming a tool of choice, due to its most efficient, and lower cost, when compared with other biotechnological tools. CRISPR technology is useful for changing DNA sequences at specific locations, it provides magnificent improvement in floriculture crops. This system is used to induce mutations or modifications in specific genomes or genes that were involved in various plant developmental processes by modifying the color of the flower by targeting its biosynthetic pathway genes and by reducing ethylene production, thus it enhances its flower longevity compared with wild types. Here, this chapter summarizes the research work done by employing new breeding tools and advanced tools like the CRISPR system, as well as other variants for crop improvement in floriculture. Our findings show that there is a future in the CRISPR system where it may be useful in mutating or altering the genes that are related to pigmentation and also for flower longevity
Exploration of stable host-plant resistant sources to sterility mosaic disease of pigeonpea (Cajanus cajan L. Huth)
No full textSterility mosaic disease (SMD) presents a major challenge in pigeonpea cultivation throughout the Indian subcontinent. Chemical control methods, such as acaricides, are neither economically viable nor sustainable, making host plant resistance the preferred approach for managing this disease. In this study, we evaluated 45 pigeonpea germplasm accessions and breeding lines for SMD resistance over two consecutive Kharif seasons (2021-22 and 2022-23). Of the 45 genotypes tested, 8 exhibited low disease incidence (0-10%) (LRG-471, ICPL 151, ICPB 2089, ICPB 2047, ICPB 2092, ICPB 2211, ICPL 85063, and ICPL 14003) and were classified as resistant. Additionally, 23 genotypes showed disease incidence between 10.1-20.0% and were categorized as moderately resistant. These resistant genotypes offer promising new sources of SMD resistance and should be considered for inclusion in future pigeonpea breeding programs aimed at improving resistance. This research provides valuable phenotypic insights and identifies stable resistant sources essential for advancing SMD resistance breeding efforts
Double-digest restriction-associated DNA sequencing-based genotyping and its applications in sesame germplasm management
Get PDFSesame (Sesamum indicum L.) is an ancient oilseed crop belonging to the family Pedaliaceae and a globally cultivated crop for its use as oil and food. In this study, 2496 sesame accessions, being conserved at the National Genebank of ICAR-National Bureau of Plant Genetic Resources (NBPGR), were genotyped using genomics-assisted double-digest restriction-associated DNA sequencing (ddRAD-seq) approach. A total of 64,910 filtered single-nucleotide polymorphisms (SNPs) were utilized to assess the genome-scale diversity. Applications of this genome-scale information (reduced representation using restriction enzymes) are demonstrated through the development of a molecular core collection (CC) representing maximal SNP diversity. This information is also applied in developing a mid-density panel (MDP) comprising 2515 hyper-variable SNPs, representing almost equally the genic and non-genic regions. The sesame CC comprising 384 accessions, a representative set of accessions with maximal diversity, was identified using multiple criteria such as k-mer (subsequence of length “k” in a sequence read) diversity, observed heterozygosity, CoreHunter3, GenoCore, and genetic differentiation. The coreset constituted around 15% of the total accessions studied, and this small subset had captured >60% SNP diversity of the entire population. In the coreset, the admixture analysis shows reduced genetic complexity, increased nucleotide diversity (π), and is geographically distributed without any repetitiveness in the CC germplasm. Within the CC, India-originated accessions exhibit higher diversity (as expected based on the center of diversity concept), than those accessions that were procured from various other countries. The identified CC set and the MDP will be a valuable resource for genomics-assisted accelerated sesame improvement program
Cultivating knowledge: the importance of integrating agriculture and farming education in Indian schools
Get PDFAmidst climate change and sustainability concerns, the imperative for agricultural education arises from the renewed focus of modern society, nature, agriculture and nutrition. Spanning primary to tertiary levels, this education encompasses diverse subjects. Elementary education instils fundamental concepts, while vocational programmes groom students for agricultural careers. At the college level, the emphasis shifts to teaching and research. Integrating agriculture into Indian schools yields multiple advantages, including enhancing fundamental life skills, nutrition comprehension, environmental consciousness and STEM education. Consequently, students are equipped with indispensable knowledge and skills, paving the way for a sustainable future in the ever-evolving world
Field-level rice yield estimations under different farm practices using the crop simulation model for better yield
Get PDFCrop yield estimation is essential for decision-making systems and insurance policy makers. Numerous methodologies for yield estimation have been developed, encompassing crop models, remote sensing techniques, and empirical equations. Each approach holds unique limitations and advantages. The primary aim of this study was to assess the accuracy of the DSSAT (Decision Support System for Agro Technology Transfer) model in predicting rice yields and LAI (Leaf Area Index) across various management methods. Additionally, the study sought to identify the optimal management practice for attaining higher yields. Crop models facilitate the expeditious evaluation of management strategies aimed at improving crop yield and analyzing the balance between production, resource efficiency, and environmental impacts. The study region selected for analysis is Karimnagar district of Telangana state. DSSAT has been chosen as the preferred tool due to its high efficiency in evaluating crop yield. The model's simulated yield was compared to the observed yield obtained from crop-cutting experiments. The results indicate a correlation of 0.81 and 0.85 between observed and simulated yields, as well as between model LAI and yield. An observation was made regarding a discrepancy between predicted and actual yields, which can be attributed to biotic stress. However, it should be noted that the current model does not account for this factor. The observed average yield was 5200 kg ha-1, whereas the projected yield was 5400 kg ha-1. The findings indicate that the model's performance is influenced by both the timing of sowing and the amount of nitrogen applied. The findings indicate that the DSSAT model has demonstrated a high level of accuracy in predicting both yields and leaf area index (LAI) across various management strategies. This study showcases the potential use of crop simulation models as a technology-driven tool to identify the most effective management strategies for rice production
Genome-Wide Comparative Analysis of Five Amaranthaceae Species Reveals a Large Amount of Repeat Content
Get PDFAmaranthus is a genus of C4 dicotyledonous herbaceous plant species that are widely distributed in Asia, Africa, Australia, and Europe and are used as grain, vegetables, forages, and ornamental plants. Amaranth species have gained significant attention nowadays as potential sources of nutritious food and industrial products. In this study, we performed a comparative genome analysis of five amaranth species, namely, Amaranthus hypochondriacus, Amaranthus tuberculatus, Amaranthus hybridus, Amaranthus palmeri, and Amaranthus cruentus. The estimated repeat content ranged from 54.49% to 63.26% and was not correlated with the genome sizes. Out of the predicted repeat classes, the majority of repetitive sequences were Long Terminal Repeat (LTR) elements, which account for about 13.91% to 24.89% of all amaranth genomes. Phylogenetic analysis based on 406 single-copy orthologous genes revealed that A. hypochondriacus is most closely linked to A. hybridus and distantly related to A. cruentus. However, dioecious amaranth species, such as A. tuberculatus and A. palmeri, which belong to the subgenera Amaranthus Acnida, have formed their distinct clade. The comparative analysis of genomic data of amaranth species will be useful to identify and characterize agronomically important genes and their mechanisms of action. This will facilitate genomics-based, evolutionary studies, and breeding strategies to design faster, more precise, and predictable crop improvement programs
The Influence of Plant Growth Modulators on Physiological Yield and Quality Traits of Sesame (Sesamum indicum) Cultivars Under Rainfed Conditions
Get PDFSesame is an important oilseed crop, and the crop yields frequently fluctuate as the crop is largely grown in rainfed and low-fertile lands. Limited water availability negatively affects many physiological processes and the final productivity of sesame. Limited work has been carried out in the past to understand the role of plant growth regulators (PGRs) in modulating sesame growth and development for optimum productivity. A field study was conducted under rainfed conditions to evaluate the response of foliar application of different PGRs such as hormonal-based gibberellic acid (20 ppm); chemical-based thiourea (500 ppm); chemical-constituting structural component-based ortho-silicic acid (380 ppm); and control (water-sprayed) on sesame cultivars: Swetha til, GT-10, TKG-22, and JCSDT-26. The PGRs foliar application was done at the vegetative (25–30 days after sowing), 50% flowering (40–45 days after sowing), and seed development (70–75 days after sowing) stages of the crop. The results revealed that application of different PGRs positively influenced the plant’s growth, physiological, yield and quality traits; however, most effective results were obtained with gibberellic acid (20 ppm), followed by ortho-silicic acid (380 ppm), and thiourea (500 ppm) improved the morphological, yield, and yield-attributing traits. The interaction between PGRs and varieties was found significant and among the sesame cultivars, swetha til followed by JCSDT-29 was found most promising. The application of PGRs has significantly improved the plant height, leaf area, number of branches, capsules, seeds/capsules, seed yield oil content, and fatty acid content compared to the control by gibberellic acid, followed by ortho-silicic acid and thiourea. The interaction between PGRs and varieties was found to be significant, and cultivar Swetha til, a white-colored cultivar performed most superiorly among the different tested cultivars in terms of growth, physiology, yield as well and quality traits when treated with GA3 at 20 ppm. The seed yield was enhanced by 25–26%, 11–12%, and 6–7% with the application of gibberellic acid, ortho-silicic acid, and thiourea, respectively, over control. Considering the findings, it can be concluded that the application of PGRs (thiourea, ortho-silicic acid, and gibberellic acid) significantly enhanced the growth, physiology, yield, and quality of sesame under rainfed conditions; however, GA3 at 20 ppm was found most effective and may not only enhance the optimum productivity but also effective in improving the quality traits of sesame