International Crops Research Institute for the Semi-Arid Tropics
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Allele Mining for Genome Designing in Pearl Millet
No full textSequencing of different crop genomes resulted into availablilty of massive sequence information in public databases. Now, it is essential to utilize this information to identify and isolate superior and novel alleles of agronomically important traits from various crop gene pools in order to utilize it for development of improved cultivars. Allele discovery is more important today because molecular breeding is being used to create crop varieties that are tailored to consumer needs. Genome plasticity is also being used to adapt to climate change scenarios using targeted and precision breeding tools that have been validated by phenomics and genomics research. With potential applications in crop development programs, allele mining is a potential method for analyzing naturally occurring allelic variation or candidate genes affecting important traits. It supports the generation of allele-specific markers to utilize in marker-assisted selection, tracking of allele evolution and discovery of novel haplotypes. In order to use allele mining in pearl millet improvement, various initiatives and concentrated allele mining activities are necessary in light of the enormous potential of this technique
Beneficial bacteria mitigate combined water and phosphorus deficit effects on upland rice
Get PDFBackground and aims
Limited water and phosphorus availability are major challenges in upland rice production. Plant–microbe interactions, especially with beneficial bacteria, have shown promise in mitigating these stresses. This study investigated the influence of microbial inoculants with hydration-promoting and phosphorus-solubilizing abilities on upland rice yield under drought and phosphorus deficiency.
Methods
Upland rice (BRS Esmeralda) plants were grown in a greenhouse with different water availability conditions (well-watered and drought), phosphorus levels (normal 200 mg dm−3 and low 20 mg dm−3), and microbial treatments (no-microorganisms and single isolates, Serratia marcescens strains BRM 32114 and BRM 63523, and combined isolates Bacillus toyonensis BRM 32110 + BRM 32114 and BRM 63523 + BRM 32114). Root and shoot traits, as well as production components, were analyzed.
Results
While the microbial treatments affected the roots, the larger effects were seen in the shoot rice plants. When both water and phosphorus were limited, grain yield decreased significantly. However, plants inoculated with beneficial bacteria showed a substantial increase in grain yield (average of 39.5% in 2019/2020 and 18.8% in 2020/2021) compared to uninoculated plants under combined stresses. This increase was especially pronounced in plants treated with BRM 63523 (strain) alone or combined with BRM 32114 (strain). These inoculated plants also showed improved photosynthetic activity (average increase of 24.6%), which may have contributed to the higher grain yield.
Conclusions
Inoculating upland rice with specific Serratia strains effectively increased shoot and root traits under combined water and phosphorous stresses. These findings highlight the potential of plant–microbe interactions for sustainable upland rice production
Association of nitrogen utilisation efficiency with sustenance of reproductive stage nitrogen assimilation, transcript abundance and sequence variation of nitrogen metabolism genes in rice (Oryza sativa L.) sub-species
No full textTo maintain yield stability and environmental sustainability of rice cultivation, improvement in nitrogen use efficiency (NUE) is essential. We identified rice genotypes showing high NUE in control (N120) and N deficient (N0) field conditions by analyzing different NUE parameters. Reproductive stage N assimilatory and signalling gene expression correlated to the variation in N utilization efficiency (NutE) variation. The sequence variation in N metabolism and signaling (NLP) genes was analyzed in selected genotypes (Apo (Indica) and Nerica-L-42 (Oryza glaberrima*Indica)). Significant non-synonymous SNPs were found in NPF2.2, PTR2, NGR9 (DEP1), Fd-GOGAT, NLP3, NLP4 and NLP5 genes of Apo, Nerica-L-42 and w.r.to japonica genotype Nipponbare. The significant variation in reproductive stage gene expression and changes in the amino acid sequence of NLP3, NLP4, and NLP5 among rice genotypes differing in NUtE is a new and potent genome editing target improving rice NUE. The non-synonymous SNPs identified in the study will be important genomic resources for improving rice NUE
Discovery of potential haplotypes associated with varying levels of vicine content due to the InDel1.4 and a coding-SNP in the VC1 gene in faba bean (Vicia faba L.)
No full textFaba bean (Vicia faba L.) is a popular legume due to its nutritional, medicinal and environmental benefits. But vicine and convicine (VC) remain as the main threats for “favism” in individuals with genetic deficiency of Glucose-6-phosphate dehydrogenase (G6PDH) enzyme. Re-sequencing-based allele mining involving allele-specific Tetra-ARMS PCR has revealed a 92 bp InDel (Insertion-Deletion), designated as “InDel1.4” in the intron-4 of VC1 gene and a coding-SNP (T/C) at position +1588 in the exon-5. Consequently, three distinct haplotypes (Hap-1, Hap-2 and Hap-3) were identified based on the size of the intron-4 and the allelic status of the SNP in exon-5. LC-MS/MS analysis confirms that the vicine concentration varied between 3.489 and 10.025 g/kg in the entire collection of germplasm. A strong correlation (r = 0.84**) was observed between haplotypes and variation in vicine concentration. Translation of the sequenced fragments revealed that, the coding-SNP doesn't not change the amino acid composition of the VC1 protein. Therefore, the coding-SNP was found to be a synonymous SNP. As the InDel1.4 was located within few hundred base pairs away from the previously reported “AT insertional-mutation”, which was responsible for very low or near-zero VC faba bean, and also shows correlation with vicine content, the InDel could be utilized for a simple, reliable and cost-effective molecular marker assisted selection and crop improvement for developing faba beans with reduced VC. The Hap-1 and Hap-2 have tremendous potential to be utilized in haplotype-based breeding for faba bean improvement to combat favism
Proteomic insights into the saliva and salivary glands of the cotton aphid, Aphis gossypii (Hemiptera: Aphididae)
No full textThe cotton aphid or melon aphid, Aphis gossypii Glover (Hemiptera: Aphididae), is a rising threat to cotton production. Aphids use needle-like stylets to puncture the plant epidermis, access the sieve tube, and ingest the plant phloem. Aphids release salivary proteins while feeding, allowing them to colonize host plants successfully. Aphid saliva consists of many constituents that facilitate the consumption of phloem sap upon partial digestion and modulate plant defense systems. The salivary proteomes of A. gossypii were studied using liquid chromatography-tandem mass spectrometry (LC–MS/MS), which resulted in the identification of 189 proteins in excised salivary glands and 95 proteins in artificial diet-fed aphid saliva, with 25 proteins commonly noticed in both proteomes. Several proteins, including CAH1711662.1, CAH1735943.1, PFF0380w, XP_027839681.2, CAH1714583.1, CAH1713131.1 and XP_027840117.2 remained unique and uncharacterized. Previously identified salivary proteins of insects, such as glucose dehydrogenase, Mp1, Mp58, peroxidase, heat shock protein (HSP), elongation factor, and aminopeptidases, were also found. The identified proteins were categorized into seven groups, viz., enzymes, cytoskeletal proteins, sheath proteins, calcium-binding proteins, transporter proteins, chromatin-, RNA-, and DNA-binding proteins, and miscellaneous proteins. Twenty-five proteins from diet-fed aphid saliva and 17 proteins in the salivary gland possessed signal peptides. This study's results offer a more detailed understanding of the salivary proteins of A. gossypii and provide the foundation for future functional studies on aphid-cotton interactions to develop new aphid control methods
The Utility and Management of Transgenic Plants with Bacillus thuringiensis Genes for Protection from Pests
No full textSUMMARY. Recombinant DNA technology offers opportunities for widening the available gene pool for crop improvement. Genetic engineering also allows the introduction of several desirable genes in a single event, and can reduce the time to introgress novel genes into elite backgrounds. Genes conferring resistance to insects have been inserted into crop plants such as cotton, maize, potato, tobacco, rice, broccoli, lettuce, walnut, apple, alfalfa, and soybean. Genetically transformed crops with Bacillus thuringiensis (Bt) genes have been deployed for cultivation primarily in the USA, China, Argentina, Canada, Mexico, South Africa, and Australia. The potential of insect-resistant transgenic plants with Bt genes can be enhanced when deployed in combination with alternate protective genes such as protease inhibitors, enzymes, and plant lectins, or in combination with insect-resistant cultivars derived through conventional breeding. While several transgenic crops with insecticidal genes have been introduced in the temperate regions, very little has been done to use this technology for improving crop production in the harsh environments of the tropics, where the need for increasing food production is most urgent. This may be due to the lack of infrastructure, biosafety regulations, intellectual property rights, or market potential. There is an urgent need to develop a scientifically sound strategy to deploy exotic and plant derived genes through transgenic plants for minimizing the extent of losses caused by insect pests. Equally important is the need for observance of biosafety regulations, a responsible public debate, and a better presentation of the benefits to sustainable crop production of a rational deployment of genetically transformed plants
Innovations, Strategies, and Policies for Building Resilience of India’s Dryland Farming to Climate Change
No full textClimate change is a real and undeniable threat to the entire civilization. India is among the most severely impacted countries with extreme weather events felt intensely on agriculture (decline in yields by 3–9%), water resources, and ecosystems, threatening food security and rural livelihoods. To address these challenges, India has been actively pursuing new programs and innovative strategies for climate-proofing agriculture through its National Action Plan on Climate Change (NAPCC); major initiatives being National Mission on Sustainable Agriculture (NMSA), National Innovations on Climate Resilient Agriculture (NICRA), and international collaborative programs: conservation agriculture (CA), landscape approach, etc., thus promoting climate-resilient agriculture through resilient crop varieties, integrated natural resources management, digital agriculture, capacity building of farmers, and supporting community-based adaptation initiatives. Results from these initiatives such as CA have shown the potential to produce more food (10–15%), increase farmers’ income (25–50%), and lower carbon footprint by 25–30%. Through a multifaceted approach, embracing innovative technologies, adaptive strategies, and supportive policies such as the National Adaptation Fund for Climate Change (NAFCC), and crop insurance schemes, India’s agriculture sector is enhancing its resilience to climate change
Genomic Selection-Driven Wheat Breeding for Superior Genetic Gains: Status Quo and Future Steps
No full textConventional breeding approaches rely on phenotypic selection, which is a crucial phase in crop breeding. Breeders have been able to make use of molecular markers to aid in breeding efforts since a large number of markers were made accessible from the early 1990s. Marker-assisted selection (MAS) is a widely employed technique in molecular breeding, predominantly applicable to traits controlled by only a few of the major genes. Most economic traits found in crops are intricate and controlled by a large number of genes, each of which has very little impact on the trait’s value, making it difficult to integrate MAS into breeding practice to the extent anticipated. This shortcoming of MAS necessitates the addition of genome-wide markers. Genomic selection (GS) is a more advanced version of MAS. The goal is to obtain more thorough and accurate selection by using genome-wide markers to quantify the impacts of all loci and afterwards calculate a genomic estimated breeding value upon which new superior genotypes are selected. Because of advancements in sequencing and genotyping technology, genomic selection (GS is now widely used in plant breeding projects across the world. Genomic selection is one of the most promising strategies for speeding up the process of breeding for improved traits. There have been many attempts to optimize the training population size, inter-individual relationships, marker type and density, and the incorporation of pedigree information, environmental covariates, and other parameters in order to increase prediction accuracy for complex traits in wheat. Now that we have access to high-throughput, in-depth imaging and phenotyping technologies, we may use this data to increase the reliability of our predictions by factoring in more relevant secondary traits. In this chapter, we present an in-depth look back at how far GS-based breeding approaches have come in the quest to improve wheat
Potential for the Exploitation of Nutritional Traits of Sweet Sorghum (Sorghum bicolor (L.) Moench) in Food Systems
No full textSweet sorghum (Sorghum bicolor (L.) Moench) is a drought-tolerant small-grain cereal which is cultivated largely by smallholder farmers in sub-Saharan Africa. It has potential as a dual-purpose crop. The grain is rich in antioxidants, and the stalks accumulate nutritious juice that can be processed into ethanol or syrup. The sweet sorghum syrup contains lower sucrose and total sugar but greater amounts of organic acids and minerals than sugarcane syrup. The biomass is used for livestock feeds. Currently, there is substantial diversity in the sweet sorghum germplasm collections from various African countries. In the future, there will be merit in enhancing sweet sorghum cultivars, probably through cytoplasmic male sterility systems. Mutation breeding, in conjunction with modern molecular tools, could also be useful in future breeding efforts. Promoting the use of sweet sorghum as an ingredient in the food and pharmaceutical industries can also offer new opportunities in the value chain
CRISPR/Cas9-mediated mutagenesis of phytoene desaturase in pigeonpea and groundnut
No full textThe CRISPR/Cas9 technology, renowned for its ability to induce precise genetic alterations in various crop species, has encountered challenges in its application to grain legume crops such as pigeonpea and groundnut. Despite attempts at gene editing in groundnut, the low rates of transformation and editing have impeded its widespread adoption in producing genetically modified plants. This study seeks to establish an effective CRISPR/Cas9 system in pigeonpea and groundnut through Agrobacterium-mediated transformation, with a focus on targeting the phytoene desaturase (PDS) gene. The PDS gene is pivotal in carotenoid biosynthesis, and its disruption leads to albino phenotypes and dwarfism. Two constructs (one each for pigeonpea and groundnut) were developed for the PDS gene, and transformation was carried out using different explants (leaf petiolar tissue for pigeonpea and cotyledonary nodes for groundnut). By adjusting the composition of the growth media and refining Agrobacterium infection techniques, transformation efficiencies of 15.2% in pigeonpea and 20% in groundnut were achieved. Mutation in PDS resulted in albino phenotype, with editing efficiencies ranging from 4 to 6%. Sequence analysis uncovered a nucleotide deletion (A) in pigeonpea and an A insertion in groundnut, leading to a premature stop codon and, thereby, an albino phenotype. This research offers a significant foundation for the swift assessment and enhancement of CRISPR/Cas9-based genome editing technologies in legume crops