Advancements and Prospects of Genome-Wide Association Studies (GWAS) in Maize

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(3), P. 1918 - 1918

Published: Feb. 5, 2024

Genome-wide association studies (GWAS) have emerged as a powerful tool for unraveling intricate genotype-phenotype across various species. Maize (

Language: Английский

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Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value

Frontiers in Plant Science, Journal Year: 2021, Volume and Issue: 12

Published: Dec. 1, 2021

Novel crop improvement approaches, including those that facilitate for the exploitation of wild relatives and underutilized species harboring much-needed natural allelic variation are indispensable if we to develop climate-smart crops with enhanced abiotic biotic stress tolerance, higher nutritive value, superior traits agronomic importance. Top among these approaches “omics” technologies, genomics, transcriptomics, proteomics, metabolomics, phenomics, their integration, whose deployment has been vital in revealing several key genes, proteins metabolic pathways underlying numerous importance, aiding marker-assisted breeding major species. Here, citing relevant examples, appraise our understanding on recent developments omics technologies how they driving quest breed climate resilient crops. Large-scale genome resequencing, pan-genomes genome-wide association studies identification analysis species-level variations, whilst RNA-sequencing driven transcriptomics provided unprecedented opportunities conducting response studies. Meanwhile, single cell is slowly becoming an tool decoding cell-specific responses, although technical experimental design challenges still need be resolved. Additionally, refinement conventional techniques advent modern, high-resolution proteomics necessitated a gradual shift from general descriptive plant protein abundances large scale protein-metabolite interactions. Especially, metabolomics currently receiving special attention, owing role metabolites play as intermediates close links phenotypic expression. Further, high throughput phenomics applications targeting new research domains such root system architecture analysis, exploration root-associated microbes improved health resilience. Overall, coupling multi-omics modern genetic engineering methods ensures all-encompassing approach developing nutritionally-rich productivity can sustainably sufficiently meet current future food, nutrition energy demands.

Language: Английский

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Full-length transcriptome and RNA-Seq analyses reveal the resistance mechanism of sesame in response to Corynespora cassiicola

BMC Plant Biology, Journal Year: 2024, Volume and Issue: 24(1)

Published: Jan. 23, 2024

Abstract Background Corynespora leaf spot is a common disease occurring in sesame, and the causes yellowing even shedding, which affects growth quality of sesame. At present, mechanism sesame resistance to this still unclear. Understanding highly important for control infection. In study, leaves resistant variety (R) susceptible (S) were collected at 0–48 hpi transcriptome sequencing, used combined third-generation long-read next-generation short-read technology approach identify some key genes main pathways related resistance. Results The gene expression levels two varieties significantly different 0, 6, 12, 24, 36 48 hpi, indicating that up-regulation differentially expressed R might enhanced Moreover, with phenotypic observations inoculated time points, we found 12 was point leading difference between molecular level. WGCNA identified modules associated resistance, screened out 10 but low S, belonged transcription factors (WRKY, AP2/ERF-ERF, NAC types) protein kinases (RLK-Pelle_DLSV, RLK-Pelle_SD-2b, RLK-Pelle_WAK types). These could be response infection by cassiicola . GO KEGG enrichment analysis showed specific enriched, manifested as biologically pathways, such plant signalling hormone transduction, plant-pathogen interaction, carbon metabolism, phenylpropanoid biosynthesis, glutathione MAPK other stress-related pathways. Conclusions This study provides an resource contributing will deepen our understanding regulation paving way further breeding

Language: Английский

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Multi-locus genome-wide association studies reveal genomic regions and putative candidate genes associated with leaf spot diseases in African groundnut (Arachis hypogaea L.) germplasm

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 13

Published: Jan. 5, 2023

Early leaf spot (ELS) and late (LLS) diseases are the two most destructive groundnut in Ghana resulting ≤ 70% yield losses which is controlled largely by chemical method. To develop resistant varieties, present study was undertaken to identify single nucleotide polymorphism (SNP) markers putative candidate genes underlying both ELS LLS. In this study, six multi-locus models of genome-wide association were conducted with best linear unbiased predictor obtained from 294 African germplasm screened for LLS as well image-based indices severity 2020 2021 8,772 high-quality SNPs a 48 K SNP array Axiom platform. Ninety-seven associated ELS, five across chromosomes 2 sub-genomes. From these, twenty-nine unique detected at least one or more traits 16 explained phenotypic variation ranging 0.01 - 62.76%, exception chromosome (Chr) 08 (Chr08), Chr10, Chr11, Chr19. Seventeen potential predicted ± 300 kbp stable/prominent positions (12 5, down- upstream, respectively). The results provide basis understanding genetic architecture germplasm, would be valuable breeding varieties upon further validation.

Language: Английский

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Current Progress, Applications and Challenges of Multi-Omics Approaches in Sesame Genetic Improvement

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(4), P. 3105 - 3105

Published: Feb. 4, 2023

Sesame is one of the important traditional oil crops in world, and has high economic nutritional value. Recently, due to novel throughput sequencing techniques bioinformatical methods, study genomics, methylomics, transcriptomics, proteomics metabonomics sesame developed rapidly. Thus far, genomes five accessions have been released, including white black seed sesame. The genome studies reveal function structure genome, facilitate exploitation molecular markers, construction genetic maps pan-genomes. Methylomics focus on level changes under different environmental conditions. Transcriptomics provide a powerful tool abiotic/biotic stress, organ development, noncoding RNAs, also some support studying abiotic stress traits. In addition, opportunities challenges multi-omics genetics breeding were described. This review summarizes current research status from perspectives hopes help for further in-depth

Language: Английский

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Mining NCBI Sequence Read Archive Database: An Untapped Source of Organelle Genomes for Taxonomic and Comparative Genomics Research

Diversity, Journal Year: 2024, Volume and Issue: 16(2), P. 104 - 104

Published: Feb. 6, 2024

The NCBI SRA database is constantly expanding due to the large amount of genomic and transcriptomic data from various organisms generated by next-generation sequencing, re-searchers worldwide regularly deposit new into database. This high-coverage information can be re-evaluated regardless original research subject. database-deposited NGS offer valuable insights genomes organelles, particularly for non-model organisms. Here, we developed an automated bioinformatics workflow called “OrgaMiner”, designed unveil high-quality mitochondrial chloroplast mining OrgaMiner, a Python-based pipeline, automatically orchestrates tools extract, assemble, annotate organelle without available genome sequences but with in SRA. To test usability feasibility “mollusca” was selected as keyword, 76 were de novo assembled annotated writing one single code. applicability pipeline expanded identify organelles diverse invertebrate, vertebrate, plant species simply specifying taxonomic name. OrgaMiner provides easy-to-use, end-to-end solution biologists mainly working taxonomy population genetics.

Language: Английский

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Examining Chlorophyll Extraction Methods in Sesame Genotypes: Uncovering Leaf Coloration Effects and Anatomy Variations

Plants, Journal Year: 2024, Volume and Issue: 13(12), P. 1589 - 1589

Published: June 7, 2024

This study focuses on optimizing chlorophyll extraction techniques, in which leaf discs are cut from places the blade to enhance concentration sesame (Sesamum indicum L.) leaves. Thirty genotypes, categorized into light green (LG), middle (MG), and deep (DG) pigment groups based coloration, were selected a larger pool of field-grown accessions. The investigation involved determining optimal Soil Plant Analysis Development (SPAD) value index measurements, quantifying concentrations, exploring solvents, selecting suitable disk positions. Significant variations content observed across greenness categories, categorization genotypes DG, MG, LG revealed correlation between appearance content. highlighted consistent relationship carotenoids chlorophyll, indicating their role adaptation warm environments. An examination positions significant gradient along blade, emphasizing need for standardized protocols. Chlorophyll experiments identified DMSO 96% ethanol, particularly those incubated 10 min at 85 °C, as effective choices. recommendation considers factors like cost-effectiveness, time efficiency, safety, environmental regulations, ensuring simplified processes. For higher extraction, focusing tips 75% localization is suggested, this consistently yields increased Furthermore, our anatomical internal structure mesophyll tissue leaves plants, primarily linked chloroplast density pigment-producing structures. Our findings, therefore, provide insightful knowledge gradients encourage use protocols that enable researchers refine experimental designs precise comparable measurements. recommended solvent choices ensure reliable outcomes plant physiology, ecology, studies.

Language: Английский

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Insights into the Drought Stress Tolerance Mechanisms of Sesame: The Queen of Oilseeds

Journal of Plant Growth Regulation, Journal Year: 2024, Volume and Issue: 43(10), P. 3370 - 3391

Published: May 20, 2024

Language: Английский

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Genome-wide association analysis uncovers the genetic architecture of tradeoff between flowering date and yield components in sesame

BMC Plant Biology, Journal Year: 2021, Volume and Issue: 21(1)

Published: Nov. 22, 2021

Unrevealing the genetic makeup of crop morpho-agronomic traits is essential for improving yield quality and sustainability. Sesame (Sesamum indicum L.) one oldest oil-crops in world. Despite its economic agricultural importance, it an 'orphan crop-plant' that has undergone limited modern selection, and, as a consequence preserved wide diversity. Here we established new sesame panel (SCHUJI) contains 184 genotypes representing phenotypic variation geographically distributed. We harnessed natural this to perform genome-wide association studies under Mediterranean climate conditions.Field-based phenotyping SCHUJI across two seasons exposed all traits. Using 20,294 single-nucleotide polymorphism markers, detected 50 genomic signals associated with these Major region on LG2 was flowering date yield-related traits, exemplified key role productivity.Our results shed light architecture interaction components may serve basis future breeding programs basin.

Language: Английский

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Genome-wide association analysis and transcriptome reveal novel loci and a candidate regulatory gene of fatty acid biosynthesis in sesame (Sesamum indicum L.)

Plant Physiology and Biochemistry, Journal Year: 2022, Volume and Issue: 186, P. 220 - 231

Published: July 21, 2022

Language: Английский

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