Deciphering the Transcriptional Regulatory Network Governing Starch and Storage Protein Biosynthesis in Wheat for Breeding Improvement

Advanced Science, Journal Year: 2024, Volume and Issue: 11(33)

Published: June 28, 2024

Starch and seed storage protein (SSP) composition profoundly impact wheat grain yield quality. To unveil regulatory mechanisms governing their biosynthesis, transcriptome, epigenome profiling is conducted across key endosperm developmental stages, revealing that chromatin accessibility, H3K27ac, H3K27me3 collectively regulate SSP starch genes with varying impact. Population transcriptome phenotype analyses highlight accessible promoter regions' crucial role as a genetic variation resource, influencing quality in core collection of accessions. Integration time-serial RNA-seq ATAC-seq enables the construction hierarchical transcriptional network identifying 42 high-confidence novel candidates. These candidates exhibit overlap regions associated size traits, functional significance validated through expression-phenotype association analysis among accessions loss-of-function mutants. Functional abscisic acid insensitive 3-A1 (TaABI3-A1) genome editing knock-out lines demonstrates its promoting accumulation while repressing biosynthesis regulation. Excellent TaABI3-A1

Language: Английский

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Efficient identification of QTL for agronomic traits in foxtail millet (Setaria italica) using RTM- and MLM-GWAS

Theoretical and Applied Genetics, Journal Year: 2024, Volume and Issue: 137(1)

Published: Jan. 1, 2024

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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Genetic dissection of grain iron and zinc, and thousand kernel weight in wheat (Triticum aestivum L.) using genome-wide association study

Scientific Reports, Journal Year: 2022, Volume and Issue: 12(1)

Published: July 20, 2022

Abstract Genetic biofortification is recognized as a cost-effective and sustainable strategy to reduce micronutrient malnutrition. Genomic regions governing grain iron concentration (GFeC), zinc (GZnC), thousand kernel weight (TKW) were investigated in set of 280 diverse bread wheat genotypes. The genome-wide association (GWAS) panel was genotyped using 35 K Axiom Array phenotyped five environments. GWAS analysis showed total 17 Bonferroni-corrected marker-trait associations (MTAs) nine chromosomes representing all the three subgenomes. TKW highest MTAs (7), followed by GZnC (5) GFeC (5). Furthermore, 14 identified with more than 10% phenotypic variation. One stable MTA i.e. AX-95025823 for both E4 E5 environments along pooled data, which located at 68.9 Mb on 6A chromosome. In silico revealed that SNPs important putative candidate genes such Multi antimicrobial extrusion protein, F-box domain, Late embryogenesis abundant LEA-18, Leucine-rich repeat domain superfamily, C3H4 type finger involved translocation, homeostasis, size modifications. novel will be validated estimate their effects different genetic backgrounds subsequent use marker-assisted selection. valuable rapid development biofortified varieties ameliorate malnutrition problems.

Language: Английский

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Genome-wide association study for grain yield and component traits in bread wheat (Triticum aestivum L.)

Frontiers in Genetics, Journal Year: 2022, Volume and Issue: 13

Published: Aug. 26, 2022

Genomic regions governing days to heading (DH), grain filling duration (GFD), number per spike (GNPS), weight (GWPS), plant height (PH), and yield (GY) were investigated in a set of 280 diverse bread wheat genotypes. The genome-wide association studies (GWAS) panel was genotyped using 35K Axiom Array phenotyped five environments. GWAS analysis showed total 27 Bonferroni-corrected marker-trait associations (MTAs) on 15 chromosomes representing all three subgenomes. GFD the highest MTAs (8), followed by GWPS (7), GY (4), GNPS (3), PH DH (2). Furthermore, 20 identified with more than 10% phenotypic variation. A stable (

Language: Английский

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High Resolution Genome Wide Association Studies Reveal Rich Genetic Architectures of Grain Zinc and Iron in Common Wheat (Triticum aestivum L.)

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: March 16, 2022

Biofortification is a sustainable strategy to alleviate micronutrient deficiency in humans. It necessary improve grain zinc (GZnC) and iron concentrations (GFeC) wheat based on genetic knowledge. However, the precise dissection of architecture underlying GZnC GFeC remains challenging. In this study, high-resolution genome-wide association studies were conducted for by three different models using 166 cultivars 373,106 polymorphic markers from 660K 90K single nucleotide polymorphism (SNP) arrays. Totally, 25 16 stable loci detected GFeC, respectively. Among them, 17 8 are likely be new quantitative trait locus/loci (QTL). Based gene annotations expression profiles, 28 promising candidate genes identified Zn/Fe uptake (8), transport (11), storage (3), regulations (6). Of 11 putative orthologs known Arabidopsis rice related homeostasis. A brief model, such as homeostasis root uptake, xylem final seed was proposed wheat. Kompetitive allele-specific PCR (KASP) successfully developed two major QTL chromosome arms 3AL 7AL, respectively, which independent thousand kernel weight plant height. The further validated bi-parental population under multi-environments. multidrug toxic compound extrusion (MATE) transporter TraesCS3A01G499300, ortholog OsPEZ2, potential gene. This study has advanced our knowledge basis provides valuable biofortification.

Language: Английский

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Genome-wide association mapping for component traits of drought and heat tolerance in wheat

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: Aug. 16, 2022

Identification of marker trait association is a prerequisite for marker-assisted breeding. To find markers linked with traits under heat and drought stress in bread wheat (Triticum aestivum L.), we performed genome-wide study (GWAS). GWAS mapping panel used this consists advanced breeding lines from the IARI programme produced by pairwise complex crosses. Phenotyping was done at multi locations namely New Delhi, Karnal, Indore, Jharkhand Pune augmented-RCBD design different moisture regimes, timely sown irrigated (IR), restricted (RI) late (LS) conditions. Yield its component traits, viz., Days to Heading (DH), Maturity (DM), Normalized Difference Vegetation Index (NDVI), Chlorophyll Content (SPAD), Canopy temperature (CT), Plant Height (PH), Thousand grain weight (TGW), Grain per spike (GWPS), Plot (PLTY) Biomass (BMS) were phenotyped. Analysis variance descriptive statistics revealed significant differences among studied traits. Genotyping using 35k SNP Wheat Breeder's Array. Population structure diversity analysis filtered 10,546 two subpopulations sufficient diversity. A large whole genome LD block size 7.15 MB obtained half decay value. Genome-wide search identified 57 unique associated various across locations. Twenty-three be stable, them nine pleiotropic also identified. In silico against IWGSC ref presence majority SNPs or near gene coding region. These can transfer genes/QTLs after validation develop climate-resilient cultivars.

Language: Английский

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Deciphering spike architecture formation towards yield improvement in wheat

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2023, Volume and Issue: 50(11), P. 835 - 845

Published: March 11, 2023

Wheat is the most widely grown crop globally, providing 20% of daily consumed calories and protein content around world. With growing global population frequent occurrence extreme weather caused by climate change, ensuring adequate wheat production essential for food security. The architecture inflorescence plays a crucial role in determining grain number size, which key trait improving yield. Recent advances genomics gene cloning techniques have improved our understanding spike development its applications breeding practices. Here, we summarize genetic regulation network governing formation, strategies used identifying studying factors affecting architecture, progress made applications. Additionally, highlight future directions that will aid regulatory mechanistic study determination targeted yield improvement.

Language: Английский

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Variations in phenological, physiological, plant architectural and yield-related traits, their associations with grain yield and genetic basis

Annals of Botany, Journal Year: 2023, Volume and Issue: 131(3), P. 503 - 519

Published: Jan. 19, 2023

Abstract Background and Aims Physiological morphological traits play essential roles in wheat (Triticum aestivum) growth development. In particular, photosynthesis is a limitation to yield. Increasing has been identified as an important strategy increase However, the genotypic variations genomic regions governing morphological, architectural remain unexplored. Methods Here, we conducted large-scale investigation of phenological, physiological, plant yield-related traits, involving 32 for 166 lines during 2018–2020 four environments, performed genome-wide association study with 90K 660K single nucleotide polymorphism (SNP) arrays. Key Results These exhibited considerable diversity panel. Higher yield was associated higher net photosynthetic rate (r = 0.41, P < 0.01), thousand-grain weight 0.36, 0.01) truncated lanceolate shape, but shorter height −0.63, flag leaf angle −0.49, spike number per square metre −0.22, 0.01). Genome-wide mapping discovered 1236 significant stable loci detected environments among using SNP markers. Trait values have cumulative effect favourable alleles increases, progress made determining phenotypic over years. Eleven elite cultivars 14 grain plot (GY) were potential parental target develop high-yielding cultivars. Conclusions This provides new insights into genetic elucidation physiological their associations GY, paving way discovering underlying gene control developing enhanced ideotypes breeding.

Language: Английский

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A high-resolution genotype–phenotype map identifies the TaSPL17 controlling grain number and size in wheat

Genome biology, Journal Year: 2023, Volume and Issue: 24(1)

Published: Aug. 28, 2023

Large-scale genotype-phenotype association studies of crop germplasm are important for identifying alleles associated with favorable traits. The limited number single-nucleotide polymorphisms (SNPs) in most wheat genome-wide (GWASs) restricts their power to detect marker-trait associations. Additionally, only a few genes regulating grain per spikelet have been reported due sensitivity this trait variable environments.We perform large-scale GWAS using approximately 40 million filtered SNPs 27 spike morphology We 132,086 significant associations and the SNP markers located within 590 peaks. additional stronger peaks by dividing into sub-traits relative results propose that genetic dissection is powerful strategy signals yield traits wheat. reveal TaSPL17 positively controls size floret meristem development, which turn leads enhanced plant. haplotypes at indicate geographical differentiation, domestication effects, breeding selection.Our study provides valuable resources improvement fast-forward solution candidate gene detection cloning

Language: Английский

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