Omics for the Improvement of Abiotic, Biotic, and Agronomic Traits in Major Cereal Crops: Applications, Challenges, and Prospects

Plants, Journal Year: 2021, Volume and Issue: 10(10), P. 1989 - 1989

Published: Sept. 23, 2021

Omics technologies, namely genomics, transcriptomics, proteomics, metabolomics, and phenomics, are becoming an integral part of virtually every commercial cereal crop breeding program, as they provide substantial dividends per unit time in both pre-breeding phases. Continuous advances omics assure efficiency cost benefits to improve crops. This review provides a comprehensive overview the established methods five major cereals, rice, sorghum, maize, barley, bread wheat. We cover evolution technologies each section independently concentrate on their use economically important agronomic well biotic abiotic stress-related traits. Advancements (1) identification, mapping, sequencing molecular/structural variants; (2) high-density transcriptomics data study gene expression patterns; (3) global targeted proteome profiling protein structure interaction; (4) metabolomic quantify organ-level, small-density metabolites, composition; (5) high-resolution, high-throughput, image-based phenomics approaches surveyed this review.

Language: Английский

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Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding

GigaScience, Journal Year: 2022, Volume and Issue: 11

Published: Jan. 1, 2022

Abstract Background The sequencing of the wheat (Triticum aestivum) genome has been a methodological challenge for many years owing to its large size (15.5 Gb), repeat content, and hexaploidy. Many initiatives aiming at obtaining reference cultivar Chinese Spring have launched in past it was achieved 2018 as result huge effort combine short-read with other resources. Reference-quality assemblies were then produced accessions, but rapid evolution technologies offers opportunities reach high-quality standards lower cost. Results Here, we report on an optimized procedure based long reads Oxford Nanopore Technology PromethION device assemble French bread Renan. Conclusions We provide most contiguous chromosome-scale assembly date. Coupled annotation RNA-sequencing data, this resource will be valuable crop community facilitate selection agronomically important traits. also framework generate complex genomes using ONT.

Language: Английский

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A catalogue of resistance gene homologs and a chromosome‐scale reference sequence support resistance gene mapping in winter wheat

Plant Biotechnology Journal, Journal Year: 2022, Volume and Issue: 20(9), P. 1730 - 1742

Published: May 14, 2022

A resistance gene atlas is an integral component of the breeder's arsenal in fight against evolving pathogens. Thanks to high-throughput sequencing, catalogues genes can be assembled even crop species with large and polyploid genomes. Here, we report on capture sequencing assembly homologs a diversity panel 907 winter wheat genotypes comprising ex situ genebank accessions current elite cultivars. In addition, use accurate long-read chromosome conformation construct chromosome-scale genome sequence cv. Attraktion, variety representative European wheat. We illustrate value our resource for breeders geneticists by (i) comparing complements plant genetic resources varieties (ii) conducting genome-wide associations scans (GWAS) fungal diseases yellow rust leaf using reference-based reference-free GWAS approaches. The content under peaks was scrutinized Attraktion.

Language: Английский

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Era of gapless plant genomes: innovations in sequencing and mapping technologies revolutionize genomics and breeding

Current Opinion in Biotechnology, Journal Year: 2023, Volume and Issue: 79, P. 102886 - 102886

Published: Jan. 13, 2023

Whole-genome sequencing and assembly have revolutionized plant genetics molecular biology over the last two decades. However, significant shortcomings in first- second-generation technology resulted imperfect reference genomes: numerous large gaps of low quality or undeterminable sequence areas highly repetitive DNA along with limited chromosomal phasing restricted ability researchers to characterize regulatory noncoding elements genic regions that underwent recent duplication events. Recently, advances long-read first gapless, telomere-to-telomere (T2T) assemblies genomes. This leap forward has potential increase speed confidence genomics experimentation while reducing costs for research community.

Language: Английский

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Sequencing trait-associated mutations to clone wheat rust-resistance gene YrNAM

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: July 19, 2023

Abstract Stripe (yellow) rust, caused by Puccinia striiformis f. sp. tritici ( Pst ), can significantly affect wheat production. Cloning resistance genes is critical for efficient and effective breeding of stripe rust resistant cultivars. One gene Yr10 CG ) underlying the locus has been cloned. However, following haplotype linkage analyses indicate presence additional gene(s) underlying/near locus. Here, we report cloning YrNAM in this region using method sequencing trait-associated mutations (STAM). encodes a non-canonical protein with NAM domain ZnF-BED domain. We show that both domains are required resistance. Transgenic harboring driven its endogenous promoter confers to races CYR32 CYR33. an ancient present wild species Aegilops longissima Ae. sharonensis ; however, it absent most cultivars, which indicates value.

Language: Английский

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A secreted protease-like protein in Zymoseptoria tritici is responsible for avirulence on Stb9 resistance gene in wheat

PLoS Pathogens, Journal Year: 2023, Volume and Issue: 19(5), P. e1011376 - e1011376

Published: May 12, 2023

Zymoseptoria tritici is the fungal pathogen responsible for Septoria blotch on wheat. Disease outcome in this pathosystem partly determined by isolate-specific resistance, where wheat resistance genes recognize specific factors triggering an immune response. Despite large number of known genes, molecular determinants involved such cultivar-specific remain largely unknown. We identified avirulence factor AvrStb9 using association mapping and functional validation approaches. Pathotyping transgenic strains Stb9 cultivars, near isogenic lines populations, showed that interacts with gene, encodes unusually gene a predicted secretion signal protease domain. It belongs to S41 family conserved across different filamentous fungi Ascomycota class may constitute core effector. also among global Z. population carries multiple amino acid substitutions caused strong positive diversifying selection. These results demonstrate contribution 'atypical' effector protein role sequence diversification escape host recognition, adding our understanding host-pathogen interactions evolutionary processes underlying adaptation.

Language: Английский

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Origin and evolution of the bread wheat D genome

Nature, Journal Year: 2024, Volume and Issue: 633(8031), P. 848 - 855

Published: Aug. 14, 2024

Bread wheat (Triticum aestivum) is a globally dominant crop and major source of calories proteins for the human diet. Compared with its wild ancestors, modern bread shows lower genetic diversity, caused by polyploidisation, domestication breeding bottlenecks

Language: Английский

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Genome-wide atlas of rust resistance loci in wheat

Theoretical and Applied Genetics, Journal Year: 2024, Volume and Issue: 137(8)

Published: July 9, 2024

Rust diseases, including leaf rust, stripe/yellow and stem significantly impact wheat (Triticum aestivum L.) yields, causing substantial economic losses every year. Breeding deployment of cultivars with genetic resistance is the most effective sustainable approach to control these diseases. The toolkit for breeders select rust has rapidly expanded a multitude loci identified using latest advances in genomics, mapping cloning strategies. goal this review was establish genome atlas that provides comprehensive summary reported associated resistance. Our mapped quantitative trait (QTL) characterised genes three rusts from 170 publications over past two decades. A total 920 QTL or were positioned across 21 chromosomes based on reference (IWGSC RefSeq v2.1). Interestingly, 26 genomic regions contained multiple suggesting they could have pleiotropic effects more We discuss range strategies exploit wealth information efficiently utilise sources resistance, stack desirable develop enhanced disease.

Language: Английский

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Chromosome-scale genome assembly of bread wheat’s wild relative Triticum timopheevii

Scientific Data, Journal Year: 2024, Volume and Issue: 11(1)

Published: April 23, 2024

Wheat (Triticum aestivum) is one of the most important food crops with an urgent need for increase in its production to feed growing world. Triticum timopheevii (2n = 4x 28) allotetraploid wheat wild relative species containing A

Language: Английский

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Fhb9, a major QTL for Fusarium head blight resistance improvement in wheat

Journal of Integrative Agriculture, Journal Year: 2024, Volume and Issue: unknown

Published: March 1, 2024

Fusarium head blight (FHB), mainly caused by graminearum, is one of the most devastating diseases wheat worldwide. Identification and validation major quantitative trait loci (QTLs) for FHB resistance without negative effects on agronomic traits critical to success in breeding FHB-resistant cultivars. In this study, a stable QTL chromosome arm 2DL was identified evaluating recombinant inbred line (RIL) population derived from Shi4185×Shijiazhuang 8 both field greenhouse experiments. mapping pedigree analyses indicated that same as QFhb-2DL previously Ji5265, therefore, designated Fhb9. Four kompetitive amplicon sequence polymorphism (KASP) markers were developed based exome capture sequencing data enhance marker density Fhb9 region, it delimited an interval between single nucleotide (SNP) KASP-12056 (533.8) KASP-525 (525.9 Mb) explained 26.0-30.1% phenotypic variation. Analysis geographic distribution allele suggested originated Huang-Huai winter region China, very low frequency modern Chinese cultivars reveals has not been widely deployed programs. Field evaluation yield-related near-isogenic lines (NILs) contrasting alleles did show any adverse those traits. showed additive effect enhancing with Fhb1. Therefore, valuable improving near-diagnostic study will facilitate its deployment

Language: Английский

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