Evolution and origin of bread wheat

The Plant Cell, Journal Year: 2022, Volume and Issue: 34(7), P. 2549 - 2567

Published: May 1, 2022

Bread wheat (Triticum aestivum, genome BBAADD) is a young hexaploid species formed only 8,500-9,000 years ago through hybridization between domesticated free-threshing tetraploid progenitor, BBAA, and Aegilops tauschii, the diploid donor of D subgenome. Very soon after its formation, it spread globally from cradle in fertile crescent into new habitats climates, to become staple food humanity. This extraordinary global expansion was probably enabled by allopolyploidy that accelerated genetic novelty acquisition traits, intergenomic interactions, buffering mutations, attractiveness bread wheat's large, tasty, nutritious grain with high baking quality. New sequences suggest elusive B subgenome distinct (unknown or extinct) rather than mosaic genome. We discuss origin progenitors conflicting archaeological evidence on where which progenitor. Wheat experienced many environmental changes throughout evolution, therefore, while might adapt current climatic changes, efforts are needed better use conserve vast gene pool biodiversity our security depends.

Language: Английский

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Genome sequences of five Sitopsis species of Aegilops and the origin of polyploid wheat B subgenome

Molecular Plant, Journal Year: 2022, Volume and Issue: 15(3), P. 488 - 503

Published: Jan. 1, 2022

Common wheat (Triticum aestivum, BBAADD) is a major staple food crop worldwide. The diploid progenitors of the A and D subgenomes have been unequivocally identified; that B, however, remains ambiguous controversial but suspected to be related species Aegilops, section Sitopsis. Here, we report assembly chromosome-level genome sequences all five Sitopsis species, namely Aegilops bicornis, Ae. longissima, searsii, sharonensis, speltoides, as well partial Amblyopyrum muticum (synonym mutica) for phylogenetic analysis. Our results reveal donor common B subgenome distinct, most probably extinct, diverged from an ancestral progenitor lineage which still extant speltoides Am. belong. In addition, identified interspecific genetic introgressions throughout evolution Triticum/Aegilops complex. various assembled sizes (4.11–5.89 Gb) with high proportions repetitive (85.99%–89.81%); nonetheless, they retain collinearity other genomes or in Differences size were primarily due independent post-speciation amplification transposons. We also set genes pertinent important agronomic traits can harnessed breeding. These newly resources provide new roadmap evolutionary studies complex, improvement.

Language: Английский

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Comparative genomic and transcriptomic analyses uncover the molecular basis of high nitrogen-use efficiency in the wheat cultivar Kenong 9204

Molecular Plant, Journal Year: 2022, Volume and Issue: 15(9), P. 1440 - 1456

Published: July 21, 2022

Language: Английский

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Einkorn genomics sheds light on history of the oldest domesticated wheat

Nature, Journal Year: 2023, Volume and Issue: 620(7975), P. 830 - 838

Published: Aug. 2, 2023

Einkorn (Triticum monococcum) was the first domesticated wheat species, and central to birth of agriculture Neolithic Revolution in Fertile Crescent around 10,000 years ago1,2. Here we generate analyse 5.2-Gb genome assemblies for wild einkorn, including completely assembled centromeres. centromeres are highly dynamic, showing evidence ancient recent centromere shifts caused by structural rearrangements. Whole-genome sequencing analysis a diversity panel uncovered population structure evolutionary history revealing complex patterns hybridizations introgressions after dispersal einkorn from Crescent. We also show that 1% modern bread aestivum) A subgenome originates einkorn. These resources findings highlight evolution provide basis accelerate genomics-assisted improvement wheat.

Language: Английский

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Deciphering recent transposition patterns in plants through comparison of 811 genome assemblies

Plant Biotechnology Journal, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 10, 2025

Summary Transposable elements (TEs) are significant drivers of genome evolution, yet their recent dynamics and impacts within among species, as well the roles host genes non‐coding RNAs in transposition process, remain elusive. With advancements large‐scale pan‐genome sequencing development open data sharing, comparative genomics studies have become feasible. Here, we performed complete de novo TE annotations identified active TEs 310 plant assemblies across 119 species seven crop populations. Using 811 high‐quality genomes, detected 13 844 553 TE‐induced structural variants (TE‐SVs), providing unprecedented resolution delineating activities. Our integrative analysis revealed a mutual evolutionary relationship between genomes. On one hand, ncRNAs involved evidenced by colocalization coactivation with TEs, may play role chromatin regulation. other drive genetic innovation promoting duplication inserting into regulatory regions. Moreover, influenced linked to growth, nutrient absorption, storage metabolism environmental adaptation, aiding domestication adaptation. This atlas not only reveals functional features activity but also highlights paving way for future exploration TE‐mediated evolution improvement strategies.

Language: Английский

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TIR-Learner, a New Ensemble Method for TIR Transposable Element Annotation, Provides Evidence for Abundant New Transposable Elements in the Maize Genome

Molecular Plant, Journal Year: 2019, Volume and Issue: 12(3), P. 447 - 460

Published: Feb. 23, 2019

Language: Английский

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Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning

International Journal of Molecular Sciences, Journal Year: 2019, Volume and Issue: 20(15), P. 3837 - 3837

Published: Aug. 6, 2019

Transposable elements (TEs) are genomic units able to move within the genome of virtually all organisms. Due their natural repetitive numbers and high structural diversity, identification classification TEs remain a challenge in sequenced genomes. Although were initially regarded as “junk DNA”, it has been demonstrated that they play key roles chromosome structures, gene expression, regulation, well adaptation evolution. A highly reliable annotation these is, therefore, crucial better understand functions To date, much bioinformatics software developed address TE detection processes, but many problematic aspects remain, such reliability, precision, speed analyses. Machine learning deep algorithms can make automatic predictions decisions wide variety scientific applications. They have tested and, more specifically for TEs, with encouraging results. In this review, we will discuss important structure, importance evolution architecture host, current classifications nomenclatures. We also methods limitations identifying classifying TEs.

Language: Английский

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A haplotype-led approach to increase the precision of wheat breeding

Communications Biology, Journal Year: 2020, Volume and Issue: 3(1)

Published: Nov. 25, 2020

Abstract Crop productivity must increase at unprecedented rates to meet the needs of growing worldwide population. Exploiting natural variation for genetic improvement crops plays a central role in increasing productivity. Although current genomic technologies can be used high-throughput identification variation, methods efficiently exploiting this potential targeted, systematic manner are lacking. Here, we developed haplotype-based approach identify diversity crop using genome assemblies from 15 bread wheat ( Triticum aestivum ) cultivars. We stringent criteria identical-by-state haplotypes and distinguish these near-identical sequences (~99.95% identity). showed that each cultivar shares ~59 % its with other sequenced cultivars detected presence extended haplotype blocks containing hundreds thousands genes across all chromosomes. found genic sequence alone was insufficient fully differentiate between haplotypes, as were commonly array-based genotyping chips due their gene centric design. successfully focused discovery novel landrace collection documented trait modern wheat. This study provides framework defining efficiency precision breeding towards optimising agronomic performance crucial crop.

Language: Английский

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Non-coding RNAs and transposable elements in plant genomes: emergence, regulatory mechanisms and roles in plant development and stress responses

Planta, Journal Year: 2019, Volume and Issue: 250(1), P. 23 - 40

Published: April 16, 2019

Language: Английский

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Genome-wide association study revealed that the TaGW8 gene was associated with kernel size in Chinese bread wheat

Scientific Reports, Journal Year: 2019, Volume and Issue: 9(1)

Published: Feb. 25, 2019

Using Wheat 90 K SNP assay, kernel-related traits of Chinese bread wheat were used to perform association mapping in 14 environments by GWAS. Results indicated that 996 and 953 4417 3172 significant SNPs for kernel length thousand-kernel weight located on the chromosome 7B. Haplotype analysis these 7B generated block containing predicted TaGW8-B1 gene. gene was further cloned sequencing a 276-bp InDel found first intron. without with designated as TaGW8-B1a TaGW8-B1b, respectively. Analysis agronomic cultivars possessed significantly wider width, more number per spike, longer length, higher spikelet spike than TaGW8-B1b. Furthermore, yield Therefore, considered potentially superior allele. Meanwhile, expression level TaGW8-B1b mature seeds qRT-PCR. It possibly suggested high positively associated size wheat. Distribution allele has been selected

Language: Английский

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