Rapid formation of stable autotetraploid rice from genome-doubled F1 hybrids of japonica–indica subspecies

Nature Plants, Год журнала: 2025, Номер unknown

Опубликована: Март 31, 2025

Theory predicts that in the absence of selection, a newly formed segmental allopolyploid will become 'autopolyploidized' if homoeologous exchanges (HEs) occur freely. Moreover, because selection against meiotic abnormalities is expected to be strong initial generations, we anticipate HEs uncommon evolved allopolyploids. Here analysed whole-genome composition 202 phenotypically homogeneous and stable rice tetraploid recombinant inbred lines (TRILs) derived from Oryza sativa subsp. japonica indica hybridization/whole-genome doubling. We measured functional traits related growth, development reproductive fitness, chromosomal behaviour TRILs. uncover factors constrain genomic TRILs, including asymmetric parental contribution exclusive uniparental segment retention. Intriguingly, some TRILs have high fertility abiotic stress resilience co-occur with largely stabilized meiosis. Our findings comprise evidence supporting evolutionary possibility HE-catalysed 'allo-to-auto' polyploidy transitions nature, implications for creating new polyploid crops. This study details process duplicated (homoeologous) chromosome 'scrambling' polyploids, indicating natural 'allo-to-autopolyploid' evolution, crop breeding.

Язык: Английский

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Production, characterization, and potential utility of a newly synthesized allohexaploid wheat Triticum kiharae

The Crop Journal, Год журнала: 2025, Номер unknown

Опубликована: Апрель 1, 2025

Язык: Английский

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Chromosome translocation affects multiple phenotypes, causes genome‐wide dysregulation of gene expression, and remodels metabolome in hexaploid wheat

The Plant Journal, Год журнала: 2023, Номер 115(6), С. 1564 - 1582

Опубликована: Июнь 2, 2023

SUMMARY Chromosomal rearrangements (CRs) may occur in newly formed polyploids due to compromised meiotic fidelity. Moreover, CRs can be more readily tolerated allowing their longer‐term retention and hence potential spreading/fixation within a lineage. The direct functional consequences of plant remain unexplored. Here, we identified heterozygous individual from synthetic allohexaploid wheat which the terminal parts long‐arms chromosomes 2D (approximately 193 Mb) 4A 167 were reciprocally translocated. Five homogeneous translocation lines including both unbalanced balanced types developed by selfing fertilization founder mutant (RT [2DL; 4AL]‐ter/1, reciprocal translocation). We investigated impacts these translocations on phenotype, genome‐wide gene expression metabolome. find that, compared with sibling wild‐type, form induced substantial changes primarily via trans ‐regulation nascent allopolyploid wheat. also manifested clear phenotypic metabolic consequences. In particular, genetically balanced, stable showed immediate enhanced reproductive fitness relative wild type. Our results underscore profound impact allopolyploids wide‐ranging consequences, suggesting are an important source genetic variation that exploited for crop breeding.

Язык: Английский

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Dosage-sensitivity shapes how genes transcriptionally respond to allopolyploidy and homoeologous exchange in resynthesized Brassica napus

Genetics, Год журнала: 2023, Номер 225(1)

Опубликована: Июнь 20, 2023

The gene balance hypothesis proposes that selection acts on the dosage (i.e. copy number) of genes within dosage-sensitive portions networks, pathways, and protein complexes to maintain balanced stoichiometry interacting proteins, because perturbations stoichiometric can result in reduced fitness. This has been called selection. Dosage is also hypothesized constrain expression responses changes, making (those encoding members proteins) experience more similar changes. In allopolyploids, where whole-genome duplication involves hybridization diverged lineages, organisms often homoeologous exchanges recombine, duplicate, delete regions genome alter pairs. Although makes predictions about response exchanges, they have not empirically tested. We used genomic transcriptomic data from 6 resynthesized, isogenic Brassica napus lines over 10 generations identify analyzed responses, tested for patterns imbalance. Groups had less variable than dosage-insensitive genes, a sign their relative constrained. difference was absent pairs whose biased toward B. A subgenome. Finally, duplication, suggesting create These findings expand our knowledge impact evolution potentially connect polyploid genomes time, homoeolog bias duplicate retention.

Язык: Английский

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Subgenomic Stability of Progenitor Genomes During Repeated Allotetraploid Origins of the Same Grass Brachypodium hybridum

Molecular Biology and Evolution, Год журнала: 2023, Номер 40(12)

Опубликована: Ноя. 24, 2023

Both homeologous exchanges and expression bias are generally found in most allopolyploid species. Whether differ between repeated speciation events from the same progenitor species remains unknown. Here, we detected a third independent recent allotetraploid origin for model grass Brachypodium hybridum. Our exchange with replacement analyses indicated absence of significant any three types wild allotetraploids, supporting integrity their subgenomes immediate creation amphidiploids. Further tests did not uncover subgenomic dominance different tissues conditions allotetraploids. This suggests balanced homeologs under similar or dissimilar ecological natural habitats. We observed that density transposons around genes was associated initial establishment subgenome dominance; rather, this feature is inherited genome. drought response were highly induced two subgenomes, likely contributing to local adaptation arid habitats event. These findings provide evidence consistency stability parental genomes across multiple allopolyploidization led at periods. study emphasizes importance selecting closely related accurately assess allopolyploids, thereby avoiding detection false when using less genomes.

Язык: Английский

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The occurrence, inheritance, and segregation of complex genomic structural variation in synthetic Brassica napus

The Crop Journal, Год журнала: 2024, Номер 12(2), С. 515 - 528

Опубликована: Фев. 7, 2024

"Synthetic" allopolyploids recreated by interspecific hybridization play an important role in providing novel genomic variation for crop improvement. Such synthetic often undergo rapid structural (SV). However, how such SV arises, is inherited and fixed, it affects traits, has rarely been comprehensively quantitively studied advanced generation lines. A better understanding of these processes will aid breeders knowing to best utilize breeding programs. Here, we analyzed three genetic mapping populations (735 DH lines) derived from crosses between conventional Brassica napus (rapeseed) lines, using whole-genome sequencing determine genome composition. We observed high tolerance large variants, particularly toward the telomeres, preferential selection balanced homoeologous exchanges (duplication/deletion events C genomes resulting retention gene/chromosome dosage chromosome pairs), including stable involving whole chromosomes ("pseudoeuploidy"). Given experimental design (all shared a common parent), were able observe that parental was regularly inherited, showed hitchhiking effects on segregation, one major factors inducing adjacent larger SV. Surprisingly, occurred at low frequencies with no significant impacts fertility yield-related traits incorporating genome-wide linkage explained significantly more variance traits. Our results provide framework detecting occurrence inheritance programs, support use parents as source trait variation.

Язык: Английский

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Hijacking a rapid and scalable metagenomic method reveals subgenome dynamics and evolution in polyploid plants

Applications in Plant Sciences, Год журнала: 2024, Номер 12(4)

Опубликована: Апрель 29, 2024

Abstract Premise The genomes of polyploid plants archive the evolutionary events leading to their present forms. However, plant numerous hurdles genome comparison algorithms for classification types and exploring dynamics. Methods Here, problem intra‐ inter‐genome examining is reframed as a metagenomic problem, enabling use rapid scalable MinHashing approach. To determine how polyploidy are described by this approach, were examined from across spectrum both k ‐mer composition frequency with range sizes. In no subgenome‐specific ‐mers identified; rather, whole‐chromosome subspaces utilized. Results Given chromosome‐scale assemblies sufficient repetitive element content, literature‐verified subgenomic genomic relationships revealed, including distinguishing auto‐ allopolyploidy putative progenitor assignment. sequences responsible rapidly evolving landscape transposable elements. An investigation into parameters revealed that downsampled space (genomic signatures) produced excellent approximations sequence similarity. Furthermore, clustering approach used signatures scrutinized ensure applicability metagenomics‐based method. Discussion easily implementable highly computationally efficient MinHashing‐based strategy enables comparative subgenomics genomics large complex genomes. Such comparisons provide evidence polyploidy‐type assignments. cases where repeat signal may not be adequate given chromosomes' global profile, alternative methods more specific but outperform

Язык: Английский

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Genome‐wide patterns of homoeologous gene flow in allotetraploid coffee

Applications in Plant Sciences, Год журнала: 2024, Номер 12(4)

Опубликована: Июнь 14, 2024

Allopolyploidy-a hybridization-induced whole-genome duplication event-has been a major driver of plant diversification. The extent to which chromosomes pair with their proper homolog vs. homoeolog in allopolyploids varies across taxa, and methods detect homoeologous gene flow (HGF) are needed understand how HGF has shaped polyploid lineages.

Язык: Английский

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Homoeologs in Allopolyploids: Navigating Redundancy as Both an Evolutionary Opportunity and a Technical Challenge - A Transcriptomics Perspective

Опубликована: Июль 4, 2024

Allopolyploidy in plants involves the merging of two or more distinct parental genomes into a single nucleus, significant evolutionary process plant kingdom. Transcriptomic analysis provides valuable insights fate duplicated genes, novelties, and environmental adaptations exhibited by allopolyploid plants. However, transcriptome profiling is challenging due to genomic redundancy, which further complicated presence multiple chromosomes sets variations among homoeologs allelic genes. Prior analysis, sub-genome phasing homoeology inference are essential for obtaining comprehensive view gene expression. This review aims clarify terminology this field, identify most aspects explain their inherent difficulties, suggest reliable analytic strategies. Furthermore, bulk RNA-seq highlighted as primary method studying expression, with an emphasis on critical steps read mapping normalization differential expression analysis.

Язык: Английский

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Subgenome phasing for complex allopolyploidy: case-based benchmarking and recommendations

Briefings in Bioinformatics, Год журнала: 2023, Номер 25(1)

Опубликована: Ноя. 22, 2023

Abstract Accurate subgenome phasing is crucial for understanding the origin, evolution and adaptive potential of polyploid genomes. SubPhaser WGDI software are two common methodologies in allopolyploids, particularly scenarios lacking known diploid progenitors. Triggered by a recent debate over subgenomic origins cultivated octoploid strawberry, we examined four well-documented complex allopolyploidy cases as benchmarks, to evaluate compare accuracy software. Our analysis demonstrates that structure phased both line with prior research, effectively tracing allopolyploid evolutionary trajectories despite limitations each Furthermore, using these validated methodologies, revisited controversial issue regarding progenitors strawberry. The results reaffirm Fragaria vesca iinumae Finally, propose recommendations enhancing future studies, recognizing integrated tools advanced research offering new roadmap robust subgenome-based phylogenetic analysis.

Язык: Английский

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