Volatile metabolome and allele-specific expression reveal mechanisms of floral scent inheritance in Prunus mume

Industrial Crops and Products, Journal Year: 2025, Volume and Issue: 226, P. 120690 - 120690

Published: Feb. 18, 2025

Language: Английский

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Heterosis and hybrid breeding

Theoretical and Applied Genetics, Journal Year: 2025, Volume and Issue: 138(4)

Published: March 11, 2025

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Interspecific hybridization in Brassica species leads to changes in agronomic traits through the regulation of gene expression by chromatin accessibility and DNA methylation

GigaScience, Journal Year: 2025, Volume and Issue: 14

Published: Jan. 1, 2025

Abstract Interspecific hybridization is a common method in plant breeding to combine traits from different species, resulting allopolyploidization and significant genetic epigenetic changes. However, our understanding of genome-wide chromatin gene expression dynamics during remains limited. This study generated two Brassica allotriploid hybrids via interspecific hybridization. We observed that accessible regions (ACRs) DNA methylation interact regulates after hybridization, ultimately influencing the agronomic hybrids. In total, 234,649 ACRs were identified parental lines hybrids; process induces changes distribution abundance their regions, particularly proximity. Genes associated with proximal more highly expressed than those distal genic ACRs. More half novel drove transgressive hybrids, upregulated genes showed enrichment metal ion binding, especially magnesium ion, calcium potassium binding. also Bna.bZIP11 single-parent activation ACR, which binds BnaA06.UF3GT promote anthocyanin accumulation F1 plays role repressing expression, unmethylated are transcriptionally active. Additionally, A-subgenome genome dosage rather methylation. The interplay among methylation, transposable elements, sRNA contributes dynamic landscape distinct patterns on genome.

Language: Английский

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

The Crop Journal, Journal Year: 2024, Volume and Issue: 12(2), P. 515 - 528

Published: Feb. 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.

Language: Английский

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Frequent spontaneous structural rearrangements promote rapid genome diversification in a Brassica napus F1 generation

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

Published: Nov. 18, 2022

In a cross between two homozygous Brassica napus plants of synthetic and natural origin, we demonstrate that novel structural genome variants from the parent cause immediate diversification among F1 offspring. Long read sequencing in twelve sister revealed five large-scale rearrangements where both parents carried different alleles but heterozygous genomes were not identical heterozygotes as expected. Such spontaneous part homoeologous exchanges or segmental deletions identified different, individual plants. The caused deletions, gene copy-number variations, diverging methylation patterns other changes large numbers genes may have been causal for unexpected phenotypic variation plants, example strong divergence plant height leaf area. This supports hypothesis de novo after polyploidization can rapidly overcome intense allopolyploidization bottlenecks to re-expand crops genetic diversity ecogeographical expansion human selection. findings imply restructuring allopolyploid interspecific hybridization, common approach breeding, considerably more drastic impact on agricultural ecosystems than extremely precise, biotechnological modifications.

Language: Английский

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Comparative transcriptomic analysis reveals the molecular mechanism underlying seedling heterosis and its relationship with hybrid contemporary seeds DNA methylation in soybean

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: Feb. 19, 2024

Heterosis is widely used in crop production, but phenotypic dominance and its underlying causes soybeans, a significant grain oil crop, remain crucial yet unexplored issue. Here, the phenotypes transcriptome profiles of three inbred lines their resulting F 1 seedlings were analyzed. The results suggest that with superior heterosis leaf size biomass exhibited more extensive recompilation transcriptional network activated greater number genes compared to parental lines. Furthermore, reprogramming observed four hybrid combinations was primarily non-additive, dominant effects being prevalent. Enrichment analysis sets differentially expressed genes, coupled weighted gene co-expression analysis, has shown emergence can be attributed related circadian rhythms, photosynthesis, starch synthesis. In addition, we combined DNA methylation data from previous immature seeds similar patterns between expression. We also found correlations levels region expression levels, as well discovery 12 hub shared or conflicted remodeling patterns. This suggests contemporary have an impact on both seedling phenotype some extent. conclusion, our study provides valuable insights into molecular mechanisms soybean practical implications for selecting varieties.

Language: Английский

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Analysis of gene expression level dominance and homoeologous expression bias in different tissues of a new synthetic amphidiploid, Raphanobrassica (Brassica rapa × Raphanus sativus)

Scientia Horticulturae, Journal Year: 2024, Volume and Issue: 339, P. 113864 - 113864

Published: Dec. 3, 2024

Language: Английский

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Integration of transcriptome and DNA methylome analysis reveals the molecular mechanism of taproot yield heterosis in radish (Raphanus sativus L.)

Horticultural Plant Journal, Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 1, 2023

Heterosis, a crucial biological phenomenon, plays vital role in determining the yield and quality of plants. Radish, an important root vegetable crop, exhibits notable heterosis terms quality. Nevertheless, specific molecular mechanism behind formation radish remains unclear. Herein, transcriptome DNA methylome analyses were performed on F1 hybrids parental lines. Expression level dominance (ELD) genes allele-specific expression (ASEG) together significantly contribute to heterosis, primarily through energy metabolism plant hormone signal transduction pathway. Additionally, increase average methylation was observed compared Interestingly, negative correlation found between differentially expressed (DEGs) gene body regions their levels NAU-LB hybrids. Conversely, contrasting trend NAU-YH Furthermore, when lines treated with 5-azacytidine, more sensitive inhibitors than parents. A significant decrease weight total sugar content control. Immunolocalization results indicated auxin hybrid under 5-azacytidine treatment. Proliferating cell nuclear antigen immunolocalization also revealed inhibition vascular cambium activity both Notably, profiles few methylated DEGs including RsSUS1, RsSUC2a, RsIAA7, RsIAA18, increased parents, suggesting potential for heterosis. Collectively, these findings would provide valuable insight into underlying taproot have facilitate genetic improvement breeding programs.

Language: Английский

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Synergy of gut microbiota and host genome in driving heterosis expression of chickens

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2024, Volume and Issue: 51(10), P. 1121 - 1134

Published: June 29, 2024

Heterosis has been widely utilized in agricultural production. Despite over a century of extensive research, the underlying mechanisms heterosis remain elusive. Most hypotheses and research have focused on genetic basis heterosis. However, potential role gut microbiota largely ignored. Here, we carefully design crossbreeding experiment with two distinct broiler breeds conduct 16S rRNA amplicon transcriptome sequencing to investigate synergistic host genes driving We find that breast muscle weight hybrids exhibits high heterosis, 6.28% higher than mid-parent value. A notable difference is observed composition function cecal between their parents. Over 90% differentially colonized expressed exhibit nonadditive patterns. Integrative analyses uncover associations microbiota, including connection expression cellular signaling pathways metabolism-related abundance Odoribacter, Oscillibacter, Alistipes hybrids. Moreover, abundances these are related better meat yield. In summary, findings highlight importance serving as crucial factors modulate chickens.

Language: Английский

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Transcriptome Shock in Developing Embryos of a Brassica napus and Brassica rapa Hybrid

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(22), P. 16238 - 16238

Published: Nov. 12, 2023

Interspecific crosses that fuse the genomes of two different species may result in overall gene expression changes hybrid progeny, called 'transcriptome shock'. To better understand pattern after genome merging during early stages allopolyploid formation, we performed RNA sequencing analysis on developing embryos Brassica rapa, B. napus, and their synthesized allotriploid hybrids. Here, show transcriptome shock occurs seeds Of homoeologous pairs, 17.1% exhibit bias, with an bias toward rapa. The level dominance also biases mainly induced by change genes from napus. Functional enrichment revealed significant differences differentially expressed (DEGs) related to photosynthesis, hormone synthesis, other pathways. Further study showed levels key transcription factors (TFs) could regulate interaction network embryo, which might be essential cause phenotype change. In conclusion, present results have global patterns between rapa provided novel insights into occurrence for harnessing heterosis.

Language: Английский

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