ArticleHeredity2013
Homoeolog expression bias and expression level dominance in allopolyploid cotton.
Article in Heredity, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 221 papers.
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Who cites it
221 citing papers in PubMed, 493 citations in OpenAlex.
- Comparative genomic characterization and germination-associated expression of DET2 and CER10 related reductases in Chenopodium quinoa.Protoplasma · 2026Article
- Day-neutral flowering candidate genes identified by selection mapping in an upland cotton (Gossypium hirsutum L.) RIL population.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Regulatory divergence of homoeologs underlies network optimization for fiber improvement in domesticated cotton.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Phased T2T genome of a tetraploid grapevine reveals segmental allopolyploid origin and allele-specific alternative splicing during fruit development.Plant physiology · 2026Article
- Harnessing polyploidy for climate-resilient crops: Lessons from the evolutionary model, allotetraploid cotton.Proceedings of the National Academy of Sciences of the United States of America · 2026Review
- The evolution of gene expression in allopolyploid cotton relative to parental diploids and induced haploids.aBIOTECH · 2026Article
- Layer-specific genetic variation unlocks secondary metabolite diversity in long-lived clonal peppermint.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Ancient Whole-Genome Duplication and Lineage-Specific Retention Shape the Diversification of bZIP Transcription Factors in Pooideae.Plants (Basel, Switzerland) · 2026Article
- A natural variation within duplicated AsWRKY49-D2 drives the subgenomic functional divergence of homeologs in salt response of allohexaploid oats.Journal of integrative plant biology · 2026Article
- Lineage-specific evolution of regulatory landscapes in a polyploid plant and its diploid progenitors.bioRxiv : the preprint server for biology · 2026Article
- Genome-wide identification of ethylene receptor protein-coding gene families in wheat and their regulated expression during development and under multiple abiotic stresses.BMC plant biology · 2026Article
- Transcript isoforms and alternative splicing in polyploid Brassica napus under heat and cold stress.Annals of botany · 2026Article
- Comparative analysis of plastid genomes from allopolyploid Tragopogon miscellus and its diploid parents.Plant biology (Stuttgart, Germany) · 2025Article
- Unveiling the wheat NTP gene family: insights from genome-wide identification and TaNTP6 haplotype analysis.BMC plant biology · 2025Article
- Genetic basis and role of exotic accessions in cultivated cotton fiber quality improvement.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- Better together: Subgenomes for allotetraploid potato wild relative Solanum acaule Bitt. reveal origins in Petota Clade 3 and 4.The plant genome · 2025Article
- Deciphering octoploid strawberry evolution with serial LTR similarity matrices for subgenome partition.Horticulture research · 2025Article
- Expression pattern changes of three homeologs in chemokine activity enhance antiviral response to herpesvirus infection in a newly synthesized alloheptaploid.BMC genomics · 2025Article
- Epigenetic insights into the domestication of tetraploid peanut.Plant physiology · 2025Article
- Nonadditive gene expression contributing to heterosis in partially heterozygous maize hybrids is predominantly regulated from heterozygous regions.The New phytologist · 2025Article
161 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Allopolyploidy is an evolutionary and mechanistically intriguing process, in that it entails the reconciliation of two or more sets of diverged genomes and regulatory interactions. In this study, we explored gene expression patterns in interspecific hybrid F(1), and synthetic and natural allopolyploid cotton using RNA-Seq reads from leaf transcriptomes. We determined how the extent and direction of expression level dominance (total level of expression for both homoeologs) and homoeolog expression bias (relative contribution of homoeologs to the transcriptome) changed from hybridization through evolution at the polyploid level and following cotton domestication. Genome-wide expression level dominance was biased toward the A-genome in the diploid hybrid and natural allopolyploids, whereas the direction was reversed in the synthetic allopolyploid. This biased expression level dominance was mainly caused by up- or downregulation of the homoeolog from the 'non-dominant' parent. Extensive alterations in homoeolog expression bias and expression level dominance accompany the initial merger of two diverged diploid genomes, suggesting a combination of regulatory (cis or trans) and epigenetic interactions that may arise and propagate through the transcriptome network. The extent of homoeolog expression bias and expression level dominance increases over time, from genome merger through evolution at the polyploid level. Higher rates of transgressive and novel gene expression patterns as well as homoeolog silencing were observed in natural allopolyploids than in F(1) hybrid and synthetic allopolyploid cottons. These observations suggest that natural selection reconciles the regulatory mismatches caused by initial genomic merger, while new gene expression conditions are generated for evaluation by selection.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.