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Transcription factor retention through multiple polyploidization steps in wheat.

Catherine E B Evans1,2, Ramesh Arunkumar1, Philippa Borrill1

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|June 24, 2022
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Summary
This summary is machine-generated.

Whole-genome duplication in wheat preferentially retains transcription factors, maintaining gene dosage. This preferential retention of transcription factors (TFs) in polyploid wheat offers potential for new breeding strategies.

Keywords:
Triticum aestivum L. (wheat)Shared Data Resourceevolutiongene balance hypothesispolyploidytranscription factors

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Area of Science:

  • Plant genomics
  • Evolutionary biology
  • Molecular genetics

Background:

  • Whole-genome duplication (WGD) is common in plant evolution, leading to gene loss.
  • Retained genes in polyploids are often dosage-sensitive regulators like transcription factors (TFs).
  • Data on TF retention in young polyploids, like bread wheat, is limited.

Purpose of the Study:

  • To investigate the retention, expression, and genetic variation of transcription factors in bread wheat (Triticum aestivum L.).
  • To compare TF dynamics across diploid, tetraploid, and hexaploid wheat lineages.
  • To assess the functional conservation and potential for gene dosage manipulation in wheat breeding.

Main Methods:

  • Comparative genomics analysis across wheat ploidy levels.
  • Assessment of gene retention patterns following hybridization and WGD events.
  • Analysis of genetic variation (missense mutations) and gene expression (coexpression) in TF homoeologs.
  • Identification of specific TF families with altered homoeolog retention.

Main Results:

  • The proportion of transcription factors increased following WGD events in wheat evolution.
  • Transcription factors were preferentially retained as homoeologous groups in tetraploid and hexaploid wheat.
  • TF homoeologs showed fewer deleterious mutations and stronger coexpression compared to other genes.
  • Specific TF families (B3, MADS-M-type, NAC) exhibited lower homoeolog retention, linked to low expression and tandem duplication.

Conclusions:

  • Transcription factors are preferentially retained in polyploid wheat genomes, indicating dosage sensitivity.
  • Functional conservation exists between TF homoeologs, with evidence of selection against deleterious mutations.
  • Variations in retention exist among TF families, influenced by expression levels and duplication patterns.
  • Targeted gene dosage alteration of TF homoeologs presents a promising avenue for wheat breeding.