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Transcription factor retention through multiple polyploidisation steps in wheat

View ORCID ProfileCatherine EB Evans, View ORCID ProfileRamesh Arunkumar, View ORCID ProfilePhilippa Borrill
doi: https://doi.org/10.1101/2022.02.15.480382
Catherine EB Evans
1Department of Crop Genetics, John Innes Centre, Norwich Research Park, NR4 7UH, UK
2School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
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Ramesh Arunkumar
1Department of Crop Genetics, John Innes Centre, Norwich Research Park, NR4 7UH, UK
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Philippa Borrill
1Department of Crop Genetics, John Innes Centre, Norwich Research Park, NR4 7UH, UK
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  • For correspondence: philippa.borrill@jic.ac.uk
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Summary

  • Whole genome duplication (WGD) is widespread in plant evolutionary history, but the mechanisms of non-random gene loss after WGD are debated. The gene balance hypothesis proposes that dosage-sensitive genes such as regulatory genes are retained in polyploids. To test this hypothesis, we analysed the retention of transcription factors (TFs) in the recent allohexaploid bread wheat (Triticum aestivum).

  • We annotated TFs in hexaploid, tetraploid and diploid wheats; compared the co-expression of homoeologous TF and non-TF triads; and analysed single nucleotide variation in TFs across cultivars.

  • We found that, following each of two hybridisation and WGD events, the proportion of TFs in the genome increased. TFs were preferentially retained over other genes as homoeologous groups in tetraploid and hexaploid wheat. Across cultivars, TF triads contain fewer deleterious missense mutations than non-TFs.

  • TFs are preferentially retained as three functional homoeologs in hexaploid wheat, in support of the gene balance hypothesis. High co-expression between TF homoeologs suggests that neo- and sub-functionalisation are not major drivers of TF retention in this young polyploid. Knocking out one TF homoeolog to alter gene dosage, using TILLING or CRISPR, could be a way to further test the gene balance hypothesis and generate new phenotypes for wheat breeding.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted February 18, 2022.
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Transcription factor retention through multiple polyploidisation steps in wheat
Catherine EB Evans, Ramesh Arunkumar, Philippa Borrill
bioRxiv 2022.02.15.480382; doi: https://doi.org/10.1101/2022.02.15.480382
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Transcription factor retention through multiple polyploidisation steps in wheat
Catherine EB Evans, Ramesh Arunkumar, Philippa Borrill
bioRxiv 2022.02.15.480382; doi: https://doi.org/10.1101/2022.02.15.480382

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