Reduced chromatin accessibility underlies gene expression differences in homologous chromosome arms of diploid Aegilops tauschii and hexaploid wheat

Abstract

Background

Polyploidy is centrally important in the evolution and domestication of plants because it leads to major genomic changes, such as altered patterns of gene expression, which are thought to underlie the emergence of new traits. Despite the common occurrence of these globally altered patterns of gene expression in polyploids, the mechanisms involved are not well understood.

Results

Using a precisely defined framework of highly conserved syntenic genes on hexaploid wheat chromosome 3DL and its progenitor 3 L chromosome arm of diploid Aegilops tauschii, we show that 70% of these gene pairs exhibited proportionately reduced gene expression, in which expression in the hexaploid context of the 3DL genes was ∼40% of the levels observed in diploid Ae tauschii. Several genes showed elevated expression during the later stages of grain development in wheat compared with Ae tauschii. Gene sequence and methylation differences probably accounted for only a few cases of differences in gene expression. In contrast, chromosome-wide patterns of reduced chromatin accessibility of genes in the hexaploid chromosome arm compared with its diploid progenitor were correlated with both reduced gene expression and the imposition of new patterns of gene expression.

Conclusions

Our pilot-scale analyses show that chromatin compaction may orchestrate reduced gene expression levels in the hexaploid chromosome arm of wheat compared to its diploid progenitor chromosome arm.

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Now published in GigaScience doi: 10.1093/gigascience/giaa070

Fu-Hao Lu 1Department Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteNeil McKenzie 1Department Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMing-Cheng Luo 3Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAnthony Hall 2Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMichael W Bevan 1Department Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: michael.bevan@jic.ac.uk

A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa070 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.

These peer reviews were as follows:

Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102301 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102302

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