The contribution of cis- And trans-acting variants to gene regulation in wild and domesticated barley under cold stress and control conditions

Matthew Haas, Axel Himmelbach, Martin Mascher

Research output: Contribution to journalArticlepeer-review

9 Scopus citations

Abstract

Barley, like other crops, has experienced a series of genetic changes that have impacted its architecture and growth habit to suit the needs of humans, termed the domestication syndrome. Domestication also resulted in a concomitant bottleneck that reduced sequence diversity in genes and regulatory regions. Little is known about regulatory changes resulting from domestication in barley. We used RNA sequencing to examine allele-specific expression in hybrids between wild and domesticated barley. Our results show that most genes have conserved regulation. In contrast to studies of allele-specific expression in interspecific hybrids, we find almost a complete absence of trans effects. We also find that cis regulation is largely stable in response to short-term cold stress. Our study has practical implications for crop improvement using wild relatives. Genes regulated in cis are more likely to be expressed in a new genetic background at the same level as in their native background.

Original languageEnglish (US)
Pages (from-to)2773-2784
Number of pages12
JournalJournal of experimental botany
Volume71
Issue number9
DOIs
StatePublished - 2020

Bibliographical note

Funding Information:
We are grateful to Nils Stein for providing seed material, and to Manuela Knauft, Susanne König, Ines Walde, and Mary Ziems for technical assistance.We also thank Andreas Czihal and Dominic Knoch for advice regarding RNA extractions, and Anne Fiebig for uploading data to the ENA.We greatly appreciate the financial support from the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG) to MM (Grant ID: MA6611/2).The authors declare no conflict of interest.

Publisher Copyright:
© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Keywords

  • Allele-specific expression
  • Barley
  • Cold stress
  • Domestication
  • Gene regulation
  • Hordeum vulgare

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