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

Matthew Haas,Martin Mascher,Axel Himmelbach,Greg Rebetzke

doi:10.1093/jxb/eraa036

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.

Highlights

Barley (Hordeum vulgare ssp. vulgare L.) is an important crop for feed, malting and to a lesser extent, human consumption (Ullrich 2010)
H. spontaneum is considered to be a useful source of beneficial alleles for barley improvement
After checking our gene expression data quality, we examined the data to see if it matches our expectations to ensure that it is reliable

Summary

Introduction

Barley (Hordeum vulgare ssp. vulgare L.) is an important crop for feed, malting and to a lesser extent, human consumption (Ullrich 2010). Vulgare L.) is an important crop for feed, malting and to a lesser extent, human consumption (Ullrich 2010). Among the first crops to be domesticated in the Fertile Crescent about 10,000 years ago (Zohary et al 2012), barley remains fully interfertile with its wild progenitor H. vulgare ssp. H. spontaneum is considered to be a useful source of beneficial alleles for barley improvement. Preferential selection of genotypes with traits beneficial to humans and the intentional breeding have narrowed the genetic diversity and altered gene expression patterns. These molecular changes have caused differences in plant architecture and growth habit between wild and domesticated relatives, collectively called the domestication syndrome (Hammer 1984; Doebley et al.2006)

Methods

Results

Conclusion