Asymmetric allele‐specific expression in relation to developmental variation and drought stress in barley hybrids

Abstract

SUMMARYIn the present study, we analysed allele-specific expression (ASE) in the selfing species barley to assess the frequency of cis-acting regulatory variation and the effects of genetic background, developmental differences and drought stress on allelic expression levels. We measured ASE ratios in 30 genes putatively involved in stress responses in five hybrids and their reciprocals, namely Hordeum spontaneum 41-1/Alexis (HAl), Hordeum spontaneum 41-1/Arta (HAr), Sloop/WI3408 (SW), Tadmor/Sloop (TS) and Tadmor/WI3408 (TW). In order to detect cis-acting variation related to drought and developmental changes, the barley hybrids were grown under control and water-limited conditions, and leaf tissue was harvested at two developmental stages. The analysis demonstrated that more than half of the genes measured (63%) showed allelic differences in expression of up to 19-fold due to cis-regulatory variation in at least one cross by treatment/stage combination. Drought stress induced changes in allelic expression ratios, indicating differences between drought responsive cis-elements. In addition, ASE differences between developmental stages suggested the presence of cis-acting elements interacting with developmental cues. We were also able to demonstrate that the levels and frequency of allelic imbalance and hence differences in cis-regulatory elements are correlated with the genetic divergence between the parental lines, but may also arise as an adaptation to diverse habitats. Our findings suggest that cis-regulatory variation is a common phenomenon in barley, and may provide a molecular basis of transgression. Differential expression of near-isogenic members of the same gene family could potentially result in hybrid lines out performing their parents in terms of expression level, timing and response to developmental and environmental cues. Identification and targeted manipulation of cis-regulatory elements will assist in breeding improved crops with a better adaptation to changing environments.

Climate Change: Seed Production and Options for Adaptation

“…Other studies have identified genetic markers and physiological traits associated with drought tolerance [141]; barley cultivars, for example, have been reported to have a 19-fold difference in the expression of genes associated with drought tolerance [143]. Drought tolerant maize cultivars developed through conventional breeding have been released in the USA [144].…”

Distinct Regulatory Changes Underlying Differential Expression of TEOSINTE BRANCHED1-CYCLOIDEA-PROLIFERATING CELL FACTOR Genes Associated with Petal Variations in Zygomorphic Flowers of Petrocosmea spp. of the Family Gesneriaceae

“…Correspondingly, gene expression modifications can arise from either cis-regulatory changes that affect transcription in an allele-specific manner or transregulatory alterations that modify the expression or activity of related factors (Wray et al, 2003;Wittkopp et al, 2004). Recently, a burgeoning amount of data have shown that distinct portions of cis-and transregulatory changes contribute to gene expression divergence in different organisms by quantifying allele-specific expression (ASE) levels in a common, heterozygous diploid individual (Wittkopp et al, 2004(Wittkopp et al, , 2008Kiekens et al, 2006;Stupar et al, 2007;Zhuang and Adams, 2007;Main et al, 2009;von Korff et al, 2009;Bell et al, 2013;Cubillos et al, 2014). In spite of advances regarding cis-and trans-actions, the detailed relationship between regulatory variations of key developmental genes and phenotypic divergences, especially some important morphological novelties, has not been extensively explored yet, particularly in plants (Rosas et al, 2010).…”

Both copy number and sequence variations affect expression of human DEFB4

“…Such a shift in expression of specific variants was reported in barley hybrids, changing the allelic ratio in some genes after drought stress (for example, ABC02113, ABC03499, ABC10029). 48 To screen for possible cis-regulatory variations causative for total DEFB4 expression or VSE, we resequenced B2 kb upstream of DEFB4 transcription start site in selected cell lines. We found five NF-kB-binding sites in the putative promoter region just upstream of the transcription start.…”