Evolutionary relationships among barley and <i>Arabidopsis</i> core circadian clock and clock-associated genes

The circadian clock regulates a multitude of plant developmental and metabolic processes. In crop species, it contributes significantly to plant performance and productivity and to the adaptation and geographical range over which crops can be grown. To understand the clock in barley and how it relates to the components in the Arabidopsis thaliana clock, we have performed a systematic analysis of core circadian clock and clock-associated genes in barley, Arabidopsis and another eight species including tomato, potato, a range of monocotyledonous species and the moss, Physcomitrella patens. We have identified orthologues and paralogues of Arabidopsis genes which are conserved in all species, monocot/dicot differences, species-specific differences and variation in gene copy number (e.g. gene duplications among the various species). We propose that the common ancestor of barley and Arabidopsis had two-thirds of the key clock components identified in Arabidopsis prior to the separation of the monocot/dicot groups. After this separation, multiple independent gene duplication events took place in both monocot and dicot ancestors. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00239-015-9665-0) contains supplementary material, which is available to authorized users

Alternative splicing of barley clock genes in response to low temperature:evidence for alternative splicing conservation

Alternative splicing (AS) is a regulated mechanism that generates multiple transcripts from individual genes. It is widespread in eukaryotic genomes and provides an effective way to control gene expression. At low temperatures, AS regulates Arabidopsis clock genes through dynamic changes in the levels of productive mRNAs. We examined AS in barley clock genes to assess whether temperature-dependent AS responses also occur in a monocotyledonous crop species. We identify changes in AS of various barley core clock genes including the barley orthologues of Arabidopsis AtLHY and AtPRR7 which showed the most pronounced AS changes in response to low temperature. The AS events modulate the levels of functional and translatable mRNAs, and potentially protein levels, upon transition to cold. There is some conservation of AS events and/or splicing behaviour of clock genes between Arabidopsis and barley. In addition, novel temperature-dependent AS of the core clock gene HvPPD-H1 (a major determinant of photoperiod response and AtPRR7 orthologue) is conserved in monocots. HvPPD-H1 showed a rapid, temperature-sensitive isoform switch which resulted in changes in abundance of AS variants encoding different protein isoforms. This novel layer of low temperature control of clock gene expression, observed in two very different species, will help our understanding of plant adaptation to different environments and ultimately offer a new range of targets for plant improvement

Specific adaptation for early maturity and height stability in icelandic spring barley

Cereal production in important growing regions is negatively influenced by climate change. This can be countered by expanding cereal production northwards in Scandinavia and Iceland, where today, barley (Hordeum vulgare L.) is primarily used as feed, as it rarely reaches malting quality. This study explores genetic factors underlying the ability of barley to mature fully in low temperature and long photoperiod. A panel of 84 spring barley lines were grown in controlled environments with different day lengths and temperatures, partially mimicking the target environment. The panel was screened for accumulated heat sum to heading, maturity, and height, all traits of importance for adaptation to the northern periphery. Subgroups with different stability and heat sum requirements were found, and day-length-neutral lines were identified. Height was temperature controlled, with lower temperature resulting in taller plants. The results were coupled to a genome-wide association study (GWAS). Despite the small panel size, the Mat-a locus was identified to have the strongest association with heat sum to heading; Ppd-H1, Mat-a, FT1, and DHAR2 with heat sum to maturity; and GA20ox1 with height. Early maturing lines with height stability have successfully been developed in Iceland, and this study confirms their performance in controlled environments for the first time. It provides insight to the mechanisms behind early maturity that will increase our ability to further adapt barley and other cereals to the northern climate. This will facilitate breeding work toward combining early maturity and height stability with traits such as quality, further enabling the northward expansion of grain production