Increased copy number at the HvFT1 locus is associated with accelerated flowering time in barley

Abstract

A precise regulation of flowering time is critical for plant reproductive success, and therefore, a better understanding of the natural variation in genes regulating the initiation of the reproductive phase is required to develop well-adapted varieties. In both monocot and dicot species, the FLOWERING LOCUS T (FT) is a central integrator of seasonal signals perceived by the leaves. The encoded mobile protein (florigen) is transmitted to the apical meristem where it induces flowering. The FT homolog in barley (Hordeum vulgare L.), designated HvFT1, was shown to correspond to the vernalization locus VRN-H3, and natural alleles for spring and winter growth habit were identified. In this study, we demonstrate that the HvFT1 allele present in the barley genetic stock (BGS213) associated with a dominant spring growth habit carries at least four identical copies of HvFT1, whereas most barley varieties have a single copy. Increased copy number is associated with earlier transcriptional up-regulation of HvFT1 and a spring growth habit. This allele is epistatic to winter alleles for VRN-H1 and VRN-H2. Among accessions with one HvFT1 copy, haplotype differences in the HvFT1 promoter and first intron are also associated with differences in flowering time, which are modulated by genetic background. These different HvFT1 alleles can be used to develop barley varieties adapted to different or changing environments. Our results, together with studies of other wheat and barley flowering genes, show that copy number variation plays an important role in the regulation of developmental processes in the temperate cereals.

Phytochrome C Is A Key Factor Controlling Long-Day Flowering in Barley

“…Tammi. The Tammi allele for Vrn-H3 was shown to include four copies of HvFT1, which is associated with earlier transcriptional up-regulation of themselves (Nitcher et al, 2013). Therefore, it was considered that the spring allele Vrn-H3 (high expression of HvFT1) is epistatic to that of HvPhyC-e and HvPhyC functions in the same pathway as Vrn-H3.…”

Copy number variation at the HvCBF4–HvCBF2 genomic segment is a major component of frost resistance in barley

“…In crops a causal relationship between copy number and phenotypic variation linked to single genomic regions has been firstly demonstrated for the barley Bot1 boron transporter gene (Sutton et al 2007). Later on, the study of the soybean Rhg1 cyst nematode resistance locus (Cook et al 2012), of the maize efflux transporter MATE1 (Maron et al 2013), and the barley flowering time determinant FT1 (Nitcher et al 2013) showed that different phenotypes in evolutionary distant plant species could be ruled by CNV gene dosage effects. A similar phenomenon was also hypothesized for the FR-H2 locus by .…”

Genome Structures and Transcriptomes Signify Niche Adaptation for the Multiple-Ion-Tolerant Extremophyte Schrenkiella parvula

“…Structural variation can lead to CNV of genes, which, in turn, affects gene dosage and transcription strength (Stranger et al, 2007;Schlattl et al, 2011;Massouras et al, 2012;Haraksingh and Snyder, 2013). In plants, many examples exist for the copy number of a gene or genome segment associated with phenotype changes (Cook et al, 2012;Li et al, 2012;Maron et al, 2013;Nitcher et al, 2013), and genome-wide CNVs appear to predict phenotypes to some extent Muñoz-Amatriaín et al, 2013). The S. parvula genome is characterized by a higher copy number of genes associated with transporter activity (Dassanayake et al, 2011a).…”

“…For example, the regulation of flowering time, crucial for reproductive success in a narrow seasonal window, has been associated with copy numbers of FLOWERING LOCUS T1 (FT1) genes in barley (Hordeum vulgare; Nitcher et al, 2013). Increased copy numbers of related genes or gene clusters have conferred adaptive traits such as an enhanced defense against pathogens (Keeling et al, 2008;Cook et al, 2012) and metal ion tolerance (Hanikenne et al, 2008;Craciun et al, 2012;Maron et al, 2013) in various plant species.…”