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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.

SUBMITTER: Nitcher R

PROVIDER: S-EPMC3664738 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Two coding variants in the APOL1 gene (G1 and G2) explain most of the high rate of kidney disease in African Americans. APOL1-associated kidney disease risk inheritance follows an autosomal recessive pattern: The relative risk of kidney disease associated with inheritance of two high-risk variants is 7-30 fold, depending on the specific kidney phenotype. We wished to determine if the variability in phenotype might in part reflect structural differences in APOL1 gene. We analyzed sequence coverage from 1000 Genomes Project Phase 3 samples as well as exome sequencing data from African American kidney disease cases for copy number variation. 8 samples sequenced in the 1000 Genomes Project showed increased coverage over a ~100kb region that includes APOL2, APOL1 and part of MYH9, suggesting the presence of APOL1 copy number greater than 2. We reasoned that such duplications should be enriched in apparent G1 heterozygotes with kidney disease. Using a PCR-based assay, we observed the presence of this duplication in additional samples from apparent G0G1 or G0G2 individuals. The frequency of this APOL1 duplication was compared among cases (n = 123) and controls (n = 255) with apparent G0G1 heterozygosity. The presence of APOL1 duplication was observed in 4.06% of cases and 0.78% controls, preliminary evidence that this APOL1 duplication may alter susceptibility to kidney disease (p = 0.03). Taqman-based copy number assays confirmed the presence of 3 APOL1 copies in individuals positive for this specific duplication by PCR assay, but also identified a small number of individuals with additional APOL1 copies of presumably different structure. These observations motivate further studies to better assess the contribution of APOL1 copy number on kidney disease risk and on APOL1 function. Investigators and clinicians genotyping APOL1 should also consider whether the particular genotyping platform used is subject to technical errors when more than two copies of APOL1 are present.

Project description:Copy number variation (CNV) is rife in eukaryotic genomes and has been implicated in many human disorders, particularly cancer, in which CNV promotes both tumorigenesis and chemotherapy resistance. CNVs are considered random mutations but often arise through replication defects; transcription can interfere with replication fork progression and stability, leading to increased mutation rates at highly transcribed loci. Here we investigate whether inducible promoters can stimulate CNV to yield reproducible, environment-specific genetic changes. We propose a general mechanism for environmentally-stimulated CNV and validate this mechanism for the emergence of copper resistance in budding yeast. By analysing a large cohort of individual cells, we directly demonstrate that CNV of the copper-resistance gene CUP1 is stimulated by environmental copper. CNV stimulation accelerates the formation of novel alleles conferring enhanced copper resistance, such that copper exposure actively drives adaptation to copper-rich environments. Furthermore, quantification of CNV in individual cells reveals remarkable allele selectivity in the rate at which specific environments stimulate CNV. We define the key mechanistic elements underlying this selectivity, demonstrating that CNV is regulated by both promoter activity and acetylation of histone H3 lysine 56 (H3K56ac) and that H3K56ac is required for CUP1 CNV and efficient copper adaptation. Stimulated CNV is not limited to high-copy CUP1 repeat arrays, as we find that H3K56ac also regulates CNV in 3 copy arrays of CUP1 or SFA1 genes. The impact of transcription on DNA damage is well understood, but our research reveals that this apparently problematic association forms a pathway by which mutations can be directed to particular loci in particular environments and furthermore that this mutagenic process can be regulated through histone acetylation. Stimulated CNV therefore represents an unanticipated and remarkably controllable pathway facilitating organismal adaptation to new environments.

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

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