Rht18 semidwarfism in wheat is due to increased GA 2-oxidaseA9 expression and reduced GA content

Semidwarfing genes have improved crop yield by reducing height, improving lodging resistance, and allowing plants to allocate more assimilates to grain growth. In wheat (Triticum aestivum), the Rht18 semidwarfing gene was identified and deployed in durum wheat before it was transferred into bread wheat, where it was shown to have agronomic potential. Rht18, a dominant and gibberellin (GA) responsive mutant, is genetically and functionally distinct from the widely used GA-insensitive semidwarfing genes Rht-B1b and Rht-D1b. In this study, the Rht18 gene was identified by mutagenizing the semidwarf durum cultivar Icaro (Rht18) and generating mutants with a range of tall phenotypes. Isolating and sequencing chromosome 6A of these "overgrowth"mutants showed that they contained independent mutations in the coding region of GA2oxA9. GA2oxA9 is predicted to encode a GA 2-oxidase that metabolizes GA biosynthetic intermediates into inactive products, effectively reducing the amount of bioactive GA (GA1). Functional analysis of the GA2oxA9 protein demonstrated that GA2oxA9 converts the intermediate GA12 to the inactive metabolite GA110. Furthermore, Rht18 showed higher expression of GA2oxA9 and lower GA content compared with its tall parent. These data indicate that the increased expression of GA2oxA9 in Rht18 results in a reduction of both bioactive GA content and plant height. This study describes a height-reducing mechanism that can generate new genetic diversity for semidwarfism in wheat by combining increased expression with mutations of specific amino acid residues in GA2oxA9

The Aquilegia genome: adaptive radiation and an extraordinarily polymorphic chromosome with a unique history

The columbine genus Aquilegia is a classic example of an adaptive radiation, involving a wide variety of pollinators and habitats. Here we present the genome assembly of A. coerulea "Goldsmith", complemented by high-coverage sequencing data from 10 wild species covering the world-wide distribution. Our analysis reveals extensive allele sharing among species, and sheds light on the complex process of radiation. We also present the remarkable discovery that the evolutionary history of an entire chromosome differed from that of the rest of the genome --- a phenomenon which we do not fully understand, but which highlights the need to consider chromosomes in an evolutionary context

Flow sorting and sequencing meadow fescue chromosome 4F.

Analysis of large genomes is hampered by a high proportion of repetitive DNA, which makes the assembly of short sequence reads difficult. This is also the case in meadow fescue (Festuca pratensis), which is known for good abiotic stress resistance and it has been used in intergeneric hybridization with ryegrasses to produce Festulolium cultivars. In this work we describe a new approach to analyze the large genome of meadow fescue, which involves reduction of sample complexity without compromising information content. This is achieved by dissecting the genome to smaller parts - individual chromosomes and groups of chromosomes. As the first step, we flow-sorted chromosome 4F and sequenced it by Illumina with ~50x coverage. This provided the first insight into the composition of the fescue genome, enabled the construction of virtual gene order of the chromosome, and facilitated detailed comparative analysis with the sequenced genomes of rice, Brachypodium, Sorghum and barley. Using GenomeZipper, we were able to confirm collinearity of chromosome 4F with barley chromosome 4H and the long arm of chromosome 5H (5HL). Several new tandem repeats were identified and physically mapped using FISH. They were found as robust cytogenetic markers for karyotyping of meadow fescue and ryegrass species and their hybrids. The ability to purify chromosome 4F opens a way for more efficient analysis of genomic loci on this chromosome underlying important traits, including freezing tolerance. Our results confirm that next generation sequencing of flow-sorted chromosomes enables an overview on chromosome structure and evolution at a resolution never achieved before

README file

README file for data in this repositor

Aquilegia kept positions

zipped text file of all genomic positions kept for population genetics analysis of 10 Aquilegia specie

biallelic SNPs

zipped vcf of all bialleleic SNPs called in 10 Aquilegia species plus Semiaquilegia. Species are referred to by short names as follows: species name.in.vcf geography Aquilegia_aurea IIUF europe Aquilegia_barnebyi IIUC north_america Aquilegia_chrysantha IIWY north_america Aquilegia_japonica IIWU asia Aquilegia_formosa IIWT north_america Aquilegia_longissima IIWX north_america Aquilegia_oxysepala IIWW asia Aquilegia_vulgaris IIUH europe Aquilegia_pubescens D14R north_america Aquilegia_sibirica IIUI asia Semiaquilegia SRR4 asi