An Autotetraploid Linkage Map of Rose (Rosa hybrida) Validated Using the Strawberry (Fragaria vesca) Genome Sequence

Polyploidy is a pivotal process in plant evolution as it increase gene redundancy and morphological intricacy but due to the complexity of polysomic inheritance we have only few genetic maps of autopolyploid organisms. A robust mapping framework is particularly important in polyploid crop species, rose included (2n = 4x = 28), where the objective is to study multiallelic interactions that control traits of value for plant breeding. From a cross between the garden, peach red and fragrant cultivar Fragrant Cloud (FC) and a cut-rose yellow cultivar Golden Gate (GG), we generated an autotetraploid GGFC mapping population consisting of 132 individuals. For the map we used 128 sequence-based markers, 141 AFLP, 86 SSR and three morphological markers. Seven linkage groups were resolved for FC (Total 632 cM) and GG (616 cM) which were validated by markers that segregated in both parents as well as the diploid integrated consensus map

Genetic dissection of fruit quality traits in the octoploid cultivated strawberry highlights the role of homoeo-QTL in their control

Fruit quality traits are major breeding targets in the Rosaceae. Several of the major Rosaceae species are current or ancient polyploids. To dissect the inheritance of fruit quality traits in polyploid fleshy fruit species, we used a cultivated strawberry segregating population comprising a 213 full-sibling F1 progeny from a cross between the variety ‘Capitola’ and the genotype ‘CF1116’. We previously developed the most comprehensive strawberry linkage map, which displays seven homoeology groups (HG), including each four homoeology linkage groups (Genetics 179:2045–2060, 2008). The map was used to identify quantitative trait loci (QTL) for 19 fruit traits related to fruit development, texture, colour, anthocyanin, sugar and organic acid contents. Analyses were carried out over two or three successive years on field-grown plants. QTL were detected for all the analysed traits. Because strawberry is an octopolyploid species, QTL controlling a given trait and located at orthologous positions on different homoeologous linkage groups within one HG are considered as homoeo-QTL. We found that, for various traits, about one-fourth of QTL were putative homoeo-QTL and were localised on two linkage groups. Several homoeo-QTL could be detected the same year, suggesting that several copies of the gene underlying the QTL are functional. The detection of some other homoeo-QTL was year-dependent. Therefore, changes in allelic expression could take place in response to environmental changes. We believe that, in strawberry as in other polyploid fruit species, the mechanisms unravelled in the present study may play a crucial role in the variations of fruit quality

A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses

<p>Abstract</p> <p>Background</p> <p>Polyploidy is important from a phylogenetic perspective because of its immense past impact on evolution and its potential future impact on diversification, survival and adaptation, especially in plants. Molecular population genetics studies of polyploid organisms have been difficult because of problems in sequencing multiple-copy nuclear genes using Sanger sequencing. This paper describes a method for sequencing a barcoded mixture of targeted gene regions using next-generation sequencing methods to overcome these problems.</p> <p>Results</p> <p>Using 64 3-bp barcodes, we successfully sequenced three chloroplast and two nuclear gene regions (each of which contained two gene copies with up to two alleles per individual) in a total of 60 individuals across 11 species of Australian <it>Poa </it>grasses. This method had high replicability, a low sequencing error rate (after appropriate quality control) and a low rate of missing data. Eighty-eight percent of the 320 gene/individual combinations produced sequence reads, and >80% of individuals produced sufficient reads to detect all four possible nuclear alleles of the homeologous nuclear loci with 95% probability.</p> <p>We applied this method to a group of sympatric Australian alpine <it>Poa </it>species, which we discovered to share an allopolyploid ancestor with a group of American <it>Poa </it>species. All markers revealed extensive allele sharing among the Australian species and so we recommend that the current taxonomy be re-examined. We also detected hypermutation in the <it>trn</it>H-<it>psb</it>A marker, suggesting it should not be used as a land plant barcode region. Some markers indicated differentiation between Tasmanian and mainland samples. Significant positive spatial genetic structure was detected at <100 km with chloroplast but not nuclear markers, which may be a result of restricted seed flow and long-distance pollen flow in this wind-pollinated group.</p> <p>Conclusions</p> <p>Our results demonstrate that 454 sequencing of barcoded amplicon mixtures can be used to reliably sample all alleles of homeologous loci in polyploid species and successfully investigate phylogenetic relationships among species, as well as to investigate phylogeographic hypotheses. This next-generation sequencing method is more affordable than and at least as reliable as bacterial cloning. It could be applied to any experiment involving sequencing of amplicon mixtures.</p

What is the significance of pore pressure in a saturated shale layer?

International audienceElectrostatic interactions, associated with negatively charged surfaces of clay minerals, produce a so-called "disjoining pressure" when diffuse layers overlap, i.e., at low porosity. Disjoining pressure is the pressure difference between the water in the clay pore space and that in a bulk solution at the same depth. Another widely used concept in clay-rocks is the "swelling pressure." It corresponds in fact to the macroscopic average of the disjoining pressure. This study proposes to determine the value of the swelling pressure of a natural material by a simple volume-averaging approach of the disjoining pressure, calculated for each clay mineral present in the material. The swelling pressure, which is dependent on the salinity of the pore fluid, is introduced into a hydrochemomechanical coupling, yielding a more general pressure diffusion equation. The results are compared to swelling pressure measurements for natural shale samples. The implications of this swelling pressure for water pressure measurements in natural formations are also discussed

Hydrochemical variations of groundwater and spring discharge of the western Great Artesian Basin, Australia: implications for regional groundwater flow

The western Great Artesian Basin (GAB) is an important water source for pastoral and town water supplies, as well as for springs containing endemic flora and fauna, within arid Australia. This study focuses on the hydrochemical variations of groundwater and spring discharge in order to determine the major geochemical processes responsible for water quality and evolution across the western GAB. Regional hydrochemical trends within groundwater generally support the modern groundwater potentiometric surface and interpreted flow paths, highlighting that these approximately represent the long-term flow paths. Additionally, the regional chemical variations along the flow paths in the western GAB are complex, with their composition being a function of several controlling processes, including location of recharge, evapo-concentration, mixing and various water–rock interactions. These processes cause groundwater east of Lake Eyre to be predominantly of Na-HCO₃ type, whereas groundwater originating from the western margin is of Na-Cl-(-SO₄) type. The GAB springs appear to be discharging water predominantly from the main GAB aquifer, the J Aquifer; however, a component of the discharging water from several springs is from a source other than the J Aquifer. Current understanding of the hydrochemical variations of groundwater and spring discharge of the western GAB can help provide constraints on groundwater flow, as well as provide an understanding of the geochemical and hydrological processes responsible for water quality evolution.Stacey C. Priestley, Paul Shand, Andrew J. Love, Laura J. Crossey, Karl E. Karlstrom, Mark N. Keppel, Daniel L. Wohling, Pauline Rousseau-Gueuti

What is the pore pressure in a saturated shale layer?

International audienceElectrostatic interactions, associated with negatively charged surfaces of clay minerals, produce a so-called "disjoining pressure" when diffuse layers overlap, i.e., at low porosity. Disjoining pressure is the pressure difference between the water in the clay pore space and that in a bulk solution at the same depth. Another widely used concept in clay-rocks is the "swelling pressure." It corresponds in fact to the macroscopic average of the disjoining pressure. This study proposes to determine the value of the swelling pressure of a natural material by a simple volume-averaging approach of the disjoining pressure, calculated for each clay mineral present in the material. The swelling pressure, which is dependent on the salinity of the pore fluid, is introduced into a hydrochemomechanical coupling, yielding a more general pressure diffusion equation. The results are compared to swelling pressure measurements for natural shale samples. The implications of this swelling pressure for water pressure measurements in natural formations are also discussed

Centromere locations in brassica A and C genomes revealed through half-tetrad analysis

Locating centromeres on genome sequences can be challenging. The high density of repetitive elements in these regions makes sequence assembly problematic, especially when using short-read sequencing technologies. It can also be difficult to distinguish between active and recently extinct centromeres through sequence analysis. An effective solution is to identify genetically active centromeres (functional in meiosis) by half-tetrad analysis. This genetic approach involves detecting heterozygosity along chromosomes in segregating populations derived from gametes (half-tetrads). Unreduced gametes produced by first division restitution mechanisms comprise complete sets of nonsister chromatids. Along these chromatids, heterozygosity is maximal at the centromeres, and homologous recombination events result in homozygosity toward the telomeres. We genotyped populations of half-tetrad-derived individuals (from Brassica interspecific hybrids) using a high-density array of physically anchored SNP markers (Illumina Brassica 60K Infinium array). Mapping the distribution of heterozygosity in these half-tetrad individuals allowed the genetic mapping of all 19 centromeres of the Brassica A and C genomes to the reference Brassica napus genome. Gene and transposable element density across the B. napus genome were also assessed and corresponded well to previously reported genetic map positions. Known centromere-specific sequences were located in the reference genome, but mostly matched unanchored sequences, suggesting that the core centromeric regions may not yet be assembled into the pseudochromosomes of the reference genome. The increasing availability of genetic markers physically anchored to reference genomes greatly simplifies the genetic and physical mapping of centromeres using half-tetrad analysis. We discuss possible applications of this approach, including in species where half-tetrads are currently difficult to isolate