Doubled haploid ramets via embryogenesis of haploid tissue cultures

Tissue culture in the oil palm business is generally concerned with the multiplication (clonal production) of dura, pisifera and tenera palms. These are all normal diploids (2n=2x=36). Sumatra Bioscience has pioneered haploid tissue culture of oil palm (n=x=18). Haploid oil palm is the first step in producing doubled haploid palms which in turn provide parental lines for F1 hybrid production. Chromosome doubling is known to occur during embryogenesis in other haploid cultures, e.g. barley anther culture. Haploid tissue cultures in oil palm were therefore set up to investigate and exploit spontaneous chromosome doubling during embryogenesis. Flow cytometry of embryogenic tissue showed the presence of both haploid (n) and doubled haploid (2n) cells indicating spontaneous doubling. Completely doubled haploid ramets were regenerated suggesting that doubling occurred during the first mitoses of embryogenesis. This is the first report of doubled haploid production in oil palm via haploid tissue culture. The method provides a means of producing a range of doubled haploids in oil palm from the 1,000 plus haploids available at Sumatra Bioscience, in addition the method also produced doubled haploid (and haploid) clones. 1

Buoyant magnetic flux ropes in a magnetized stellar envelope: Idealized numerical 2.5-D MHD simulations

Context: The context of this paper is buoyant toroidal magnetic flux ropes, which is a part of flux tube dynamo theory and the framework of solar-like magnetic activity. Aims: The aim is to investigate how twisted magnetic flux ropes interact with a simple magnetized stellar model envelope--a magnetic "convection zone"--especially to examine how the twisted magnetic field component of a flux rope interacts with a poloidal magnetic field in the convection zone. Method: Both the flux ropes and the atmosphere are modelled as idealized 2.5-dimensional concepts using high resolution numerical magneto-hydrodynamic (MHD) simulations. Results: It is illustrated that twisted toroidal magnetic flux ropes can interact with a poloidal magnetic field in the atmosphere to cause a change in both the buoyant rise dynamics and the flux rope's geometrical shape. The details of these changes depend primarily on the polarity and strength of the atmospheric field relative to the field strength of the flux rope. It is suggested that the effects could be verified observationally.Comment: 8 pages, 5 figures (9 files), accepted by A&

A simple, high throughput method to locate single copy sequences from Bacterial Artificial Chromosome (BAC) libraries using High Resolution Melt analysis

BACKGROUND: The high-throughput anchoring of genetic markers into contigs is required for many ongoing physical mapping projects. Multidimentional BAC pooling strategies for PCR-based screening of large insert libraries is a widely used alternative to high density filter hybridisation of bacterial colonies. To date, concerns over reliability have led most if not all groups engaged in high throughput physical mapping projects to favour BAC DNA isolation prior to amplification by conventional PCR. RESULTS: Here, we report the first combined use of Multiplex Tandem PCR (MT-PCR) and High Resolution Melt (HRM) analysis on bacterial stocks of BAC library superpools as a means of rapidly anchoring markers to BAC colonies and thereby to integrate genetic and physical maps. We exemplify the approach using a BAC library of the model plant Arabidopsis thaliana. Super pools of twenty five 384-well plates and two-dimension matrix pools of the BAC library were prepared for marker screening. The entire procedure only requires around 3 h to anchor one marker. CONCLUSIONS: A pre-amplification step during MT-PCR allows high multiplexing and increases the sensitivity and reliability of subsequent HRM discrimination. This simple gel-free protocol is more reliable, faster and far less costly than conventional PCR screening. The option to screen in parallel 3 genetic markers in one MT-PCR-HRM reaction using templates from directly pooled bacterial stocks of BAC-containing bacteria further reduces time for anchoring markers in physical maps of species with large genomes

Methods of producing haploid and doubled haploid oil palms

The present invention relates to haploid oil palm plants and homozygous doubled haploid oil palm plants. The invention also relates to methods for producing and selecting haploid and doubled haploid plants. More particularly, but not exclusively, the method may be used for selecting haploid and doubled haploid oil palm plants. Haploid and doubled haploid plants are selected by a large-scale screening based on a combination of the phenotype with the use of molecular methods combined with flow cytometry techniques to identify haploid and doubled haploid plants. More particularly, a method for selecting haploid and doubled haploid plants is described comprising: (a) germinating seeds; (b) selecting seedlings with atypical phenotype; (c) assessing heterozygosity using markers; (d) isolating cells from the seedlings and determining the DNA content of the cells; and (e) isolating and purifying the DNA and using defined molecular markers to characterise the genotype of the plant. The haploid oil palm plants may be used for producing homozygous doubled haploid oil palms: doubled haploids may be intercrossed to produce uniform F.sub.1 hybrids of superior properties

BAC-HAPPY mapping (BAP mapping): a new and efficient protocol for physical mapping

Physical and linkage mapping underpin efforts to sequence and characterize the genomes of eukaryotic organisms by providing a skeleton framework for whole genome assembly. Hitherto, linkage and physical “contig” maps were generated independently prior to merging. Here, we develop a new and easy method, BAC HAPPY MAPPING (BAP mapping), that utilizes BAC library pools as a HAPPY mapping panel together with an Mbp-sized DNA panel to integrate the linkage and physical mapping efforts into one pipeline. Using Arabidopsis thaliana as an exemplar, a set of 40 Sequence Tagged Site (STS) markers spanning ~10% of chromosome 4 were simultaneously assembled onto a BAP map compiled using both a series of BAC pools each comprising 0.7x genome coverage and dilute (0.7x genome) samples of sheared genomic DNA. The resultant BAP map overcomes the need for polymorphic loci to separate genetic loci by recombination and allows physical mapping in segments of suppressed recombination that are difficult to analyze using traditional mapping techniques. Even virtual “BAC-HAPPY-mapping” to convert BAC landing data into BAC linkage contigs is possible.Giang T. H. Vu, Paul H. Dear, Peter D. S. Caligari and Mike J. Wilkinso

Flux-loss of buoyant ropes interacting with convective flows

We present 3-d numerical magneto-hydrodynamic simulations of a buoyant, twisted magnetic flux rope embedded in a stratified, solar-like model convection zone. The flux rope is given an initial twist such that it neither kinks nor fragments during its ascent. Moreover, its magnetic energy content with respect to convection is chosen so that the flux rope retains its basic geometry while being deflected from a purely vertical ascent by convective flows. The simulations show that magnetic flux is advected away from the core of the flux rope as it interacts with the convection. The results thus support the idea that the amount of toroidal flux stored at or near the bottom of the solar convection zone may currently be underestimated.Comment: 5 pages, 3 figures. Accepted for publication in Astronomy & Astrophysic

The Rise of Active Region Flux Tubes in the Turbulent Solar Convective Envelope

We use a thin flux tube model in a rotating spherical shell of turbulent convective flows to study how active region scale flux tubes rise buoyantly from the bottom of the convection zone to near the solar surface. We investigate toroidal flux tubes at the base of the convection zone with field strengths ranging from 15 kG to 100 kG at initial latitudes ranging from 1 degree to 40 degrees with a total flux of 10^22 Mx. We find that the dynamic evolution of the flux tube changes from convection dominated to magnetic buoyancy dominated as the initial field strength increases from 15 kG to 100 kG. At 100 kG, the development of Omega-shaped rising loops is mainly controlled by the growth of the magnetic buoyancy instability. However, at low field strengths of 15 kG, the development of rising Omega-shaped loops is largely controlled by convective flows, and properties of the emerging loops are significantly changed compared to previous results in the absence of convection. With convection, rise times are drastically reduced (from years to a few months), loops are able to emerge at low latitudes, and tilt angles of emerging loops are consistent with Joy's Law for initial field strengths of greater than or equal to 40 kG. We also examine other asymmetries that develop between the leading and following legs of the emerging loops. Taking all the results together, we find that mid-range field strengths of approximately 40 - 50 kG produce emerging loops that best match the observed properties of solar active regions.Comment: Accepted for publication in The Astrophysical Journa

Solar dynamo model with nonlocal alpha-effect

The first results of the solar dynamo model that allows for the diamagnetic effect of inhomogeneous turbulence and the nonlocal alpha-effect due to the rise of magnetic loops are discussed. The nonlocal alpha-effect is not subject to the catastrophic quenching related to the conservation of magnetic helicity. Given the diamagnetic pumping, the magnetic fields are concentrated near the base of the convection zone, although the distributed-type model covers the entire thickness of the convection zone. The magnetic cycle period, the equatorial symmetry of the field, its meridional drift, and the polar-to-toroidal field ratio obtained in the model are in agreement with observations. There is also some disagreement with observations pointing the ways of improving the model.Comment: To appear in Astronomy Letters, 10 pages, 5 figure

Production of haploids and doubled haploids in oil palm

Background: Oil palm is the world’s most productive oil-food crop despite yielding well below its theoretical maximum. This maximum could be approached with the introduction of elite F1 varieties. The development of such elite lines has thus far been prevented by difficulties in generating homozygous parental types for F1 generation. Results: Here we present the first high-throughput screen to identify spontaneously-formed haploid (H) and doubled haploid (DH) palms. We secured over 1,000 Hs and one DH from genetically diverse material and derived further DH/mixoploid palms from Hs using colchicine. We demonstrated viability of pollen from H plants and expect to generate 100% homogeneous F1 seed from intercrosses between DH/mixoploids once they develop female inflorescences. Conclusions: This study has generated genetically diverse H/DH palms from which parental clones can be selected in sufficient numbers to enable the commercial-scale breeding of F1 varieties. The anticipated step increase in productivity may help to relieve pressure to extend palm cultivation, and limit further expansion into biodiverse rainforest

A retrospective of the GREGOR solar telescope in scientific literature

In this review, we look back upon the literature, which had the GREGOR solar telescope project as its subject including science cases, telescope subsystems, and post-focus instruments. The articles date back to the year 2000, when the initial concepts for a new solar telescope on Tenerife were first presented at scientific meetings. This comprehensive bibliography contains literature until the year 2012, i.e., the final stages of commissioning and science verification. Taking stock of the various publications in peer-reviewed journals and conference proceedings also provides the "historical" context for the reference articles in this special issue of Astronomische Nachrichten/Astronomical Notes.Comment: 6 pages, 2 color figures, this is the pre-peer reviewed version of Denker et al. 2012, Astron. Nachr. 333, 81