Current advances in genomics and breeding of leaf chicory (Cichorium intybus L.)

This review gives an overview of agricultural topics on a non-model species, in other words, leaf chicory. Often classified as a minor crop, \u201cRadicchio\u201d, the Italian name of leaf chicory, is assuming a very important role at both a local and national level, as it characterizes a high proportion of the agricultural income of suited areas. Botanical classification along the genus Cichorium is reported and a detailed description of the most important cultivated biotypes typical of northern Italy is presented. A special consideration is reserved to breeding aspects, from molecular marker-assisted selection to the implementation of the first genome draft and leaf transcriptomes. Sexual barriers, for example, self-incompatibility or male-sterility, are described in great detail with the aim to be utilized for breeding purposes. The main aspects of seed production are also critically presented. In conclusion, the present work is a sort of handbook to better understand this orphan crop and it is mainly directed to breeders and seed producers dealing with leaf chicory

El Roque de Los Muchachos Site Characteristics. III. Analysis of Atmospheric Dust and Aerosol Extinction

Canary Islands are normally interested by dominant North-East winds that, in some meteorological conditions, can transport sand at high altitude from the Sahara desert. The dust may affect the efficiency of the telescopes and decreases the transparency of the sky. In order to maximize the scientific return of the telescopes located at the ORM, we present an analysis of the atmospheric dust content and its effects on astronomical observations. B, V and I dust aerosol astronomical extinction are derived. Using a 5 years series database of data taken from the four channel TNG dust monitor, we compute a mean hourly and daily values of the dust content. We have detected particles having size 0.3, 0.5, 1.0 and 5.0 um. Using a power law we have derived the content of 10.0 um particles. We found a typical local dust concentration ranging from 3x10^6 particles per cubic meter at 0.3 um, to 10^3 at 5.0 um and 10 at 10.0 um, increasing up to 3 order of magnitudes during the dust storms, with a relative higher increase of 1.0, 5.0 and 10.0 um particles. The number of local dust storm events is the same in winter- and summertime, but, the average background and storm-related increases in the dust concentration in summer are significantly higher than in winter. In a uniform approximation, during the dust storms, an average height of the dust layer of 2.5 km above the telescope is inferred. During the sand storms La Palma Island is affected by an almost uniform layer extending up to 5 km above the sea level, down, at least the height of the telescope. The visible extinction is dominated by particles at 1.0, 5.0 and 10.0 um. In agreement with the results from Carlsberg Automatic Meridian Circle (CAMC) we find a typical extinction during dust storms of about 0.2 mag/airmass.Comment: Accepted for publication in A&A. 9 pages, 11 figures. This work is the continuation of a series of papers concerning a detailed study of the Astroclimatology at ORM. The two previous papers (both Lombardi et al.) have reference PASP.2006.118.1198-1204 and PASP.2007.119.292-30

A method for genotyping elite breeding stocks of leaf chicory (Cichorium intybus L.) by assaying mapped microsatellite marker loci

BACKGROUND: Leaf chicory (Cichorium intybus subsp. intybus var. foliosum L.) is a diploid plant species (2n = 18) of the Asteraceae family. The term "chicory" specifies at least two types of cultivated plants: a leafy vegetable, which is highly differentiated with respect to several cultural types, and a root crop, whose current industrial utilization primarily addresses the extraction of inulin or the production of a coffee substitute. The populations grown are generally represented by local varieties (i.e., landraces) with high variation and adaptation to the natural and anthropological environment where they originated, and have been yearly selected and multiplied by farmers. Currently, molecular genetics and biotechnology are widely utilized in marker-assisted breeding programs in this species. In particular, molecular markers are becoming essential tools for developing parental lines with traits of interest and for assessing the specific combining ability of these lines to breed F1 hybrids. RESULTS: The present research deals with the implementation of an efficient method for genotyping elite breeding stocks developed from old landraces of leaf chicory, Radicchio of Chioggia, which are locally dominant in the Veneto region, using 27 microsatellite (SSR) marker loci scattered throughout the linkage groups. Information on the genetic diversity across molecular markers and plant accessions was successfully assessed along with descriptive statistics over all marker loci and inbred lines. Our overall data support an efficient method for assessing a multi-locus genotype of plant individuals and lineages that is useful for the selection of new varieties and the certification of local products derived from Radicchio of Chioggia. CONCLUSIONS: This method proved to be useful for assessing the observed degree of homozygosity of the inbred lines as a measure of their genetic stability; plus it allowed an estimate of the specific combining ability (SCA) between maternal and paternal inbred lines on the basis of their genetic diversity and the predicted degree of heterozygosity of their F1 hybrids. This information could be exploited for planning crosses and predicting plant vigor traits (i.e., heterosis) of experimental F1 hybrids on the basis of the genetic distance and allelic divergence between parental inbred lines. Knowing the parental genotypes would allow us not only to protect newly registered varieties but also to assess the genetic purity and identity of the seed stocks of commercial F1 hybrids, and to certificate the origin of their food derivatives

Near-infrared thermal emissivity from ground based atmospheric dust measurements at ORM

We present an analysis of the atmospheric content of aerosols measured at Observatorio del Roque de los Muchachos (ORM; Canary Islands). Using a laser diode particle counter located at the Telescopio Nazionale Galileo (TNG) we have detected particles of 0.3, 0.5, 1.0, 3.0, 5.0 and 10.0 um size. The seasonal behavior of the dust content in the atmosphere is calculated. The Spring has been found to be dustier than the Summer, but dusty conditions may also occur in Winter. A method to estimate the contribution of the aerosols emissivity to the sky brightness in the near-infrared (NIR) is presented. The contribution of dust emission to the sky background in the NIR has been found to be negligible comparable to the airglow, with a maximum contribution of about 8-10% in the Ks band in the dusty days.Comment: 6 pages, 3 figures, 6 tables, accepted for publication in MNRA

Breeding F1 Hybrid Varieties of Leaf Chicory Through Marker-Assisted Selection Schemes

Cichorium (Cichorium intybus subsp. intybus var. foliosum L.) comprises diploid plant species (2n=18) belonging to the Asteraceae family. These species are biennial or, in the wild, perennial species. They are naturally allogamous due to an efficient sporophytic self-incompatibility system. In addition, outcrossing is promoted by a floral morpho-phenology unfavorable to selfing in the absence of pollen donors (i.e., proterandry, wherein the anthers mature before the pistils) and a favorable competition of allo-pollen grains and tubes (i.e., pollen that is genetically diverse from that produced by the seed parents, usually called auto-pollen). Long appreciated as medical plants by the ancient Greeks and Romans, Cichorium spp. are currently among the most important cultivated vegetable crops. They are generally used as components in fresh salads or, more rarely, cooked according to local traditions and alimentary habits. Although this crop does not contribute greatly to the total agricultural income of each country, it is very important at the local level, as it characterizes the agriculture of limited areas, where from 80 to 90% of the country’s production is concentrated. This is indeed the case of Italy, where the Veneto region accounts for 66% of the national acreage and 59% of the national production of the particular type of red or variegated chicory known as “Radicchio”. Radicchio production was for a long time based on farmer’s populations, which are yearly selected and maintained and whose seed is usually reutilized on farm but may also be sold through private and not officially registered transactions. All these populations, obtained by mass selection and maintained through the inter-crossing of selected parents, have to be considered highly heterozygous and genetically heterogeneous whose behaviour and level of adaptation to different environments and/or cultural conditions depend on the frequency of favourable genes or gene combinations. In each breeding program, selection schemes and methods that can be used and the varietal types than can be breed, depend on plant reproductive barriers (e.g. self-incompatibility) and pollination system (e.g. allogamous), and thus on the genetic structure of populations. As a matter of fact, the strong self-incompatibility system found in chicory hinders obtaining highly homozygous parents, made it generally difficult to propose an efficient F1 seed production scheme. Despite the difficulties encountered in obtaining inbred lines by repeated selfing, the recent discovery of spontaneous male-sterile mutants increased the interest towards the production of F1 hybrid varieties. Indeed, male-sterility, or the inability of plants to produce functional pollen, is needful to the commercial production of hybrid seed by crossing parental inbred lines appropriately selected through progeny tests for assessing their specific combining ability. In this project we developed a genotyping method using molecular markers, useful for assessing the homozygosity and genetic stability of single inbred lines and for measuring the specific combining ability between maternal and paternal inbred lines on the basis of their genetic diversity. This information could be exploited for planning crosses and predicting the heterosis of experimental F1 hybrids on the basis of the allelic divergence and genetic distance of the parental lines. Knowing the parental genotypes would enable not only to protect newly registered varieties but also to assess the genetic purity and identity of the seed stocks of commercial F1 hybrids, and to certificate the origin of their food derivatives. Modern marker-assisted breeding (MAB) technology based on traditional methods using molecular markers such as SSRs and SNPs, without relations to genetic modification (GM) techniques, will now be planned and adopted for breeding of vigorous and uniform F1 hybrids combining quality, uniformity, and productivity traits in the same genotypes. Furthermore, this research project deals with the discovery and genetic analysis of four male-sterile mutants in this species. These mutants, which to the best of our knowledge are the first spontaneous male-sterile mutants ever discovered and described in Radicchio, were characterized in great details for the developmental pathway of micro-sporogenesis and gametogenesis, and the inheritance pattern of the gene underlying the male-sterility trait. A quick molecular diagnostic assay was also developed for the early marker-assisted selection of the genotype associated to male-sterile plants. Hence, male-sterile mutants object of this PhD project were demonstrated to be controlled by a single nuclear gene (ms1) that acts at the recessive status. We were able to map the male-sterility gene on a well saturated and characterized linkage group in a chromosomal region spanning 7.3 cM and 5.8 cM from the ms1 locus. On the whole, this information was crucial to plan a Genotyping-by-Sequencing experiment based on BC1 progenies with the aim of narrowing down the genomic window containing the gene for male-sterility in leaf chicory. Finally, the sequencing and assembly of the first genome draft of leaf chicory, will contribute to increase and reinforce the reliability of Italian seed firms and local activities of the Veneto region associated with the cultivation and commercialization of Radicchio plant varieties and food products; the seed market of this species will have the chance to become highly professional and more competitive at the national and international levels. We assembled a genome draft of an estimated size of 760 Mb. We obtained 58,392,530 and 389,385,400 raw reads through the MySeq and HiSeq platforms, respectively. Overall, we identified 66,785 SSR containing regions. Original data from the bioinformatic assembly of the first genome draft of Radicchio, along with the most relevant findings that emerged from an extensive de novo gene prediction and in silico functional annotation of more than 18,000 unigenes are critically discussed. To uncover the sequence of a given genome means to gain a robust scientific background and technological knowhow, which in short time can play a crucial role in addressing and solving issues related to the cultivation and protection of modern Radicchio varieties. In fact, we are confident that our efforts will extend the current knowledge of the genome organization and gene composition of leaf chicories, which is crucial in the development of new tools and diagnostic markers useful for our breeding strategies, and allow researchers for more focused studies on chromosome regions controlling relevant agronomic traits of Radicchio. In conclusion, the present work is a sort of handbook to better understand the world of a non-model species, i.e. leaf chicory, and it is mainly directed to breeders and seed producers dealing with leaf chicory

Toward a First High-quality Genome Draft for Marker-assisted Breeding in Leaf Chicory, Radicchio (Cichorium intybus L.)

Radicchio (Cichorium intybus subsp. intybus var. foliosum L.) is one of the most important leaf chicories, used mainly as a component for fresh salads. Recently, we sequenced and annotated the first draft of the leaf chicory genome, as we believe it will have an extraordinary impact from both scientific and economic points of view. Indeed, the availability of the first genome sequence for this plant species will provide a powerful tool to be exploited in the identification of markers associated with or genes responsible for relevant agronomic traits, influencing crop productivity and product quality. The plant material used for the sequencing of the leaf chicory genome belongs to the Radicchio of the Chioggia type. Genomic DNA was used for library preparation with the TruSeq DNA Sample Preparation chemistry (Illumina). Sequencing reactions were performed with the Illumina platforms HiSeq and MySeq, and sequence reads were then assembled and annotated. We are confident that our efforts will extend the current knowledge of the genome organization and gene composition of leaf chicory, which is crucial for developing new tools and diagnostic markers useful for our breeding strategies in Radicchio

Broadband near-infrared astronomical spectrometer calibration and on-sky validation with an electro-optic laser frequency comb

The quest for extrasolar planets and their characterisation as well as studies of fundamental physics on cosmological scales rely on capabilities of high-resolution astronomical spectroscopy. A central requirement is a precise wavelength calibration of astronomical spectrographs allowing for extraction of subtle wavelength shifts from the spectra of stars and quasars. Here, we present an all-fibre, 400 nm wide near-infrared frequency comb based on electro-optic modulation with 14.5 GHz comb line spacing. Tests on the high-resolution, near-infrared spectrometer GIANO-B show a photon-noise limited calibration precision of <10 cm/s as required for Earth-like planet detection. Moreover, the presented comb provides detailed insight into particularities of the spectrograph such as detector inhomogeneities and differential spectrograph drifts. The system is validated in on-sky observations of a radial velocity standard star (HD221354) and telluric atmospheric absorption features. The advantages of the system include simplicity, robustness and turn-key operation, features that are valuable at the observation sites

Optical pulsations from a transitional millisecond pulsar

Weakly magnetic, millisecond spinning neutron stars attain their very fast rotation through a 1E8-1E9 yr long phase during which they undergo disk-accretion of matter from a low mass companion star. They can be detected as accretion-powered millisecond X-ray pulsars if towards the end of this phase their magnetic field is still strong enough to channel the accreting matter towards the magnetic poles. When mass transfer is much reduced or ceases altogether, pulsed emission generated by particle acceleration in the magnetosphere and powered by the rotation of the neutron star is observed, preferentially in the radio and gamma-ray bands. A few transitional millisecond pulsars that swing between an accretion-powered X-ray pulsar regime and a rotationally-powered radio pulsar regime in response to variations of the mass in-flow rate have been recently identified. Here we report the detection of optical pulsations from a transitional pulsar, the first ever from a millisecond spinning neutron star. The pulsations were observed when the pulsar was surrounded by an accretion disk and originated inside the magnetosphere or within a few hundreds of kilometres from it. Energy arguments rule out reprocessing of accretion-powered X-ray emission and argue against a process related to accretion onto the pulsar polar caps; synchrotron emission of electrons in a rotation-powered pulsar magnetosphere seems more likely.Comment: 32 pages, 7 figures. The first two authors contributed equally to this wor

GIANO-TNG spectroscopy of red supergiants in the young star cluster RSGC3

The Scutum complex in the inner disk of the Galaxy has a number of young star clusters dominated by red supergiants that are heavily obscured by dust extinction and observable only at infrared wavelengths. These clusters are important tracers of the recent star formation and chemical enrichment history in the inner Galaxy. During the technical commissioning and as a first science verification of the GIANO spectrograph at the Telescopio Nazionale Galileo, we secured high-resolution (R=50,000) near-infrared spectra of five red supergiants in the young Scutum cluster RSGC3. Taking advantage of the full YJHK spectral coverage of GIANO in a single exposure, we were able to measure several tens of atomic and molecular lines that were suitable for determining chemical abundances. By means of spectral synthesis and line equivalent width measurements, we obtained abundances of Fe and iron-peak elements such as Ni, Cr, and Cu, alpha (O, Mg, Si, Ca, Ti), other light elements (C, N, F, Na, Al, and Sc), and some s-process elements (Y, Sr). We found average half-solar iron abundances and solar-scaled [X/Fe] abundance patterns for most of the elements, consistent with a thin-disk chemistry. We found depletion of [C/Fe] and enhancement of [N/Fe], consistent with standard CN burning, and low 12C/13C abundance ratios (between 9 and 11), which require extra-mixing processes in the stellar interiors during the post-main sequence evolution. We also found local standard of rest V(LSR)=106 km/s and heliocentric V(HEL)=90 km/s radial velocities with a dispersion of 2.3 km/s. The inferred radial velocities, abundances, and abundance patterns of RSGC3 are very similar to those previously measured in the other two young clusters of the Scutum complex, RSGC1 and RSGC2, suggesting a common kinematics and chemistry within the Scutum complex