Application of a high-resolution genetic map for chromosome-scale genome assembly and fine QTLs mapping of seed size and weight traits in castor bean.

Castor bean (Ricinus communis L., Euphorbiaceae) is a critical biodiesel crop and its seed derivatives have important industrial applications. Due to lack of a high-density genetic map, the breeding and genetic improvement of castor bean has been largely restricted. In this study, based on a recombinant inbred line (RIL) population consisting of 200 individuals, we generated 8,896 high-quality genomic SNP markers and constructed a high-resolution genetic map with 10 linkage groups (LGs), spanning 1,852.33 centiMorgan (cM). Based on the genetic map, 996 scaffolds from the draft reference genome were anchored onto 10 pseudo-chromosomes, covering 84.43% of the castor bean genome. Furthermore, the quality of the pseudo-chromosome scale assembly genome was confirmed via genome collinearity analysis within the castor bean genome as well as between castor bean and cassava. Our results provide new evidence that the phylogenetic position of castor bean is relatively solitary from other taxa in the Euphorbiaceae family. Based on the genetic map, we identified 16 QTLs that control seed size and weight (covering 851 candidate genes). The findings will be helpful for further research into potential new mechanisms controlling seed size and weight in castor bean. The genetic map and improved pseudo-chromosome scale genome provide crucial foundations for marker-assisted selection (MAS) of QTL governing important agronomic traits, as well as the accelerated molecular breeding of castor bean in a cost-effective pattern.

Assessment of attractiveness of cassava as a roosting plant for the melon fly, Bactrocera cucurbitae, and the Oriental fruit fly, B. dorsalis.

Application of bait spray to crop borders is a standard approach for suppression of melon fly, Bactrocera cucurbitae (Coquillett) (Diptera: Tephritidae) populations and may also be of value for suppression of oriental fruit fly, B. dorsalis (Hendel) populations. Establishment of preferred roosting hosts as crop borders may help to improve suppression of both fruit fly species by providing sites for bait spray applications. In an area-wide B. cucurbitae suppression trial, the question was raised as to whether cassava, Manihot esculenta Crantz (Euphorbiales: Euphorbiaceae), could be used as a B. cucurbitae roosting host. M. esculenta was of interest as a roosting host because, in contrast to many other identified preferred roosting hosts, it would also be a crop potentially increasing the productivity of the crop production system overall. As a short-lived and shrubby perennial, M. esculenta potentially constitutes a crop with more persistent roosting foliage than an annual crop such as corn, Zea mays L. (Cyperales: Poaceae), that has often been planted as a roosting host for B. cucurbitae control. Using protein-baited traps set amidst potted plants placed adjacent to a papaya Carica papaya L. (Violales: Caricaceae) orchard known to have established populations of B. cucurbitae and B. dorsalis, the effectiveness of M. esculenta as a roosting host was assessed by comparing its attractiveness to that of castor bean, Ricinus communis L (Malpighiales: Euphorbiaceae), previously identified as one of the most attractive roosting hosts for B. cucurbitae, and to corn, a crop which has been planted as a roosting host for help in B. cucurbitae control. The results showed that use of M. esculenta as a roosting host is comparable to use of R. communis by both B. cucurbitae and B. dorsalis. These results provide encouragement to incorporate M. esculenta on a farm as a trap crop (i.e. site for bait spray application). This has the advantage of having the trap crop be a crop on its own (as opposed to castor bean) and, among prospective crops that could be used as a trap crop, has foliage more persistent than an annual trap crop such as corn.

A phloem-enriched cDNA library from Ricinus: insights into phloem function.

The aim of this study was to identify genes that are expressed in the phloem. Increased knowledge of phloem regulation will contribute to our understanding of its many roles, from transport of solutes to information about interactions with pathogens. A cDNA library constructed from phloem-enriched sap exuding from cut Ricinus communis (L.) hypocotyls was sequenced. To assess contamination from other tissues, two libraries were constructed: one using the first 15 min of exudation and the other from sap collected after 120 min of exudation had elapsed. Of 1012 clones sequenced, 158 unique transcripts were identified. The presence of marker molecules such as profilin, the low occurrence of chloroplast-related mRNAs, and the sieve element localization of constituent mRNA using in situ hybridization were consistent with a phloem origin of the sap. Functional analysis of the cDNAs revealed classifications including ribosomal function, interaction with the environment, transport, DNA/RNA binding, and protein turnover. An analysis of the closest Arabidopsis thaliana (L.) homologue for each clone indicated that genes involved in cell localization, protein synthesis, tissue localization, organ localization, organ differentiation, and cell fate were represented at twice the level occurring in the whole Arabidopsis genome. The transcripts found in this phloem-enriched library are discussed in the context of phloem function and the relationship between the companion cell and sieve element.

Flow encoded NMR spectroscopy for quantification of metabolite flow in intact plants.

An NMR flow quantification technique applicable to metabolite flow in plants is presented. It combines flow sensitive magnetization preparation with slice selective spectroscopy. Flow encoded NMR spectroscopy is described to quantify, for the first time, flow velocities of metabolites in plants non-invasively. Flow sensitivity is introduced by magnetization preparation based on a stimulated echo experiment, prior to slice selective spectroscopy. For flow quantification eight different flow-weighted spectra are collected. With this flow preparation very slow flow velocities down to 0.1mm/s can be detected and small amounts of flowing metabolites can be observed despite the large background signal of stationary and flowing water. Important sequence optimization steps include appropriate choice of experimental parameters used for flow encoding as well as complete balancing of eddy currents from the flow encoding gradients. The method was validated in phantom experiments and applied in vivo. Examples of quantitative flow measurements of water and metabolites in phantoms and plants are provided to demonstrate the reliability and the performance of flow encoded spectroscopy.

Long-distance signalling from roots to shoots assessed: the flooding story.

Several kinds of signal may be generated when roots are exposed to an environmental stress. Some, but not all, are conveyed to shoots in the transpiration stream. Principles are summarized that may help establish experimentally the presence or intensity of root signals transported by transpiration. In many dryland species, flooding of the soil induces developmental responses in the shoot such as epinastic leaf curvature, stomatal closure and slowing of leaf expansion. These reactions compensate for diminished input of resources from the roots. They lend themselves to the study of root-to-shoot signalling by commencing after a time lag of only a few hours, by persisting for several days and by being highly reproducible. Evidence implicating chemical and hydraulic signals in promoting stomatal closure and epinastic curvature in flooded plants is reviewed. Further progress will depend upon examining a wider range of putative signals, accounting for any interactions between them and improving methods for the evaluation of signal durability in transit, and effectiveness at target sites.

Fast NMR flow measurements in plants using FLASH imaging.

A fast method for quantitative NMR imaging of flow velocities in intact plants is described. The purpose of this method is to observe dynamic changes of flow velocity in the xylem of plants after fast changes of environmental conditions. The spatial image resolution is 47 x 188 micrometer(2) in-plane. The method applies a fast gradient echo sequence (FLASH). Compared to other flow NMR imaging sequences, the imaging time was reduced by a factor of 6 with comparable signal-to-noise ratio. A complete flow measurement consists of a set of 8 different flow weighted images with a total acquisition time of 3.5 min.