Omics-directed Reverse Genetics Enables the Creation of New Productivity Traits for the Vegetable Oil Crop Canola

Bayer CropScience is a leader in the oilseed rape seeds business with a 2013 market share of 50% in Canada, based on the creation and use of a unique hybridization system enabling the development of high-yielding canola (B.napus) InVigor® hybrids. For the European markets, Bayer is developing non-transgenic hybrids that will be complemented with differentiating traits. To this end, a highly effective mutagenesis-based and omics-directed reverse genetics platform was established which enables the creation of novel productivity traits in canola.The reverse genetics process involves three major steps described in the following figure.The selection of relevant homoeologs is facilitated by Bayer's B.napus genome sequence and transcript atlas. The genome sequence allows the in silico identification of functional homoeologs and the transcript atlas enables to prioritize on homoeologs that are highly expressed in the right tissues. A new trait is created by stacking relevant mutant alleles in a single line. Bayer CropScience is using its canola reverse genetics platform to improve certain canola characteristics including pod shattering, grain yield and oil composition and to develop traits such as herbicide tolerance. Pod shatter reduction was the first trait developed with the platform. A first pod shatter-reduced InVigor hybrid, L140P, was commercially grown in Canada during the 2014 summer season. Bayer CropScience has established and is successfully using a this biotech-based platform for the improvement of the productivity of canola. The resulting traits do not require regulation and can be deployed in all continents. The major limitation of reverse genetics is that the scope of modification is limited to the crops’ own gene content and the expression levels of these genes

Ocean current connectivity propelling the secondary spread of a marine invasive comb jelly across western Eurasia

Publication history: Accepted - 15 February 2018; Published - 16 May 2018.Aim: Invasive species are of increasing global concern. Nevertheless, the mechanisms driving further distribution after the initial establishment of non-native species remain largely unresolved, especially in marine systems. Ocean currents can be a major driver governing range occupancy, but this has not been accounted for in most invasion ecology studies so far. We investigate how well initial establishment areas are interconnected to later occupancy regions to test for the potential role of ocean currents driving secondary spread dynamics in order to infer invasion corridors and the source–sink dynamics of a non-native holoplanktonic biological probe species on a continental scale. Location: Western Eurasia. Time period: 1980s–2016. Major taxa studied: ‘Comb jelly’ Mnemiopsis leidyi. Methods: Based on 12,400 geo-referenced occurrence data, we reconstruct the invasion history of M. leidyi in western Eurasia. We model ocean currents and calculate their stability to match the temporal and spatial spread dynamics with large-scale connectivity patterns via ocean currents. Additionally, genetic markers are used to test the predicted connectivity between subpopulations. Results: Ocean currents can explain secondary spread dynamics, matching observed range expansions and the timing of first occurrence of our holoplanktonic non-native biological probe species, leading to invasion corridors in western Eurasia. In northern Europe, regional extinctions after cold winters were followed by rapid recolonizations at a speed of up to 2,000 km per season. Source areas hosting year-round populations in highly interconnected regions can re-seed genotypes over large distances after local extinctions. Main conclusions: Although the release of ballast water from container ships may contribute to the dispersal of non-native species, our results highlight the importance of ocean currents driving secondary spread dynamics. Highly interconnected areas hosting invasive species are crucial for secondary spread dynamics on a continental scale. Invasion risk assessments should consider large-scale connectivity patterns and the potential source regions of non-native marine species.Danish Council for Independent Research; Grant/Award Number: DFF-1325-00102B; FP7 People: Marie-Curie Actions, Grant/Award Number: MOBILEX, DFF - 1325-00025; EU, BONUS, BMBF, Grant/ Award Number: 03F0682; Excellence Cluster “Future Ocean”, Grant/Award Number: CP153

Unique regulation of the Calvin cycle in the ultrasmall green alga Ostreococcus

Glyceraldehyde-3-phosphate dehydrogenase (GapAB) and CP12 are two major players in controlling the inactivation of the Calvin cycle in land plants at night. GapB originated from a GapA gene duplication and differs from GapA by the presence of a specific C-terminal extension that was recruited from CP12. While GapA and CP12 are assumed to be generally present in the Plantae (glaucophytes, red and green algae, and plants), up to now GapB was exclusively found in Streptophyta, including the enigmatic green alga Mesostigma viride. However, here we show that two closely related prasinophycean green algae, Ostreococcus tauri and Ostreococcus lucimarinus, also possess a GapB gene, while CP12 is missing. This remarkable finding either antedates the GapA/B gene duplication or indicates a lateral recruitment. Moreover, Ostreococcus is the first case where the crucial CP12 function may be completely replaced by GapB-mediated GapA/B aggregation

2007b. Unique regulation of the calvin cycle in the ultrasmall green alga Ostreococcus

Abstract. Glyceraldehyde-3-phosphate dehydrogenase (GapAB) and CP12 are two major players in controlling the inactivation of the Calvin cycle in land plants at night. GapB originated from a GapA gene duplication and differs from GapA by the presence of a specific C-terminal extension that was recruited from CP12. While GapA and CP12 are assumed to be generally present in the Plantae (glaucophytes, red and green algae, and plants), up to now GapB was exclusively found in Streptophyta, including the enigmatic green alga Mesostigma viride. However, here we show that two closely related prasinophycean green algae, Ostreococcus tauri and Ostreococcus lucimarinus, also possess a GapB gene, while CP12 is missing. This remarkable finding either antedates the GapA/B gene duplication or indicates a lateral recruitment. Moreover, Ostreococcus is the first case where the crucial CP12 function may be completely replaced by GapB-mediated GapA/B aggregation

Hydrogen peroxide-induced gene expression across kingdoms: a comparative analysis

Cells react to oxidative stress conditions by launching a defense response through the induction of nuclear gene expression. The advent of microarray technologies allowed monitoring of oxidative stress-dependent changes of transcript levels at a comprehensive and genome-wide scale, resulting in a series of inventories of differentially expressed genes in different organisms. We performed a meta-analysis on hydrogen peroxide (H2O2)-induced gene expression in the cyanobacterium Synechocystis PCC 6803, the yeast Saccharomyces cerevisiae and Schizosaccharomyces pombe, the land plant Arabidopsis thaliana, and the human HeLa cell line. The H2O2-induced gene expression in both yeast species was highly conserved and more similar to the A. thaliana response than that of the human cell line. Based on the expression characteristics of genuine antioxidant genes, we show that the antioxidant capacity of microorganisms and higher eukaryotes is differentially regulated. Four families of evolutionarily conserved eukaryotic proteins could be identified that were H2O2 responsive across kingdoms: DNAJ domain-containing heat shock proteins, small guanine triphosphate-binding proteins, Ca2+-dependent protein kinases, and ubiquitin-conjugating enzymes

Genome-wide analysis of core cell cycle genes in the unicellular green alga Ostreococcus tauri

The cell cycle has been extensively studied in various organisms, and the recent access to an overwhelming amount of genomic data has given birth to a new integrated approach called comparative genomics. Comparing the cell cycle across species shows that its regulation is evolutionarily conserved; the best-known example is the pivotal role of cyclin-dependent kinases in all the eukaryotic lineages hitherto investigated. Interestingly, the molecular network associated with the activity of the CDK-cyclin complexes is also evolutionarily conserved, thus, defining a core cell cycle set of genes together with lineage-specific adaptations. In this paper, we describe the core cell cycle genes of Ostreococcus tauri, the smallest free-living eukaryotic cell having a minimal cellular organization with a nucleus, a single chloroplast, and only one mitochondrion. This unicellular marine green alga, which has diverged at the base of the green lineage, shows the minimal yet complete set of core cell cycle genes described to date. It has only one homolog of CDKA, CDKB, CDKD, cyclin A, cyclin B, cyclin D, cyclin H, Cks, Rb, E2F, DP, DEL, Cdc25, and Wee L We have also added the APC and SCF E3 ligases to the core cell cycle gene set. We discuss the potential of genome-wide analysis in the identification of divergent orthologs of cell cycle genes in different lineages by mining the genomes of evolutionarily important and strategic organisms

The first green lineage cdc25 dual-specificity phosphatase

The Cdc25 protein phosphatase is a key enzyme involved in the regulation of the G(2)/M transition in metazoans and yeast. However, no Cdc25 ortholog has so far been identified in plants, although functional studies have shown that an activating dephosphorylation of the CDK-cyclin complex regulates the G(2)/M transition. In this paper, the first green lineage Cdc25 ortholog is described in the unicellular alga Ostreococcus tauri. It encodes a protein which is able to rescue the yeast S. pombe cdc25-22 conditional mutant. Furthermore, microinjection of GST-tagged O. tauri Cdc25 specifically activates prophase-arrested starfish oocytes. In vitro histone H1 kinase assays and anti-phosphotyrosine Western Blotting confirmed the in vivo activating dephosphorylation of starfish CDK1-cyclinB by recombinant O. tauri Cdc25. We propose that there has been coevolution of the regulatory proteins involved in the control of M-phase entry in the metazoan, yeast and green lineages