Genome structure and evolution in the cruciferous tribe Thlaspideae (Brassicaceae)

Whole-genome duplications (WGDs) and chromosome rearrangements (CRs) play the key role in driving the diversification and evolution of plant lineages. Although the direct link between WGDs and plant diversification is well documented, relatively few studies focus on the evolutionary significance of CRs. The cruciferous tribe Thlaspideae represents an ideal model system to address the role of large-scale chromosome alterations in genome evolution, as most Thlaspideae species share the same diploid chromosome number (2n = 2x = 14). Here we constructed the genome structure in 12 Thlaspideae species, including field pennycress (Thlaspi arvense) and garlic mustard (Alliaria petiolata). We detected and precisely characterized genus- and species-specific CRs, mostly pericentric inversions, as the main genome-diversifying drivers in the tribe. We reconstructed the structure of seven chromosomes of an ancestral Thlaspideae genome, identified evolutionary stable chromosomes versus chromosomes prone to CRs, estimated the rate of CRs, and uncovered an allohexaploid origin of garlic mustard from diploid taxa closely related to A. petiolata and Parlatoria cakiloidea. Furthermore, we performed detailed bioinformatic analysis of the Thlaspideae repeatomes, and identified repetitive elements applicable as unique species- and genus-specific barcodes and chromosome landmarks. This study deepens our general understanding of the evolutionary role of CRs, particularly pericentric inversions, in plant genome diversification, and provides a robust base for follow-up whole-genome sequencing efforts.     

Molecular tools enabling pennycress (Thlaspi arvense) as a model plant and oilseed cash cover crop

Thlapsi arvense L. (pennycress) is being developed as a profitable oilseed cover crop for the winter fallow period throughout the temperate regions of the world, controlling soil erosion and nutrients run‐off on otherwise barren farmland. We demonstrate that pennycress can serve as a user‐friendly model system akin to Arabidopsis that is well‐suited for both laboratory and field experimentation. We sequenced the diploid genome of the spring‐type Spring 32‐10 inbred line (1C DNA content of 539 Mb; 2n = 14), identifying variation that may explain phenotypic differences with winter‐type pennycress, as well as predominantly a one‐to‐one correspondence with Arabidopsis genes, which makes translational research straightforward. We developed an Agrobacterium‐mediated floral dip transformation method (0.5% transformation efficiency) and introduced CRISPR‐Cas9 constructs to produce indel mutations in the putative FATTY ACID ELONGATION1 (FAE1) gene, thereby abolishing erucic acid production and creating an edible seed oil comparable to that of canola. We also stably transformed pennycress with the Euonymus alatus diacylglycerol acetyltransferase (EaDAcT) gene, producing low‐viscosity acetyl‐triacylglycerol‐containing seed oil suitable as a diesel‐engine drop‐in fuel. Adoption of pennycress as a model system will accelerate oilseed‐crop translational research and facilitate pennycress’ rapid domestication to meet the growing sustainable food and fuel demands.     

Conserving Britain's biodiversity. I:Thlaspi perfoliatum L. (Brassicaceae), Cotswold Pennycress

This paper describes the decline and conservation work carried out on the rare, statutorily protected species Thlaspi perfoliatum L. (Brassicaceae), Cotswold Pennycress, in England. This plant has been recorded historically in a total of about 45 native and 37 introduced sites. Surveys between 1986 and 1997 found populations in nine native sites and three introduced sites, suggesting an 80% loss of native and 92% loss of introduced colonies. The main reasons for decline are probably agricultural improvements, quarrying and neglect of management. The plant is a winter annual of open grassland and screes on Oolite limestone, which requires maintenance of open conditions for long-term survival. Current and recommended forms of management of sites are outlined. Only two sites have appropriate statutory protection.     

A draft genome of field pennycress (Thlaspi arvense) provides tools for the domestication of a new winter biofuel crop

Field pennycress (Thlaspi arvense L.) is being domesticated as a new winter cover crop and biofuel species for the Midwestern United States that can be double-cropped between corn and soybeans. A genome sequence will enable the use of new technologies to make improvements in pennycress. To generate a draft genome, a hybrid sequencing approach was used to generate 47 Gb of DNA sequencing reads from both the Illumina and PacBio platforms. These reads were used to assemble 6,768 genomic scaffolds. The draft genome was annotated using the MAKER pipeline, which identified 27,390 predicted protein-coding genes, with almost all of these predicted peptides having significant sequence similarity to Arabidopsis proteins. A comprehensive analysis of pennycress gene homologues involved in glucosinolate biosynthesis, metabolism, and transport pathways revealed high sequence conservation compared with other Brassicaceae species, and helps validate the assembly of the pennycress gene space in this draft genome. Additional comparative genomic analyses indicate that the knowledge gained from years of basic Brassicaceae research will serve as a powerful tool for identifying gene targets whose manipulation can be predicted to result in improvements for pennycress.     

Efficacy of Organic Soil Amendments for Management of Heterodera glycines in Greenhouse Experiments

In a repeated greenhouse experiment, organic soil amendments were screened for effects on population density of soybean cyst nematode (SCN), Heterodera glycines, and soybean growth. Ten amendments at various rates were tested: fresh plant material of field pennycress, marigold, spring camelina, and Cuphea; condensed distiller’s solubles (CDS), ash of combusted CDS, ash of combusted turkey manure (TMA), marigold powder, canola meal, and pennycress seed powder. Soybeans were grown for 70 d in field soil with amendments and SCN eggs incorporated at planting. At 40 d after planting (DAP), many amendments reduced SCN egg population density, but some also reduced plant height. Cuphea plant at application rate of 2.9% (amendment:soil, w:w, same below), marigold plant at 2.9%, pennycress seed powder at 0.5%, canola meal at 1%, and CDS at 4.3% were effective against SCN with population reductions of 35.2%, 46.6%, 46.7%, 73.2%, and 73.3% compared with control, respectively. For Experiment 1 at 70 DAP, canola meal at 1% and pennycress seed powder at 0.5% reduced SCN population density 70% and 54%, respectively. CDS at 4.3%, ash of CDS at 0.2%, and TMA at 1% increased dry plant mass whereas CDS at 4.3% and pennycress seed powder at 0.1% reduced plant height. For Experiment 2 at 70 DAP, amendments did not affect SCN population nor plant growth. In summary, some amendments were effective for SCN management, but phytoxicity was a concern.     

Winter oilseed production for biofuel in the US Corn Belt: opportunities and limitations

Interest from the US commercial aviation industry and commitments established by the US Navy and Air Force to use renewable fuels has spurred interest in identifying and developing crops for renewable aviation fuel. Concern regarding greenhouse gas emissions associated with land‐use change and shifting land grown for food to feedstock production for fuel has encouraged the concept of intensifying current prominent cropping systems through various double cropping strategies. Camelina (Camelina sativa L.) and field pennycress (Thlaspi arvense L.) are two winter oilseed crops that could potentially be integrated into the corn (Zea mays L.)–soybean [(Glycine max (L.) Merr.] cropping system, which is the prominent cropping system in the US Corn Belt. In addition to providing a feedstock for renewable aviation fuel production, integrating these crops into corn–soybean cropping systems could also potentially provide a range of ecosystem services. Some of these include soil protection from wind and water erosion, soil organic C (SOC) sequestration, water quality improvement through nitrate reduction, and a food source for pollinators. However, integration of these crops into corn–soybean cropping systems also carries possible limitations, such as potential yield reductions of the subsequent soybean crop. This review identifies and discusses some of the key benefits and constraints of integrating camelina or field pennycress into corn–soybean cropping systems and identifies generalized areas for potential adoption in the US Corn Belt.     

Soybean Cyst Nematode Population Development and its Effect on Pennycress in a Greenhouse Study

Midwest crop production is dominated by two summer annual crops grown in rotation, viz., corn (Zea mays L.) and soybean (Glycine max L.). Winter oilseed crops, such as pennycress (Thlaspi arvense L.), can provide ecosystem and economic benefits when added to the corn–soybean rotation. However, adding a new crop adds risks, such as increased pest pressure. The objectives of this study were to (i) evaluate population development of three soybean cyst nematode (SCN; Heterodera glycines) biotypes on three pennycress genotypes and susceptible soybean and (ii) determine whether SCN inoculation level influenced plant biomass. SCN population density and biomass were determined after 60 d in the greenhouse. At the inoculation level of 2,000 eggs/100 cm³ soil, the average egg density for the three pennycress genotypes was 1,959 eggs/100 cm³ soil, lower than that for the susceptible soybean ‘Sturdy’ (9,601 eggs/100 cm³ soil). At the inoculation level of 20,000 eggs/100 cm³ soil, the average egg density for the three pennycress genotypes was 6,668 eggs/100 cm³ soil, lower than that for ‘Sturdy’ (40,740 eggs/100 cm³ soil). The inoculation level did not affect plant biomass. Pennycress is an alternative host to SCN under greenhouse conditions but is a less suitable host than soybean.