Management of pennycress as a winter annual cash cover crop. A review

Potential insect threats to pennycress, Thlaspi arvense (Brassicales: Brassicaceae), an emerging oilseed cover crop

Pennycress (Thlaspi arvense L.) is an annual plant in temperate regions that often grows as a weed. Pennycress is being domesticated as a new winter cover crop and oilseed crop for incorporation in the Midwest United States corn-soybean rotation, where it could offer economic and environmental benefits. While pennycress is gaining attention as a promising new crop, there remains a significant gap in understanding its interaction with insect communities and agroecosystems. This review compiles available information on insect herbivores (potential pests) and beneficial insects associated with pennycress growing in the wild (natural areas) or as a weed in agricultural areas. The limited knowledge on the response of pennycress to stressors (defoliation, stem injury and stand loss) similar to injury that could be caused by insects is also compiled here. By shedding light on the insects associated with pennycress and how pennycress might respond to injury from insect pests, this review sets the stage for further research and development of integrated pest management programs for insect pests of this new crop.

Transcriptomic and lipidomic analysis of the differential pathway contribution to the incorporation of erucic acid to triacylglycerol during Pennycress seed maturation

Thlaspi arvense (Pennycress) is an emerging feedstock for biofuel production because of its high seed oil content enriched in erucic acid. A transcriptomic and a lipidomic study were performed to analyze the dynamics of gene expression, glycerolipid content and acyl-group distribution during seed maturation. Genes involved in fatty acid biosynthesis were expressed at the early stages of seed maturation. Genes encoding enzymes of the Kennedy pathway like diacylglycerol acyltransferase1 (TaDGAT1), lysophosphatidic acid acyltransferase (TaLPAT) or glycerol 3-phosphate acyltransferase (TaGPAT) increased their expression with maturation, coinciding with the increase in triacylglycerol species containing 22:1. Positional analysis showed that the most abundant triacylglycerol species contained 18:2 at sn-2 position in all maturation stages, suggesting no specificity of the lysophosphatidic acid acyltransferase for very long chain fatty acids. Diacylglycerol acyltransferase2 (TaDGAT2) mRNA was more abundant at the initial maturation stages, coincident with the rapid incorporation of 22:1 to triacylglycerol, suggesting a coordination between Diacylglycerol acyltransferase enzymes for triacylglycerol biosynthesis. Genes encoding the phospholipid-diacylglycerol acyltransferase (TaPDAT1), lysophosphatidylcholine acyltransferase (TaLPCAT) or phosphatidylcholine diacylglycerolcholine phosphotransferase (TaPDCT), involved in acyl-editing or phosphatidyl-choline (PC)-derived diacylglycerol (DAG) biosynthesis showed also higher expression at the early maturation stages, coinciding with a higher proportion of triacylglycerol containing C18 fatty acids. These results suggested a higher contribution of these two pathways at the early stages of seed maturation. Lipidomic analysis of the content and acyl-group distribution of diacylglycerol and phosphatidyl-choline pools was compatible with the acyl content in triacylglycerol at the different maturation stages. Our data point to a model in which a strong temporal coordination between pathways and isoforms in each pathway, both at the expression and acyl-group incorporation, contribute to high erucic triacylglycerol accumulation in Pennycress.

Transposon dynamics in the emerging oilseed crop Thlaspi arvense

Genome evolution is partly driven by the mobility of transposable elements (TEs) which often leads to deleterious effects, but their activity can also facilitate genetic novelty and catalyze local adaptation. We explored how the intraspecific diversity of TE polymorphisms might contribute to the broad geographic success and adaptive capacity of the emerging oil crop Thlaspi arvense (field pennycress). We classified the TE inventory based on a high-quality genome assembly, estimated the age of retrotransposon TE families and comprehensively assessed their mobilization potential. A survey of 280 accessions from 12 regions across the Northern hemisphere allowed us to quantify over 90,000 TE insertion polymorphisms (TIPs). Their distribution mirrored the genetic differentiation as measured by single nucleotide polymorphisms (SNPs). The number and types of mobile TE families vary substantially across populations, but there are also shared patterns common to all accessions. Ty3/Athila elements are the main drivers of TE diversity in T. arvense populations, while a single Ty1/Alesia lineage might be particularly important for transcriptome divergence. The number of retrotransposon TIPs is associated with variation at genes related to epigenetic regulation, including an apparent knockout mutation in BROMODOMAIN AND ATPase DOMAIN-CONTAINING PROTEIN 1 (BRAT1), while DNA transposons are associated with variation at the HSP19 heat shock protein gene. We propose that the high rate of mobilization activity can be harnessed for targeted gene expression diversification, which may ultimately present a toolbox for the potential use of transposition in breeding and domestication of T. arvense.

Metabolic and transcriptomic study of pennycress natural variation identifies targets for oil improvement

Pennycress (Thlaspi arvense L.), a member of the Brassicaceae family, produces seed oil high in erucic acid, suitable for biodiesel and aviation fuel. Although pennycress, a winter annual, could be grown as a dedicated bioenergy crop, an increase in its seed oil content is required to improve its economic competitiveness. The success of crop improvement relies upon finding the right combination of biomarkers and targets, and the best genetic engineering and/or breeding strategies. In this work, we combined biomass composition with metabolomic and transcriptomic studies of developing embryos from 22 pennycress natural variants to identify targets for oil improvement. The selected accession collection presented diverse levels of fatty acids at maturity ranging from 29% to 41%. Pearson correlation analyses, weighted gene co-expression network analysis and biomarker identifications were used as complementary approaches to detect associations between metabolite level or gene expression and oil content at maturity. The results indicated that improving seed oil content can lead to a concomitant increase in the proportion of erucic acid without affecting the weight of embryos. Processes, such as carbon partitioning towards the chloroplast, lipid metabolism, photosynthesis, and a tight control of nitrogen availability, were found to be key for oil improvement in pennycress. Besides identifying specific targets, our results also provide guidance regarding the best timing for their modification, early or middle maturation. Thus, this work lays out promising strategies, specific for pennycress, to accelerate the successful development of lines with increased seed oil content for biofuel applications.

Evaluation of soybean selection and sowing date in a continuous cover relay-cropping system with pennycress

Pennycress (Thlaspi arvense L.) is a new winter annual oilseed crop that can be integrated as a “cash cover crop” in Midwestern USA cropping systems. Relay-cropping pennycress with soybean [Glycine max (L.) Merr.] has been shown as an effective way to produce three crops over 2 years while providing living cover on the agricultural landscape nearly year-round. However, management improvements are needed to optimize pennycress and soybean production in this new system. A 2-year field study was conducted to evaluate three soybean interseeding dates (based on pennycress growth stage) and three soybean cultivars (varied in maturity date) on the overall productivity of this relay system. Interseeding dates were SD1 (rosette stage), SD2 (bolting stage), and SD3 (initial flowering), and soybean cultivars were MG0.2 (early), MG1.1 (standard), and MG1.7 (late). In the second season, relaying soybean reduced pennycress seed yield compared with its monocrop counterpart, but the reduction was lowest (23%) at SD2. Cultivar maturity group impacted soybean seed yields in the relay system, which for MG0.2, MG1.1, and MG1.7 averaged 2,589, 3,196, and 3,445 kg ha−1, respectively. Although there was soybean yield drag associated with relay cropping, the seed yield of the MG1.7 cultivar relay interseeded at SD2 was not significantly different from a monocropped MG1.1 soybean using conventional practice (CP; winter fallow, no pennycress). The results indicate that relay interseeding of longer maturity (MG1.7) soybean for the region at the bolting stage (SD2) of pennycress optimized overall system productivity while keeping the continuous living cover on the agricultural landscape. More research will likely be needed to improve soybean selection and management regionally for this unique relay system.

Effective Mechanisms for Improving Seed Oil Production in Pennycress (Thlaspi arvense L.) Highlighted by Integration of Comparative Metabolomics and Transcriptomics

Pennycress is a potentially lucrative biofuel crop due to its high content of long-chain unsaturated fatty acids, and because it uses non-conventional pathways to achieve efficient oil production. However, metabolic engineering is required to improve pennycress oilseed content and make it an economically viable source of aviation fuel. Research is warranted to determine if further upregulation of these non-conventional pathways could improve oil production within the species even more, which would indicate these processes serve as promising metabolic engineering targets and could provide the improvement necessary for economic feasibility of this crop. To test this hypothesis, we performed a comparative biomass, metabolomic, and transcriptomic analyses between a high oil accession (HO) and low oil accession (LO) of pennycress to assess potential factors required to optimize oil content. An evident reduction in glycolysis intermediates, improved oxidative pentose phosphate pathway activity, malate accumulation in the tricarboxylic acid cycle, and an anaplerotic pathway upregulation were noted in the HO genotype. Additionally, higher levels of threonine aldolase transcripts imply a pyruvate bypass mechanism for acetyl-CoA production. Nucleotide sugar and ascorbate accumulation also were evident in HO, suggesting differential fate of associated carbon between the two genotypes. An altered transcriptome related to lipid droplet (LD) biosynthesis and stability suggests a contribution to a more tightly-packed LD arrangement in HO cotyledons. In addition to the importance of central carbon metabolism augmentation, alternative routes of carbon entry into fatty acid synthesis and modification, as well as transcriptionally modified changes in LD regulation, are key aspects of metabolism and storage associated with economically favorable phenotypes of the species.

Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates

Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field-based model species for genetics and epigenetics. The availability of a high-quality reference genome is vital for understanding pennycress physiology and for clarifying its evolutionary history within the Brassicaceae. Here, we present a chromosome-level genome assembly of var. MN106-Ref with improved gene annotation and use it to investigate gene structure differences between two accessions (MN108 and Spring32-10) that are highly amenable to genetic transformation. We describe non-coding RNAs, pseudogenes and transposable elements, and highlight tissue-specific expression and methylation patterns. Resequencing of forty wild accessions provided insights into genome-wide genetic variation, and QTL regions were identified for a seedling colour phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across the Brassicaceae.

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.

Plant Breeding for Intercropping in Temperate Field Crop Systems: A Review

Monoculture cropping systems currently dominate temperate agroecosystems. However, intercropping can provide valuable benefits, including greater yield stability, increased total productivity, and resilience in the face of pest and disease outbreaks. Plant breeding efforts in temperate field crops are largely focused on monoculture production, but as intercropping becomes more widespread, there is a need for cultivars adapted to these cropping systems. Cultivar development for intercropping systems requires a systems approach, from the decision to breed for intercropping systems through the final stages of variety testing and release. Design of a breeding scheme should include information about species variation for performance in intercropping, presence of genotype × management interaction, observation of key traits conferring success in intercropping systems, and the specificity of intercropping performance. Together this information can help to identify an optimal selection scheme. Agronomic and ecological knowledge are critical in the design of selection schemes in cropping systems with greater complexity, and interaction with other researchers and key stakeholders inform breeding decisions throughout the process. This review explores the above considerations through three case studies: (1) forage mixtures, (2) perennial groundcover systems (PGC), and (3) soybean-pennycress intercropping. We provide an overview of each cropping system, identify relevant considerations for plant breeding efforts, describe previous breeding focused on the cropping system, examine the extent to which proposed theoretical approaches have been implemented in breeding programs, and identify areas for future development.

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.

CRISPR/Cas9-Induced fad2 and rod1 Mutations Stacked With fae1 Confer High Oleic Acid Seed Oil in Pennycress (Thlaspi arvense L.)

Pennycress (Thlaspi arvense L.) is being domesticated as an oilseed cash cover crop to be grown in the off-season throughout temperate regions of the world. With its diploid genome and ease of directed mutagenesis using molecular approaches, pennycress seed oil composition can be rapidly tailored for a plethora of food, feed, oleochemical and fuel uses. Here, we utilized Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 technology to produce knockout mutations in the FATTY ACID DESATURASE2 (FAD2) and REDUCED OLEATE DESATURATION1 (ROD1) genes to increase oleic acid content. High oleic acid (18:1) oil is valued for its oxidative stability that is superior to the polyunsaturated fatty acids (PUFAs) linoleic (18:2) and linolenic (18:3), and better cold flow properties than the very long chain fatty acid (VLCFA) erucic (22:1). When combined with a FATTY ACID ELONGATION1 (fae1) knockout mutation, fad2 fae1 and rod1 fae1 double mutants produced ∼90% and ∼60% oleic acid in seed oil, respectively, with PUFAs in fad2 fae1 as well as fad2 single mutants reduced to less than 5%. MALDI-MS spatial imaging analyses of phosphatidylcholine (PC) and triacylglycerol (TAG) molecular species in wild-type pennycress embryo sections from mature seeds revealed that erucic acid is highly enriched in cotyledons which serve as storage organs, suggestive of a role in providing energy for the germinating seedling. In contrast, PUFA-containing TAGs are enriched in the embryonic axis, which may be utilized for cellular membrane expansion during seed germination and seedling emergence. Under standard growth chamber conditions, rod1 fae1 plants grew like wild type whereas fad2 single and fad2 fae1 double mutant plants exhibited delayed growth and overall reduced heights and seed yields, suggesting that reducing PUFAs below a threshold in pennycress had negative physiological effects. Taken together, our results suggest that combinatorial knockout of ROD1 and FAE1 may be a viable route to commercially increase oleic acid content in pennycress seed oil whereas mutations in FAD2 will likely require at least partial function to avoid fitness trade-offs.

Technologies enabling rapid crop improvements for sustainable agriculture: example pennycress (Thlaspi arvense L.)

Growing concerns over food insecurity and ecosystems health related to population growth and climate change have challenged scientists to develop new crops, employing revolutionary technologies in combination with traditional methods. In this review, we discuss the domestication of the oilseed-producing cover crop pennycress, which along with the development of other new crops and improvements to farming practices can provide sustainable solutions to address malnutrition and environmental impacts of production agriculture. We highlight some of the new technologies such as bioinformatics-enabled next-generation sequencing and CRISPR genome editing in combination with traditional mutation breeding that has accelerated pennycress development as a new crop and a potential model system. Furthermore, we provide a brief overview of the technologies that can be integrated for improving pennycress and other crops and the status of pennycress development using these technologies.