Heat stress during seed development leads to impaired physiological function and plasticity in seed oil accumulation in Camelina sativa

Camelina sativa, a member of the Brassicaceae, is a low-cost, renewable oilseed crop that produces seeds up to 40% oil by weight with high potential for use in food, feed, and biofuel applications. Camelina seeds contain high levels of the fatty acids α-linolenic acid (C18:3), linoleic acid (C18:2), oleic acid (C18:1), and gondoic acid (C20:1), which have high nutritional and industrial value. The impact of climate change, especially increased frequency and amplitude of heat waves, poses a serious threat to crop productivity. In this study, we evaluated the effect of elevated temperatures post-anthesis on the developing seeds of C. sativa and performed physiological, morphological, and chemical characterizations at 7, 14, 21, and 28 days post-anthesis (DPA), as well as at maturity. While the seed oil accumulation peaked at 21 DPA under control conditions, reaching 406mg/g dry weight, under heat stress it was only 186mg/g. Physiologically, transpiration rate (E) and internal CO2 concentration (Ci) increased between 2 to 9 days post-stress imposition and overall net photosynthesis was impaired. Seed yield, seed weight, and oil content reduced by 84.5%, 38.5% and 54.1% respectively. We demonstrate that post-anthesis heat stress causes severe yield losses and developmental plasticity in fatty acid accumulation in oilseeds

Cold stress induces differential gene expression of retained homeologs in Camelina sativa cv Suneson

Camelina sativa (L.) Crantz, a member of the Brassicaceae, has potential as a biofuel feedstock which is attributable to the production of fatty acids in its seeds, its fast growth cycle, and low input requirements. While a genome assembly is available for camelina, it was generated from short sequence reads and is thus highly fragmented in nature. Using long read sequences, we generated a chromosome-scale, highly contiguous genome assembly (644,491,969 bp) for the spring biotype cultivar ‘Suneson’ with an N50 contig length of 12,031,512 bp and a scaffold N50 length of 32,184,682 bp. Annotation of protein-coding genes revealed 91,877 genes that encode 133,355 gene models. We identified a total of 4,467 genes that were significantly up-regulated under cold stress which were enriched in gene ontology terms associated with “response to cold” and “response to abiotic stress”. Coexpression analyses revealed multiple coexpression modules that were enriched in genes differentially expressed following cold stress that had putative functions involved in stress adaptation, specifically within the plastid. With access to a highly contiguous genome assembly, comparative analyses with Arabidopsis thaliana revealed 23,625 A. thaliana genes syntenic with 45,453 Suneson genes. Of these, 24,960 Suneson genes were syntenic to 8,320 A. thaliana genes reflecting a 3 camelina homeolog to 1 Arabidopsis gene relationship and retention of all three homeologs. Some of the retained triplicated homeologs showed conserved gene expression patterns under control and cold-stressed conditions whereas other triplicated homeologs displayed diverged expression patterns revealing sub- and neo-functionalization of the homeologs at the transcription level. Access to the chromosome-scale assembly of Suneson will enable both basic and applied research efforts in the improvement of camelina as a sustainable biofuel feedstock

Genome Editing for Crop Improvement – Applications in Clonally Propagated Polyploids With a Focus on Potato (Solanum tuberosum L.)

Genome-editing has revolutionized biology. When coupled with a recently streamlined regulatory process by the U.S. Department of Agriculture and the potential to generate transgene-free varieties, genome-editing provides a new avenue for crop improvement. For heterozygous, polyploid and vegetatively propagated crops such as cultivated potato, Solanum tuberosum Group Tuberosum L., genome-editing presents tremendous opportunities for trait improvement. In potato, traits such as improved resistance to cold-induced sweetening, processing efficiency, herbicide tolerance, modified starch quality and self-incompatibility have been targeted utilizing CRISPR/Cas9 and TALEN reagents in diploid and tetraploid clones. However, limited progress has been made in other such crops including sweetpotato, strawberry, grapes, citrus, banana etc., In this review we summarize the developments in genome-editing platforms, delivery mechanisms applicable to plants and then discuss the recent developments in regulation of genome-edited crops in the United States and The European Union. Next, we provide insight into the challenges of genome-editing in clonally propagated polyploid crops, their current status for trait improvement with future prospects focused on potato, a global food security crop

Overcoming Self-Incompatibility in Diploid Potato Using CRISPR-Cas9

Potato breeding can be redirected to a diploid inbred/F1 hybrid variety breeding strategy if self-compatibility can be introduced into diploid germplasm. However, the majority of diploid potato clones (Solanum spp.) possess gametophytic self-incompatibility that is primarily controlled by a single multiallelic locus called the S-locus which is composed of tightly linked genes, S-RNase (S-locus RNase) and multiple SLFs (S-locus F-box proteins), which are expressed in the style and pollen, respectively. Using S-RNase genes known to function in the Solanaceae gametophytic SI mechanism, we identified S-RNase alleles with flower-specific expression in two diploid self-incompatible potato lines using genome resequencing data. Consistent with the location of the S-locus in potato, we genetically mapped the S-RNase gene using a segregating population to a region of low recombination within the pericentromere of chromosome 1. To generate self-compatible diploid potato lines, a dual single-guide RNA (sgRNA) strategy was used to target conserved exonic regions of the S-RNase gene and generate targeted knockouts (KOs) using a Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (Cas9) approach. Self-compatibility was achieved in nine S-RNase KO T0 lines which contained bi-allelic and homozygous deletions/insertions in both genotypes, transmitting self compatibility to T1 progeny. This study demonstrates an efficient approach to achieve stable, consistent self-compatibility through S-RNase KO for use in diploid potato breeding approaches

Evaluation of Methods to Assess in vivo Activity of Engineered Genome-Editing Nucleases in Protoplasts

Genome-editing is being implemented in increasing number of plant species using engineered sequence specific nucleases (SSNs) such as Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated systems (CRISPR/Cas9), Transcription activator like effector nucleases (TALENs), and more recently CRISPR/Cas12a. As the tissue culture and regeneration procedures to generate gene-edited events are time consuming, large-scale screening methodologies that rapidly facilitate validation of genome-editing reagents are critical. Plant protoplast cells provide a rapid platform to validate genome-editing reagents. Protoplast transfection with plasmids expressing genome-editing reagents represents an efficient and cost-effective method to screen for in vivo activity of genome-editing constructs and resulting targeted mutagenesis. In this study, we compared three existing methods for detection of editing activity, the T7 endonuclease I assay (T7EI), PCR/restriction enzyme (PCR/RE) digestion, and amplicon-sequencing, with an alternative method which involves tagging a double-stranded oligodeoxynucleotide (dsODN) into the SSN-induced double stranded break and detection of on-target activity of gene-editing reagents by PCR and agarose gel electrophoresis. To validate these methods, multiple reagents including TALENs, CRISPR/Cas9 and Cas9 variants, eCas9(1.1) (enhanced specificity) and Cas9-HF1 (high-fidelity1) were engineered for targeted mutagenesis of Acetolactate synthase1 (ALS1), 5-Enolpyruvylshikimate- 3-phosphate synthase1 (EPSPS1) and their paralogs in potato. While all methods detected editing activity, the PCR detection of dsODN integration provided the most straightforward and easiest method to assess on-target activity of the SSN as well as a method for initial qualitative evaluation of the functionality of genome-editing constructs. Quantitative data on mutagenesis frequencies obtained by amplicon-sequencing of ALS1 revealed that the mutagenesis frequency of CRISPR/Cas9 reagents is better than TALENs. Context-based choice of method for evaluation of gene-editing reagents in protoplast systems, along with advantages and limitations associated with each method, are discussed

Impact of Blue Light on Plant Growth, Flowering and Accumulation of Medicinal Flavones in <i>Scutellaria baicalensis</i> and <i>S. lateriflora</i>

Scutellaria baicalensis Georgi (Baikal skullcap) and S. lateriflora (American skullcap) are two ethnobotanical medicinal plants used to treat gastrointestinal, respiratory, and inflammatory disorders, in addition to demonstrated anti-cancer properties. The predominant bioactive compounds produced in these species are unique 4′-deoxyflavones, in roots of S. baicalensis and leaves of S. lateriflora, making these two species suitable to study the effects of light quality on flavone accumulation in aerial and underground tissues. Light emitting diodes were used to study the impact of blue-dominated spectrum on the accumulation of bioactive flavones. Eight major flavones, including 4′-deoxyflavones baicalein, wogonin, baicalin, wogonoside and chrysin, along with 4′-hydroxyflavones scutellarein, scutellarin and apigenin, were quantified using HPLC in high flavone accumulating tissues. Aerial tissues directly exposed to blue light in S. lateriflora showed an increase in the concentrations of scutellarein by 18.7%, scutellarin by 296%, and baicalin by 31.6%. While the roots in S. baicalensis also had significant increases in baicalein by 154% and wogonin by 76% in response to blue light, there was a slight reduction in their respective glycosides baicalin and wogonoside as well as a decrease in total flavone content. Blue light resulted in compact skullcap plants with early flowering and modified flavone profiles

Table_1_Heat stress during seed development leads to impaired physiological function and plasticity in seed oil accumulation in Camelina sativa.xlsx

Camelina sativa, a member of the Brassicaceae, is a low-cost, renewable oilseed crop that produces seeds up to 40% oil by weight with high potential for use in food, feed, and biofuel applications. Camelina seeds contain high levels of the fatty acids α-linolenic acid (C18:3), linoleic acid (C18:2), oleic acid (C18:1), and gondoic acid (C20:1), which have high nutritional and industrial value. The impact of climate change, especially increased frequency and amplitude of heat waves, poses a serious threat to crop productivity. In this study, we evaluated the effect of elevated temperatures post-anthesis on the developing seeds of C. sativa and performed physiological, morphological, and chemical characterizations at 7, 14, 21, and 28 days post-anthesis (DPA), as well as at maturity. While the seed oil accumulation peaked at 21 DPA under control conditions, reaching 406mg/g dry weight, under heat stress it was only 186mg/g. Physiologically, transpiration rate (E) and internal CO2 concentration (Ci) increased between 2 to 9 days post-stress imposition and overall net photosynthesis was impaired. Seed yield, seed weight, and oil content reduced by 84.5%, 38.5% and 54.1% respectively. We demonstrate that post-anthesis heat stress causes severe yield losses and developmental plasticity in fatty acid accumulation in oilseeds.</p