Transcriptome and Gene Regulatory Network Analyses in Camelina Nitrogen Response and Seed Development
Authors:
Fernando Henrique Correr* (fernando.correr@montana.edu), Racheal Upton, Chaofu Lu, and Jennifer Lachowiec
Institutions:
Montana State University
URLs:
Goals
Camelina is a Brassica oilseed crop that has great potential to become a sustainable source of bioenergy in the U. S. However, the low nitrogen use efficiency and the low seed and oil yield compared to other major oilseed crops hinder this potential. The goal of this project is to decipher the genetic and physiological mechanisms that determine the nitrogen use efficiency and oilseed yield during the most critical processes of the camelina life cycle: 1) how camelina, in partnership with soil microbes, maximizes its ability to absorb and assimilate nitrogen into vegetative biomass; and 2) upon the transition to reproductive growth, how nitrogen is efficiently remobilized from senescing tissues (leaves and silicles) into sinks (seeds) to optimize yield potential by increasing seed size and enhancing oil synthesis.
Abstract
Camelina (Camelina sativa (L.) Crantz) is an oilseed with potential as a crop for second generation biofuel production. To achieve sustainable production of camelina oil, the energy-consuming inputs need to be optimized, especially reducing the amount of nitrogen in the production system. Researchers need to obtain a systems-level understanding of genetic and physiological mechanisms that may be used to enhance the nitrogen use efficiency (NUE) and to improve agronomic and seed traits in camelina. The team grew three C. sativa accessions–Suneson, Cam 70 and Cam 116-under two nitrogen conditions of 0.55 mM and 5.5 mM of nitrate in the nutrient solution, and assessed the transcriptomes of six organs–flower, 10 days after fertilization (DAF) seed, pod, leaf, stem, and root. The largest number of differentially expressed genes (DEGs) is due to the genotype effect for almost all tissues; but differences attributed to nitrogen input are remarkable in flower, pod, and stem. The team identified functional terms enriched with DEGs due to nitrogen, which involved mostly in abiotic responses and changes in photosynthesis-associated processes. In seeds, researchers also identified significant differences in genes of the phenylpropanoid pathway, biosynthesis of flavonoids, and maintenance of seed dormancy.
There is a lack of knowledge in processes that regulate the development of camelina seeds and affect their viability. The previous study showed that the miR167A overexpression results in lower levels of α-linolenic acid, but also larger seeds and delayed seed maturation in camelina (Na et al, 2019). Researchers therefore aimed to identify genes responsible for this altered seed development through a co-expression weighted network analysis. Researchers examined published gene expression profiles of the camelina wildtype (cv. Suneson) and miR167OE, a transgenic line overexpressing miR167A, at 8, 10 and 12 days after flowering (DAF). One group of co-expressed genes increased in expression from 8 to 10-12 DAF in miR167OE; however, their expression levels at 10-12 DAF was similar to those in Suneson at 8 DAF. In this group, the team found significant enrichment of genes in auxin response, seed oilbody biogenesis, seed maturation and seed germination. Genes with the opposite expression pattern included those with functions in the flavonoid biosynthesis pathway including BANYLUS and multiple members of the TRANSPARENT TESTA family. They are potentially involved in the determination of seed coat color but also can influence other seed traits. In addition to genes found in the enrichment analysis, the team also identified other candidates involved in seed germination: DELAY OF GERMINATION 1 (DOG1), ABA-HYPERSENSITIVE GERMINATION 1 (AHG1) and FIE2. The expression profiles of those genes showed profound differences at 8 DAF in miR167OE compared to all the other samples. Based on the patterns of expression in these genes, researchers hypothesized that earlier germination occurs in miR167OE compared to Suneson despite delayed seed maturation. This was confirmed by a germination assay to evaluate the germination rates of both genotypes for two weeks, and the transgenic genotype indeed germinated faster. These outcomes provide evidence that besides changing the oil profile, miR167A overexpression also interferes with seed development and maturation, resulting in faster germination rates in miR167OE.
References
Na, G., et al. 2019. “Enhancing Micro RNA 167A Expression in Seed Decreases the α‐Linolenic Acid Content and Increases Seed Size in Camelina sativa.” The Plant Journal 98(2), 346–58.
Funding Information
This research is supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomic Science program Award No. DE-SC0021369.