Camelina, an ancient oilseed once used across Europe and Asia, has reemerged as a sustainable crop due to its high omega-3 content, ability to grow on marginal land, and potential as a source for aviation biofuel. Unlike many traditional crops, camelina is an allohexaploid formed through hybridization of three subgenomes. However, its low genetic diversity and lack of well-characterized breeding material have limited its advancement. To fully harness camelina's potential, researchers must untangle its complex genomic architecture and identify unique genetic resources for targeted breeding. Due to these challenges, deeper investigations into its genome structure and population diversity are urgently needed.
A research team from Michigan State University and partner institutions has assembled a high-quality genome of the camelina cultivar “Suneson”, shedding new light on this polyploid oilseed's breeding potential. Published (DOI: 10.1093/hr/uhae247) on September 9, 2024, in Horticulture Research, the study combines third-generation sequencing with population genetics and transcriptome analyses of over 220 accessions. The team’s comprehensive findings on subgenome dynamics, genetic structure, and regulatory elements promise to transform camelina breeding and accelerate its role in sustainable agriculture and biofuel development.
The researchers used long-read PacBio sequencing to reconstruct a nearly gap-free genome of the camelina variety “Suneson”. Compared to older assemblies, the new genome captured ~19 Mb of previously unresolved sequence and identified over 5,000 new protein-coding genes. When resequencing 222 diverse accessions, the team found overall low genetic diversity (π = 0.00086), with the SG3 subgenome notably less diverse but showing the highest heterozygosity. Population structure analysis uncovered 13 distinct genetic clusters, including two wild populations from Europe and Georgia.
Interestingly, SG3 was previously considered universally dominant in gene expression. However, transcriptome data from six tissues showed that SG3's dominance was restricted to floral and fruit organs, which are critical for yield. Furthermore, SG3 contained significantly more long intergenic noncoding RNAs (lincRNAs), which are implicated in stress responses. The team also annotated transposable elements across subgenomes and found SG3 harbored the most active TEs, potentially influencing gene regulation. These nuanced insights challenge earlier views and suggest tissue-specific regulatory complexity within polyploid genomes.
“This work provides an essential genomic toolkit for both basic and applied research in camelina,” said Dr. Patrick Edger, senior author of the study. “By improving the reference genome and uncovering new layers of expression and population diversity, we now have a clearer roadmap to develop more resilient and productive cultivars. This is a significant leap forward for camelina as a model species and bioenergy crop.”
With aviation industries seeking low-carbon fuel alternatives, camelina’s oil-rich seeds offer a promising path. This new genomic resource not only refines the tools available for molecular breeding but also enables precision editing of stress-resistance genes and floral traits critical to yield. The identification of genetically distinct cultivars and wild types provides valuable targets for creating heterotic groups. As breeding programs work to enhance camelina's productivity and stress tolerance, this study sets the stage for genome-informed strategies that can expand its cultivation across diverse environments and elevate its role in green energy solutions.
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References
DOI
10.1093/hr/uhae247
Original Source URL
https://doi.org/10.1093/hr/uhae247
Funding information
This work was supported by the Department of Energy Office of Biological and Environmental Research (Grant no. DE-SC0022987 to E.G. and P.P.E.), National Science Foundation (NSF) Postdoctoral Research Fellowship in Biology (PRFB-2109178 to J.R.B.; PRFB-2208944 to K.A.B), National Science Foundation Plant Genome (PGRP-2029959 to P.P.E.), National Science Foundation (IOS-2023310 and NSF DBI-2243562 to A.D.L.N).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.