Exploring genetic diversity, population structure, and subgenome differences in the allopolyploid Camelina sativa: implications for future breeding and research studies

Abstract

Camelina (Camelina sativa), an allohexaploid species, is an emerging aviation biofuel crop that has been the focus of resurgent interest in recent decades. To guide future breeding and crop improvement efforts, the community requires a deeper comprehension of subgenome dominance, often noted in allopolyploid species, “alongside an understanding of the genetic diversity” and population structure of material present within breeding programs. We conducted population genetic analyses of a C. sativa diversity panel, leveraging a new genome, to estimate nucleotide diversity and population structure, and analyzed for patterns of subgenome expression dominance among different organs. Our analyses confirm that C. sativa has relatively low genetic diversity and show that the SG3 subgenome has substantially lower genetic diversity compared to the other two subgenomes. Despite the low genetic diversity, our analyses identified 13 distinct subpopulations including two distinct wild populations and others putatively representing founders in existing breeding populations. When analyzing for subgenome composition of long non-coding RNAs, which are known to play important roles in (a)biotic stress tolerance, we found that the SG3 subgenome contained significantly more lincRNAs compared to other subgenomes. Similarly, transcriptome analyses revealed that expression dominance of SG3 is not as strong as previously reported and may not be universal across all organ types. From a global analysis, SG3 “was only significant higher expressed” in flower, flower bud, and fruit organs, which is an important discovery given that the crop yield is associated with these organs. Collectively, these results will be valuable for guiding future breeding efforts in camelina.

Acknowledgements

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).

Author contributions

P.P.E, E.G., and J.R.B. conceived the project. J.R.B., S.K.G., and E.G.P. collected samples and S.K.P. and M.M.L. extracted DNA and RNA for sequencing. J.R.B analyzed camelina resequencing data, K.A.B. analyzed camelina homoeolog-expression bias, A.E.P. assembled and annotated the genome, S.J.T. annotated TEs, K.P. and C.E.R. annotated lncRNAs. Y.S.L, J.R.B., F.G.C and S.K.G. manually curated target genes. J.R.B. P.P.E., A.D.L.N., and E.G. wrote the manuscript. All authors gave feedback and comments on the final manuscript version.

Data availability

The reference genome and transcriptome of C. sativa variety “Suneson” will be publicly available after publication at CamRegBase (https://camregbase.org/) and CoGe (https://genomevolution.org/coge/). Raw RNAseq reads and HiFi genomic and transcriptomic reads have been submitted to NCBI SRA under accession numbers SRX25825928-SRX25825946, SRX25826254, SRX25827247, and SRX25827248.

Conflict of interest

The authors declare no conflict of interest.

Supplementary Data

Supplementary data is available at Horticulture Research online.

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