Genetic diversity and population structure of a Camelina sativa spring panel

Authors: Luo, Zinan; BROCK, JORDAN - Washington University; Dyer, John; KUTCHAN, TONI - Danforth Plant Science Center; AUGUSTIN, MEGAN - Danforth Plant Science Center; SCACHTMAN, DANIEL - University Of Nebraska; GE, YUFENG - University Of Nebraska; FAHLGREN, NOAH - Danforth Plant Science Center; Abdel-Haleem, Hussein

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/5/2019
Publication Date: 2/20/2019
Citation: Luo, Z., Brock, J., Dyer, J.M., Kutchan, T., Augustin, M., Scachtman, D., Ge, Y., Fahlgren, N., Abdel-Haleem, H.A. 2019. Genetic diversity and population structure of a Camelina sativa spring panel. Frontiers in Plant Science. 10:184. https://doi.org/10.3389/fpls.2019.00184.
DOI: https://doi.org/10.3389/fpls.2019.00184

Interpretive Summary: Camelina sativa (L. Crantz), a crop originated from southeastern Europe and southwestern Asia, is showing renewed public interest due to its exceptional level of omega-3 essential fatty acids and high seed oil content. These oil qualities, combined with positive agronomic attributes such as early maturity, low-input requirements for water, nutrients and pesticides, broader adaptability to diverse environments and resistance against insects and pathogens, make C. sativa an ideal alternative resource for biofuel and animal feedstock in the development of sustainable agriculture. Studies on genetic diversity and population structure are important for characterizing the natural selection history and genetic relationships among C. sativa accessions. And these will facilitate the faster genetic enhancement and efficient breeding progresses such as marker-assisted selection. In this study, high-throughput genotyping-by-sequencing technology was used to explore genetic diversity and adaptation among Camelina sativa accessions and the possibility of utilizing single nucleotide polymorphic markers for genomic analyses in Camelina genetic enhancement. Based on our data, the panel was genetically diverse. This level of genetic diversity could be the basis for developing new Camelina cultivars with desirable characteristics such as high yield potential, high oil production and tolerance to abiotic stress while being adapted to diverse environments. Moreover, our study identified two subpopulations which could be explained by their geographical differentiation and natural selection and regional adaptation history. The subpopulation that originated mainly from former soviet-union region is more diverse than the subpopulation that originated from Germany, based on genetic differentiation estimators. Knowledge of population structure and genetic diversity of Camelina sativa accessions is important for future genetic studies such as genomic selection, marker-assisted selection and genome-wide association studies.

Technical Abstract: There is a need to explore renewable alternatives (e.g., biofuels) that can produce energy sources to help reduce the reliance on fossil oils. In addition, the consumption of fossil oils adversely affects the environment and human health via the generation of waste water, greenhouse gases, and waste solids. Camelina sativa, originated from southeastern Europe and southwestern Asia, is being re-embraced as an industrial oilseed crop due to its high seed oil content (36–47%) and high unsaturated fatty acid composition (>90%), which are suitable for jet fuel, biodiesel, high-value lubricants and animal feed. C. sativa’s agronomic advantages include short time to maturation, low water and nutrient requirements, adaptability to adverse environmental conditions and resistance to common pests and pathogens. These characteristics make it an ideal crop for sustainable agricultural systems and regions of marginal land. However, the lack of genetic and genomic resources has slowed the enhancement of this emerging oilseed crop and exploration of its full agronomic and breeding potential. Here, a core of 213 spring C. sativa accessions was collected and genotyped. The genotypic data was used to characterize genetic diversity and population structure to infer how natural selection and plant breeding may have affected the formation and differentiation within the C. sativa natural populations, and how the genetic diversity of this species can be used in future breeding efforts. A total of 6,192 high-quality single nucleotide polymorphisms (SNPs) were identified using genotypingby-sequencing (GBS) technology. The average polymorphism information content (PIC) value of 0.29 indicate moderate genetic diversity for the C. sativa spring panel evaluated in this report. Population structure and principal coordinates analyses (PCoA) based on SNPs revealed two distinct subpopulations. Sub-population 1 (POP1) contains accessions that mainly originated from Germany while the majority of POP2 accessions (>75%) were collected from Eastern Europe. Analysis of molecular variance (AMOVA) identified 4% variance among and 96% variance within subpopulations, indicating a high gene exchange (or low genetic differentiation) between the two subpopulations. These findings provide important information for future allele/gene identification using genome wide association studies (GWAS) and marker-assisted selection (MAS) to enhance genetic gain in C. sativa breeding programs.