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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Weed and Insect Biology Research » Research » Publications at this Location » Publication #412363
Research Project: Biology of Weed-Crop Interactions to Improve Weed Management Strategies in Northern Agro-ecosystems

Location: Weed and Insect Biology Research

Title: Assembly and analysis of sequence from a spring and winter type Camelina sativa by whole genome PacBio Hifi technologies

Author
item ONTANO, ANDREW - University Of Georgia
item Dobrin, Barbara
item Smith, Timothy - Tim
item ABERNATHY, BRIAN - University Of Georgia
item Sthapit Kandel, Jinita
item SHAIKH, TM - Missouri State University
item RAHMAN, MUKHLESUR - North Dakota State University
item Anderson, James
item Vaughn, Justin
item Horvath, David

Submitted to: Industrial Crops and Products
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/29/2024
Publication Date: 8/8/2024
Citation: Ontano, A., Dobrin, B.H., Smith, T.P., Abernathy, B., Sthapit Kandel, J., Shaikh, T., Rahman, M., Anderson, J.V., Vaughn, J.N., Horvath, D.P. 2024. Assembly and analysis of sequence from a spring and winter type Camelina sativa by whole genome PacBio Hifi technologies. Industrial Crops and Products. 221:119346. https://doi.org/10.1016/j.indcrop.2024.119346.
DOI: https://doi.org/10.1016/j.indcrop.2024.119346

Interpretive Summary: Camelina sativa is a new biofuel crop and potential cash cover-crop suitable for the northern great plains. However, breeding and research of camelina has been hampered by the lack of a high quality genome assembly and lack of genetic tools to study agronomic traits. To solve this problem, new sequencing technologies that are capable of producing contiguous chromosome length sequences were used to sequence two camelina varieties that differed in the ability to withstand freezing temperatures and also in their ability to flower without a winter chilling period. Additionally, these two varieties were crossed and the progeny were sequenced as well. These sequences will be a powerful tool to begin assessing the mechanisms that allow early flowering and freezing tolerance and assist breeders and other scientists to improve many agronomic traits in this new crop.

Technical Abstract: Camelina sativa is an emerging oilseed crop with potential for intercropping with more traditional cash crops. Until very recently, the only reference genome was produced by short read technologies and was considerably fragmented. We developed a cross between the spring biotype CO46 and the winter biotype Joelle that showed significant differences in their vernalization requirements and their freezing tolerance after cold acclimation. The resulting offspring were selfed and the F2 lines were advanced by single see descent to the F6:7 stage. To facilitate mapping of traits in this population we performed Long read sequencing using PacBio HiFi technology. Here we report the assembly and annotation of these two parental lines. Both assemblies formed 20 chromosomal units with a genome size of 679,629,983 and 559,281,586 bases for CO46 nd Joelle respectively. Assessment of completeness by BUSCO analysis indicated the CO46 and Joelle genomes were 99.6 and 99.4% complete respectively. Gene annotation however indicated that the Joelle assembly had a small number of missing gene sequences, and this was further shown by the presence of gaps when the assemblies were aligned and compared. Skim-sequencing of the F6:7 recombinant inbred lines resulted in 823,142 markers that mapped to variants identified by comparisons of the parental genome sequences. These sequences provide a valuable resource for breeders seeking to improve the food and industrial attributes of camelina.