Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates

Authors: NUNN, ADAM - University Of Leipzig; RODRIGUEZ, ISACC - Gregor Mendel Institute; TANDUKAR, ZENITH - University Of Minnesota; FRELS, KATHERINE - University Of Nebraska; CONTRERAS-GARRIDO, ADRIAN - Max Planck Institute For Developmental Biology; CARBONELL-BEJERANO, PABLO - Max Planck Institute For Developmental Biology; ZHANG, PANPAN - University Of Perpignan; RAMOS, DANIELA - Gregor Mendel Institute; JANDRASITS, KATHARINA - Gregor Mendel Institute; LANZ, CHRISTA - Max Planck Institute For Developmental Biology; BRUSA, ANTHONY - University Of Minnesota; MIROUZE, MARIE - Max Planck Institute For Developmental Biology; Dorn, Kevin; JARVIS, BRICE - Illinois State University; SEDBROOK, JOHN - Illinois State University; WYSE, DONALD - University Of Minnesota; OTTO, CHRISTIAN - Ecseq Bioinformatics; LANGENBERGER, DAVID - Ecseq Bioinformatics; WEIGEL, DETLEF - Max Planck Institute For Developmental Biology; MARKS, M - University Of Minnesota; ANDERSON, JAMES - University Of Minnesota; BECKER, CLAUDE - Gregor Mendel Institute; CHOPRA, RATAN - University Of Minnesota

Submitted to: Plant Biotechnology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/23/2021
Publication Date: 1/6/2022
Citation: Nunn, A., Rodriguez, I., Tandukar, Z., Frels, K., Contreras-Garrido, A., Carbonell-Bejerano, P., Zhang, P., Ramos, D., Jandrasits, K., Lanz, C., Brusa, A., Mirouze, M., Dorn, K.M., Jarvis, B., Sedbrook, J., Wyse, D., Otto, C., Langenberger, D., Weigel, D., Marks, M.D., Anderson, J., Becker, C., Chopra, R. 2022. Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates. Plant Biotechnology Journal. 20(5):944-963. https://doi.org/10.1111/pbi.13775.
DOI: https://doi.org/10.1111/pbi.13775

Interpretive Summary: Field pennycress (Thlaspi arvense) is cold-hardy weed species and is currently being bred as a potential new oilseed and cover crop. Over the past decade, rapid improvements have been made in pennycress using genomics-assisted breeding by identifying critical domestication traits to remove the weedy traits and improve oil and seed meal characteristics. ARS researchers in Fort Collins, CO characterized critical genetic variation in pennycress germplasm resources to identify genetic controls of important traits. This research serves as a foundational resource for breeding and has applicability to the full family of crops known as Brassicas.

Technical Abstract: Thlaspi arvense (Field Pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without new land displacement. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible genetic field-based model species. The availability of a high quality reference genome is vital for untangling the genetic control of pennycress development and to understand its evolutionary history within the Brassicaceae. Here, we present a chromosome-level genome assembly of var. MN106-Ref with improved annotations and highlight transcript variation for two of the accessions (MN108 and Spring32-10) that are highly amenable to genetic transformation. In addition, we classified small RNAs, pseudogenes, and transposable elements, and highlighted tissue specific expression and methylation patterns. Resequencing of forty wild accessions identified genetic variation and putative QTL regions for flowering time and a leaf color phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across Brassicaceae.