Ta Ta for now: Thlapsi arvense (pennycress), an emerging model for genetic analyses
2018; Wiley; Volume: 96; Issue: 6 Linguagem: Inglês
10.1111/tpj.14172
ISSN1365-313X
Autores Tópico(s)Photosynthetic Processes and Mechanisms
ResumoThe Plant JournalVolume 96, Issue 6 p. 1091-1092 Research HighlightFree Access Ta Ta for now: Thlapsi arvense (pennycress), an emerging model for genetic analyses Sheila McCormick, Research Highlights EditorSearch for more papers by this author Sheila McCormick, Research Highlights EditorSearch for more papers by this author First published: 10 December 2018 https://doi.org/10.1111/tpj.14172Citations: 2 Linked article: This is a Research Highlight about Ratan Chopra et al. To view this article visit https://doi.org/10.1111/tpj.14147. AboutSectionsPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinked InRedditWechat Thlapsi arvense (common name pennycress) is a weed in the Brassicaceae family. Its most remarkable feature is that it can survive at very low temperatures (−25°C). Pennycress was therefore proposed as a crop that could fill the several month gap between the fall harvest and spring planting dates for corn and soybean. But will farmers adopt it as an alternative crop? That is, can it produce a product that will be valuable enough to justify the production costs? Pennycress is called a weed for a reason. For example, the seeds don't germinate uniformly and harvestability is not ideal; plants can lodge (fall down), pods sometimes shatter too early and the seeds are small. Furthermore, the erucic acid content is too high for human consumption. Several modifications to plant architecture, oil content and quality will be needed to domesticate pennycress (reviewed by Sedbrook et al., 2014). In the highlighted paper (Chopra et al., 2018), the Marks and Sedbrook labs present tools that will help in these domestication efforts. A companion paper (McGinn et al., 2018) presents other desirable tools for using pennycress as a complementary model to Arabidopsis, i.e. a floral dip method for Agrobacterium transformation and a demonstration that CRISPR-Cas9 gene editing is feasible in pennycress. The highlighted paper has 15 authors: developing tools is a multi-faceted endeavor! David Marks is a professor who had focused on trichome development in Arabidopsis for more than 25 years, but in 2012 he was captivated by the idea of helping to develop a new crop, in some ways analogous to his work during his postdoc, when he developed tools for Arabidopsis research (Feldman and Marks, 1987). David had learned about pennycress from his colleague Donald Wyse, founder of the Forever Green Initiative (www.forevergreen.umn.edu), which aims to develop new annual and perennial crops. As a student and postdoc, John Sedbrook had studied cell expansion and trophic responses in Arabidopsis, but as a professor at Illinois State he switched his focus to developing cellulosic and oilseed bioenergy crops. The Marks and Sedbrook labs have been collaborating since the fall of 2012, due to a chance dinner meeting after David had given a seminar at Illinois State. From the Marks lab, the first author, Ratan Chopra is a postdoc, with previous experience in molecular breeding and genomics using peanut and sorghum. Kevin Dorn was a graduate student, while Evan Johnson and Erin Daniels were former technicians and Kirk Amundson was an undergraduate; Nicole Folstad is the current technician. From the Sedbrook lab, both Michaela McGinn and Maliheh Esfahanian are graduate students. Donald Wyse and Kevin Betts, his technician, worked on agronomic aspects, as did James Anderson and two members of his group (Katherine Frels, a postdoc and Kayla Altendorf, a graduate student). As the schematic in Figure 1 shows, Chopra et al. (2018) focused on mutagenizing seed, then screened the M2 populations for obvious phenotypes and carried out whole genome sequencing of selected lines. The Marks lab had previously generated a draft genome and transcriptomics resources for pennycress (Dorn et al., 2015). In Chopra et al. (2018) they aligned the draft pennycress genome to the Arabidopsis genome and showed that synteny was substantial, thus hypothesizing that the Arabidopsis genome could be used as a guide for identifying causal mutations in the pennycress mutant populations. Their Data S5 lists over 16 000 pennycress genes with mutations as well as the closest Arabidopsis homolog for each. Figure 1Open in figure viewerPowerPoint Pennycress mutants derived from mutagenized seeds were identified in the field and subjected to whole gene sequencing. Sequences were analyzed using the Arabidopsis database to identify candidate causative mutations. The sequences were also used to create a gene index for identification of additional mutants. Image credit: Ratan Chopra. To demonstrate the efficacy of using Arabidopsis to guide mutant analyses in pennycress, they used the flavonoid biosynthesis pathway, which contributes to the oxidized tannins in the seed coat (oxidized tannins are anti-nutritional and thus a target for domestication). The flavonoid biosynthetic pathway and the relevant transcription factors have been well studied in Arabidopsis (i.e. the transparent testa mutants, reviewed in Appelhagen et al., 2014). They therefore identified M2 plants whose M3 seeds had seed coat pigment differences, and after whole genome sequencing were able to identify pennycress mutants in several of the relevant transcription factors and in most of the genes encoding biosynthetic enzymes. In addition, they established that GL3 in pennycress is important for seed coat color, although that is not true for GL3 in Arabidopsis, and they identified a transparent testa mutation in a novel gene that had not been identified in Arabidopsis. There are many applications for these mutant populations and the presented gene index, both for domestication efforts and for basic research. For example, they have used Near Infrared Spectroscopy (NIRS) to rapidly assess seed quality traits and thereby identify useful pennycress mutants (Chopra et al., 2019). Similarly, genes underlying differences in seed size, seed maturation, pod shattering and flowering time are known in Arabidopsis (and/or in Brassica), so it should be straightforward to combine the analogous pennycress mutants. Furthermore, numerous genes that are duplicated in Arabidopsis are present as single copies in pennycress, suggesting that studying their function will be easier in pennycress. Pennycress is easy to grow and is larger than Arabidopsis and thus more amenable for biochemistry (more tissue), and can be used in field and environmental studies. Now is the time for pennycress! References Appelhagen, I., Thiedig, K., Nordholt, N., Schmidt, N., Huep, G., Sagasser, M. and Weisshaar, B. (2014) Update on transparent testa mutants from Arabidopsis thaliana: characterisation of new alleles from an isogenic collection. Planta, 240, 955– 970. CrossrefCASPubMedWeb of Science®Google Scholar Chopra, R., Johns, E.B., Daniels, E. et al. (2018) Translational genomics using Arabidopsis as a model enables the characterization of pennycress genes through forward and reverse genetics. Plant J. 96, 1093– 1105. Wiley Online LibraryCASWeb of Science®Google Scholar Chopra, R., Foldstad, N., Lyons, J. et al. (2019) The adaptable use of Brassica NIRS calibration equations to identify pennycress variants to facilitate the rapid domestication of a new winter oilseed crop. Ind. Crops Prod. 128, 55– 61. CrossrefWeb of Science®Google Scholar Dorn, K.M., Fankhauser, J.D., Wyse, D.L. and Marks, M.D. (2015) A draft genome of field pennycress (Thlaspi arvense) provides tools for the domestication of a new winter biofuel crop. DNA Res. 22, 121– 131. CrossrefCASPubMedWeb of Science®Google Scholar Feldman, K.A. and Marks, M.D. (1987) Agrobacterium-mediated transformation of germinating seeds of Arabidopsis thaliana: a non-tissue culture approach. Mol. Gen. Genet. 208, 1– 9. CrossrefWeb of Science®Google Scholar McGinn, M., Phippen, W.B., Chopra, R. et al. (2018) Molecular tools enabling pennycress (Thlaspi arvense) as a model plant and oilseed cash cover crop. https://doi.org/10.1111/pbi.13014. Google Scholar Sedbrook, J.C., Phippen, W.B. and Marks, M.D. (2014) New approaches to facilitate rapid domestication of a wild plant to an oilseed crop: example pennycress (Thlaspi arvense L.). Plant Sci. 227, 122– 132. CrossrefCASPubMedWeb of Science®Google Scholar Citing Literature Volume96, Issue6December 2018Pages 1091-1092 FiguresReferencesRelatedInformation
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