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Front. Plant Sci. | doi: 10.3389/fpls.2019.01211

Editorial: Setaria as a Model Genetic System to Accelerate Yield Increases in Cereals, Forage Crops, and Bioenergy Grasses

  • 1Botany, Oklahoma State University, United States
  • 2Donald Danforth Plant Science Center, United States
  • 3CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), South Asia, India
  • 4Boyce Thompson Institute, United States

Setaria is a model C4 grass in the tribe Paniceae of the subfamily Panicoideae, closely related to switchgrass, napier grass and pearl millet, and in the sister tribe to important crops such as maize, sorghum and sugar cane. The model comprises two species, foxtail millet (S. italica), domesticated in the Yellow River valley in China approximately 9-11,000 years ago, and its wild progenitor, green foxtail (S. viridis), which is one of the world’s most widespread weeds. Setaria, particularly green foxtail, differs from its more important biofuels and crop relatives in that it is small in stature, fast-cycling, and has a small genome. As such it is ideally suited to greenhouse and growth experiments, as well as being capable of being grown in field plots. Over the last ten years, numerous resources have been created for both species, including annotated genomes, mutant and field collections, transformation protocols, and gene atlases. Some of these advances were detailed in a volume in the Springer Crop Genetics and Genomics volume released in 2017 (Doust and Diao, editors), and the current collection of papers in this Research Topic, covering domestication, developmental genetics, mutant analysis, microbiomes, and technical advances, shows how far the field has progressed even in the short time since that volume.

Several papers deal with the genetics of domestication and improvement. Hu et al. presents an overview of domestication and improvement in Setaria, focusing on key traits that differ between foxtail millet and its wild progenitor green foxtail. Focusing on the domestication and improvement traits of shattering, plant architecture and flowering time, the paper summarizes known information and points out new opportunities for improvement in drought stress and nutrient efficiencies. Odonkor et al. takes the theme of domestication further and investigates the genetic basis of shattering in Setaria in more detail. Through mapping and gene expression analyses the authors pinpoint the ortholog of sorghum SH1 as being likely to underlie the QTL of largest effect, with a second small QTL in the vicinity of the ortholog of rice qSH1. These results are significant because they suggest that there might be a common genetic control of shattering across the grasses. Chaluvadi and Bennetzen also look at the effects of domestication, but focus below ground, contrasting soil microbiome differences between wild and domesticated Setaria. They point out key differences in the microbiotic assemblages of domesticated versus wild accessions and suggest that domestication has selected for specific associations in the root and rhizosphere.

Other papers deal with gene expression analyses. Zhu et al. present a co-expression study of early inflorescence development in green foxtail. Six developmental stages were identified, containing stage specific co-expression modules with homologs of known developmental genes from maize and rice, suites of transcription factors, as well as unknown genes. This study will be important for comparative analyses and gene discovery in Setaria.

Three papers detail screening and characterization of mutants related to C4 photosynthesis, Kranz structure, and chloroplast biogenesis in foxtail millet. Luo et al. detail their studies on identifying EMS mutants of foxtail millet that show variation in anatomical structure, especially related to Kranz anatomy. The genetic basis of Kranz anatomy, an essential part of C4 photosynthesis in grasses, has been exceedingly difficult to elucidate, and the 14 mutants identified by Luo et al. represent an important new set of resources for genetic analysis. Another two papers describe the identification of genes responsible for chloroplast biogenesis and a range of other phenotypes. Zhang, Tang, et al. identify the Setaria ortholog of deoxycytidine monophosphate deaminase (DCD), a key enzyme in dTTP biosynthesis. Surprisingly, the expression of this gene in Setaria differs from that in rice (a C3 plant) and shows similar patterns of expression to C4 photosynthesis genes. This may provide new avenues for understanding the differing roles of this essential gene in C3 and C4 grasses. Zhang, Zhi et al. describes the identification of an ATP-independent metalloprotease that is required for chloroplast development, photosystem II function, leaf senescence, and ABA signal response. This is the first report characterizing this gene’s functions in C4 plants.

Setaria is also an excellent vehicle for stress studies, including drought, salt and low nutrient levels. The paper by Kaur et al. details the role of an Arabidopsis Type III G Protein AGG3 in monocots, using the over-expression of the Arabidopsis gene in Setaria to gain insight into its function in C4 grasses. In doing so, Kaur et al. reveal that several traits are correlated with gene expression level whilst others appear to exhibit allele-specific expression. Traits related to stress were positively affected, including responses to salt and low nitrogen.

The papers that seek to understand the genetic control of development and response to the environment all rest on a requirement for accurate and sensitive phenotyping. Two papers directly address this issue. Acharya et al. conduct multiple phenotypic assays of Setaria to optimize growth conditions under multiple hormonal and abiotic streses. This is very important to provide a secure base of information for the Setaria community to conduct further phenotypic assays. A very different tack is taken by Desai et al., who use neural net classification combined with movement analysis of time-lapse imagery to track flower opening in Setaria. This trait is particularly tricky to track in Setaria, where knowledge of timing of anther appearance is critical for the success of controlled crosses and for breeding for favorable opening times in hot field environments.

Finally, Van Eck provides a review of Setaria viridis transformation approaches, where she discusses tissue culture-based and floral dip approaches, and concludes that tissue culture-based methods are the most reliable, though technically demanding. Simplification of tissue-based approaches and successful optimization of the floral dip method - the holy grail of monocot transformation- are necessary for Setaria to reach its full potential as a model system.

While by no means being a comprehensive review of all activity in Setaria to date, these articles provide a unique insight into the value and potential of the Setaria model system.

Keywords: Setaria, Green foxtail, foxtail millet, C4 Photosynthesis, grass, Poaceae

Received: 03 Apr 2019; Accepted: 03 Sep 2019.

Copyright: © 2019 Doust, Brutnell, Upadhyaya and Van Eck. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Andrew N. Doust, Oklahoma State University, Botany, Stillwater, 74075, OK, United States, andrew.doust@okstate.edu