Sequencing and functional validation of the <scp>JGI </scp><i>Brachypodium distachyon</i> T‐<scp>DNA</scp> collection

Hsia, Mon Mandy; O’Malley, Ronan; Cartwright, Amy; Nieu, Rita; Gordon, Sean P.; Kelly, Sandra; Williams, Tina; Wood, Delilah F.; Zhao, Yunjun; Bragg, Jennifer; Jordan, Mark C.; Pauly, Markus; Ecker, Joseph R.; Gu, Yong; Vogel, John P.

doi:10.1111/tpj.13582

Cited by 37 publications

(34 citation statements)

References 43 publications

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“…To study BdPYL1 involvement in ABA perception, we analyzed a BdPYL1 T-DNA insertion line JJ20227-Bdpyl1-1 ( Figure S7; Bragg et al, 2012;Hsia et al, 2017). T-DNA insertion in BdPYL1 includes a 4 9 35S enhancer that drives the majority of the BdPYL1 coding sequence in an anti-sense conformation.…”

Section: Bdpyl1 Function As An Aba Receptormentioning

confidence: 99%

Non‐redundant functions of the dimeric ABA receptor BdPYL1 in the grass Brachypodium

et al. 2017

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Abiotic stresses have severe detrimental effects on agricultural productivity worldwide. Abscisic acid (ABA) levels rise in response to abiotic stresses, and play a role in coordinating physiological responses. ABA elicits its effects by binding a family of soluble receptors, increasing affinity of the receptors to type 2C phosphatases (PP2Cs) leading to phosphatase inhibition. In the current study, we conducted a comprehensive analysis of the ABA signaling pathway in the cereal model grass Brachypodium distachyon. The Brachypodium genome encodes a family of 10 functionally conserved ABA receptors. The 10th in the series, BdPYL10, encodes a defective receptor and is likely a pseudogene. Combinatorial protein interaction assay further validated computational analysis, which grouped Brachypodium ABA receptors into three subfamilies, similarly to Arabidopsis classification. Brachypodium subfamily III receptors inhibited PP2C activity in vitro and complemented Arabidopsis quadruple (pyr1/pyl1/pyl2/pyl4) mutant. BdPYL1 T-DNA mutant exhibited clear ABA hyposensitivity phenotypes during seedling establishment and in mature plants. Single receptor predominance is in agreement with high transcriptional abundance of only a small Brachypodium ABA receptors subset, harboring the higher marginal significance of BdPYL1. Our findings suggest that unlike the highly redundant ABA core signaling components of Arabidopsis, Brachypodium encompasses a more compact and specialized ABA receptor apparatus. This organization may contribute to plant adaptations to ecological niches. These results lay the groundwork for targeting the prominent ABA receptors for stress perception in grasses, and reveal functional differences and commonalities between monocots and eudicots.

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Section: Bdpyl1 Function As An Aba Receptormentioning

confidence: 99%

Non‐redundant functions of the dimeric ABA receptor BdPYL1 in the grass Brachypodium

et al. 2017

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“…Agrobacterium tumefaciens AGL1, a supervirulent strain, has been used for the majority of B. distachyon transformations (Alves et al., ; Bragg et al., ; Hsia et al., ; Vogel & Hill, ). However, a recent study found that A. rhizogenes strain 18r12v can also transform B. distachyon with efficiency comparable to or slightly higher than that of AGL1 (Collier et al., ).…”

Section: Commentarymentioning

confidence: 99%

“…The protocol described here has been successfully employed to create over 22,000 T‐DNA mutants (Bragg et al., ; Hsia et al., ) and has been used for studying individual genes, including the functional validation of the flowering‐time gene FT (Qin et al., ; Wu et al., ) and wheat male sterile gene Ms2 (Ni et al., ), among others.…”

Section: Commentarymentioning

confidence: 99%

Agrobacterium‐Mediated Transformation of Brachypodium distachyon

et al. 2019

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Brachypodium distachyon is an excellent model system for the grasses and has been adopted as a research organism by many laboratories around the world. It has all of the biological traits required for a model system, including small stature, short life cycle, small genome, simple growth requirements, and a close relationship to major crop plants (cereals). In addition, numerous resources have been developed for working with this species, including genome sequences for many lines, sequenced mutant collections, and a large, freely available germplasm collection. Fortunately, among grasses B. distachyon is one of the most easily transformed species, an absolute necessity for a model system. Agrobacterium‐mediated transformation is the preferred method to transform plants because it usually results in simple insertions of target DNA. In this article, we describe a method for Agrobacterium‐mediated transformation of the inbred B. distachyon lines Bd21 and Bd21‐3. Embryogenic callus induced from immature embryos is co‐cultivated with Agrobacterium tumefaciens strain AGL1 or Agrobacterium rhizogenes strain 18r12v. Hygromycin and paromomycin are used as selective agents, with comparable transformation efficiencies (defined as the percentage of co‐cultivated callus that produce transgenic plants) of 40% to 70%. It takes 20 to 30 weeks to obtain T1 seeds starting from the initial step of dissecting out immature embryos. This protocol has been shown to be efficient and facile in several studies that resulted in the creation of over 22,000 T‐DNA mutants. © 2019 by John Wiley & Sons, Inc.

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“…Thus, research on model grasses such as Setaria viridis and Brachypodium distachyon can inform growth strategies for many crops (Brutnell et al, 2015). B. distachyon is gaining popularity as a model grass because of its small genome, short generation time, genetic tractability, and the availability of extensive germplasm and mutant collections (Hsia et al, 2017). Additionally, since it uses C 3 carbon (C) fixation, it is a good laboratory model plant relevant to cereal crops such as barley (Hordeum vulgare), rice (Oryza sativa), and wheat (Triticum aestivum).…”

Section: Introductionmentioning

confidence: 99%

Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass

et al. 2019

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Summary There is a dynamic reciprocity between plants and their environment: soil physiochemical properties influence plant morphology and metabolism, and root morphology and exudates shape the environment surrounding roots. Here, we investigate the reproducibility of plant trait changes in response to three growth environments. We utilized fabricated ecosystem (Eco FAB ) devices to grow the model grass Brachypodium distachyon in three distinct media across four laboratories: phosphate‐sufficient and ‐deficient mineral media allowed assessment of the effects of phosphate starvation, and a complex, sterile soil extract represented a more natural environment with yet uncharacterized effects on plant growth and metabolism. Tissue weight and phosphate content, total root length, and root tissue and exudate metabolic profiles were consistent across laboratories and distinct between experimental treatments. Plants grown in soil extract were morphologically and metabolically distinct, with root hairs four times longer than with other growth conditions. Further, plants depleted half of the metabolites investigated from the soil extract. To interact with their environment, plants not only adapt morphology and release complex metabolite mixtures, but also selectively deplete a range of soil‐derived metabolites. The Eco FAB s utilized here generated high interlaboratory reproducibility, demonstrating their value in standardized investigations of plant traits.

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Sequencing and functional validation of the JGI Brachypodium distachyon T‐DNA collection

Cited by 37 publications

References 43 publications

Non‐redundant functions of the dimeric ABA receptor BdPYL1 in the grass Brachypodium

Non‐redundant functions of the dimeric ABA receptor BdPYL1 in the grass Brachypodium

Agrobacterium‐Mediated Transformation of Brachypodium distachyon

Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass

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