The lignin toolbox of the model grass Setaria viridis

Ferreira, Sávio Siqueira; Simões, Marcella Siqueira; Carvalho, Gabriel Garon; Lima, Leydson Gabriel Alves de; Svartman, Raphael Mendes de Almeida; Cesarino, Igor

doi:10.1007/s11103-019-00897-9

Cited by 30 publications

(16 citation statements)

References 121 publications

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“…We found only two putative AtqCOMT genes in A. tequilana, while three genes have been identified in A. fourcroydes , A. sisalana , and the hybrid H11648 [ 19 ], findings similar to that found in maize [ 58 ] but different from the 18 genuine COMT and COMT-like sequences found in sugarcane transcriptomes [ 59 ]. For CAD genes, the existence of multiple orthologous found in A. tequilana is also consistent is a high number CAD genes reported in fiber-producing Agave species [ 19 ], and other monocots, such as rice (12 genes) and Setaria viridens (11 genes) [ 60 , 61 ]. For the rest of cellulose and phenylpropanoid pathway genes, they were grouped in small families or even classified as unigenes, comparable with that reported in A. fourcroydes , A. sisalana , and the hybrid H11648 [ 17 , 19 ].…”

Section: Discussionsupporting

confidence: 75%

Transcriptome Mining Provides Insights into Cell Wall Metabolism and Fiber Lignification in Agave tequilana Weber

Maceda-López

Góngora-Castillo

Ibarra-Laclette

et al. 2022

Plants

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Resilience of growing in arid and semiarid regions and a high capacity of accumulating sugar-rich biomass with low lignin percentages have placed Agave species as an emerging bioenergy crop. Although transcriptome sequencing of fiber-producing agave species has been explored, molecular bases that control wall cell biogenesis and metabolism in agave species are still poorly understood. Here, through RNAseq data mining, we reconstructed the cellulose biosynthesis pathway and the phenylpropanoid route producing lignin monomers in A. tequilana, and evaluated their expression patterns in silico and experimentally. Most of the orthologs retrieved showed differential expression levels when they were analyzed in different tissues with contrasting cellulose and lignin accumulation. Phylogenetic and structural motif analyses of putative CESA and CAD proteins allowed to identify those potentially involved with secondary cell wall formation. RT-qPCR assays revealed enhanced expression levels of AtqCAD5 and AtqCESA7 in parenchyma cells associated with extraxylary fibers, suggesting a mechanism of formation of sclerenchyma fibers in Agave similar to that reported for xylem cells in model eudicots. Overall, our results provide a framework for understanding molecular bases underlying cell wall biogenesis in Agave species studying mechanisms involving in leaf fiber development in monocots.

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Section: Discussionsupporting

confidence: 75%

Transcriptome Mining Provides Insights into Cell Wall Metabolism and Fiber Lignification in Agave tequilana Weber

Maceda-López

Góngora-Castillo

Ibarra-Laclette

et al. 2022

Plants

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“…Transformation is efficient and amenable to CRISPR–Cas9-mediated mutagenesis. These features have enabled the use of S. viridis for studies of photosynthetic mechanisms 3 , drought tolerance 4 , cell wall composition 5 , floral and inflorescence development 6 , leaf anatomy 7 , secondary metabolism 8 , plant microbiomes 9 , aluminum tolerance 10 , defense responses 11 and even inspiration for engineering applications 12 (Supplementary Fig. 1 ).…”

Section: Mainmentioning

confidence: 99%

A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci

et al. 2020

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Wild and weedy relatives of domesticated crops harbor genetic variants that can advance agricultural biotechnology. Here we provide a genome resource for the wild plant green millet (Setaria viridis), a model species for studies of C4 grasses, and use the resource to probe domestication genes in the close crop relative foxtail millet (Setaria italica). We produced a platinum-quality genome assembly of S. viridis and de novo assemblies for 598 wild accessions and exploited these assemblies to identify loci underlying three traits: response to climate, a ‘loss of shattering’ trait that permits mechanical harvest and leaf angle, a predictor of yield in many grass crops. With CRISPR–Cas9 genome editing, we validated Less Shattering1 (SvLes1) as a gene whose product controls seed shattering. In S. italica, this gene was rendered nonfunctional by a retrotransposon insertion in the domesticated loss-of-shattering allele SiLes1-TE (transposable element). This resource will enhance the utility of S. viridis for dissection of complex traits and biotechnological improvement of panicoid crops.

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“…For example, the Caffeoyl-shikimate esterase (CSE) [101], the bifunctional phenylalanine/tyrosine ammonia lyase (PTAL) [102] and a bifunctional cytosolic ascorbate peroxidase functioning as C3H [103] are missing links in the phenylpropanoid pathway that have only recently been discovered. There are ~511 genes in the phenylpropanoid pathway of SP80-3280 (Table 2), whereas other species like Arabidopsis thaliana and the model C4 grass Setaria viridis have only 26 [104] and 56 [105], respectively. Gaps in our knowledge include how monolignols, the lignin monomers, are transported to the apoplast for polymerization [106].…”

Section: Linking Genomic Data To Biomass Improvement By Exploring Thementioning

confidence: 99%

Genomic resources for energy cane breeding in the post genomics era

Diniz

Ferreira

Caten

et al. 2019

Computational and Structural Biotechnology Journal

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Sugarcane is one of the most sustainable energy crops among cultivated crops presenting the highest tonnage of cultivated plants. Its high productivity of sugar, bioethanol and bioelectricity make it a promising green alternative to petroleum. Furthermore, the myriad of products that can be derived from sugarcane biomass has been driving breeding programs towards varieties with a higher yield of fiber and a more vigorous and sustainable performance: the energy cane. Here we provide an overview of the energy cane including plant description, breeding efforts, types, and end-uses. In addition, we describe recently published genomic resources for the development of this crop, discuss current knowledge of cell wall metabolism, bioinformatic tools and databases available for the community.

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The lignin toolbox of the model grass Setaria viridis

Cited by 30 publications

References 121 publications

Transcriptome Mining Provides Insights into Cell Wall Metabolism and Fiber Lignification in Agave tequilana Weber

Transcriptome Mining Provides Insights into Cell Wall Metabolism and Fiber Lignification in Agave tequilana Weber

A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci

Genomic resources for energy cane breeding in the post genomics era

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