Transcriptional dynamics during cell wall removal and regeneration reveals key genes involved in cell wall development in rice

Sharma, Rita; Tan, Feng; Jung, Ki‐Hong; Sharma, Manoj K.; Peng, Zhaohua; Ronald, Pamela C.

doi:10.1007/s11103-011-9819-4

Cited by 19 publications

(19 citation statements)

References 93 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Similarly, Sorghum Transcription Factor Database provides sequence information for about 1826 predicted transcription factors loci belonging to 56 families in S. bicolor [108]. Because of significant microcolinearity between sorghum, rice, and Brachypodium genomes [8], tools developed for rice/ Brachypodium [19, 109] can serve as an important framework to strengthen the functional genomic studies in sorghum.…”

Section: Molecular Markers Genome Sequence and Dna Polymorphismsmentioning

confidence: 99%

Sweet sorghum as biofuel feedstock: recent advances and available resources

Mathur

Umakanth

Tonapi

et al. 2017

Biotechnol Biofuels

Self Cite

198

119

View full text Add to dashboard Cite

Sweet sorghum is a promising target for biofuel production. It is a C4 crop with low input requirements and accumulates high levels of sugars in its stalks. However, large-scale planting on marginal lands would require improved varieties with optimized biofuel-related traits and tolerance to biotic and abiotic stresses. Considering this, many studies have been carried out to generate genetic and genomic resources for sweet sorghum. In this review, we discuss various attributes of sweet sorghum that make it an ideal candidate for biofuel feedstock, and provide an overview of genetic diversity, tools, and resources available for engineering and/or marker-assisting breeding of sweet sorghum. Finally, the progress made so far, in identification of genes/quantitative trait loci (QTLs) important for agronomic traits and ongoing molecular breeding efforts to generate improved varieties, has been discussed.

show abstract

Section: Molecular Markers Genome Sequence and Dna Polymorphismsmentioning

confidence: 99%

Sweet sorghum as biofuel feedstock: recent advances and available resources

Mathur

Umakanth

Tonapi

et al. 2017

Biotechnol Biofuels

Self Cite

198

119

View full text Add to dashboard Cite

show abstract

“…This is not surprising given that plants have many unique properties, e.g., the complex cell wall with a structure and biological role quite different from what is found in any other organisms. Identification of such plant unique families will require isolation of mutants through forward genetics screens or indications, e.g., from gene expression and localization analyses (Manfield et al, 2004; Brown et al, 2005; Persson et al, 2005; Oikawa et al, 2010; Mutwil et al, 2011; Sharma et al, 2011). To estimate the number of such unidentified GTs that might be present is very difficult.…”

Section: Future Perspectivesmentioning

confidence: 99%

Plant Glycosyltransferases Beyond CAZy: A Perspective on DUF Families

Hansen¹,

Harholt²,

Oikawa³

et al. 2012

Front. Plant Sci.

View full text Add to dashboard Cite

The carbohydrate active enzyme (CAZy) database is an invaluable resource for glycobiology and currently contains 45 glycosyltransferase families that are represented in plants. Glycosyltransferases (GTs) have many functions in plants, but the majority are likely to be involved in biosynthesis of polysaccharides and glycoproteins in the plant cell wall. Bioinformatic approaches and structural modeling suggest that a number of protein families in plants include GTs that have not yet been identified as such and are therefore not included in CAZy. These families include proteins with domain of unknown function (DUF) DUF23, DUF246, and DUF266. The evidence for these proteins being GTs and their possible roles in cell wall biosynthesis is discussed.

show abstract

“…In addition to their primary role in polysaccharide degradation, mounting genetic evidence suggests that several plant glycoside hydrolases are involved in biosynthesis, assembly and reorganization of cell wall polysaccharides (Minic, 2008; Sharma et al, 2011). The GH9 family genes encoding endo-1,4-β-glucanases, for example, are involved in cellulose biosynthesis (Nicol et al, 1998; Molhoj et al, 2002; Xie et al, 2013) and the xyloglucan endotransglucosylase/hydrolases (XETs) of the GH16 family have been implicated in synthesis and remodeling of xyloglucans (Rose et al, 2002; Jan et al, 2004; Yokoyama et al, 2004).…”

Section: Resultsmentioning

confidence: 99%

Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research

et al. 2013

Self Cite

View full text Add to dashboard Cite

Glycoside hydrolases (GH) catalyze the hydrolysis of glycosidic bonds in cell wall polymers and can have major effects on cell wall architecture. Taking advantage of the massive datasets available in public databases, we have constructed a rice phylogenomic database of GHs (http://ricephylogenomics.ucdavis.edu/cellwalls/gh/). This database integrates multiple data types including the structural features, orthologous relationships, mutant availability, and gene expression patterns for each GH family in a phylogenomic context. The rice genome encodes 437 GH genes classified into 34 families. Based on pairwise comparison with eight dicot and four monocot genomes, we identified 138 GH genes that are highly diverged between monocots and dicots, 57 of which have diverged further in rice as compared with four monocot genomes scanned in this study. Chromosomal localization and expression analysis suggest a role for both whole-genome and localized gene duplications in expansion and diversification of GH families in rice. We examined the meta-profiles of expression patterns of GH genes in twenty different anatomical tissues of rice. Transcripts of 51 genes exhibit tissue or developmental stage-preferential expression, whereas, seventeen other genes preferentially accumulate in actively growing tissues. When queried in RiceNet, a probabilistic functional gene network that facilitates functional gene predictions, nine out of seventeen genes form a regulatory network with the well-characterized genes involved in biosynthesis of cell wall polymers including cellulose synthase and cellulose synthase-like genes of rice. Two-thirds of the GH genes in rice are up regulated in response to biotic and abiotic stress treatments indicating a role in stress adaptation. Our analyses identify potential GH targets for cell wall modification.

show abstract

Transcriptional dynamics during cell wall removal and regeneration reveals key genes involved in cell wall development in rice

Cited by 19 publications

References 93 publications

Sweet sorghum as biofuel feedstock: recent advances and available resources

Sweet sorghum as biofuel feedstock: recent advances and available resources

Plant Glycosyltransferases Beyond CAZy: A Perspective on DUF Families

Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research

Contact Info

Product

Resources

About