DNA methylation and gene expression regulation associated with vascularization in Sorghum bicolor.
Gina M Turco, Kaisa Kajala, Govindarajan Kunde-Ramamoorthy, Chew-Yee Ngan, Andrew Olson, Shweta Deshphande, Denis Tolkunov, Barbara Waring, Scott Stelpflug, Patricia Klein, Jeremy Schmutz, Shawn Kaeppler, Doreen Ware, Chia-Lin Wei, J Peter Etchells, Siobhan M Brady
Author Information
Gina M Turco: Department of Plant Biology and Genome Center, UC Davis, Davis, CA, 95616, USA.
Kaisa Kajala: Department of Plant Biology and Genome Center, UC Davis, Davis, CA, 95616, USA.
Govindarajan Kunde-Ramamoorthy: DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
Chew-Yee Ngan: DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
Andrew Olson: Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.
Shweta Deshphande: DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
Denis Tolkunov: DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
Barbara Waring: Department of Plant Biology and Genome Center, UC Davis, Davis, CA, 95616, USA.
Scott Stelpflug: Department of Agronomy and Great Lakes Bioenergy Research Center, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706, USA.
Patricia Klein: Institute for Plant Genomics and Biotechnology and Department of Horticultural Sciences, Texas A and M University, College Station, TX, 77843, USA.
Jeremy Schmutz: DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
Shawn Kaeppler: Department of Agronomy and Great Lakes Bioenergy Research Center, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706, USA.
Doreen Ware: Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.
Chia-Lin Wei: DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
J Peter Etchells: Department of Plant Biology and Genome Center, UC Davis, Davis, CA, 95616, USA. ORCID
Siobhan M Brady: Department of Plant Biology and Genome Center, UC Davis, Davis, CA, 95616, USA.
Plant secondary cell walls constitute the majority of plant biomass. They are predominantly found in xylem cells, which are derived from vascular initials during vascularization. Little is known about these processes in grass species despite their emerging importance as biomass feedstocks. The targeted biofuel crop Sorghum bicolor has a sequenced and well-annotated genome, making it an ideal monocot model for addressing vascularization and biomass deposition. Here we generated tissue-specific transcriptome and DNA methylome data from sorghum shoots, roots and developing root vascular and nonvascular tissues. Many genes associated with vascular development in other species show enriched expression in developing vasculature. However, several transcription factor families varied in vascular expression in sorghum compared with Arabidopsis and maize. Furthermore, differential expression of genes associated with DNA methylation were identified between vascular and nonvascular tissues, implying that changes in DNA methylation are a feature of sorghum root vascularization, which we confirmed using tissue-specific DNA methylome data. Roots treated with a DNA methylation inhibitor also showed a significant decrease in root length. Tissues and organs can be discriminated based on their genomic methylation patterns and methylation context. Consequently, tissue-specific changes in DNA methylation are part of the normal developmental process.
