title: Changes in cell wall polysaccharide composition, gene transcription and alternative splicing in germinating barley embryos.
abstract: Barley (Hordeum vulgare L.) seed germination initiates many important biological processes such as DNA, membrane and mitochondrial repairs. However, little is known on cell wall modifications in germinating embryos. We have investigated cell wall polysaccharide composition change, gene transcription and alternative splicing events in four barley varieties at 24h and 48 h germination. Cell wall components in germinating barley embryos changed rapidly, with increases in cellulose and (1,3)(1,4)-β-D-glucan (20-100%) within 24h, but decreases in heteroxylan and arabinan (3-50%). There were also significant changes in the levels of type I arabinogalactans and heteromannans. Alternative splicing played very important roles in cell wall modifications. At least 22 cell wall transcripts were detected to undergo either alternative 3' splicing, alternative 5' splicing or intron retention type of alternative splicing. These genes coded enzymes catalyzing synthesis and degradation of cellulose, heteroxylan, (1,3)(1,4)-β-D-glucan and other cell wall polymers. Furthermore, transcriptional regulation also played very important roles in cell wall modifications. Transcript levels of primary wall cellulase synthase, heteroxylan synthesizing and nucleotide sugar inter-conversion genes were very high in germinating embryos. At least 50 cell wall genes changed transcript levels significantly. Expression patterns of many cell wall genes coincided with changes in polysaccharide composition. Our data showed that cell wall polysaccharide metabolism was very active in germinating barley embryos, which was regulated at both transcriptional and post-transcriptional levels.
authors.affiliation: Australian Export Grains Innovation Centre, 3 Baron-Hay Court, South Perth, WA 6155, Australia. Electronic address: Qisen.zhang@aegic.org.au.
authors.forename: Qisen
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Western Barley Genetics Alliance, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia. Electronic address: Xiao-Qi.Zhang@murdoch.edu.au.
authors.forename: Xiaoqi
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Agriculture Flagship, CSIRO, Black Mountain, ACT 2601, Australia. Electronic address: Filomena.Pettolino@csiro.au.
authors.forename: Filomena
authors.initials: F
authors.lastname: Pettolino
authors.affiliation: Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, WA 6155, Australia. Electronic address: Gaofeng.zhou@agric.wa.gov.au.
authors.forename: Gaofeng
authors.initials: G
authors.lastname: Zhou
authors.affiliation: Australian Export Grains Innovation Centre, 3 Baron-Hay Court, South Perth, WA 6155, Australia; Western Barley Genetics Alliance, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia; Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, WA 6155, Australia. Electronic address: c.li@murdoch.edu.au.
authors.forename: Chengdao
authors.initials: C
authors.lastname: Li
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D002473:Cell Wall / Q000201:enzymology / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018525:Germination / Q000235:genetics*; D001467:Hordeum / Q000196:embryology* / Q000201:enzymology / Q000235:genetics*; D005810:Multigene Family; D009711:Nucleotides / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D011134:Polysaccharides / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics; D012639:Seeds / Q000235:genetics*; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic; D014990:Xylans / Q000378:metabolism; D047071:beta-Glucans / Q000378:metabolism
chemical_list: D009711:Nucleotides; D010940:Plant Proteins; D011134:Polysaccharides; D012333:RNA, Messenger; D014157:Transcription Factors; D014990:Xylans; D047071:beta-Glucans; C067858:beta-glucan, (1-3)(1-4)-
keywords: Alternative splicing; Cell wall; Differentially expressed gene; Germination; Polysaccharide; RNA-sequencing