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Transcriptome analysis reveals season-specific rbcS gene expression profiles in diploid perennial ryegrass (Lolium perenne L.)

Sathish, Puthigae, Withana, Nimali, Biswas, Margaret, Bryant, Catherine, Templeton, Kerry, Al-Wahb, Muhannad, Smith-Espinoza, Claudia, Roche, John R., Elborough, Kieran M., Phillips, Jonathan R.
Plant biotechnology journal 2007 v.5 no.1 pp. 146-161
DNA, Lolium perenne, autumn, databases, diploidy, expressed sequence tags, forage, gene expression, genes, genetic engineering, grasses, lawns and turf, nuclear genome, outcrossing, pastures, ribulose-bisphosphate carboxylase, seasonal variation, spring, summer, tissues, transcriptome, transcriptomics, winter
Perennial ryegrass (Lolium perenne L.) is a major grass species used for forage and turf throughout the world, and gains by conventional breeding have reached a plateau. Perennial ryegrass is an outcrossing, self-incompatible diploid (2n = 2x = 14) with a relatively large genome (4067 Mbp/diploid genome; Evans, G.M., Rees, H., Snell, C.L. and Sun, S. (1972) The relation between nuclear DNA amount and the duration of the mitotic cycle. Chrom. Today, 3, 24-31). Using tissues sourced from active pastures during the peak of the autumn, winter, spring and summer seasons, we analysed the ryegrass transcriptome employing a Serial Analysis of Gene Expression (SAGE[trade mark sign]) protocol, with the dual goals of understanding the seasonal changes in perennial ryegrass gene expression and enhancing our ability to select genes for genetic manipulation. A total of 159 002 14-mer SAGE[trade mark sign] tags was sequenced and mapped to the perennial ryegrass DNA database, comprising methyl-filtered (GeneThresher®) and expressed sequence tag (EST) sequences. The analysis of 14 559 unique SAGE[trade mark sign] tags, which were present more than once in our SAGE[trade mark sign] library, revealed 964, 1331, 346 and 131 exclusive transcripts to autumn, winter, spring and summer, respectively. Intriguingly, our analysis of the SAGE[trade mark sign] tags revealed season-specific expression profiles for the small subunit of ribulose-1,5-bisphosphate carboxylase (Rubisco), LprbcS. The transcript level for LprbcS was highest in spring, and then decreased gradually between summer and winter. Five different copies of LprbcS were revealed in ryegrass, with one possibly producing splice variant transcripts. Two highly expressed LprbcS genes were reported, one of which was not active in autumn. Another LprbcS gene showed an inverse expression profile to the autumn inactive LprbcS in a manner to compensate the expression level.