Perennial ryegrass (Lolium perenne L.) is an important grass species for both forage and amenity purposes for temperate regions worldwide. It is envisaged that breeding efforts may be enhanced with the assistance of new breeding technologies such as genomic selection. A major step towards genomic selection will be the availability of a reference genome, and efforts are underway within our group to deliver this. An important step in de novo assembly will be defining the gene set, and the availability of transcriptome sequencing data will greatly aid gene prediction and validation, and the development of functional markers for improved ryegrass breeding. Therefore, the goal of this study is to analyze a de novo assembly of the perennial ryegrass transcriptome from the same inbred genotype being used for de novo genome assembly. Furthermore, we also conducted de novo transcriptome assembly with other heterozygous genotypes to enable SNP discovery for marker-assisted selection (MAS) and to determine the number of synonymous and non-synonymous SNPs. In this study we have preformed RNA-seq analysis of leaf, stem, inflorescence, leaf sheath, root and meristem from the inbred and heterozygous genotypes; to get a good representation of the transcriptome.
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International Plant & Animal Genome XXI (PAG XXI), 2013