The Complete Chloroplast Genome Sequence of Perennial Ryegrass (Lolium perenne L.) Reveals Useful Polymorphisms Among European Ecotypes

To date, more than 130 complete chloroplast genome sequences of plants have been published. Thirteen of these sequences belong to Poaceae species. But the complete chloroplast genome sequence of the important forage species, perennial ryegrass, was hitherto unknown. We sequenced, assembled and annotated the entire chloroplast genome of Lolium perenne 'Cashel', and searched it for single nucleotide polymorphism (SNPs) and simple sequence repeats (cpSSRs). The chloroplast genome sequence of L. perenne is 135,282 bp long and encodes 128 genes. Forty SNPs were found within the sequenced sample of 'Cashel'. Thirty mononucleotide cpSSRs of more than ten base pairs length were detected and we designed primers to amplify and sequence twelve of the most variable of these regions. Length variation and SNP variation of these markers was assessed on a set of 15 Irish and 15 European ecotypes. The results revealed a total of 21 haplotypes across all ecotypes and these were suitable to detect genetic diversity among and within L. perenne accessions.