SNP Discovery in Olive Tree Using Illumina Transcriptome Sequencing

The improvement of single nucleotide polymorphism (SNP) markers in olive offers the opportunity to utilize DNA markers in many new areas of genetic variation, linkage mapping, population structure analysis, association genetics, map-based gene isolation, and plant breeding. The main objective of this study was to discover single nucleotide polymorphisms (SNP) for olive using high-throughput next generation sequencing and to develop SNP assays for cultivar identification. Transcriptome sequencing was performed isolating mRNA samples from 5 distinct olive genotypes (Siyah Salamuralık, Yun Celebi, Yuvarlak Celebi, Hirhali Celebi and Halhali 3) using Illumina next generation sequencing technology. Approximately 28.4 million reads for Siyah Salamuralik, 28.9 from Yun Celebi, 26.8 from Yuvarlak Celebi, 30.2 from Hirhali Celebi and 30.6 million from Halhali-3 were obtained by sequencing gene transcripts derived from mRNA samples. After sequencing, 21.152 contigs were found to have reads aligned to the Genbank sequences revealing which biological process they are responsible for metabolic process (18%),  cellular process (15%), developmental process (11%), biological regulation (%10) etc. and then they were used in gene associated SNP identification. This study is the first effort to characterize the olive transcriptome comprehensively and may provide insights into the characterisation of olive cultivar.