Genome-Wide SNP Discovery in Indonesian Pepper (Capsicum annum L.)

• Pepper (Capsicum annuum L.), an herbaceous diploid species, is an important and strategic horticultural crop in Indonesia and satisfies people’s spicy taste worldwide. To gain a better understanding of genome information for future breeding, six varieties of peppers were paired-end re-sequenced of their whole genome. Their sequence variation revealed 26,079,616 variants, of which one DNA variation was shown in every 101 bases. Of total variant, approximately 94.7% were SNPs and the remaining were indels (insertion/deletion). Abundant SNPs were shared among varieties and some private SNPs could be unique to the Indonesian pepper. Of the 175,885 SNPs with functional classes, 60.5% were mis-sense mutation and only small portion was silent mutation (1.9%). Such mutation might modify amino acid composition encoding protein, leading to phenotypic change. Ratio of transition and transversion (1.9:1) indicated the higher quality of these sequences. Around 0.62% variants identified within coding region indicated their relation with important genes in pepper as shown by the functional annotation with Gene Ontology (GO). For SNP validation, 48 SNPs were chosen and most of the SNPs detected by bioinformatic tools were confirmed by re-sequencing with Sanger Method. Based on the confirmed SNPs, at least 68% sequences identity were sharing between two genotypes (Tanjung and Lembang-1). The informative genome-wide SNPs and the confirmation in our study could be useful to develop molecular markers for genetic studies, fingerprinting and marker-assisted selection in pepper breeding program.