Construction of DNA fingerprint for chili pepper varieties using SNAP markers

Abstract

Establishing the genetic identity of crop varieties has been considered essential for protecting plant breeder and farmer rights, particularly in developing countries like Indonesia. DNA fingerprint using molecular markers is important to give an unambiguous characteristic pattern as a valuable tool for genetic identification. In this study, eight Single Nucleotide Amplified Polymorphism (SNAP) markers were developed and applied to fingerprint 23 varieties of chili pepper. Polymorphism Information Content (PIC) detected in each primer ranged from 0.14 to 0.36 with an average of 0.17. The average of gene diversity was 0.20 among all varieties for total SNAP markers. A phylogenetic tree was subsequently constructed based on their genotypic scores for selected six markers, which separated the 23 varieties into three major groups. The cluster consisted of 2, 5 or 16 varieties. The DNA fingerprints were translated into capital letters representing presence and absence of allele, and they revealed the specific identity of five varieties. A number of varieties possessed the same DNA fingerprint profiles indicating their close genetic distance. Eventhough these SNAP markers were not able to distinguish each variety according to its unique allelic composition, this study could serve as preliminary information to establish genetic fingerprints of chili pepper varieties in Indonesia. Similar studies in the future will benefit from the SNAP found in this study.