PRELIMINARY EVALUATION ON THE SNP MARKERS FOR THE MALAYSIAN COMMERCIAL COCOA CLONES
Authors: Lea Johnsiul, Sairan Asim, Nuraziawati Mat Yazik
Journal Issue: Malaysian Cocoa Journal, Volume 13(1)/2021
Keywords: Theobroma cocoa, SNP marker, Malaysian cocoa commercial clone, clone verification, planting material.
Published On: 1/11/2021
Abstract
Accurate identification of individual genotypes is important for cocoa (Theobroma cacao L.) breeding, planting, propagation and germplasm conservation. Single nucleotide polymorphism (SNP) is the current preferred markers for DNA fingerprinting in most crops including cocoa, nevertheless, a SNP panel with a minimum number of SNPs for optimal clone verification for Malaysian cocoa commercial clones is still unavailable. The development of single nucleotide polymorphism (SNP) markers in cocoa provides an effective way to do high-throughput genotyping system for cocoa commercial clones’ verification. A set of 94 SNP loci of varying sizes were assembled and assessed to determine their ability to distinguish among a set of two samples from each of 53 Malaysian cocoa commercial clones. The genotyped data obtained were of high quality with very little missing data and good coverage of all samples. Based on this study, a set of 15 SNP markers were selected to be the core SNP panel for verifying the Malaysian cocoa commercial clones with the exception of two clones which were found to be different at only one SNP loci.