SNP GENOTYPING: THE KASP ASSAY IN THEOBROMA CACAO
Authors: Roslina, M.S1, Nuraziawati M.Y, Aizat, J, Ahmad K, M.J, Navies, M., Alias A, Rosmin, K.
Journal Issue: Malaysian Cocoa Journal, Volume 14/2022
Keywords: Assay, SNPs, cocoa, traits, KASP
Published On: 10/05/2022
Abstract
The validation of a marker is designing an assay based on the discovered polymorphism and then genotyping a panel of diverse germplasm and segregating the population. The ultimate goal of the study was to develop a reliable, rapid, and inexpensive polymerase chain reaction (PCR)-based method to genotype SNPs previously associated with desirable phenotypes in cocoa. The KASP genotyping assay utilizes a unique form of competitive allele-specific PCR combined with a novel, homogeneous, fluorescence-based reporting system. It is used to identify and measure genetic variation occurring at the nucleotide level to detect single nucleotide polymorphisms (SNPs) or inserts and deletions (InDels). The KASP technology is suitable for use on various equipment platforms and provides flexibility regarding the number of SNPs and the number of samples to be analyzed. Three hundred eighty-four cocoa leaves were collected from Bagan Datuk, Tawau, Madai, PPBK, and KKIP. These samples were collected in three replicates and to be tested with a total of 75 SNPs were used for the KASP assays. These final SNPs were selected for various traits such as; resistance to CPB, VSD and Black Pod, high yielding cocoa, and high cocoa butter. The KASP assays developed in this study were efficient and versatile for determining different traits studied. On average, the method is more straightforward than other methods, fast, and reproducible.