Next-generation sequencing technologies have resulted in the identification of a large number of single nucleotide polymorphism (SNP) markers in the genome. In comparison to other marker systems such as amplified fragment length polymorphisms and simple sequence repeats, SNP markers are amenable to automation, high-throughput, and cost-effective genotyping (Saxena et al., 2018). SNP markers are commonly used for genetic improvement through various studies such as construction of genetic map (Ting et al., 2023), elucidation of marker-trait associations, genome- wide association studies and genomic selection (Serdari et al., 2024; Kwong et al., 2017). SNP genotyping was performed using either fixed- arrays or genotyping-by-sequencing platforms. In the oil palm industry, most of the biotechnology research is currently using sequencing-based DNA markers for genomics-guided breeding. Utilisation of sequencing-based DNA markers require additional bioinformatics analysis and the cost per data point is higher compared to array-based with optimised SNP panel. Moreover, genotype calls of sequencing are not consistent across different experiments.
Main researcher: Dr. Chan Pek Lan
E-mail: chanpl@mpob.gov.my