Oil Palm SSR Resource Interface (Opsri) – Web-Based Bioinformatic Analysis Pipeline for SSR Mining

Abstract

Co-dominant simple sequence repeat (SSRs) are popular DNA markers, widely applied in oil palm genetic studies, especially in genetic mapping, marker-trait association, diversity analysis and detecting illegitimacy.A repository having detailed information on SSRs and their inheritance profiles in specific breeding lines is lacking in Malaysia. Such a database enables prioritising polymorphic SSRs for screening, identification of which otherwise can be expensive and time consuming. As such, to facilitate and accelerate development of informative SSRs, oil palm SSR resource interface (OPSRI) was established and currently contains information on 1983 markers that were genotyped successfully across several oil palm breeding lines. OPSRI is a well-structured database that can expedite marker development and reduce redundancy in the on-going efforts at developing DNA markers for genetic analysis of oil palm. The system has been integrated with MISA, Primer3, ORF search script and BLAST to enable SSR identification. This study also characterised a large number of expressed sequence tags (EST)-SSRs using an in-silico approach. The information within the OPSRI database can help accelerate research in oil palm as well as in crops such as coconut and date palm which have a high level of synteny and marker-transferability with oil palm.

OIL PALM ECONOMIC PERFORMANCE IN MALAYSIA AND R&D PROGRESS IN 2022

“…Generally, linking of markers to traits of interest and pilling up favourable alleles in the next generation could improve breeding efficiency. To assist with the use of markers in breeding, Rosli et al (2022) described the establishment of the Oil Palm SSR Resource Database (OPSRI), a highly structured database that can facilitate the development of SSR based molecular markers. Signalling the increase in the repertoire of DNA markers available to the oil palm community, the establishment of intron polymorphism (IP) markers was also reported, in particular for the enhancement of fatty acid composition.…”