RESEARCH ARTICLE

Journal of Oil Palm Research Vol. 34 (4) December 2022, p. 643-656

OIL PALM SSR RESOURCE INTERFACE (OPSRI) – WEB-BASED BIOINFORMATIC ANALYSIS PIPELINE FOR SSR MINING

ROZANA ROSLI1 *; MOHD AMIN AB HALIM 1; TING NGOOT-CHIN1 ; NOORHARIZA MOHD ZAKI1 ; JAYANTHI NAGAPPAN1 ; RAJINDER SINGH1 ; LESLIE LOW ENG-TI1 and ZETI-AZURA MOHAMED-HUSSEIN2,3

DOI: https://doi.org/10.21894/jopr.2022.0008
Received: 6 January 2021   Accepted: 9 December 2021   Published Online: 28 January 2022
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 withMISA, 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.

KEYWORDS:


1 Malaysian Palm Oil Board,
6 Persiaran Institusi, Bandar Baru Bangi,
43000 Kajang, Selangor, Malaysia.

2 Department of Applied Physics,
Faculty of Science and Technology
Universiti Kebangsaan Malaysia,
43600 UKM Bangi, Selangor, Malaysia.

3 Centre for Bioinformatics Research,
Institute of Systems Biology (INBIOSIS)
Universiti Kebangsaan Malaysia,
43600 UKM Bangi, Selangor, Malaysia.

* Corresponding author e-mail: lizana@mpob.gov.my