Genetic Diversity Analysis of Three Salak (Salacca zalacca) Populations by Using SCOPA Markers
Reflinur Reflinur *
Research Center for Applied Botany, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Cibinong, Bogor 16911, West Java, Indonesia.
Adhitya Pratama Putra
Department of Agronomy, Faculty of Agriculture, Gadjah Mada University, Yogyakarta 55281, Yogyakarta, Indonesia.
Aziz Purwantoro
Department of Agronomy, Faculty of Agriculture, Gadjah Mada University, Yogyakarta 55281, Yogyakarta, Indonesia.
Zidni Muflikhati
Food Biotechnology Research Center, Bina Nusantara University, Palmerah 11480, Jakarta, Indonesia.
Kristianto Nugroho
Research Center for Horticulture, Research Organization for Agricultural and Food, National Research and Innovation Agency (BRIN), Cibinong, Bogor 16911, West Java, Indonesia.
Rerenstradika Tizar Terryana
Research Center for Applied Botany, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Cibinong, Bogor 16911, West Java, Indonesia.
Andi Isti Sakinah
Research Center for Applied Botany, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Cibinong, Bogor 16911, West Java, Indonesia.
Tasliah Tasliah
Research Center for Applied Botany, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Cibinong, Bogor 16911, West Java, Indonesia.
Lina Herlina
Research Center for Applied Botany, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Cibinong, Bogor 16911, West Java, Indonesia.
Muh Aswad Ashan
Biology Doctoral Program, School of Life Science and Technology, Bandung Institute of Technology (Institut Teknologi Bandung), Bandung 40132, West Java, Indonesia.
Ifa Manzila
Research Center for Horticulture, Research Organization for Agricultural and Food, National Research and Innovation Agency (BRIN), Cibinong, Bogor 16911, West Java, Indonesia.
Muhammad Ace Suhendar
Research Center for Food Crops, Research Organization for Agricultural and Food, National Research and Innovation Agency (BRIN), Cibinong, Bogor 16911, West Java, Indonesia.
Amalia Prihaningsih
Directorate for Laboratory Management, Research Facilities, and Science and Technology Park, National Research and Innovation Agency (BRIN), Cibinong, Bogor 16911, West Java, Indonesia.
Muh. Dzulkifly Ashan
Department of Agricultural Production Technology, Pangkajene State Agricultural Polytechnic, 90761 Pangkep, South Sulawesi, Indonesia.
Azis Natawijaya
Innovation Center, Corporate Development, PT. Bumitama Gunajaya Agro (Bumitama Agri Ltd.), South Jakarta 12160, Jakarta, Indonesia.
*Author to whom correspondence should be addressed.
Abstract
Salacca zalacca (Gaert.) Voss, commonly known as salak, is a native Indonesian fruit with high economic value. Developing superior salak varieties is crucial for enhancing national production, and high genetic uniformity is one key requirement for varietal release. This study aimed to analyse the genetic diversity of three salak populations (F3 female, F4 female, and F4 male) generated from a cross between the Pade Bali and Mawar cultivars, both sourced from PT. Benih Sumber Andalan. DNA was amplified using SCOPA markers, an improved version of SCAR markers, and analysed using NTSYS-pc 2.1 and GenAlEx. Amplification with four SCOPA primers (SCOPA-1, SCOPA-3, SCOPA-5, and SCOPA-6) produced 23 loci, of which 22 were polymorphic (95.65% polymorphism), indicating high effectiveness in detecting genetic variation. The F3 female population had the lowest heterozygosity value (0.139), followed by the F4 male (0.261) and F4 female (0.343) populations, suggesting greater genetic segregation in populations with larger sample sizes. AMOVA results showed that 89% of genetic variance occurred within populations and 11% between populations. PCoA and dendrogram analyses revealed relatively consistent clustering patterns and identified individuals with potentially unique alleles. These findings demonstrate the effectiveness of SCOPA markers in evaluating genetic diversity and their potential use in the early sex determination of salak seedlings. The genetic information obtained provides a foundation for future salak breeding programmes, particularly for the selection of elite genotypes and the conservation of valuable germplasm.
Keywords: DNA marker, genetic diversity, heterozygosity, Salacca zalacca (Gaert.) Voss, SCOPA markers, SCAR markers