Genetic diversity of Indonesia milkfish (Chanos chanos) using amplified fragment length polymorphism (AFLP) analysis

Abstract

Genetic diversity of milkfish (Chanos chanos) from Indonesia was investigated using amplified fragment length polymorphism (AFLP) markers. A total of 255 loci were detected by combination of seven primers from 130 individuals collected at seven locations. AFLP analysis provided useful information in determining genetic variation for milkfish from different locations. The proportion of polymorphic loci and heterozygosity among populations ranged from 12 to 72% and 0.041 to 0.187, respectively. Genetic differentiation (F_ST) and Nei’s genetic distance among populations ranged from 0.214 to 0.732 and 0.016 to 0.302, respectively. Analysis of molecular variance supported significant differences between variance among populations when compared with variance within populations. The neighbor joining tree revealed four significantly distinct milkfish populations in Indonesian coastal waters. AFLP analyses may reveal historical patterns of milkfish genetic population structure in Indonesian coastal waters. The information derived from this study is useful to identify populations and categorize their population of origin to design a long term management program such as genetic improvement by selective breeding.

Key words: Chanos chanos, milkfish, genetic structure, Indonesia, amplified fragment length polymorphism (AFLP).