Polymorphism Study of vtg1 and igf3 Genes from Osteochilus vittatus and Cyprinus carpio as Candidate Molecular Markers for Egg-Quality Selection

The bonylip barb ( Osteochilus vittatus ) and common carp ( Cyprinus carpio ) are major freshwater aquaculture species in Indonesia; however, inconsistent egg quality remains a critical constraint to hatchery performance and seed reliability. The vitellogenin 1 ( vtg1 ) gene is essential for yolk precursor synthesis, while insulin-like growth factor-3 ( igf3 ) regulates ovarian function and oocyte maturation. Polymorphisms within these genes may therefore serve as candidate molecular markers for egg- quality selection. This study characterised polymorphisms in vtg1 and igf3 and identified restriction enzymes suitable for PCR–RFLP analysis. Twenty-five mature females per species were sampled. PCR amplification revealed variation in amplicon size and number: vtg1 produced a single amplicon in O. vittatus (655–844 bp), whereas in C. carpio it produced 1 or 2 amplicons (696–889 bp). For igf3 , O. vittatus generally produced a single amplicon (2737–3870 bp), whereas C. carpio typically produced two amplicons (2176–3286 bp). High-quality sequencing data were obtained only for O. vittatus ; sub-optimal chromatograms in C. carpio prevented reliable contig assembly and downstream enzyme prediction. In silico digestion identified five enzymes for vtg1 (TaqI, MboII, PstI, AcuI, and RsaI) and two for igf3 (MseI and MfeI) in O. vittatus . These findings provide the first molecular-level evidence supporting the development of vtg1 - and igf3 -based polymorphism screening as candidate markers for egg-quality selection in freshwater aquaculture.