Development and application of functional gene-based SSR markers for enhancing color and genetic stability in Taiwan red Tilapia (Oreochromis spp.)

Abstract

Red tilapia (Oreochromis spp.) is highly valued in the market because of its vibrant coloration and higher price compared to that of standard tilapia. However, current red tilapia strains frequently exhibit undesirable black and dark red blotches that diminish their market value and pose a challenge to the aquaculture industry. The genetic basis of these strains remains unclear and complicates their breeding and cultivation. Body color formation in tilapia is a complex quantitative trait regulated by multifunctional genes. Herein, biological materials from a long-term selection of Taiwan red tilapias were used to evaluate body surface color variation across two generations. We developed microsatellite markers targeting seven key functional genes involved in pigment synthesis, using the Taiwan Tilapia Transcriptome Database. Our findings demonstrated significant variations in body color parameters among Taiwan red tilapia seedlings, with genetics identified as the primary factor influencing skin color stability. Genotyping of functional genes revealed significant associations (P <0.001) with various body color phenotypes. Recessive alleles had differential effects on color fading and redness compared to dominant alleles, with allelic combinations driving genetic diversification and phenotypic expression. Furthermore, we identified that microsatellite sequence variations in sox10 gene, potentially alters amino acid sequences. These findings offer crucial insights into the molecular selection and hybridization of high-quality Taiwan red tilapia varieties. The developed markers are promising tools for verifying hybrid and self-crossing strains along with establishing pure Taiwan red tilapia strains. Their use can significantly improve production and value by providing aquaculture farmers and consumers with a broad selection of high-quality options.