IDENTIFICATION OF POTENTIAL NON-SYNONYMOUS SNPS ASSOCIATED WITH GROWTH TRAITS IN HYBRID COMMON CARP USING RNA-SEQ

Abstract

Common carp (Cyprinus carpio) is a traditionally important freshwater aquaculture species in many countries. Conventional selective breeding, when combined with molecular genetics, plays a crucial role in improving growth rate, productivity, and economic efficiency. This study applied RNA-sequencing technology to identify potential non-synonymous single-nucleotide polymorphisms (nsSNPs) in two hybrid carp groups (fast-growing and slow-growing), derived from crosses between pure Hungarian and Vietnamese carp lines. After sequencing, the total number of filtered reads was approximately 24.6 million in the fast-growing group (FG) and 24.8 million in the slow-growing group (SG), with mapping rates of 87.64% and 84.79%, respectively. A total of 333,328 SNPs were identified in FG and 453,729 in SG, with 138,837 SNPs shared between the two groups. Statistical analysis revealed 1,984 SNPs significantly associated with growth differences, distributed across 47 chromosomes. Functional annotation indicated that most nsSNPs were located in genes related to carbon and energy metabolism. Notably, 37 potential nsSNPs were detected in genes such as Myogenic Factor 6, Myozenin, and Myosin, which are known to be involved in muscle development and growth regulation. These findings provide valuable insights and a scientific foundation for improving the efficiency of fast-growing common carp breeding programs in Vietnam.