Development of Single Nucleotide Polymorphism and Association Analysis with Growth Traits for Black Porgy (Acanthopagrus schlegelii)

Abstract

Black porgy is an important marine aquaculture fish species whose production is at the fifth position in all kinds of marine-cultured fishes in China. In this study, Illumina high-throughput sequencing technology was used to sequence the total RNA of black porgy. Sixty-one candidate SNPs (Single Nucleotide Polymorphism) were screened out and genotyped through GATK4 (Genome Analysis ToolKit) software and MALDI-TOF MS (Matrix-Assisted Laser Desorption/ Ionization Time of Flight Mass Spectrometry). The experimental results showed that a total of sixty SNPs were successfully genotyped, with a success rate of 98.36%. The results of principal component analysis and correlation analysis of growth traits showed that body weight was the first principal component, with a cumulative contribution rate of 74%. There were significant correlations (p < 0.05) or extremely significant correlations (p < 0.01) between different growth traits. The results of genetic parameter analysis and association analysis showed that scaffold12-12716321, scaffold13-4787950, scaffold2-13687576 and scaffold290-11890 were four SNPs that met the requirement of polymorphic information content and conformed to the Hardy–Weinberg equilibrium. There were significant differences between their genotype and the phenotype of growth traits. The four SNP molecular markers developed in this research will lay a foundation for further exploration of molecular markers related to the growth traits of black porgy and will provide a scientific reference for the further study of its growth mechanisms. At the same time, these molecular markers can be applied to the production practices of black porgy, so as to realize selective breeding at the molecular level and speed up the breeding process.

Single nucleotide polymorphism SNP19140160 A > C is a potential breeding locus for fast-growth largemouth bass (Micropterus salmoides)

“…SNPs are variants with low redundancy and high coverage in the genome, and they can be used to facilitate high-throughput genotyping [34]. They have been widely used to construct high-density genetic linkage maps and discover QTL and economic trait-related genes [35][36][37]. Li et al (2017) used RNA-seq data to mine for fast-growth-related SNPs in largemouth bass.…”

Single nucleotide polymorphism SNP19140160 A>C is a potential breeding locus for fast-growth largemouth bass (Micropterus salmoides)

“…SNPs are variants with low redundancy and high coverage in the genome, and they can be used to facilitate high-throughput genotyping [34]. They have been widely used to construct high-density genetic linkage maps and discover QTL and economic trait-related genes [35][36][37]. Li et al (2017) used RNA-seq data to mine for fast-growth-related SNPs in largemouth bass.…”

A Cold-Inducible RNA Binding Protein Gene from Acanthopagrus schlegelii: Molecular Characterization, Expression, and Association with Apoptosis to Low-Temperature Stress

“…Black porgy (Acanthopagrus schlegelii) belongs to the family Sparidae in the order Perciformes [1], which is widely distributed along the western Pacifc coast because of its wide temperature and salinity tolerance. It is an essential coastal economic fsh in China, Japan, and Southeast Asia [2].…”