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

Abstract

Abstract Background Largemouth bass (Micropterus salmoides) has significant economic value as a high-yielding fish species in China’s freshwater aquaculture industry. Determining the major genes related to growth traits and identifying molecular markers associated with these traits serve as the foundation for breeding strategies involving gene pyramiding. In this study, using restriction-site associated DNA sequencing (RAD-seq) data to identify single nucleotide polymorphism (SNP) loci potentially associated with extreme growth differences between fast-growth and slow-growth groups in the F1 generation of a largemouth bass population. Results We subsequently identified associations between these loci and specific candidate genes related to four key growth traits (body weight, body length, body height, and body thickness) based on SNP genotyping. In total, 4,196,486 high-quality SNPs were distributed across 23 chromosomes. Using a population-specific genotype frequency threshold of 0.7, we identified 30 potential SNPs associated with growth traits. Among the 30 SNPs, three SNPs (SNP9639603, SNP9639605, and SNP23355498) were significantly correlated with one trait, body length, in the F1 generation, and one SNP (SNP19140160) was significantly linked with four traits (body weight, height, length, and thickness) in the F1 generation. Two potential genes were identified at the loci of the related markers, with fam174b being closely linked with growth, development, and feeding. The average body weight of the group with four dominant genotypes at these SNP loci in the F1 generation population (703.86 g) was 19.63% higher than that of the group without dominant genotypes at these loci (588.36 g). Conclusions Thus, these four markers could be used to construct a population with dominant genotypes at loci related to fast growth. These findings demonstrate how markers can be used to identify genes related to fast growth, and will be useful for molecular marker-assisted selection breeding of high-quality largemouth bass.