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

• Published in: BMC genomics 2024-01, Vol.25 (1), p.64-64, Article 64
• Main Authors: Hua, Jixiang, Zhong, Chunyi, Chen, Wenhua, Fu, Jianjun, Wang, Jian, Wang, Qingchun, Zhu, Geyan, Li, Yan, Tao, Yifan, Zhang, Maoyou, Dong, Yalun, Lu, Siqi, Liu, Wenting, Qiang, Jun
• Format: Article
• Language: English
• Subjects: Aquaculture; Aquaculture industry; Bass; Biomarkers; Body height; Body length; Body weight; Breeding; Chromosomes; DNA sequencing; Dominant genotypes; Fish; Fishes; Fishing; Fresh water; Freshwater aquaculture; Freshwater fish; Gene polymorphism; Genes; Genetic aspects; Genetic diversity; Genomes; Genotype & phenotype; Genotypes; Genotyping; Growth; Growth traits; Height; Largemouth bass; Marker-assisted selection; Micropterus salmoides; Nucleotide sequencing; Nucleotides; Polymorphism; RAD-seq; Single nucleotide polymorphisms; Single-nucleotide polymorphism; SNP; Software; Thickness
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-024-09962-0

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, we screened 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 F generation of a largemouth bass population. 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, SNP19140160, SNP9639603, SNP9639605, and SNP23355498 showed significant associations; three of them (SNP9639603, SNP9639605, and SNP23355498) were significantly associated with one trait, body length, in the F generation, and one (SNP19140160) was significantly linked with four traits (body weight, height, length, and thickness) in the F generation. The markers SNP19140160 and SNP23355498 were located near two growth candidate genes, fam174b and ppip5k1b, respectively, and these candidate genes were closely linked with growth, development, and feeding. The average body weight of the group with four dominant genotypes at these SNP loci in the F generation population (703.86 g) was 19.63% higher than that of the group without dominant genotypes at these loci (588.36 g). 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 in the breeding of high-quality largemouth bass.