Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China.
Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
BMC Genomics. 2024 Jan 16;25(1):64. 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.
大口黑鲈（Micropterus salmoides）在中国淡水养殖业中是一种高产量的鱼类，具有重要的经济价值。确定与生长性状相关的主效基因，并鉴定与这些性状相关的分子标记，是涉及基因聚合的育种策略的基础。在这项研究中，我们筛选了限制相关 DNA 测序（RAD-seq）数据，以鉴定 F 代大鳞大麻哈鱼群体中快速生长和缓慢生长组之间极端生长差异相关的单核苷酸多态性（SNP）位点。
我们随后根据 SNP 基因分型，确定了这些位点与与四个关键生长性状（体重、体长、体高和体厚）相关的特定候选基因之间的关联。总共在 23 条染色体上分布了 4196486 个高质量的 SNPs。使用群体特异性基因型频率阈值为 0.7，我们鉴定了 30 个与生长性状相关的潜在 SNP。在 30 个 SNP 中，SNP19140160、SNP9639603、SNP9639605 和 SNP23355498 表现出显著的关联；其中三个（SNP9639603、SNP9639605 和 SNP23355498）与 F 代的一个生长性状（体长）显著相关，一个（SNP19140160）与 F 代的四个性状（体重、高度、体长和厚度）显著相关。标记 SNP19140160 和 SNP23355498 分别位于两个生长候选基因 fam174b 和 ppip5k1b 的附近，这些候选基因与生长、发育和摄食密切相关。在 F 代群体中具有这些 SNP 位点四个优势基因型的组的平均体重（703.86 g）比没有这些位点优势基因型的组高 19.63%（588.36 g）。
因此，这四个标记可以用于构建与快速生长相关的优势基因型群体。这些发现表明了如何利用标记识别与快速生长相关的基因，并将有助于大口黑鲈优质品种的分子标记辅助选择。
