Agudelo John F G, Mastrochirico-Filho Vito A, Garcia Baltasar F, Ariede Raquel B, Yáñez José M, Valladão Gustavo M R, Hashimoto Diogo T
Universidade Estadual Paulista (Unesp), Centro de Aquicultura da Unesp, Jaboticabal, SP, Brazil.
Universidade Estadual Paulista (Unesp), Faculdade de Ciências, Bauru, SP, Brazil.
Genet Mol Biol. 2024 Sep 2;47(3):e20230364. doi: 10.1590/1678-4685-GMB-2023-0364. eCollection 2024.
In South America, Tambaqui (Colossoma macropomum) stands as the primary target for aquaculture, yet breeding programs for this Amazon native species are in their early stages. While high-density single nucleotide polymorphism (SNP) arrays are pivotal for aquaculture breeding, their costs can be prohibitive for non- or semi-industrial species. To overcome this, a cost-effective approach involves developing low-density SNP arrays followed by genotype imputation to higher densities. In this study, a 1K SNP array for tambaqui was created and validated, offering a balance between SNP quantity and genome representativity. The imputation accuracy from various SNP densities to a medium-density array was evaluated, with the 1K density demonstrating the best trade-off (accuracy of 0.93). This subset was further utilized to construct a commercial array through Agriseq™ targeted genotyping-by-sequencing, validated in 192 DNA samples, affirming its high quality for genotyping tambaqui. The low-density SNP array, with genome-wide coverage and high polymorphism, emerges as an effective tool for exploring genetic variation within diverse populations. Population analyses using the 1K panel proved to be an efficient tool for genetic characterization of sampled broodstocks, making it a valuable resource for genetic improvement programs targeting this Amazon native species.
在南美洲，坦巴基鱼（巨脂鲤）是水产养殖的主要目标物种，但针对这种亚马逊本土物种的育种计划尚处于早期阶段。虽然高密度单核苷酸多态性（SNP）阵列对水产养殖育种至关重要，但其成本对于非工业化或半工业化养殖的物种来说可能过高。为克服这一问题，一种经济有效的方法是先开发低密度SNP阵列，然后通过基因型填补提高到更高密度。在本研究中，构建并验证了一种用于坦巴基鱼的1K SNP阵列，该阵列在SNP数量和基因组代表性之间取得了平衡。评估了从各种SNP密度到中密度阵列的填补准确性，1K密度表现出最佳权衡（准确性为0.93）。该子集进一步用于通过Agriseq™靶向测序基因分型构建商业阵列，并在192个DNA样本中进行了验证，证实其用于坦巴基鱼基因分型的高质量。这种具有全基因组覆盖和高多态性的低密度SNP阵列，成为探索不同种群内遗传变异的有效工具。使用1K面板进行的群体分析被证明是对采样亲鱼进行遗传特征分析的有效工具，使其成为针对这种亚马逊本土物种的遗传改良计划的宝贵资源。
