High-Throughput Single Nucleotide Polymorphism (SNP) Discovery and Validation Through Whole-Genome Resequencing in Nile Tilapia (Oreochromis niloticus).

摘要: Nile tilapia (Oreochromis niloticus) is the second most important farmed fish in world and a sustainable source of protein for human consumption. Several genetic improvement programs have been established this species world. Currently, estimation of genetic merit breeders typically based on genealogical phenotypic information. Genome-wide information can be exploited to efficiently incorporate traits that are difficult measure into breeding goal. Thus, single nucleotide polymorphisms (SNPs) required investigate phenotype–genotype associations determine genomic basis economically traits. We performed de novo SNP discovery three different populations tilapia. A total 29.9 million non-redundant SNPs were identified through Illumina (HiSeq 2500) whole-genome resequencing 326 individual samples. After applying several filtering steps, including removing genotype site quality, presence Mendelian errors, non-unique position genome, 50,000 high-quality selected development custom BeadChip panel. These highly informative analyzed showing between 43,869 (94%) 46,139 (99%) Hardy-Weinberg Equilibrium; 37,843 (76%) 45,171(90%) with minor allele frequency (MAF) higher than 0.05; 43,450 (87%) 46,570 (93%) MAF 0.01. The 50K panel developed current work will useful dissection relevant traits, enhancing selection, as well supporting studies using dense genome-wide