Abstract
Next-generation sequencing and pool sequencing have been widely used in SNP (single-nucleotide polymorphism) detection and population genetics research; however, there are few reports on SNPs related to the growth of Penaeus vannamei. The purpose of this study was to call SNPs from rapid-growing (RG) and slow-growing (SG) individuals’ transcriptomes and use DNA pool sequencing to assess the reliability of SNPs. Two parameters were applied to detect SNPs. One parameter was the p-values generated using Fisher’s exact test, which were used to calculate the significance of allele frequency differences between RG and SG. The other one was the AFI (minor allele frequency imbalance), which was defined to highlight the fold changes in MAF (minor allele frequency) values between RG and SG. There were 216,015 hypothetical SNPs, which were obtained based on the transcriptome data. Finally, 104 high-quality SNPs and 96,819 low-quality SNPs were predicted. Then, 18 high-quality SNPs and 17 low-quality SNPs were selected to assess the reliability of the detection process. Here, 72.22% (13/18) accuracy was achieved for high-quality SNPs, while only 52.94% (9/17) accuracy was achieved for low-quality SNPs. These SNPs enrich the data for population genetics studies of P. vannamei and may play a role in the development of SNP markers for future breeding studies.
Highlights
Penaeus vannamei is a widely farmed penaeid shrimp
singlenucleotide polymorphisms (SNPs) widely exist in the genome, and they serve as suitable markers for linkage maps, genome-wide association studies (GWAS), and marker-assisted selection (MAS) of target traits [8,9,10,11,12,13,14,15,16]
52,476,282; 54,200,380; 59,824,174; 55,354,830; 54,220,100; and 43,292,594 high-quality reads were obtained. These high-quality, clean reads were mapped to the rRNA database, the unmapped reads were used for subsequent analysis
Summary
With the development of culture technology, higher-density farming has become a trend. Genetic studies have been conducted to understand the molecular mechanisms of target traits in P. vannamei, such as linkage map construction [1,2,3,4] and quantitative trait locus detection [5,6]. As a major shrimp cultured in China, there are few genetic markers of P. vannamei for growth performance. SNPs widely exist in the genome, and they serve as suitable markers for linkage maps, genome-wide association studies (GWAS), and marker-assisted selection (MAS) of target traits [8,9,10,11,12,13,14,15,16]. There have been several studies to discover SNPs associated with the phenotypes of interest [17,18,19,20]; the available information for genetic diversity studies is still insufficient
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