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Abstract
High-density single-nucleotide polymorphism (SNP) genotyping array is an essential tool for genetic analyses of animals and plants. Large yellow croaker (Larimichthys crocea) is one of the most commercially important marine fish species in China. Although plenty of SNPs have been identified in large yellow croaker, no high-throughput genotyping array is available. In this study, a high-throughput SNP array named NingXin-I with 600K SNPs was developed and evaluated. A set of 82 large yellow croakers were collected from different locations of China and re-sequenced. A total of 9.34M SNPs were identified by mapping sequence reads to the large yellow croaker reference genome. About 1.98M candidate SNPs were selected for further analyses by using criteria such as SNP quality score and conversion performance in the final array. Finally, 579.5K SNPs evenly distributed across the large yellow croaker genome with an average spacing of 1.19 kb were proceeded to array production. The performance of NingXin-I array was evaluated in 96 large yellow croaker individuals from five populations, and 83.38% SNPs on the array were polymorphic sites. A further test of the NingXin-I array in five closely related species in Sciaenidae identified 26.68–56.23% polymorphic SNP rate across species. A phylogenetic tree inferred by using the genotype data generated by NingXin-I confirmed the phylogenetic distance of the species in Sciaenidae. The performance of NingXin-I in large yellow croaker and the other species in Sciaenidae suggested high accuracy and broad application. The NingXin-I array should be valuable for quantitative genetic studies, such as genome-wide association studies (GWASs), high-density linkage map construction, haplotype analysis, and genome-based selection.
Highlights
Large yellow croaker (Larimichthys crocea) is a commercially important marine fish species native to the northwestern Pacific, generally found in temperate waters
The large yellow croaker samples collected from wild stocks and cultured population, combined with the de novo whole-genome re-sequencing technique, guaranteed that the developed NingXin-I single-nucleotide polymorphism (SNP) array will perform well across different populations and that it will be broadly useful for population genetics and genome-assisted breeding of large yellow croaker
The SNP genotyping rate and polymorphic SNP rate may change with software parameters, population diversity, and sample size, the high polymorphic SNP rate across wild and cultured populations of large yellow croaker compared with other species still provides solid evidence of the good design and reliability of the NingXin-I array
Summary
Large yellow croaker (Larimichthys crocea) is a commercially important marine fish species native to the northwestern Pacific, generally found in temperate waters. It is one of the traditional species favored by Chinese consumers. The global production of large yellow croaker was 269,300 tons in 2016 [Food and Agriculture Organization (FAO)]. More than 99% of the large yellow croaker was produced by China. Large yellow croaker is the top marine aquaculture species in China according to the annual yield (Bureau of Fisheries of the Ministry of Agriculture 2019). Large yellow croaker strains with a high level of disease resistance, fast growth rate, and high tolerance to stresses are desperately needed
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