Development and Evaluation of a High-Throughput Single-Nucleotide Polymorphism Array for Large Yellow Croaker...

Area of Science:

• Aquaculture Genomics
• Marine Biology
• Molecular Genetics

Background:

• The large yellow croaker (Larimichthys crocea) is a vital commercial marine fish in China.
• Existing genetic analyses are limited by the absence of a high-throughput genotyping array.
• Single-nucleotide polymorphism (SNP) arrays are crucial for genetic research in various species.

Purpose of the Study:

• To develop and evaluate a novel high-throughput SNP genotyping array for the large yellow croaker.
• To provide a tool for advanced genetic analyses and breeding programs in this species.

Main Methods:

• Whole-genome re-sequencing of 82 large yellow croakers to identify millions of SNPs.
• Selection of approximately 1.98 million candidate SNPs based on quality and performance metrics.
• Design and production of the NingXin-I array with 579,500 SNPs, evenly distributed across the genome.
• Evaluation of the array's performance in 96 individuals from five large yellow croaker populations and five related Sciaenidae species.

Main Results:

• The NingXin-I array contains 579,500 SNPs with an average spacing of 1.19 kb.
• An 83.38% SNP polymorphism rate was observed in large yellow croaker populations.
• Polymorphic SNP rates ranged from 26.68% to 56.23% in closely related Sciaenidae species.
• Phylogenetic analysis using the array data confirmed species relationships within Sciaenidae.

Conclusions:

• The NingXin-I array demonstrates high accuracy and broad applicability in large yellow croaker and related species.
• This array is a valuable tool for quantitative genetic studies, including GWAS, linkage mapping, and genomic selection.
• The development facilitates significant advancements in the genetic improvement and conservation of large yellow croaker.