Development and evaluation of 50 K liquid SNP array for blunt snout bream (Megalobrama amblycephala)

Abstract

Blunt snout bream (Megalobrama amblycephala) is an economically important herbivorous fish native to China. However, the lack of high-efficient genotyping tools has impeded the genomic breeding programs for M. amblycephala. SNP array, an important genotyping platform, is crucial for implementing genomic selection. In this study, we employed the genotyping by liquid hybridization capture sequencing technology to create a multiple single-nucleotide polymorphism (mSNP) liquid array named Fangxin-I, which comprised 49,173 evenly distributed SNP loci across the 24 chromosomes of M. amblycephala. The array was designed for the comprehensive assessment of allelic variations across the genome of M. amblycephala. A total of 79.59 % of the array loci were of high-quality, with a genotyping success rate of 98.63 % across 52 individuals. The average genotype concordance rates reached 96.56 % between batches, and 99.40 % within batches. The comparison of the genotyping results between the SNP array and whole-genome re-sequencing indicated a genotype concordance of 98.32 %. Fangxin-I SNP array was subsequently employed for population genetics and genetic sex identification to validate its efficiency and accuracy. The analysis results indicated that the phylogenetic trees constructed for six populations of M. amblycephala, using the genotyping data from the Fangxin-I SNP array and the identified genomic loci from re-sequencing, reflected similar genetic relationships. Fangxin-I demonstrated a high accuracy in the genetic sex identification, affirming its effectiveness in both population genetics and genetic sex determination. Additionally, the array was used for genome-wide association study and identified the loci related to the resistance of Aeromonas hydrophila in M. amblycephala mainly on chromosomes 2, 4, 11 and 20. In summary, Fangxin-I SNP array will serve as an instrumental platform for high-quality genotyping, thereby facilitating the genomic selection breeding of M. amblycephala.