Development and validation of a 40 K liquid SNP array for the mud crab (Scylla paramamosain)

Abstract

Genomic selection (GS) and genome-wide association studies (GWAS) have been widely implemented to accelerate the genetic improvement of important economic traits. Developing an efficient and reliable high-throughput genotyping tool is the premise and basis of implementing GS and GWAS on the mud crab (Scylla paramamosain). In this study, leveraging the whole-genome resequencing data of 146 mud crabs from the southeast coast of China, a total of 16,714,943 high-quality SNPs were discovered. Based on polymorphic information content and evenly distribution on 49 chromosomes, a total of 40,352 SNPs was selected to develop a 40 K liquid SNP array (named “Xiexin No. 1”) using the genotyping by target sequencing (GBTS) technology. The genotyping performance test showed that this SNP array had a high site polymorphism (over 92.70%) and individual calling rate (97.02%). Furthermore, the mean of SNP concordance, genotype concordance, non-reference sensitivity, and non-reference discrepancy between “Xiexin No. 1” SNP array and resequencing were identified to be 0.986, 0.954, 0.942, and 0.097, respectively. Using this SNP array data, the genomic heritabilities were evaluated as 0.887 ± 0.065, 0.643 ± 0.108, 0.599 ± 0.111, and 0.624 ± 0.111 for body weight (BW), carapace length (CL), carapace length (CW), and body height (BH) in a cultured population (233 crabs). Furthermore, five significant SNPs associated with growth traits were identified by GWAS. After annotation, one candidate gene (XP_027221997.1) associated with BW and one candidate gene (XP_027210446.1) associated with CW and BH were identified. Most importantly, the prediction accuracy of GBLUP for BW, BH, CL, and CW were 0.535 ± 0.064, 0.544 ± 0.101, 0.574 ± 0.087, and 0.585 ± 0.083, with the unbiasedness values of 0.988 ± 0.22, 1.015 ± 0.274, 1.011 ± 0.196 and 1.037 ± 0.235. In conclusion, the “Xiexin No. 1” SNP array provides an efficient and reliable platform for high-quality genotyping, which would greatly promote the genetic studies and thus accelerate the genetic improvement of mud crabs.