SNP- and haplotype-based GWAS of growth-related traits in Pacific white shrimp Litopenaeus vannamei

The Pacific white shrimp Litopenaeus vannamei ( L. vannamei ) is a very important aquaculture species. A better understanding of the genetic mechanisms underlying the growth-related traits is crucial for the development of the shrimp aquaculture industry. In this study, a genome-wide association study (GWAS) based on both single-nucleotide polymorphisms (SNPs) and haplotypes was conducted for the body weight trait in L. vannamei . The heritability of body weight was estimated as moderate (0.37 ± 0.06) based on 56,651 SNPs from 1106 individuals genotyped with the “Zhongke Xin No.2” SNP chip. A total of 30 SNPs and 42 haplotypes were identified as body weight-associated markers. Furthermore, 47 candidate genes were annotated around the significantly associated SNPs and haplotypes. Among these genes, four of them, including SOCS5 , EcR , Eip75 , and E75 , showed significantly different expression levels between shrimp with fast and slow growth. Notably, EcR , Eip75 , E75 , and another molting-related gene, HR3 , might act as a molecular module to regulate growth in L. vannamei . These results not only contribute to clarifying the genetic mechanisms underlying shrimp growth but also provide valuable genetic markers for molecular breeding programs.