Genome-wide Association Study Identifies SNPs and Candidate Genes Associated with Abdominal Meat Weight and Meat Yield of red Swamp Crayfish Procambarus clarkii.

Red swamp crayfish (Procambarus clarkii) is an economically important freshwater species in the world. The abdominal meat weight (AMW) and meat yield (MY) are the principal economic traits of the species. To identify SNPs and candidate genes associated with AMW and MY of the species, a genome-wide association study (GWAS) was conducted to genotype 410 individuals using a 50 K liquid-phase breeding SNP array. A total of 46,367 high-quality SNPs was identified. The Mixed Linear Model (MLM), Fixed and random model Circulating Probability Unification (FarmCPU), and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) models were identified to be suitable for GWAS analysis of AMW and MY of the species. Eleven significant SNPs were identified to be associated with AMW and ten SNPs with MY trait, respectively. Seven candidate genes (FOXO, UBE4A, RAP2B, CCNO, CDK7, Mlp84B, and HK1) were linked to AMW trait, while three candidate genes (NDFIP1, PRKG1, and ADCY5) were associated with MY trait based on KEGG and GO enrichment analyses. These candidate genes are primarily involved in biological processes including cell cycle arrest, apoptosis, oxidative stress response, and metabolic homeostasis. The results would benefit to understanding the genetic basis of abdominal meat weight and meat yield traits and providing potential molecular markers for genetic improvement of crayfish.