Black carp (Mylopharyngodon piceus) is an economically important freshwater aquaculture species in China, and improvement of growth traits is a major objective in its breeding. In a previous genome-wide association study (GWAS), nlrp3 was identified as a candidate gene for body weight and body length. In this study, we further analyzed genetic variation in the nlrp3 region and validated its association with growth traits in black carp. A discovery dataset of 537 black carp individuals retained from the previous GWAS cohort and an independent validation population of 275 additional individuals were analyzed for body weight (BW) and body length (BL). Linkage disequilibrium (LD) analysis identified 24 LD blocks in the coding region of nlrp3, and the GWAS lead SNP, Chr05₄2410277, was located within the first prominent LD block containing six candidate SNPs. Local LD analysis showed strong linkage among these six SNPs, with most pairwise D′ values ranging from 0. 99 to 1. 00. In the discovery population, four SNPs showed significant associations with growth traits, and haplotype analysis identified eight common haplotypes, with clear haplotype-dependent differences in BW. In the validation population, four SNPs were polymorphic, and three of them were significantly associated with both BW and BL. In addition, the full-length cDNA of black carp nlrp3 was 3126 bp, encoding a protein of 1033 amino acids. Expression analysis showed that nlrp3 was expressed in all examined tissues, with significantly higher expression in the intestine and muscle, whereas significant differences between fast-growing and slow-growing individuals were observed only in the liver. This study provides further insight into the genetic basis of growth traits in black carp and suggests that variants in the nlrp3 region may serve as useful molecular markers for selective breeding.
Cao et al. (Mon,) studied this question.