Genome-wide association study reveals markers and candidate genes associated with growth in the rice flower carp, an economic fish species of integrated rice-fish culture in China

The rice flower carp ( Cyprinus carpio ) is an important fish in integrated rice-fishery farming. Here, we performed the first genome-wide association study (GWAS) for seven growth traits (including body mass, total length, height, width, caudal-peduncle depth, and eye spacing) 200 samples using 369,688 high-quality SNPs 42,225 indels obtained by double-digest genotyping-by-sequencing (ddGBS). morphometrics of these were highly correlated (Pearson’s correlation coefficients = 0.74–0.99, p < 0.001). GWAS detected 15, 5, 4, 26, 7, 16, 17 loci significant associated (-log10P ≥ 5) with spacing, respectively. Subsequently, within 50 kb upstream downstream regions surrounding loci, 38, 19, 18, 20, 52, 27, 37 candidate genes detected, Importantly, B6_4352672 A8_4978825 significantly more than five traits. These results showed will be helpful future marker-assisted selection (MAS). Interestingly, chromosomes A8 B25 had many traits, most which shared among multiple growth-related indicated that chromosome may closely related to Our findings not only help understand genetic architecture but facilitate identification towards breeding faster-growing future.