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