Estimating genetic parameters of muscle imaging trait with 2b-RAD SNP markers in Zhikong scallop (Chlamys farreri)

Genetic improvement is a crucial tool to deal with the increasing demand for high-quality, sustainably produced meat in the scallop industry. Breeding programs are based on genetic parameters, such as heritability, genetic correlations, and breeding values (BVs). By X-ray technology, we used adductor muscle area percentage (AMAP) obtained by dividing adductor muscle area (AMA) by shell area (SA) in an X-ray scallop image as a novel muscle imaging trait in a non-invasive manner. The goals of this study are 1) to estimate the genetic parameters of the muscle imaging trait AMAP and the adductor muscle weight percentage (AMWP), which is traditionally determined by weighing after dissection causing low efficiency in measurement and failure to collect data in vivo, and 2) to compare estimation accuracies of breeding values of AMAP and AMWP in a Zhikong scallop (Chlamys farreri) population. 2b-RAD SNPs were applied in 449 two-year-old healthy and active Zhikong scallops randomly sampled from an artificially bred population in the same culture sea area. The estimates of SNP-based heritability conducted using all SNPs (17,495 SNPs with MAF > 2%) were 0.551 (S.E. 0.07) for AMAP and 0.515 (S.E. 0.08) for AMWP, respectively. Chromosome-wise heritabilities for AMAP and AMWP were regressed against the chromosome lengths with significant linear trends (P = 0.02969 and P = 0.03043), implying that the genetic contribution to muscle trait is scattered across the genome and driven by many loci with small effect rather than a few causal loci with a large effect. The phenotypic and genetic correlations between AMAP and AMWP were 0.769 (S.E. 0.002) and 0.917 (S.E 0.043), suggesting that we can use the image-based trait AMAP in substitution for the muscle growth trait AMWP for genetic improvement of meat in live scallops. The impact of population genome structure (e.g., the effective population size Ne), number of independent chromosome segments (Me), SNP marker densities, and training population sizes on genomic prediction accuracy of AMAP and AMWP was investigated as well. These results will provide important reference information and methodology basis for breeding through image-based traits in scallops.