Deciphering the genetic basis and prediction genomic estimated breeding values of heat tolerance in Zhikong scallop Chlamys farreri

The changes in seawater temperature due to global warming have produced profound influences on the growth, survival and production of aquatic species. Therefore, improving the performance of these species under heat stress is crucial for the sustainable development of aquaculture. Genomic selection, as a method of genetic improvement of economic traits, has great potential and value in cultivation of new strains with adaptation advantages. In present study, 1060 Zhikong scallops Chlamys farreri, an economically important species, were exposed to a gradient heating experiment to obtain individuals with heat tolerance. Among them, 154 individuals died firstly during experiment were considered as heat-sensitive group (HS), and 156 still alive after recovering for 7 days were taken as heat-tolerant group (HT). Then, these 310 individuals were sequenced, and 35,507 single nucleotide polymorphisms (SNPs) of 289 scallops were genotyped for genome wide association study (GWAS) and genomic prediction analysis. The results showed that seven SNPs and two genes (PNC1 and RASD1) were significant associated with heat tolerance trait in C. farreri. In addition, the heat tolerance trait of C. farreri was moderately heritable, and the heritability of survival status and survival time was 0.52 ± 0.04 and 0.24 ± 0.03, respectively. Furthermore, genomic best linear unbiased prediction (GBLUP) and Bayes B models were proved to be more suitable for genomic breeding value predictions of heat tolerance trait in C. farreri. The accuracy of genomic estimated breeding value could be stabilized when the number of markers reached 8 k. Population size could improve the accuracy of breeding value predictions and the accuracy has not reach a plateau yet in our study. Taken together, the findings obtained in this study provide insights into the genetic basis of heat tolerance in C. farreri and contribute to the genetic improvement of scallop and other related species.