Genome-wide Association Mapping for Heat Shock Tolerance in Mercenaria mercenaria through SNP Microarray Analysis

This study aimed to establish a genome-wide association for heat tolerance using the newly developed 66K SNP array for Mercenaria mercenaria. Northern quahogs from three local farms were combined for a heat challenge by increasing temperature at 1°C per day from 24°C to 35°C (Phase I), maintaining at 35°C for two days before decreasing to 27°C within the next 24 hr, then to 24°C within 24 hr. Survival-time analysis showed different survivals among quahogs from these three farms during the heat challenge. Mortality during the temperature increase period (Phase I) was 38, 46, and 55%, and after the temperature decrease was 36, 30, and 29%. For the survivors, no changes were found in body weight before and after the heat shock challenges (p < 0.265). The PCA analyses of SNP frequencies indicated significant genetic differences associated with clam survival under heat stress across the different farms. The fastStructure analysis also revealed the proportions of different ancestral components within the clams, highlighting the genetic factors that may contribute to their varying survival rates under heat stress. The heritability of the heat tolerance traits was 0.680 ± 0.063. GWAS analysis indicated that one SNP exhibited a significant association with the time-to-death trait of northern quahogs and was in chromosome 7. More significant SNPs (p < 10-3.5) were inside genes that have been reported to function in heat tolerance such as serine/threonine-protein kinase 31 and carbohydrate sulfotransferase 11, and some genes found within 50K bp far from SNP sites have a relationship with heat tolerance such as toll-like receptors 4 and 6 (TLRs 4 and TLRs 6), uracil-DNA glycosylase, and a disintegrin and metalloproteinase with thrombospondin motifs gon-1 (ADAMTs). Overall, these findings highlight the power of high-throughput approaches for the identification of superior clam genotypes for further breeding. 633 samples