A genome-wide association study of heat tolerance in Pacific abalone based on genome resequencing

Abstract

China produces nearly 90% of the world's abalone. The Pacific abalone, Haliotis discus hannai, is the main cultured species. Because of the southward migration to subtropical areas from its natural temperate habitat, abalone can be grown at suitable temperatures for an extended time, and the growth period has been greatly shortened. However, the survival rate declines sharply with high temperatures, especially in summer. Therefore, heat tolerance has been one of the most important economic traits for abalone farming, and accelerating genetic improvements has become the priority of breeding research. In this study, a genome-wide association study (GWAS) was performed using genome resequencing to identify the loci associated with the heat tolerance of abalone. A total of 1,431,014 single nucleotide polymorphisms (SNPs) were identified. Among these, 27 SNPs showed significant associations with heat tolerance. Thirty candidate genes were identified near these SNPs. Most of these genes were related to metabolism, ion channels, signal transduction, or DNA repair. In particular, genes mdhc (malate dehydrogenase, cytoplasmic), achβ3 and ach92 (acetylcholine receptors), and cah2 and cah7 (carbonic anhydrase) have been demonstrated to be associated with heat response in previous studies in mollusks, corroborating the accuracy and reliability of the GWAS results. The results should be useful for marker-assisted selection (MAS), which would accelerate the genetic improvement of heat tolerance of abalone, and promote the understanding of the molecular mechanisms underlying heat tolerance in Pacific abalone or other shellfish.