Genomic insights into thermal tolerance in pacific abalone: Implications for food security and sustainable aquaculture

Heatwaves driven by climate change make thermal tolerance a key economic trait in aquaculture. Pacific abalone ( Haliotis discus hannai ) experiences recurrent summer die-offs, yet the genetic basis of heat resilience remains unclear. In this study, a mixed-family group composed of 210 families was constructed to monitor growth and summer survival rates of under sea- and land-based aquaculture systems. Heart rate–derived Arrhenius Breakpoint Temperature (ABT) was used to evaluate thermal tolerance, revealing significantly higher ABT in land-based (29.59 ± 1.21 °C) than in sea-based systems (29.19 ± 1.24 °C), and in common-shell-color (29.45 ± 1.24 °C) than in red-shell-color abalone (29.05 ± 1.06 °C). Survival rates were also higher in land-based farms (63.77% vs. 47.30%), although both systems experienced high summer mortality, highlighting the vulnerability of this species to thermal stress. A genome-wide association study (GWAS) of 630 individuals identified 23 single nucleotide polymorphisms (SNPs) associated with ABT., including a cluster of 10 SNPs on chromosome 13. The 23 SNPs were mapped to 21 genes, with notable candidates including tm117 and anxa6 (apoptosis), nktr and ubxn4 (protein homeostasis), and ddx58 , qvr , vwa7 , and lin41 (immunity). The expression of 11 genes changed significantly after acute heat stress, supporting their functional relevance. Collectively, these loci, genes, and pathways present testable targets for selective breeding and future genomic selection, with the aim of producing more heat-resilient abalone. This approach has the potential to reduce heat-induced losses and enhance production stability under warming conditions, thus contributing to food security in abalone aquaculture. • The cumulative mortality rate of annual cultivation of Pacific abalone in southern China was over 50%. • Heat stress genes in abalone identified by GWAS and transcriptomic evidence. • 23 SNPs linked to thermal tolerance, with a major cluster on chromosome 13. • Key genes were linked to apoptosis, protein homeostasis, and immune pathways. • Genomic markers support selective breeding to enhance food safety in aquaculture.