Genome-wide association analyses reveal genotype-by-environment interactions of growth and organ weights in gilthead seabream (Sparus aurata)

Gilthead seabream is one of the most important fish species for Mediterranean aquaculture. More than 80% of the genetically improved fingerlings of this species originate from a single country, Greece. A previous study revealed moderate genotype-by-environment (G x E) interactions for growth traits and organ weights between commercial production sites in Greece and Spain. The main objectives of this study were to identify QTLs and genes associated with growth traits and organ weights in gilthead seabream and to identify the biological processes and pathways controlling these traits under different temperature environments. For growth traits, we found fourteen genome-wide suggestive SNP effects in Spain. A strong peak between 1.97 Mb to 4.69 Mb on chromosome (chr) 22 was shared among three growth traits (harvest weight, fillet weight and thermal growth coefficient). Fourteen genome-wide suggestive SNP effects were also identified in Greece. However, none overlap with those found in Spain. Two SNPs on chr5 (chr5:5729959, chr5:2336903) and two SNPs on chr6 (chr6:1957732, chr6:3659811) were associated with all three growth traits. For organ weights, a total of 15 SNPs were associated above the suggestive threshold in Spain. Four SNPs (chr22:1966940, chr22:6094383, chr22:67838, chr15:16798259) are shared between viscera weight and liver weight, while one SNP (chr22:67838) is shared among viscera, liver and heart weight. Interestingly, three of these four SNPs (chr22:1966940, chr22:67838, and chr15:16798259) also overlap with significant SNPs associated with growth traits. None of the SNPs associated with viscera weight, liver weight and heart weight are shared with Greece. GO and KEGG functional enrichment analyses showed that light absorption and ECM-receptor interaction are significantly enriched with growth traits QTLs in Spain but not in Greece. For organ weights, response to stimulus is the most prominent process in Spain, while cell adhesion, and regulation of phosphorylation are more prominent in Greece. Genomic architectures for growth traits and organ weights differ between environments. These findings not only explain part of the G x E interactions, but also give insight into how genetics determines differences in how environmental conditions affect growth and organ weights.