Family-based transcriptomic profiling of Atlantic salmon skin and head kidney in response to Lepeophtheirus salmonis infestation under physiological and elevated temperatures

• Different families of Atlantic salmon exhibit distinct transcriptional responses to sea lice infestation. • Family-based transcriptomic analysis holds significant potential for identifying potential molecular biomarkers linked to sea lice resistance/susceptibility in Atlantic salmon. • Remarkable transcriptomic alterations were observed in Atlantic salmon exposed to elevated (20 °C) compared to standard (10 °C) temperature conditions. • Both sea lice infestation and thermal stress influenced transcriptional changes in the skin and head kidney of Atlantic salmon. This study explored transcriptomic alterations in the skin and head kidney of Atlantic salmon ( Salmo salar ) from multiple families in response to infestation with the salmon louse ( Lepeophtheirus salmonis ) at the chalimus and adult stages, under elevated (20 °C) versus standard (10 °C) temperature conditions. Family-specific transcriptomic comparisons identified several candidate genes potentially associated with variation in host responses among families to sea lice, as reflected by differential expression patterns between families with varying lice densities. These biomarkers were primarily involved in immune function (e.g., cd209, cd22, btn2a1, h2-q9, c1qb, muc2, muc5ac, sntx-b, kbas ), tissue repair (e.g., krt13, tgm2, mmp9, mmp13 ), inflammation (e.g., nlrp1, il1b, nlrc3, nlrp12 ), iron homeostasis (e.g., hbb1, ftm ) and stress response (e.g., hspa8, herc3 ). Under elevated temperature conditions (20 °C), 124 and 324 shared differentially expressed genes (DEGs) were respectively identified in the skin and head kidney of lice-infested salmon. RNA-seq analysis revealed consistent modulation of several thermal stress biomarkers (e.g., serpinh1, hsp90aa1, hspa8, cirbp, fkbp10 ) in both chalimus- and adult-infested salmon under elevated temperature conditions, along with pronounced differences in the diversity of transcriptomic alterations and biological pathways compared to fish parasitized under standard temperature. Our results provide insights into molecular signatures that can help to differentiate more and less susceptible salmon families, supporting the development of selective breeding strategies for improved sea lice management. The temperature-related transcriptomic changes highlighted the climate adaptation strategies adopted by salmon, as well as their potential vulnerability to long-term shifts in water temperature.