Genome-Wide Detection of Copy Number Variation and Association Studies With Physiological and Anatomical Indicators...

Indicators of heat stress response are heritable complex traits with polygenic inheritance. Copy number variations (CNV) are important genomic structural variations that may be linked to climatic adaptation by influencing the phenotypic variability of traits related to thermal stress and disease resistance in animals. Therefore, the primary objectives of this study were to detect CNV and CNV regions (CNVR) in pigs and explore their associations with physiological and anatomical indicators of HS response in lactating sows. A total of 4184 autosomal genome CNV (4012 deletions and 172 duplications) were detected in 969 animals. CNVR were identified by merging CNV with at least 1-bp overlap, which enabled the identification of 236 autosomal CNVR. The association analyses led to the identification of three CNVR significantly associated with ear skin temperature and one CNVR significantly associated with vaginal temperature considering all records, vaginal temperature measured at 8:00 h, and hair density. Eleven genes harboured the CNVR with significant associations. In summary, various CNV and CNVR were identified in crossbred maternal-line pigs, including CNVR significantly associated with physiological and anatomical heat stress response indicators in lactating sows. Candidate genes involved in immune and stress responses overlapped with the significant CNVR, suggesting that they may contribute to climatic resilience in pigs. The findings of this study contribute to better understanding the genetic background of heat stress response in lactating sows.