Combined molecular and statistical approach identified the role of key haplotypes in caprine SOD3 gene during thermal stress

Abstract

The study identified a single nucleotide polymorphism (SNP) in the SOD3 gene using high-resolution melting analysis, forming four haplotypes (haplotypes 1, 2, 3, and 4). The correlation between these haplotypes and key physiological (rectal and skin temperature, heart rate, respiration rate, pulse rate) and biochemical (ALP, albumin, bilirubin, cholesterol, glucose, urea, ALT) traits was analyzed under thermal stress using statistical techniques like heat mapping, random forest analysis (RFA), principal component analysis (PCA), and multi-scale dimensional plotting (MSDP). RFA indicated that the SOD3 polymorphism significantly influenced physiological (rectal temperature, respiration, skin temperature) and biochemical (bilirubin, total protein, ALP) traits. Animals with haplotypes 2 and 3 exhibited lower physiological values and weak associations between physiological and biochemical traits, indicating higher heat tolerance. Both MSDP and PCA confirmed that haplotypes 1 and 4 strongly regulated most traits, while haplotypes 2 and 3 had weaker effects. Thus, molecular and statistical methods helped identify heat-tolerant animals for future breeding programs.