Comparative analysis of the extreme meat color transcriptome reveals key regulatory genes and identifies potential SNPs in Leiqiong cattle

BACKGROUND: Leiqiong cattle, an indigenous beef breed from southern China, possess remarkable adaptability to tropical climates and demonstrate significant market potential owing to their high-quality meat. Meat color serves as a critical quality trait that strongly influences consumer preference and commercial value. Meat color in beef is primarily governed by myoglobin redox chemistry, mitochondrial activity, and post-mortem metabolism-processes modulated by oxidative stress, chaperone networks, and glycolytic flux. While these pathways are recognized in commercial breeds, their genetic architecture in heat-adapted, tropical cattle like Leiqiong remains unknown. Here, we bridge this gap by integrating transcriptomics and targeted genotyping to uncover breed-specific regulatory mechanisms. RESULTS: To elucidate the genetic basis of meat color variation, we conducted transcriptome sequencing and comparative analysis between light- and dark-colored meat samples from 8 cattle. We identified 490 differentially expressed genes (328 upregulated and 162 downregulated), among which GSTP1, HSPA2, and LDHD emerged as key candidate genes. Polymorphism screening revealed 25 SNPs across these loci in 100 cattle, with association analysis confirming the significant effects of specific variants (GSTP1: g.45441935G > A, g.4544191937G > A, g.45444424G > A; HSPA2: g.77680461G > A; LDHD: g.2453066T > G) on meat color phenotypes. CONCLUSIONS: Our integrated analysis identified GSTP1, HSPA2, and LDHD as key candidate genes and revealed specific SNPs significantly associated with meat color variation in Leiqiong cattle. These findings provide novel insights into the breed-specific genetic mechanisms underlying this trait and supply preliminary molecular markers that could inform future marker-assisted selection strategies aimed at improving meat color.