Genetic Variation in Zebu Cattle Breeds Based on Growth-related Genes

Genetic variations in growth-related genes (e.g., MSTN, LEP, STAT5) have been shown to influence growth traits, including growth rate, average daily gain, and birth weight. Malaysian zebu cattle, particularly the locally adapted Kedah-Kelantan (KK) and KK Elit (KKE), are important genetic resources for tropical beef production. Characterising genetic variation across Malaysian zebu breeds provides valuable insights into breed differentiation and supports genetic improvement strategies. A total of 95 zebu cattle from three zebu breeds (KK, KKE and Nelore) were genotyped using a Fluidigm targeted 54 single nucleotide polymorphisms (SNPs) in 36 growth-related genes associated with growth traits. Following quality control, 33 polymorphic SNPs with minor allele frequency (MAF) > 0.01 were retained. Genetic variation parameters including observed heterozygosity (Ho), expected heterozygosity (He), MAF, polymorphism information content (PIC), and Hardy-Weinberg equilibrium (HWE) were calculated using the snpReady R package. Breed differentiation was examined using fixation index (Fst). PIC value ranged from 0.02 to 0.38, with the majority of SNPs classified as moderately informative (0.25 < PIC < 0.50). Across all SNPs, PIC values ranged from 0.02 to 0.38, with the majority classified as moderately informative (0.25 < PIC < 0.50). Three SNPs (rs136507921, rs380173310, and rs797743111) showed the highest PIC values. When averaged by breed, PIC was similar across the three populations, highest in KK (0.20), followed by KKE (0.18) and Nelore (0.17).  Of 33 SNPs, 10 showed significant deviation from HWE expectations (p < 0.05). The Fst heatmap showed moderate genetic differentiation between Nelore and the KK lineage breeds at these growth-related candidate loci, with KK and KKE being closest (Fst = 0.061), consistent with their shared genetic background, while Nelore shows the greatest divergence, particularly from KKE (Fst = 0.102). This study characterises genetic variation at growth-related candidate gene loci across two Malaysian zebu cattle breeds. Breed-level differences in allele frequencies and heterozygosity at these loci highlight genetic differences between the local KK lineage and Nellore.