Polymorphism of splicing factor 3A subunit 3/PstI gene and its association with the performance of Madura cows (Bos indicus)

Background and Aim: Madura cattle (Bos indicus), a native Indonesian breed, are primarily raised for meat production and possess unique genetic characteristics shaped by crossbreeding with Bos javanicus, Bos taurus, and B. indicus. Despite their cultural and economic importance, limited molecular studies have explored candidate genes influencing their productive traits. This study aimed to identify the single-nucleotide polymorphism (SNP) g.1292A>T (rs473122879) in intron 2 of the Splicing Factor 3A Subunit 3 (SF3A3) gene and to evaluate its association with key phenotypic traits in Madura cows. Materials and Methods: A total of 49 adult Madura cows (>3 years) were sampled from two breeding locations: Java (n = 29) and Madura Island (n = 20). Body weight, withers height, hip height, body length (BL), and heart girth were measured using standardized morphometric techniques. Genomic DNA was extracted from whole blood and subjected to polymerase chain reaction (PCR) amplification targeting a 633 bp fragment of the SF3A3 gene. Genotyping of SNP g.1292A>T was performed using PCR-restriction fragment length polymorphism with PstI enzyme digestion. Sequencing analysis was conducted for genotype confirmation. Genetic diversity indices and Hardy–Weinberg equilibrium were assessed, and association between genotype and phenotypic traits was evaluated using a general linear model. Results: Two genotypes, TT (0.69) and AT (0.31), were identified; the AA genotype was absent in all samples. The polymorphism was under Hardy–Weinberg equilibrium (χ2 < 3.84) with a moderate polymorphic information content (PIC = 0.23). A significant association was found between SF3A3/PstI polymorphism and BL in cows from Madura Island (p < 0.05), with heterozygous (AT) individuals exhibiting superior morphometric traits compared to TT homozygotes. Conclusion: The SF3A3/PstI gene is polymorphic in Madura cows and exhibits moderate genetic diversity. The presence of the g.1292A>T SNP is significantly associated with BL, particularly in animals from their native breeding environment. These findings suggest the potential utility of SF3A3/PstI as a genetic marker in molecular selection strategies aimed at improving Madura cattle productivity.