Maternal origins and genetic diversity of Sabahan swamp buffalo using mitochondrial cytochrome b gene

The swamp buffalo (Bubalus bubalis carabanensis) plays a crucial role in agriculture across Southeast Asia but is increasingly underutilized in regions like Sabah, Malaysia. This study presents the first comprehensive statewide genetic assessment of Sabahan swamp buffalo using mitochondrial cytochrome b (cytb) gene sequences to investigate maternal origins and assess genetic diversity. Blood samples were collected from 211 individuals across eight locations in Sabah. DNA extraction and PCR amplification successfully yielded 198 high-quality cytb sequences. Comparative analysis with 1745 publicly available sequences revealed that 197 Sabahan buffalo belong to the SA1 haplogroup, which is common across Southeast Asia. Only four haplotypes were identified, with one dominant haplotype found in 190 individuals, indicating remarkably low genetic diversity (haplotype diversity = 0.088; nucleotide diversity = 0.00031). An additional river buffalo haplotype detected in one phenotypically swamp buffalo suggests introgression from Murrah buffalo. Analysis of molecular variance (AMOVA) showed that 96.29% of genetic variation occurred within populations, with minimal differentiation among them. Φ_ST comparisons suggest Sabah's buffalo are genetically closer to Chinese swamp buffalo populations than those from South Asia, supporting a maternal lineage via the China-Taiwan-Philippines dispersal route. Spatial autocorrelation analysis indicated localized gene flow, while demographic reconstruction via Bayesian Skyline Plot suggested long-term population stability with recent expansion. These findings highlight the limited maternal genetic variation within Sabahan swamp buffalo, likely stemming from a founder effect during introduction to Borneo and minimal subsequent genetic inflow. The study provides critical insight into the evolutionary history and population structure of Sabah's swamp buffalo, with implications for conservation and livestock improvement strategies aimed at bolstering genetic diversity and productivity in the region.