Sequencing & Pangenomes

Genotyping using High-Resolution Melting (HRM) analysis of buffaloes in Bangladesh

---

Abstract

Buffaloes are central to agrarian systems in Bangladesh and South Asia, where Bubalus bubalis predominates, and breeding decisions must balance genetic improvement with conservation while accounting for strong economic constraints. In this study, 62 buffaloes were analyzed with the specific aim of establishing an economically viable analytical pipeline to determine whether Bangladeshi Indigenous river buffaloes and their crossbred progeny were genetically comparable to the well-defined Murrah breed, rather than to isolate or redefine breeds. For pure and selective breeding, it was mandatory to maintain breed purity. But for practical breeding purposes, both Indigenous and their crossbreds were analytically grouped and treated as Indigenous-type, reflecting the reality that crossbred progeny were not genetically confined, whereas Murrah represented a fixed, managed breed population. High-Resolution Melting (HRM) analysis was integrated with phylogenetic and population-genetic approaches using two microsatellite markers (CSSM033, CSSM047) and one SNP marker (K-CN). Beyond melting temperature shifts, HRM curves were interpreted using color-coded pattern analysis, focusing on curve shape, relative position, and clustering behavior. Murrah samples consistently formed compact and coherent curve clusters, while Indigenous buffaloes showed broader dispersion, and their crossbred samples occupied intermediate or overlapping positions, indicating admixture but not Murrah equivalence. At the sequence level, allelic variation was assessed through haplotypes, yielding 16 unique haplotypes per locus (Hd = 1.000), which were used in AMOVA based on aligned sequences. Results showed that most genetic variation resided within populations (71.56à¢â‚¬â€œ90.05%), with FST values ranging from 0.099 to 0.284, demonstrating low to high differentiation alongside ongoing gene flow. The consistent separation of Murrah from the Indigenous and crossbred groups across HRM, phylogenetic reconstruction, and AMOVA confirms that Indigenous and crossbred/mixed buffaloes were genetically distinct from Murrah. Collectively, these findings validate HRM as a scalable, low-cost screening tool that complements buffalo SNP chips by enabling rapid, field-relevant decisions on genetic similarity, breed purity, admixture, and introgression prior to genome-wide analyses.

Keywords: 2026

How to Cite:

Deb, G., Tahira, K., Alam, M., Mostari, M., Majumder, M., Miah, M., Paul, O., Sarker, H. & Hossain, S., (2026) “Genotyping using High-Resolution Melting (HRM) analysis of buffaloes in Bangladesh”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286923. doi: https://doi.org/10.31274/wcgalp.24167

Rights: 1