Characterization of an Iranian buffalo population at CSN1S1 and CSN3 loci

Water buffalo is globally recognized as an important species for agriculture and local economies in many regions of the world. River buffaloes are found from eastern Asia to Europe. In Iran, there are three main buffalo breeds including Azeri, Khuzestani and Mazandarani. However, local sub-populations (or breeds) exist, mainly identified on geographical origin with little or no documented phenotypic or genetic differences. Buffalo milk qual ity plays a key role in dairy processing, being the curd formation dependent on total protein and fat content. In this respect, casein variants are known to influence the yield according to the specific genotype at CSN3 and CSN1S1 loci. The aim of this study was to characterise a local Iranian buffalo population of the Pareh Sar area (Gilan province, IRAN) for the SNP AJ005430:c.578C>T at CSN1S1 and HQ677596:c.536C>T at CSN3 and compare it with the literature data in the Italian Mediterranean buffaloes (IMB). DNA was isolated from 89 buffalo individual blood samples. A duplex artificially created restriction site (ACRS) PCR was carried out using at the same time four primers for generating two ampl icons, 86 bp for the CSN1S1 and 160 bp for the CSN3. Enzymatic digestion was performed by MboI and HinfI endonucleases. The electrophoresis run on a 3% agarose gel in TBE 0.5× at 90V for 45min allowed the simultaneous identification of the genotypes for both loci. Population statistics were run on collected data. The population analysis showed that minor allele frequencies (MAF) were 0.318 for the CSN1S1 T (allele A) and 0.275 for the CSN3 T (allele X2). No departure from HW equilibrium was detected. MAF of CSN1S1 was different (Z=2.48, p=0.013) from published data on IMB (0.425), but this was not observed for CSN3. No linkage disequilibrium (LD) was detected between the markers (r2 = 0) and all four possible haplotypes were found. The higher frequency (0.496) was discovered for the CSN1S1 B-CSN3 X1 and a similar result was also found in the IMB (BX1, 0.553). The most favourable haplotype for dairy purposes (CSN1S1 A-CSN3 X2) showed the lower frequency (0.094) in the Iranian population. Conversely, the AX2 haplotype had a frequency of 0.279 in the IMB. This result leaves genetic improvement oppor tunities in both populations for this trait, considered as one of the most relevant for its influence on protein content and chee semaking properties.