Exploration of Genetic Variability in Stearoyl‐ CoA Desaturase 1 (SCD1) Gene and Association of Its Variants With Production and Reproduction Traits in Murrah Buffaloes

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The objective of this study was to explore the genetic variability in the SCD1 gene and its association with performance traits in 100 Murrah buffaloes. Two regions of the gene, i.e., 400 and 752 bp fragments of exon 5 and exon 1, respectively, were amplified via PCR, and genotyping was done using the RFLP technique. The fragments of the SCD1 gene were digested with Nco1 and Taq1 enzymes, respectively. In the present study, monomorphic patterns were revealed for the exon 5 region, and polymorphic patterns were revealed for the exon 1 region of the SCD1 gene. The exon 1 region of the SCD1 gene revealed two types of genotypes, i.e., AA (752 bp) and AC (752, 620 and 132 bp) after digestion with the Taq1 restriction enzyme. The frequencies of 'A' and 'C' alleles were found to be 0.95 and 0.05, and genotypic frequencies for AA and AC were 0.89 and 0.11, respectively, in Murrah buffaloes. Results of the Chi-square test showed that the population was in Hardy-Weinberg equilibrium with respect to the targeted loci. The association analysis revealed that individuals having the AA genotype had better production performance, while individuals with the AC genotype had comparatively better reproduction performance; however, there was no statistically significant association among the genotypes and performance traits. Further, a total of 10 samples of the exon 1 region of the SCD1 gene were Sanger sequenced. Multiple alignments of the sequenced samples were done using BioEdit software. On comparison of sequencing results with the reference sequence of the Italian Mediterranean river buffalo (EMBL-FM876222), polymorphism was noticed at one position, i.e., g.300 C>T in two samples out of the total 10 samples. Sequenced samples were also compared with the reference sequence of Bos taurus (AY241932.1). A total of 13 nucleotide changes were observed, out of which seven were transversions and six were transitions. An insertion of nucleotide 'G' was also observed at position 1400, and two novel SNPs were observed, i.e., g.1581 C>T and g.1992 G>C. It was concluded that nucleotide changes at different locations in Murrah buffaloes as compared to Bos taurus can be used as selection signatures in Murrah buffaloes.