The positional candidate diacylglycerol O-acyltransferase (DGAT1) gene affecting milk fat percentage is reported in Indian buffaloes (Bubalus bubalis). A comparison with Chinese buffalo (Bubalus bubalis) revealed eight exonic single nucleotide polymorphisms (SNPs), five of which were non-synonymous. A total of 19 SNPs were observed among diverse buffalo breeds in India. A Unique 22 base insertion has been reported in the intron between exon ten and eleven.

We report the myostatin gene sequence of Bos indicus cattle in comparison to Bos taurus. B. indicus genomic sequence was obtained by overlapping PCR amplification of genomic DNA. Exon splice sites were confirmed by mRNA sequencing. There were 5 exonic single nucleotide polymorphisms (SNP) only one of which was a non-synonymous mutation that resulted in a serine to asparagine (S214N) amino acid substitution. The B. indicus gene has two insertions of 16 and 12 bases in the first intron. In addition, SNPs in the 3' UTR and intronic regions are also reported.

The sequence of myostatin gene (growth differentiation factor 8 [GDF 8]) in Indian riverine buffalo (Bubalus bubalis) is reported. The genomic DNA as well as mRNA were sequenced. The sequence is conserved across all the livestock species. Five nonsynonymous changes as compared to cattle were found in this study and were also confirmed by mRNA sequence. Two intronic single nucleotide polymorphisms (SNPs) were identified in buffalo.

The paternally inherited Y chromosome markers have been used widely in population genetic studies to trace paternal lineages, to understand differences in migration pattern and populations admixture in animals. In the absence of crossing over, Y-chromosomal markers in the non-recombining male-specific region (MSY) are mostly transmitted as a haplotype. Recent studies of five polymorphic sites on DDX3Y, UTY and ZFY genes of bull MSY assisted in the identification of three haplogroups (Y1, Y2 and Y3) in contemporary cattle. Here we report the screening of five SNPs (ZFY9-120> C/T; ZFY10-655> C/T; DDX3Y1-425>C/T; DDX3Y7 -123>C/T and UTY19-423>C/A) of bull MSY employing optimized and validated allele-specific PCR (AS-PCR) protocols that are useful in effective differentiation of bull/semen samples of Bos indicus and Bos taurus origin. Three haplogroups (Y1, Y2 and Y3) were identified in the present study by the screening of 181 bulls from 10 native cattle breeds and 50 HF crossbred. Y1 and Y2 haplogroups were restricted to HF crossbred with a frequency of 0.98 and 0.02, respectively. The high frequency of Y1 haplogroups is possibly due to the occurrence of Y1 lineage predominantly in HF bulls. All the native cattle breeds were observed to have pure indicine lineage (Y3). These cost effective AS-PCR protocols may be useful for reliable and accurate genotyping of Y-SNPs in diverse native cattle breeds, exotic and crossbred cattle populations.

In bovines, duplication of major histocompatibility complex (MHC) class II DQ genes increase the advantage of high genetic polymorphism in the region multifold to produce better immune response and population fitness. In this study, the DQA gene duplication was explored at MHC class II locus in mithun (Bos frontalis, Bofr), a unique bovine of North-East region of India. A 776 nucleotide long genomic region encompassing hyper-variable exon 2 of Bofr-DQA was amplified in 79 mithuns and digested with Hae III restriction enzyme for PCR-RFLP analysis. The analysis revealed some of the restriction patterns, which were carrying the total fragment size of the alleles aggregating more than a heterozygous condition. Colony PCR-RFLP of clones of mithun DQA by Hinf I enzyme revealed a total of three DQA alleles in single PCR product. The RFLP of direct PCR and clone (colony) PCR products indicated the amplification of three DQA alleles at a time, suggesting duplication of the DQA locus in mithun. Further, the RFLP based typing of mithun DQA locus revealed the presence of five different DQA1 and DQA2 alleles in different combinations during duplication in mithun population. The duplication of DQA, carrying both DQA1 and DQA2 alleles gene was found to be present in nearly half of the mithun population. In mithun, similar to other bovines, DQA gene duplication may have much importance in creating more and diversified MHC class II molecules, thus conferring an advantage to bind with a more number of pathogenic antigens.