ABSTRACT
The DRB3 gene is an MHC class II gene that has a high degree of polymorphism with more than 100 alleles described in cattle. This variation contributes to differences among individuals in immune responsiveness and disease resistance. In this study, we searched for allelic variants in exon 2 of the DRB3 gene in 80 river buffaloes of three breeds in Brazil using a PCR-RFLP technique. The PCR product showed genetic polymorphism when digested with RsaI, PstI or HaeIII restriction enzymes. In total, 16 restriction patterns were identified: nine restriction patterns and 16 genotypes were found with RsaI; four restriction patterns and nine genotypes were found with HaeIII; and, three restriction patterns and four genotypes were found with PstI. Three RFLP patterns were exclusive to Jafarabadi buffaloes (RsaI-b, RsaI-c and RsaI-f) and three others were only observed in Mediterranean buffaloes (RsaI-g, RsaI-h and PstI-y). Jafarabadi buffaloes had a larger number of RFLP patterns than Mediterranean and Murrah breeds. The analysis showed that the DRB3 exon 2 was highly polymorphic, with the highest degree of polymorphism in Mediterranean buffaloes. This study provides the first assessment of allelic variation among three different buffalo breeds from Brazil and provides a basis for further investigations into the association between the DRB3 alleles and disease resistance.
Subject(s)
Buffaloes/genetics , Histocompatibility Antigens Class II/genetics , Alleles , Animals , Brazil , Cattle , Exons/genetics , Gene Frequency/genetics , Polymerase Chain Reaction , Polymorphism, Genetic/genetics , Polymorphism, Restriction Fragment LengthABSTRACT
Recent developments in methodologies for genomic analyses have enabled a significant advance in understanding of the river buffalo genome. The S1PR1 gene has been mapped to buffalo chromosome 6 and bovine chromosome 3; this gene is of interest as it is a candidate for marbling in meat, an important economic trait. Here, we performed next generation sequencing in a buffalo BAC DNA clone and obtained a 54.5-kb sequence encompassing the entire buffalo S1PR1 gene as well as the 27 kb upstream region and the 22 kb downstream region. The gene had a total length of 4716 bp, including three exons and two introns; exons 1 and 2 were classified as non-protein-coding. In comparison with homologues from other species, the structural organization of buffalo S1PR1 was closest to that of the goat and in both species exon 2 of the gene was non-protein-coding. One hundred and nine repetitive elements were found within the buffalo gene and its boundary regions, with 50 SINE repeats being the most abundant. Alignment of S1PR1 sequences from the Murrah and Mediterranean breeds revealed two nucleotide substitutions (g.1176C>G and g.2740T>C), which represent potential SNPs that could be used in further studies of buffalo genetic structure.
Subject(s)
Buffaloes/metabolism , Genes , Receptors, Lysosphingolipid/genetics , Amino Acid Sequence , Animals , Buffaloes/genetics , DNA , High-Throughput Nucleotide Sequencing , Molecular Sequence Data , Polymorphism, Single Nucleotide , Receptors, Lysosphingolipid/chemistry , Receptors, Lysosphingolipid/metabolism , Repetitive Sequences, Nucleic Acid , Sequence Alignment , Sequence Analysis, DNAABSTRACT
River buffalo chromosome 1 (BBU1) is a sub-metacentric chromosome homologous to bovine chromosomes 1 and 27. In this study, we constructed a new framework radiation hybrid (RH) map from BBU1 using BBURH5000 panel adding nine new genes (ADRB3, ATP2C1, COPB2, CRYGS, P2RY1, SLC5A3, SLC20A2, SST, and ZDHHC2) and one microsatellite (CSSM043) to the set of markers previously mapped on BBU1. The new framework RH map of BBU1 contained 141 markers (55 genes, 2 ESTs, 10 microsatellites, and 74 SNPs) distributed within one linkage group spanning 2832.62 centirays. Comparison of the RH map to sequences from bovine chromosomes 1 and 27 revealed an inversion close to the telomeric region. In addition, we ordered a set of 34 scaffolds from the buffalo genome assembly UMD_CASPUR_WB_2.0. The RH map could provide a valuable tool to order scaffolds from the buffalo genome sequence, contributing to its annotation.
