Characterization of bovine MHC DRB3 diversity in Latin American Creole cattle breeds

• Published in: Gene Vol. 519; no. 1; pp. 150 - 158
• Main Authors: Giovambattista, Guillermo, Takeshima, Shin-nosuke, Ripoli, Maria Veronica, Matsumoto, Yuki, Franco, Luz Angela Alvarez, Saito, Hideki, Onuma, Misao, Aida, Yoko
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 25.04.2013
• Subjects: Alleles; Amino Acid Sequence; Animals; BoLA-DRB3 polymorphism; Breeding; Cattle - genetics; Exons; Gene Frequency; Genetic Markers; Hartón del Valle; Histocompatibility Antigens Class II - genetics; Latin American Creole cattle; Major histocompatibility complex class II; Molecular Sequence Data; Phylogeny; Polymerase Chain Reaction; Polymorphism, Genetic; Principal Component Analysis; Selection, Genetic; Sequence-based typing; Yacumeño; PCs; SBT; Major histocompatibility complex class II; ho; Yacumeño; MHC; dn; Sequence-based typing; Hartón del Valle; PCA; ds; UPGMA; na; HWE; BoLA-DRB3 polymorphism; Latin American Creole cattle; IPD; NJ; BoLA; he; PCR; RFLP
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2013.01.002

In cattle, bovine leukocyte antigens (BoLAs) have been extensively used as markers for diseases and immunological traits. However, none of the highly adapted Latin American Creole breeds have been characterized for BoLA gene polymorphism by high resolution typing methods. In this work, we sequenced exon 2 of the BoLA class II DRB3 gene from 179 cattle (113 Bolivian Yacumeño cattle and 66 Colombian Hartón del Valle cattle breeds) using a polymerase chain reaction sequence-based typing (PCR-SBT) method. We identified 36 previously reported alleles and three novel alleles. Thirty-five (32 reported and three new) and 24 alleles (22 reported and two new) were detected in Yacumeño and Hartón del Valle breeds, respectively. Interestingly, Latin American Creole cattle showed a high degree of gene diversity despite their small population sizes, and 10 alleles including three new alleles were found only in these two Creole breeds. We next compared the degree of genetic variability at the population and sequence levels and the genetic distance in the two breeds with those previously reported in five other breeds: Holstein, Japanese Shorthorn, Japanese Black, Jersey, and Hanwoo. Both Creole breeds presented gene diversity higher than 0.90, a nucleotide diversity higher than 0.07, and mean number of pairwise differences higher than 19, indicating that Creole cattle had similar genetic diversity at BoLA-DRB3 to the other breeds. A neutrality test showed that the high degree of genetic variability may be maintained by balancing selection. The FST index and the exact G test showed significant differences across all cattle populations (FST=0.0478; p<0.001). Results from the principal components analysis and the phylogenetic tree showed that Yacumeño and Hartón del Valle breeds were closely related to each other. Collectively, our results suggest that the high level of genetic diversity could be explained by the multiple origins of the Creole germplasm (European, African and Indicus), and this diversity might be maintained by balancing selection. ► This is the first report of BoLA-DRB3 diversity in Creole cattle, using PCR-SBT. ► Creole cattle have high diversity despite the reduction of its population size. ► Three new BoLA-DRB3 alleles were detected in the Creole cattle breeds. ► Data suggested that BoLA-DRB3 diversity can be maintained by balancing selection. ► PCA and tree showed that Creole cattle trend to cluster together.