Diversity of the BoLA-DRB3 Gene in Cattle Breeds From Tropical and Subtropical Regions of South America

Background Bovine leukocyte antigens (BoLA) are widely used as markers of disease and immunological traits in cattle because of their primary function in the recognition of pathogens by the immune system. To date, however, the characterization of BoLA gene polymorphisms in Latin American Zebu and mixed zebuine breeds is scarce. By a sequence-based typing method, here we sequenced exon 2 of BoLA class II DRB3 gene of 264 animals from the five breeds (Creole, Brahman, Braford, Brangus and Nellore) most commonly used in northern Argentina. Results The taurine and zebuine breeds contained 61 previously reported alleles. Genetic diversity was high at allelic and molecular levels, particularly in the mixed breeds. Neutrality tests revealed that none of the breeds shows the even gene frequency distribution expected under a balanced selection scenario. The FST index shows significant differences across all populations (FST=0.052, P < 0.001), indicating a substantial differentiation between breeds. UPGMA trees and Metric multidimensional scaling (MDS) analysis show that, as expected, Creole is distantlyrelated to the other zebuinebreeds. Among them, Brahman, Braford and Brangus cluster closer together than with Nellore. These data are consistent with the historical and geographical origin of these breeds. A peptide binding region sequence analysis at the aminoacid level revealed that, despite the nucleotide diversity among the breeds, the key aminoacids involved in peptide recognition are greatly conserved. Conclusions This is the first report of BoLA-DRB3 diversity in pure and mixed zebuine cattle breeds from Argentina. Knowledge ofBoLA-DRB3 variability in breeds adapted to tropical and subtropical environments contributes not only to ongoing efforts to catalog bovine MHC allele frequencies by breed and location but also to the design of peptide-based vaccines.

Genetic Diversity and Affinity Among Five Tibeto-Burman Tribal Populations of Northern India: A Study on Eight Alu Markers

The study attempts to ascertain an analysis of eight Arthrobacter luteus (Alu) insertion loci (ACE, TPA25, PV92, HS4.32, FXIIIB, D1, A25, B65) carried out in five tribal populations (Raji, Buxa, Jaunsari, Tharu and Bhotia) of Uttarakhand, Northern India. Total genomic DNA was extracted and amplification of genomic DNA by PCR analysis was carried out to examine the distribution of Alu (+) and Alu (–) genotypes from eight Alu loci. Genetic distance, genetic identity, pairwise Fst values and corresponding p values were computed between each pair of populations through analysis of molecular variance (AMOVA) for each Alu loci. The populations exhibited high levels of intra population variations and low levels of inter population differentiation with the average Fst value of inter population being 0.05896, which was expected to be more as the Fst value of intra population was 0.06780. Phylogenetic tree was constructed by using the neighbour-joining (NJ) method and multidimensional (MDS) plot to trace out the genetic affinity between populations. The present data showed that Raji and Buxa community were an ancestral population and Jaunsari, Tharu and Bhotia were diverged latter from Buxa community. The present study is an effort to generate a basic gene frequency distribution data at eight polymorphic Alu loci among five autochthonous groups of Uttarakhand.

333. HETEROGENEITY OF GENE EXPRESSION IN BOVINE SMALL FOLLICLES

Small antral follicles <5 mm in bovine ovaries undergo one of two fates: further growth and selection to become the dominant follicle for ovulation, or atresia. Atresia can occur before, during or after selection. As follicle grow past >5 mm there is upregulation in expression of focimatrix genes and later upregulation of the LH receptor and steroidogenic enzymes, especially aromatase, in the granulosa cells. For follicles at sizes >5 mm entering atresia the granulosa cells are the first in the follicle to die. Thus expression of genes in granulosa cells is critical to the fate of the follicle. To examine granulosa cells of small follicles we collected bovine ovaries and dissected follicles, removed part of the follicle wall for subsequent classification of health or atresia, and harvested the remaining granulosa cells for RNA isolation. Follicles examined included small follicles (<5 mm), both healthy (n = 10) and atretic (n =5), and healthy large follicles (>10 mm, n = 4). RNA was hybridized to Affymetrix GeneChip Bovine Genome Arrays and the results were analysed using Partek Genomics Suite software. The number of genes which were 2 fold differentially regulated between large and small follicles by Benjamini Hochberg post hoc test (False Discovery Rate, P < 0.05) was 2408 and between healthy and atretic small follicles was 4931. The coefficient of variation (CV; SD/mean × 100) for the expression level of each gene for each group was calculated. A gene frequency distribution indicated greater heterogeneity in expression levels in small follicles in comparison to large follicles. Furthermore, the greatest variability in genes in small follicles includes those that are either up or down regulated due to atresia or growth. We therefore conclude that variability in small follicles is a consequence of alternative fates that small follicle can undergo.

The divergence of a polygenic system subject to stabilizing selection, mutation and drift

SummaryPolygenic variation can be maintained by a balance between mutation and stabilizing selection. When the alleles responsible for variation are rare, many classes of equilibria may be stable. The rate at which drift causes shifts between equilibria is investigated by integrating the gene frequency distribution W̅2NΠ(pq)4Nμ−1. This integral can be found exactly, by numerical integration, or can be approximated by assuming that the full distribution of allele frequencies is approximately Gaussian. These methods are checked against simulations. Over a wide range of population sizes, drift will keep the population near an equilibrium which minimizes the genetic variance and the deviation from the selective optimum. Shifts between equilibria in this class occur at an appreciable rate if the product of population size and selection on each locus is small (Nsα2 < 10). The Gaussian approximation is accurate even when the underlying distribution is strongly skewed. Reproductive isolation evolves as populations shift to new combinations of alleles: however, this process is slow, approaching the neutral rate (≈ μ) in small populations.