13 research outputs found
Candidate Gene Approach for Parasite Resistance in Sheep – Variation in Immune Pathway Genes and Association with Fecal Egg Count
<div><p>Sheep chromosome 3 (Oar3) has the largest number of QTLs reported to be significantly associated with resistance to gastro-intestinal nematodes. This study aimed to identify single nucleotide polymorphisms (SNPs) within candidate genes located in sheep chromosome 3 as well as genes involved in major immune pathways. A total of 41 SNPs were identified across 38 candidate genes in a panel of unrelated sheep and genotyped in 713 animals belonging to 22 breeds across Asia, Europe and South America. The variations and evolution of immune pathway genes were assessed in sheep populations across these macro-environmental regions that significantly differ in the diversity and load of pathogens. The mean minor allele frequency (MAF) did not vary between Asian and European sheep reflecting the absence of ascertainment bias. Phylogenetic analysis revealed two major clusters with most of South Asian, South East Asian and South West Asian breeds clustering together while European and South American sheep breeds clustered together distinctly. Analysis of molecular variance revealed strong phylogeographic structure at loci located in immune pathway genes, unlike microsatellite and genome wide SNP markers. To understand the influence of natural selection processes, SNP loci located in chromosome 3 were utilized to reconstruct haplotypes, the diversity of which showed significant deviations from selective neutrality. Reduced Median network of reconstructed haplotypes showed balancing selection in force at these loci. Preliminary association of SNP genotypes with phenotypes recorded 42 days post challenge revealed significant differences (P<0.05) in fecal egg count, body weight change and packed cell volume at two, four and six SNP loci respectively. In conclusion, the present study reports strong phylogeographic structure and balancing selection operating at SNP loci located within immune pathway genes. Further, SNP loci identified in the study were found to have potential for future large scale association studies in naturally exposed sheep populations.</p></div
Bayesian clustering of 713 sheep under assumption of 2 to 6 clusters without a priori population information.
<p>The breed names are given below the box plot and the geographical origin indicated above the box plot with the individuals of different breeds separated by vertical black lines.</p
Details of candidate genes under study and involved in different KEGG immune pathways.
<p>Details of candidate genes under study and involved in different KEGG immune pathways.</p
Location of sheep breeds sampled for the present study.
<p>Location of sheep breeds sampled for the present study.</p
Three dimensional scattergram of first three principal components derived from pairwise F<sub>ST</sub> (a) across 41 SNP loci and (b) across 27 SNP loci among different sheep populations.
<p>(BAN-Bangladeshi; COR-Corriedale; PAM-Pampinta; JUN-Junin; BER-Bergschaf; TEX-Texel; KSF-Krainersteinschaf; MUF-Mouflon; KAR-Karakachanska; SHU-Shumenska; KUL-Karakul; THA-Thalli; KAC-Kachi; KAJ-Kajli; HAM-Hamdani; SHA-Shal; PAT-Pattanam; NEL-Nellore; MRS-Madras Red; MEC-Mecheri; IFT-Indonesian Fat Tail; ITT-Indonesian Thin Tail).</p
Values of haplotype diversity and statistics for testing departures from neutrality (Haplotypes reconstructed from 13 SNPs in chromosome 3-R Method).
<p>Values of haplotype diversity and statistics for testing departures from neutrality (Haplotypes reconstructed from 13 SNPs in chromosome 3-R Method).</p
UPGMA radial tree constructed using pair-wise allele sharing distance among different sheep breeds.
<p>(Numbers at nodes indicate bootstrap values out of 10000 resampled datasets).</p
Mean diversity indices and number of loci deviating from Hardy-Weinberg equilibrium in different sheep breeds at 41 SNP loci.
<p>Mean diversity indices and number of loci deviating from Hardy-Weinberg equilibrium in different sheep breeds at 41 SNP loci.</p
Details of candidate genes, chromosome location, genomic location and strand genotyped at 41 SNP loci under study.
<p>Details of candidate genes, chromosome location, genomic location and strand genotyped at 41 SNP loci under study.</p
Least squares ANOVA of parasite resistance characteristics (log transformed fecal egg count, body weight change and packed cell volume change 42 days post challenge at different SNP loci in experimentally challenged sheep (Pampinta and Corriedale, Indonesian Thin Tailed and Indonesian fat tailed).
*<p>FDR – Benjamini-Hochberg False Discovery Rate corrected P-value.</p