Browsing by Author "Kathiravan, Periasamy"
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ArticleItem Open Access Candidate Gene Approach for Parasite Resistance in Sheep – Variation in Immune Pathway Genes and Association with Fecal Egg Count(2014) Kathiravan, Periasamy; Rudolf, Pichler; Mario, Poli; Silvina, Cristel; Bibiana, Cetra; Daniel, Medus; Muladno, Bas; Thiruvenkadan, AK; Saravanan, Ramasamy; et al.; TANUVASSheep 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.ArticleItem Open Access Genetic diversity analysis of major Sri Lankan goat populations usingmicrosatellite and mitochondrial DNA D-loop variations(2017) Pradeepa, Silva; Dematawewa, CMB; Kurukulasuriyaa, Maheshika; Utsunomiya, Yuri T.; José Fernando, Garcia; Rudolf, Pichler; Thiruvenkadan, AK; Saravanan, Ramasamy; Jian-Lin, Hane; Kathiravan, Periasamy; TANUVASThe present study aimed at the genetic characterization of five major goat populations of Sri Lankaincluding four indigenous populations (Jaffna Local – JFL, Kottukachchiya – KOT, Southern – SLS andNorth Central – SNC) and one stabilized crossbred (German Boer x indigenous goats, also known as “SriLankan Boer” – SLB). Genetic diversity was evaluated using 15 microsatellite markers and the mitochon-drial DNA D-loop variation. Allelic diversity and observed and expected heterozygosities were moderate,but less than Eurasian and Indian goat breeds. The overall mean estimated inbreeding coefficient (FIS)was 0.069 and significant heterozygote deficiency was detected in JFL (P < 0.001), KOT (P < 0.01) and SLS(P < 0.05), indicating population-specific drift or selection of the loci assessed. Genetic differentiationamong populations was low and the phylogenetic clustering pattern was in line with the geographicallocation of goat populations. Although pair-wise Cavalli-Sforza and Edwards chord distance clustered SLSand SLB separately from the rest of the populations, Bayesian clustering clearly showed lack of discretegenetic structure in Sri Lankan goat populations despite significant morphological and phenotypic differ-ences among them. Mitochondrial DNA D-loop sequences revealed significantly high haplotype diversitywith the existence of maternal haplogroups ‘A’ and ‘B’. Analysis of mtDNA sequences indicated maternalorigins of Jaffna Local, Kotukachchiya and Sri Lankan South distinct from the other goat populations.ArticleItem Open Access Short tandem repeat (STR) based genetic diversity and relationship ofdomestic sheep breeds with primitive wild Punjab Urial sheep (Ovisvignei punjabiensis)(Elsevier, 2017) Rudolf, Pichler; Tanveer, Hussain; Wu Xu; Anam, Aftab; Masroor Ellahi, Babar; Thiruvenkadan, AK; Saravanan, Ramasamy; Atanaska, Teneva; Kiala, Sebastinoa; Moumouni, Sanou; Amadou, Traore; Adama, Dialloa; Kathiravan, Periasamy; TANUVAStIn this study, short tandem repeat (STR) genotypes of 466 sheep from eleven domestic breeds located inAsia, Africa, Europe and Latin America were compared with wild Asian Urial sheep and captive Mouflontype sheep to assess genetic diversity and relationship among them. Analysis of sheep breeds at 19short tandem repeat (STR) loci revealed higher diversity in wild Punjab Urial sheep and domestic sheepfrom West Asia followed by Europe and Latin America as compared to South Asia, consistent with thehistory of sheep domestication. The average inter-individual allele sharing distance within breed wasfound to be lowest in South Asian sheep as compared to West Asian, European and Latin American sheeppopulations. The estimated global FSTrevealed 15.9% of total variation attributable to between breeddifferences. Investigation of genetic relationship by phylogeny revealed four distinct clusters; the firstcluster formed by four South Asian sheep breeds, the second cluster formed by Iraqi and Bulgarian sheepbreeds; the third cluster formed by Iranian, Austrian, Burkina Faso and Peruvian sheep breeds and thefourth cluster formed by Punjab Urial and captive mouflon type sheep. Principal components analysisrevealed individuals from Punjab Urial sheep population being distributed close to the cluster of WestAsian and East European sheep (Hamdani-Karakachanska-West Palminska) while being distinct fromthe cluster of four Indian breeds. Analysis of molecular variance (AMOVA) was performed to assess thedistribution of STR variation as a function of both breed membership and geographic origin, the resultsof which revealed the structure based on phylogeny to be evidently stronger than the structure basedon geographic origin. Bayesian clustering of individuals without prior population information revealedthe most appropriate K with nine genetic clusters. In conclusion, the present study showed the PunjabUrial sheep being genetically closer to West Asian and East European sheep breeds as compared to SouthAsian sheep breeds. The microsatellite based nuclear DNA variations, thus confirmed the wild PunjabUrial sheep did not share any recent common ancestry with Asian domestic sheep, as reported earlierbased on mitochondrial sequence variations