8_Iran_Cattle_Breeds_geno

The file contains genotypes of 8 Iranian cattle breeds (75 animals). The file is in a compressed rds format and can be used and modified in R

Mitochondrial DNA sequence variation in Iranian native dogs

<p>The dog mtDNA diversity picture from wide geographical sampling but from a small number of individuals per region or breed, displayed little geographical correlation and high degree of haplotype sharing between very distant breeds. For a clear picture, we extensively surveyed Iranian native dogs (<i>n</i> = 305) in comparison with published European (<i>n</i> = 443) and Southwest Asian (<i>n</i> = 195) dogs. Twelve haplotypes related to haplogroups A, B and C were shared by Iranian, European, Southwest Asian and East Asian dogs. In Iran, haplotype and nucleotide diversities were highest in east, southeast and northwest populations while western population had the least. Sarabi and Saluki dog populations can be assigned into haplogroups A, B, C and D; Qahderijani and Kurdi to haplogroups A, B and C, Torkaman to haplogroups A, B and D while Sangsari and Fendo into haplogroups A and B, respectively. Evaluation of population differentiation using pairwise <i>F</i>_ST generally revealed no clear population structure in most Iranian dog populations. The genetic signal of a recent demographic expansion was detected in East and Southeast populations. Further, in accordance with previous studies on dog-wolf hybridization for haplogroup d2 origin, the highest number of d2 haplotypes in Iranian dog as compared to other areas of Mediterranean basin suggests Iran as the probable center of its origin. Historical evidence showed that Silk Road linked Iran to countries in South East Asia and other parts of the world, which might have probably influenced effective gene flow within Iran and these regions. The medium nucleotide diversity observed in Iranian dog calls for utilization of appropriate management techniques in increasing effective population size.</p

Genetic Variation of Goat Interferon Regulatory Factor 3 Gene and Its Implication in Goat Evolution

<div><p>The immune systems are fundamentally vital for evolution and survival of species; as such, selection patterns in innate immune loci are of special interest in molecular evolutionary research. The interferon regulatory factor (<i>IRF</i>) gene family control many different aspects of the innate and adaptive immune responses in vertebrates. Among these, <i>IRF3</i> is known to take active part in very many biological processes. We assembled and evaluated 1356 base pairs of the <i>IRF3</i> gene coding region in domesticated goats from Africa (Nigeria, Ethiopia and South Africa) and Asia (Iran and China) and the wild goat (<i>Capra aegagrus</i>). Five segregating sites with θ value of 0.0009 for this gene demonstrated a low diversity across the goats’ populations. Fu and Li tests were significantly positive but Tajima’s D test was significantly negative, suggesting its deviation from neutrality. Neighbor joining tree of <i>IRF3</i> gene in domesticated goats, wild goat and sheep showed that all domesticated goats have a closer relationship than with the wild goat and sheep. Maximum likelihood tree of the gene showed that different domesticated goats share a common ancestor and suggest single origin. Four unique haplotypes were observed across all the sequences, of which, one was particularly common to African goats (MOCH-K14-0425, Poitou and WAD). In assessing the evolution mode of the gene, we found that the codon model d_N/d_S ratio for all goats was greater than one. <a href="http://www.baidu.com/link?url=kkqzjLCQ_0ML92i5pxFn22m8yH-Ee0kuL6OdTRr1Ko76Iu8UyUCCRDpL8jgIpt2B4NUepOc7MJC9vWhiozorAK" target="_blank">Phylogenetic Analysis by Maximum Likelihood (PAML)</a> gave a ω₀ (d_N/d_S) value of 0.067 with LnL value of -6900.3 for the first Model (M1) while ω2 = 1.667 in model M2 with LnL value of -6900.3 with positive selection inferred in 3 codon sites. Mechanistic empirical combination (MEC) model for evaluating adaptive selection pressure on particular codons also confirmed adaptive selection pressure in three codons (207, 358 and 408) in <i>IRF3</i> gene. Positive diversifying selection inferred with recent evolutionary changes in domesticated goat <i>IRF3</i> led us to conclude that the gene evolution may have been influenced by domestication processes in goats.</p></div

Population statistics and neutrality test in <i>IRF3</i> gene in goats alone and goats with Sheep.

<p>Population statistics and neutrality test in <i>IRF3</i> gene in goats alone and goats with Sheep.</p

Accession Identification for goat <i>IRF3</i> Sequences downloaded from NCBI and NextGen Capra Project for Moroccan and Iranian goats.

<p>Accession Identification for goat <i>IRF3</i> Sequences downloaded from NCBI and NextGen Capra Project for Moroccan and Iranian goats.</p

The phylogeny of goat <i>IRF3</i> gene was inferred by the maximum likelihood (ML) method using the PhyML program in MEGA software to analyze aligned sequences and this tree was rooted using the <i>Ovis aries IRF3</i> gene sequence.

<p>MOCH = Moroccan goats; IRCH = Iranian goats; WAD = West African Dwarf.</p

Chromosome identity, number of exons and mutations in codons under positive selection pressure in <i>IRF3</i> gene.

<p>Chromosome identity, number of exons and mutations in codons under positive selection pressure in <i>IRF3</i> gene.</p

Inference of positive selection in <i>IRF3</i> genes using two pairs of models in Phylogenetic Analysis by Maximum Likelihood (PAML).

<p>Inference of positive selection in <i>IRF3</i> genes using two pairs of models in <a href="http://www.baidu.com/link?url=kkqzjLCQ_0ML92i5pxFn22m8yH-Ee0kuL6OdTRr1Ko76Iu8UyUCCRDpL8jgIpt2B4NUepOc7MJC9vWhiozorAK" target="_blank">Phylogenetic Analysis by Maximum Likelihood (PAML)</a>.</p

Neighbor joining phylogenetic trees for goat <i>IRF3</i> gene sequences constructed by Neighbor-joining (NJ) method in MEGA 6.0 with bootstrap value set to 1000 and <i>Ovis aries IRF3</i> gene sequence as outgroup.

<p>MOCH = Moroccan goats; IRCH = Iranian goats; WAD = West African Dwarf.</p

Selection pressures among goat <i>IRF3</i> gene sequences using mechanistic empirical combination (MEC) model of selecton online tool.

<p>Yellow and brown highlights represent positive selection, grey and white highlights represent neutral selection and purple highlight represent negative selection on codons.</p