Integrated analysis of inflammatory mRNAs, miRNAs, and lncRNAs elucidates the molecular interactome behind bovine mastitis.

Mastitis is known as intramammary inflammation, which has a multifactorial complex phenotype. However, the underlying molecular pathogenesis of mastitis remains poorly understood. In this study, we utilized a combination of RNA-seq and miRNA-seq techniques, along with computational systems biology approaches, to gain a deeper understanding of the molecular interactome involved in mastitis.

Hitchhiking Mapping of Candidate Regions Associated with Fat Deposition in Iranian Thin and Fat Tail Sheep Breeds Suggests New Insights into Molecular Aspects of Fat Tail Selection.

The fat tail is a phenotype that divides indigenous Iranian sheep genetic resources into two major groups. The objective of the present study is to refine the map location of candidate regions associated with fat deposition, obtained via two separate whole genome scans contrasting thin and fat tail breeds, and to determine the nature of the selection occurring in these regions using a hitchhiking approach. Zel (thin tail) and Lori-Bakhtiari (fat tail) breed samples that had previously been run on the Illumina Ovine 50 k BeadChip, were genotyped with a denser set of SNPs in the three candidate regions using a Sequenom Mass ARRAY platform.

Genome Diversity and the Origin of the Arabian Horse.

The Arabian horse, one of the world's oldest breeds of any domesticated animal, is characterized by natural beauty, graceful movement, athletic endurance, and, as a result of its development in the arid Middle East, the ability to thrive in a hot, dry environment. Here we studied 378 Arabian horses from 12 countries using equine single nucleotide polymorphism (SNP) arrays and whole-genome re-sequencing to examine hypotheses about genomic diversity, population structure, and the relationship of the Arabian to other horse breeds. We identified a high degree of genetic variation and complex ancestry in Arabian horses from the Middle East region.

Study of whole genome linkage disequilibrium patterns of Iranian water buffalo breeds using the Axiom Buffalo Genotyping 90K Array.

Accuracy of genome-wide association studies, and the successful implementation of genomic selection depends on the level of linkage disequilibrium (LD) across the genome and also the persistence of LD phase between populations. In the present study LD between adjacent SNPs and LD decay between SNPs was calculated in three Iranian water buffalo populations. Persistence of LD phase was evaluated across these populations and effective population size (Ne) was estimated from corrected r2 information.

Genetic Diversity of Persian Arabian Horses and Their Relationship to Other Native Iranian Horse Breeds.

The principal aims of this study were to explore genetic diversity and genome-wide selection signatures in Persian Arabian horses and to determine genetic relationship of Persian Arabians with other Iranian horse breeds. We evaluated 71 horses from 8 matrilineal strains tracing to 47 mares from the mid to late 19th century, using the equine 670k single nucleotide polymorphism (SNP) BeadChip. Mean observed and expected heterozygosity were (0.

A genome-wide scan for signatures of selection in Azeri and Khuzestani buffalo breeds.

Background: Identification of genomic regions that have been targets of selection may shed light on the genetic history of livestock populations and help to identify variation controlling commercially important phenotypes. The Azeri and Kuzestani buffalos are the most common indigenous Iranian breeds which have been subjected to divergent selection and are well adapted to completely different regions. Examining the genetic structure of these populations may identify genomic regions associated with adaptation to the different environments and production goals.

MHC haplotype diversity in Persian Arabian horses determined using polymorphic microsatellites.

Previous research on the equine major histocompatibility complex (MHC) demonstrated strong correlations between haplotypes defined by polymorphic intra-MHC microsatellites and haplotypes defined using classical serology. Here, we estimated MHC diversity in a sample of 124 Arabian horses from an endangered strain native to Iran (Persian Asil Arabians), using a validated 10-marker microsatellite panel. In a group of 66 horses related as parent-offspring pairs or half-sibling groups, we defined 51 MHC haplotypes, 49 of which were new.

Neural network and SVM classifiers accurately predict lipid binding proteins, irrespective of sequence homology.

Due to the central roles of lipid binding proteins (LBPs) in many biological processes, sequence based identification of LBPs is of great interest. The major challenge is that LBPs are diverse in sequence, structure, and function which results in low accuracy of sequence homology based methods. Therefore, there is a need for developing alternative functional prediction methods irrespective of sequence similarity.

The relation between the genetic architecture of quantitative traits and long-term genetic response.

The genetic architecture of a quantitative trait refers to the number of genetic variants, allele frequencies, and effect sizes of variants that affect a trait and their mode of gene action. This study was conducted to investigate the effect of four shapes of allelic frequency distributions (constant, uniform, L-shaped and U-shaped) and different number of trait-affecting loci (50, 100, 200, 500) on allelic frequency changes, long term genetic response, and maintaining genetic variance. To this end, a population of 440 individuals composed of 40 males and 400 females as well as a genome of 200 cM consisting of two chromosomes and with a mutation rate of 2.

Detecting novel SNPs and breed-specific haplotypes at calpastatin gene in Iranian fat- and thin-tailed sheep breeds and their effects on protein structure.

Calpastatin has been introduced as a potential candidate gene for growth and meat quality traits. In this study, genetic variability was investigated in the exon 6 and its intron boundaries of ovine CAST gene by PCR-SSCP analysis and DNA sequencing. Also a protein sequence and structural analysis were performed to predict the possible impact of amino acid substitutions on physicochemical properties and structure of the CAST protein.

Underlying functional genomics of fat deposition in adipose tissue.

The objective of this study was to gain insight into the underlying mechanisms of fat deposition. Two sheep breeds with large fat-tail (Lori-Bakhtiari) and with thin-tail (Zel) were used as models. To determine important and key candidate lipid metabolism related genes, comparative genomic approaches were employed.

Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition.

Background: Identification of genomic regions that have been targets of selection for phenotypic traits is one of the most important and challenging areas of research in animal genetics. However, currently there are relatively few genomic regions identified that have been subject to positive selection. In this study, a genome-wide scan using ~50,000 Single Nucleotide Polymorphisms (SNPs) was performed in an attempt to identify genomic regions associated with fat deposition in fat-tail breeds.