جستجوی مقالات مرتبط با کلیدواژه "caspian" در نشریات گروه "علوم دام"

Horses have played an important role in the history of Iranians during different centuries. They kept horses for various aims such as agriculture, transportation, sport, food sources. Iran has a suitable climatic, social and economic potential for keeping and breeding horses, that is why it has been created different breeds using the selection and breeding. But due to problems such as mechanization, lack of government support, export ban, high costs of breeding and maintenance, import of foreign horses, lack of proper planning, interest in keeping horses has decreased. So, unfortunately, only a few native Iranian breeds remain. Additional investigation of the equine genomic architecture is critical for a better understanding of the equine genome, as well as for expanded comparisons across diverse mammalian species. Turkmen and Caspian horses are well-known breeds of Iranian horse breeds. These breeds were historically selected to perform distinct tasks and therefore may harbor a wealth of unique variation at the genome level. Copy number variation (CNV) along with single nonucleotide polymorphisms (SNPs) play a key role in genetic diversity in livestock species. CNVs, a term that refers to a change in the number of copies of a genomic segment, are responsible for more sequence differences between individuals than SNPs and are considered to be a major source of genetic variation contributing to differences in phenotypes (Beckmann et al, 2007). Several studies identified copy number variations in horses using different techniques (Doan et al, 2012). Part of these studies tried to establish associations between CNVs and a specific trait, a disease or even gene expression (Schurink et al, 2017). Most of these studies found either no association or inconclusive associations as the number of horses with phenotypic information or with specific CNVs were limited. For example, a 62 kb duplication on Equus caballus (ECA) chromosome 10 seemed to be related to recurrent laryngeal neuropathy (Dupuis et al, 2013). However, little is known about CNV in Iranian horses.

In this study, detection of CNVs and CNVRs were performed based on SNP data from Caspian and Turkman horse breeds were genotyped via Equine70k SNP beadchip. PennCNV software was only used to detect CNV on autosomes. The PennCNV algorithm was only applied to autosomes (command: -lastchr 26) to identify individual-based CNVs. To increase the confidence of the detected CNVs, quality control was performed by employing standard exclusions of the LRR (standard deviation of LRR) <0.3, a BAF drift <0.01 and a waviness factor <0.05. We classified the status of these CNV into two categories: “loss” (CNV containing a deletion) and “gain” (CNV containing a duplication). The CNVRs were determined by aggregating the overlapping CNVs with CNVRuler. BioMart in the Ensembl database and DAVID was employed to identify genes located in CNVRs and GO terms and KEGG pathway analyses respectively. Quantitative real-time PCR (qPCR) was applied to validate the CNVRs that were detected in this study.

A total of 202 and 105 CNVs and CNVRs were identified in the studied horses, respectively, which cover 1.08% of the horse genome. The number CNVs in Caspian breed were 1.6 times more than Turkmen. Also, the average size of CNVs in Caspian breed was longer than Turkmen. In both breeds, the genetic event of gain was higher than the genetic event of deletion. In Caspian breed, chromosomes 1, 3, 12, and in the Turkmen breed, chromosomes 1, 6 and 12 showed the most changes in CNVs, respectively. Functional analysis showed that the identified CNVRs overlapped with 434 genes and the most of these genes were common between the two horse breeds (more than 60%). Among these genes, PPARG and GALR have potential related with breed-specific traits. The KEGG pathway analysis also identified several pathways that are significantly enriched in olfactory sensory perception, chemical stimulus sensory perception, antigen processing, and G protein signaling pathway. Also, 60% of successfully detected CNVRs were confirmed by Real-time qPCR. The results of this study were compared with the results of eight other studies. For example, we concluded that the average size of the CNVRs detected by the 70k arrays and the 50K arrays were significantly larger than obtained by the CGH and NGS arrays. This may be due to the relatively low coverage and non-uniform distribution of SNP in the equine genome in SNP arrays. Possible reasons for the differences between our results and some CNV studies can be related to different parameters such as sample size and genetic background, different detection platforms and CNV retrieval algorithms, CNV definitions and CNVRs, as well as random error estimation methods (Pinto et al. 2011).

CNVs can describe part of the phenotypic diversity and adaptation evidence in Iranian horses. With regard to Genes identified in a number of cellular components, biological processes and molecular functions within CNVRs, the importance of such CNVRs and the possible effect needs to be studied and may interest insight into the functional and adaptive consequence of CNVs in horse. In total, the number of CNVs in the Caspian breed was greater than in the Turkmen breed, and also the CNV length in the number of copies in the Caspian breed was greater than in the Turkmen breed. In both breeds, there were overlapping genes with CNVRs that were significantly enriched in biological pathways, including sensory perception, immunity, and metabolism. This is the first CNV report on Turkmen and Caspian horses and the findings of this study could provide valuable information for better understanding of the horse genome and also the important performance traits with CNVRs and associated genes for the future studies in horse breeds.

Due to having historical value and climatic diverse, Iran has unique horse breeds. Unfortunately, due to the lack of attention and control of the import of foreign breeds into this rich
genetic source, huge damage has been created. Therefore, many horse breeds in the country got crossbred and their racial purity reduced. Knowing the genetic structure of native breeds will play an important role in their safeguarding and ensuring of their survival. Indigenous breeds, due to their unique characteristics, are considered as part of the genetic resources of the country, and their genetic structure will help them to protect and develop eugenic programs.

 This study was conducted on 136 horses including Taleshi (25 samples), Caspian (49 samples) and Arabic (62 samples) breeds from their breeding areas. Taleshi horse samples was captured from local stock in the Guilan province, Caspian samples was captured from horse riding clubs around Tehran and Guilan provinces, and Arabian samples was captured from horse riding clubs around the provinces of Tehran, Khuzestan and Alborz. They were unrelated and selected randomly. The race recognition of horses was based on books published by the Federation of Equestrian and their phenotypic characteristics. After determining of the concentration and uniformity of the concentration of extracted DNA, all individuals under study were conducted for 12 microsatellite markers recommended by the Animal Genetic Association (ISAG) to determine the genotype in order to estimate the parameters such as heterozygosity, inbreeding, Hardy and Weinberg equilibrium, and so on and find an appropriate strategy to maintain these valuable breeds. The number of observed alleles (na), and effective (ne), observed heterozygosity (Ho) and the Expectation case (He), Shannon index (I), inbreeding coefficient (ISF), genetic distance, genetic similarity, Hardy-Weinberg equilibrium, and phylogeny tree between races were calculated using POPGENE 1.31 software.

 All of the used markers were multi-shaped and the ASB17 markers with 12 alleles and HMS6 produced the highest and lowest number of alleles with 6 alleles, respectively.
The highest and lowest expected heterozygosity were calculated in VHL20 (0.78) and ASB23 (0.62) markers, and the average Shannon index for all sites was 1.72. Hardy Weinberg balance
analysis by Chi square test showed that except ASB2 and HMS3 markers in Taleshi breed, ASB17 and HTG4 markers in the Caspian breed and ASB17 markers in the Arabic breed, all markers had a significant deviation from Hardy and Weinberg equilibrium (P <0.05). The highest observed heterozygosity was related to AHT5 marker (0.81) and the lowest observed heterozygote was related to ASB17 and HTG4 markers (0.68). The Shannon index, like the observed heterozygosity, shows the amount of genetic diversity, and because the maximum value is equal to Ln (n), it is useful to express the genetic diversity of multi-formed sites. The highest and lowest values of Shannon index were 1.96 and 1.46, respectively, for VHL20 and HTG4 markers. Given the fact that the VHL20 marker showed the highest and the HTG4 marker showed the least effective allele, so the calculated values for the Shannon index are justified. Phylogeny diagram showed that Caspian and Taleshi horses were placed in one branch and Arab horses in separate branch.

Breeds with fewer populations are more at risk for genetic changes and extinction. Reducing of the genetic diversity of indigenous populations will result in the loss of many useful
genes, especially those that are compatible with different environments and resistant to regional diseases. Undoubtedly, it is very important to pay attention to the genetic diversity of small-sized
population of breeds such as Taleshi and Caspian. The results of this study showed that due to the low number of Caspian and Taleshi horses, genetic diversity is still at a high level, so it would be hoped that by adopting the principled measures, we would prevent their extinction in the long duration.