Whole genome wide identification and annotation of genetic variations in camels is in its first steps. The aim of this study was the identification of genome wide variants, functional annotations of them and enrichment analysis of affected genes using whole genome sequencing data of three dromedary camels. The genomes of two Iranian female dromedary camels that mostly used to produce meat and milk were sequenced to 41.9-fold and 38.6-fold coverage. A total of 4,727,238 single-nucleotide polymorphisms (SNPs) and 692,908 indels (insertions and deletions) were found by mapping raw reads to the dromedary reference assembly (GenBank Accession: GCA_000767585.1). In-silico functional annotation of the discovered variants in under study samples revealed that most SNPs (2,305,738; 48.78%) and indels (339,756; 49.03%) were located in intergenic regions. A comparison of the identified SNPs with those of the African camel (BioProject Accession: PRJNA269274) indicated that they had 993,474 SNPs in common. We found 15,168 non-synonymous SNPs in the shared variants of the three camels that could affect gene function and protein structure. Obtained results revealed that there were 7085, 6271 and 4688 non-synonymous SNPs among the 3436, 3058 and 2882 genes in the specific gene sets of Yazd dromedary, Trod dromedary and African dromedary, respectively. The list of genes predicted to be affected by non-synonymous variants in different individuals was subjected to gene ontology (GO) enrichment analysis.

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The population size of Bactrian camels is smaller than dromedary, and they are distributed in cold and mountain regions and are also at the risk of extinction in some countries such as Iran. To identify and investigate the genome-wide variations, whole-genome sequencing of two Iranian Bactrian camels were performed with 37.4- and 42.6-fold coverage for the first time. Along with Iranian Bactrian camels, sequencing data from two Mongolian domestic and two wild Bactrian camels deposited in the NCBI were reanalyzed. The analysis eventuated to the identification of 4,908,998, 4,485,725, and 4,706,654 SNPs for Iranian, Mongolian domestic, and wild Bactrian camels, respectively. Also, INDEL variations ranged from 358,311 to 533,188 in all six camels. Results of variants annotation in all samples revealed that more than 88 percent of SNPs and INDELs were located in the intergenic and intronic regions. We found that 800,530 SNPs were common among all studied camels, containing 4,046 missense variants that affected 2,428 genes. Investigation of common genes among all camels containing the missense SNPs showed that there are 98 zinc finger and 4 fertility-related genes (ZP1, ZP2, ZP4, and ZPBP) in this set.

Transposable elements (TEs) along with simple sequence repeats (SSRs) are prevalent in eukaryotic genome, especially in mammals. Repetitive sequences form approximately one-third of the camelid genomes, so study on this part of genome can be helpful in providing deeper information from the genome and its evolutionary path. Here, in order to improve our understanding regarding the camel genome architecture, the whole genome of the two dromedaries (Yazdi and Trodi camels) was sequenced. Totally, 92- and 84.3-Gb sequence data were obtained and assembled to 137,772 and 149,997 contigs with a N50 length of 54,626 and 54,031 bp in Yazdi and Trodi camels, respectively. Results showed that 30.58% of Yazdi camel genome and 30.50% of Trodi camel genome were covered by TEs. Contrary to the observed results in the genomes of cattle, sheep, horse, and pig, no endogenous retrovirus-K (ERVK) elements were found in the camel genome. Distribution pattern of DNA transposons in the genomes of dromedary, Bactrian, and cattle was similar in contrast with LINE, SINE, and long terminal repeat (LTR) families. Elements like RTE-BovB belonging to LINEs family in cattle and sheep genomes are dramatically higher than genome of dromedary. However, LINE1 (L1) and LINE2 (L2) elements cover higher percentage of LINE family in dromedary genome compared to genome of cattle. Also, 540,133 and 539,409 microsatellites were identified from the assembled contigs of Yazdi and Trodi dromedary camels, respectively. In both samples, di-(393,196) and tri-(65,313) nucleotide repeats contributed to about 42.5% of the microsatellites. The findings of the present study revealed that non-repetitive content of mammalian genomes is approximately similar. Results showed that 9.1 Mb (0.47% of whole assembled genome) of Iranian dromedary’s genome length is made up of SSRs. Annotation of repetitive content of Iranian dromedary camel genome revealed that 9,068 and 11,544 genes contain different types of TEs and SSRs, respectively. SSR markers identified in the present study can be used as a valuable resource for genetic diversity investigations and marker-assisted selection (MAS) in camel-breeding programs.

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The aim of this study was to identify variations of vasoactive intestinal peptide (VIP) and VIP receptor-1 (VIPR-1) genes that might be associated with turkey reproductive traits. One hundred twenty turkey hens were recorded for age at first egg (AFE), first egg weight (FEW), egg number (EN), total egg weight (TEW), laying period (LP), and broodiness. The DNA was isolated from blood samples and subjected to PCR amplification of the meleagrine VIP and VIPR-1 genes. The SNPs were detected by single-strand conformation polymorphism and the variant DNA fragments were sequenced. One mutation in 3’-UTR of VIP (G5846A) and two SNPs in intron 2 of VIPR-1 (C17687T and A17690T) were found, all of them novel. The associations of the three detected SNPs with the reproductive traits of turkeys were evaluated. The detected polymorphisms were used for marker-trait association analyses. The results of association analysis showed that G5846A on 3’ UTR of VIP has a significant association with LP, EN, TEW, and AFE. The G allele of G5846A was the favourable SNP allele for LP, EN, and TEW traits. The AA genotype of A17690T on intron 2 of VIPR-1 was significantly associated with higher LP, EN, and TEW. AGAA haplotype showed association with higher EN and TEW. These results suggest that the SNPs in 3’-UTR of VIP and intron 2 of VIPR-1 genes may influence egg production traits in turkey hens.Keywords: broodiness, candidate gene, egg production, single nucleotide polymorphism, VIPR-1

The aim of this study was to investigate the effects of dietary supplementation of protected fish oil (FO) and Persia fat ® (PF) on the quality of Moghani ram semen. For this purpose, a total of 96 ejaculates were collected from 12 healthy mature Moghani rams, which were divided into three distinct groups (n = 4) and were assigned to one of three experimental diets. The first group (control) received a diet supplemented with palm oil (PO), while the second and third groups received encapsulated FO and PF, respectively. After primary evaluation, semen samples of each group were pooled to eliminate individual differences, and then evaluated for semen concentration and volume. Afterwards, the samples were diluted with a Tris-based extender and frozen with a standard protocol. After thawing, motion kinetics, viability, membrane functionality and abnormality were assessed. The results showed that the group that received FO had significanty higher viability (quadratic), progressive motility (PM) (%), average path velocity (VAP) (µm/s), curvilinear velocity (VCL) (µm/s) (linear), amplitude of lateral head displacement (ALH) (µm) (quadratic) and sperm concentration (linear) than the others. Additionally, total motility (TM) (%) and straight-line velocity (VSL) (µm/s) were significantly higher in the groups that received FO and PF compared with the control (quadratic) The results indicated that sperm abnormalities in the control group were significantly higher than the other groups. In conclusion, enrichment of the diet with FO or Persia fat could enhance ram sperm quality after freeze-thawing process.