Sex-specific genetic parameter estimates of body weight in Mazandaran indigenous chickens.

Body weight is an economically important trait in poultry that shows sexual dimorphism (SD). In the present study, variation in SD in Mazandaran native chickens was investigated in terms of the (Co) variance components and genetic parameters of body weight between males and females. Studied traits were body weights at hatch (BW1), 8 weeks (BW8) and 12 weeks of age (BW12). Also, for weight at sexual maturity (WSM) covariance components were only estimated in females. Cross-sex direct and maternal correlations were also estimated for studied traits except for WSM. For this purpose, a deep 21-generation pedigree and body weight data (57,576 BW1, 72,925 BW8, 62,727 BW12 and, 42,496 WSM) were used. Evaluation of SD of body weight was performed using six bivariate animal models with and without considering the genetic and permanent maternal environmental effects under the restricted maximum likelihood method in WOMBAT software. Model with direct additive genetic effects and maternal genetic effects without covariance between them was identified as the best model for BW1 and BW8. The Model including direct additive genetic effects and permanent maternal environmental effects was the best model for BW12 and WSM. Direct heritability (h2) estimates for BW1, BW8 and, BW12 were, respectively, 0.05 ± 0.013, 0.17 ± 0.02 and, 0.25 ± 0.03 in males and, 0.05 ± 0.012, 0.15 ± 0.01 and 0.21 ± 0.01 in females. Also, the direct heritability of WSM based on univariate analysis in females was estimated to be 0.40 ± 0.01. Maternal heritability ( h m 2 ) varied from 0.39 ± 0.01 (BW1) to 0.04 ± 0.009 (BW8) in males, and 0.36 ± 0.10 (BW1) to 0.04 ± 0.006 (BW8) in females. The correlation between direct genetic effects between males and females for BW1 was not significantly different from one. The direct genetic correlation between the two sexes for BW8 and BW12 was significantly different from 1 concluding that these traits are dimorphic in terms of direct genetic effects and therefore independent selection in both sexes is possible.

Characterization of the mitochondrial Huso huso genome and new aspects of its organization in the presence of tandem repeats in 12S rRNA.

BACKGROUND: The sturgeon group has been economically significant worldwide due to caviar production. Sturgeons consist of 27 species in the world. Mitogenome data could be used to infer genetic diversity and investigate the evolutionary history of sturgeons. A limited number of complete mitogenomes in this family were sequenced. Here, we annotated the mitochondrial Huso huso genome, which revealed new aspects of this species. RESULTS: In this species, the mitochondrial genome consisted of 13 genes encoding proteins, 22tRNA and 2rRNA, and two non-coding regions that followed other vertebrates. In addition, H. huso had a pseudo-tRNA-Glu between ND6 and Cytb and a 52-nucleotide tandem repeat with two replications in 12S rRNA. This duplication event is probably related to the slipped strand during replication, which could remain in the strand due to mispairing during replication. Furthermore, an 82 bp repeat sequence with three replications was observed in the D-loop control region, which is usually visible in different species. Regulatory elements were also seen in the control region of the mitochondrial genome, which included termination sequences and conserved regulatory blocks. Genomic compounds showed the highest conservation in rRNA and tRNA, while protein-encoded genes and nonencoded regions had the highest divergence. The mitochondrial genome was phylogenetically assayed using 12 protein-encoding genes. CONCLUSIONS: In H. huso sequencing, we identified a distinct genome organization relative to other species that have never been reported. In recent years, along with the advancement in sequencing identified more genome rearrangements. However, it is an essential aspect of researching the evolution of the mitochondrial genome that needs to be recognized.

Identification, Isolation, Cloning, and Expression of a New Alkaline Serine Protease Gene from Native Iranian Bacillus sp. RAM 53 for Use in the Industry.

Proteases are one of the most important and widely applicable proteolytic enzymes that are used in various industries. The aim of this study was to identify, isolate, characterize, and clone the new extracellular alkaline protease from the native bacterium Bacillus sp. RAM53 that was isolated from rice fields in Iran. In this study, first, the primary assay of protease production was performed. The bacteria were cultured in a nutrient broth culture medium at 37° C for 48 h, and then, the enzyme extraction was performed. Enzyme activity was measured by standard methods in the range of 20 to 60 °C and the range of pH 6.0 to 12. Degenerate primers were designed to alkaline protease gene sequences. The isolated gene was cloned into the pET28a+ vector, the positive clones were transferred to Escherichia coli BL21, and the expression of the recombinant enzyme was optimized. The results showed that the optimum temperature and pH of the alkaline protease were 40° C and 9.0, respectively, and were stable at 60° C for 3 h. The molecular weight of the recombinant enzyme was 40 kDa in SDS-PAGE. The recombinant alkaline protease was inhibited by the PMSF inhibitor, indicating that the enzyme was serine protease. The results showed that the sequence alignment of the enzyme gene with the other alkaline protease gene sequences related to Bacillus was 94% identity. The result of Blastx showed about 86% identity to the S8 peptidase family in Bacillus cereus and Bacillus thuringiensis and other Bacillus species. The enzyme may be useful for various industries.

Association of allelic polymorphisms of IGFALS gene with growth traits in Makouei and Ghezel sheep breeds.

Insulin-like growth factor-binding protein acid-labile subunit (IGFALS) encodes a protein which binds to IGF1 and IGFBP-3 to regulate the growth, differentiation, and other physiological processes. The aim of this study was the identification of allelic polymorphisms of the IGFALS gene using the PCR-RFLP technique and evaluation of their association with growth traits. For this end, 120 blood samples were randomly collected from each breed. Following amplification of an 1113-bp fragment of exon 1 and a part of intron 1 of the IGFLAS gene, genotyping was conducted by three restriction enzymes including HinfI, MscI, and PvuII. The results showed that only one allele was observed in IGFALS-PvuII site, while in IGFLAS-MscI site, three AA, AB, and BB genotypes with the frequencies of 17.5%, 32%, and 50.5% and 11%, 37.5%, and 51.5% were observed in Makouei and Ghezel sheep breeds, respectively. Additionally, in the IGFLAS-HinfI site, two AB and BB genotypes with the frequency of 34.2% and 65.8% were observed in Makouei sheep and AA, AB, and BB genotypes with the frequency of 9%, 21%, and 70% were observed in Ghezel sheep. So that, Makouei sheep with AB genotype had more chest girth (CG) compared with other genotypes. Furthermore, a significant association was observed between the genotypes of IGFLAS-HinfI with birth weight (BW) in Ghezel and BW, weaning weight (BW3), and CG in Makouei sheep. Haplotype analysis revealed an association between paternal haplotypes and BW in both Ghezel and Makouei breeds. So that, AAB and ABB haplotypes showed more BW than others in Makouei and Ghezel sheep, respectively.

Comparison of parametric, semiparametric and nonparametric methods in genomic evaluation.

Access to dense panels of molecular markers has facilitated genomic selection in animal breeding. The purpose of this study was to compare the nonparametric (random forest and support vector machine), semiparametric reproducing kernel Hilbert spaces (RKHS), and parametric methods (ridge regression and Bayes A) in prediction of genomic breeding values for traits with different genetic architecture. The predictive performance of different methods was compared in different combinations of distribution of QTL effects (normal and uniform), two levels of QTL numbers (50 and 200), three levels of heritability (0.1, 0.3 and 0.5), and two levels of training set individuals (1000 and 2000). To do this, a genome containing four chromosomes each 100-cM long was simulated on which 500, 1000 and 2000 evenly spaced single-nucleotide markers were distributed. With an increase in heritability and the number of markers, all the methods showed an increase in prediction accuracy (P<0.05). By increasing the number of QTLs from 50 to 200, we found a significant decrease in the prediction accuracy of breeding value in all methods (P<0.05). Also, with the increase in the number of training set individuals, the prediction accuracy increased significantly in all statistical methods (P<0.05). In all the various simulation scenarios, parametric methods showed higher prediction accuracy than semiparametric and nonparametric methods. This superior mean value of prediction accuracy for parametric methods was not statistically significant compared to the semiparametric method, but it was statistically significant compared to the nonparametric method. Bayes A had the highest accuracy of prediction among all the tested methods and, is therefore, recommended for genomic evaluation.

Genome-Wide Identification of Microsatellites and Transposable Elements in the Dromedary Camel Genome Using Whole-Genome Sequencing Data.

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.

Cloning, expression and characterization of a novel alkaline serine protease gene from native Iranian Bacillus sp.; a producer of protease for use in livestock.

The use of proteases in the last decade has been welcomed in livestock and poultry industries and has led to significant results such as improved feed conversion ratio, weight gain and increased growth performance. In the present study, isolation and identification of a novel alkaline protease from Iranian Bacillus species was performed in order to use in livestock feed. After primary isolation of bacteria from soil samples of rice fields and early detection of bacterial genus, the zymogram plate was performed for evaluation of production extracellular proteases. Of the 11 strains producing protease, one strain that produced more enzymes was selected to continue the work. Characterization of alkaline protease was done using specific enzyme assays. To confirm the genus of isolates as well as to identify the species close to, molecular analysis of 16S rRNA gene sequence was done. After that, bioinformatics analysis carried out in NCBI database for searching bacterial alkaline proteases gene sequences. The primer designed based on gene homology of close species for extraction of alkaline protease gene. The results showed that the enzyme extract had the highest activity at pH 9.0 and 50 °C. The 16S rRNA gene sequence was submitted for the strain called Bacillus sp. RAM on the NCBI site. According to the results of the phylogenetic tree, the bacterium was belonged to Bacillus genus and Bacillus sp. RAM was close to Thuringiensis C405. The isolated alkaline protease gene successfully cloned in pET28a and transferred to the expression host E.coli BL21. The expression of the protease gene was evaluated by SDS-PAGE electrophoresis. The induced recombinant cells expressed the protease and revealed molecular weight band of about 38 kDa. According to the enzyme properties, this alkaline protease can useful for application in animal industry.

Genetic variants analysis of three dromedary camels using whole genome sequencing data.

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.

Detection of QTL for greasy fleece weight in sheep using a 50 K single nucleotide polymorphism chip.

Genome-wide association studies (GWAS) have introduced an influential tool in the search for quantitative trait loci (QTL) influencing economically important traits in sheep. To identify QTL associated with greasy fleece weight, a GWAS with 50 K single nucleotide polymorphisms (SNPs) was performed in a Baluchi sheep population. Association with greasy fleece weights was tested using the software Plink. The results of our GWAS provided three novel SNP markers and candidate genes associated with greasy fleece weight. A total of three chromosome-wide significant associations were detected for SNP on chromosomes 17 and 20 affecting greasy fleece weight across the four shearing. One of the significant SNP markers was located within ovine known genes namely FAM101A. Further investigation of these identified regions in validation studies will facilitate the identification of strong candidate genes for wool production in sheep.

In Silico Analysis of L1/L2 Sequences of Human Papillomaviruses: Implication for Universal Vaccine Design.

The aim of this study was to design a multiepitope universal vaccine for major human papillomavirus (HPV) structural proteins, L1/L2, by bioinformatics models. For this purpose, we predicted the most probable immunogenic epitopes of L1 and L2 from common high-risk HPV 16, 18, 31, and 45 beside high prevalent type 6 and 11 based on BCPREDS defaulted model, while solvent accessibility of structure was extrapolated. The three-dimensional molecular model of L1 protein was constructed by Swiss Model server, whereas sequence alignment provided model for prediction of L2 protein epitopes. After that, N-glycosylation sites were excluded from estimated epitope regions. Then, by other bioinformatics analyses, 20 epitopes were selected and fused in tandem repeats, reverse translated, and codon optimized to relevant sequence. The final protein parameters such as antigenicity were analyzed by protean program. Evaluation of new recombinant protein sequence indicated a molecular weight of 41.8 kDa with 400 amino acids beside positive charge. The computed isoelectric point (pI) value indicated the acidic nature of final product. The aliphatic index showed low thermal stability of this construct and the Grand Average Hydropathicity value was negative (-0.494). Analyzed plot showed that major parts of new protein construct had hydrophilic property, thus harboring antigenic potency. After all, sequence of final construct reverse translated to DNA and this codon-optimized sequence showed Codon Adaptation Index (CAI) of >0.8 for expression in Escherichia coli. Finally, this sequence ligated into pET28a bacterial expression vector. The new recombinant proteins harboring 20 B cell epitope seem to be suitable antigens based on computational methods as a universal vaccine candidate for HPVs.