Isolation and characterization of SNP markers of rainbow trout (Onchorhynchus mykiss Walbaum, 1792) from transcriptomic sequences.

Rainbow trout (Onchorhynchus mykiss) is one of the most important freshwater aquaculture fish in Iran. It is necessary to develop available molecular marker such as SNPs, which represent a useful tool in detecting adaptive signals in populations and also parentage assignment for O. mykiss. Genetic architecture of broodstock populations is important for breeding programs, as it enables decisions on broodstock screening and genomic selection. In this study, 52 novel single nucleotide polymorphism (SNP) markers for O. mykiss were discovered and validated based on transcriptome sequencing, by means of paired-end sequencing in an Illumina HiSeq 2500 platform. The SNPs were identified through liver transcriptome sequencing from fifteen samples. The observed and expected heterozygosities ranged from 0.177 to 1.000 and 0.239 to 0.638, respectively. The minimum allele frequency (MAF) ranged from 0.166 to 0.489. Among these SNP loci, twenty-two loci showed significant departures from the Hardy-Weinberg equilibrium after Bonferroni correction (p < 0.05) and significant linkage disequilibrium was found. The SNP markers identified in this research could be useful for novel studies, such as those related to associations between high-resolution molecular markers and quantitative traits studies. Moreover, these SNP markers would be used in genetic studies helping economic performance improvement and management of this species.

Characterization of novel genotyping-by-sequencing (GBS)-based simple sequence repeats (SSRs) and their application for population genomics of Capoeta aculeata (Valenciennes, 1844).

BACKGROUND: The species Capoeta aculeata (Valenciennes, 1844) is one of the most important freshwater species endemic to Iran. However, the investigation of the population genetic structure of this species is limited by the low number of molecular markers currently described. METHODS AND RESULTS: In this study, we implemented next generation sequencing technology to identify polymorphic microsatellite markers and investigate the population genetic structure of C. aculeata sampled from three geographical sites in Iran. We characterized and developed 36 novel polymorphic microsatellite markers and these loci were examined in 120 individuals from three populations occurring in the Zagros basin. The average number of alleles per locus varied from 1.7 to 16 (average = 7.89). The results showed that, the polymorphism information content (PIC) of these simple sequence repeat (SSR) loci varied from 0.254 to 0.888. The observed heterozygosity (HO) per locus ranged from 0.170 to 0.881, while the expected heterozygosity (HE) per locus was from 0.170 to 0.881. Among these SSR loci, 20 loci deviated significantly from the Hardy-Weinberg equilibrium after Bonferroni correction (p < 0.05). CONCLUSIONS: These microsatellite markers could provide a valuable tool for future population and conservation genetics studies of C. aculeate and other closely related species.

Dietary Immunogen® modulated digestive enzyme activity and immune gene expression in Litopenaeus vannamei post larvae.

Pacific white shrimp Litopenaeus vannamei (Boone, 1931) is an important economical shrimp species worldwide, especially in the Middle East region, and farming activities of this species have been largely affected by diseases, mostly viral and bacterial diseases. Scientists have started to use prebiotics for bolstering the immune status of the animal. This study aimed to investigate the influence of Immunogen® on growth, digestive enzyme activity and immune related gene expression of Litopenaeus vannamei post-larvae. All post-larvae were acclimated to the laboratory condition for 14 days. Upon acclimation, shrimps were fed on different levels of Immunogen® (0, 0.5, 1 and 1.5 g kg-1) for 60 days. No significant differences were detected in weight gain, specific growth rate (SGR) and food conversion ratio (FCR) in shrimp post-larvae in which fed with different levels of Immunogen® and control diet. The results showed that digestive enzymes activity including protease and lipase increased with different amounts of Immunogen® in the shrimp diet. Protease activity increased with 1.5 g kg-1 Immunogen® after 60 days and lipase activity increased with 1 and 1.5 g kg-1 Immunogen® after 30 and 60 days of the trial respectively (P < 0.05), while amylase activity did not change in response to different levels of Immunogen® (P > 0.05). The expression of immune related genes including, prophenoloxidase, crustin and g-type lysozyme increased with diet 1.5 g kg-1 Immunogen® (P < 0.05) while expression of penaeidin gene increased only with experimental diet 1 g kg-1 of Immunogen®. These results indicated that increase in digestive enzymes activity and expression of immune related genes could modulate the Immunogen® in the innate immune system in L. vannamei in this study.

An Integrated Bioinformatics Approach to Identify Network-Derived Hub Genes in Starving Zebrafish.

The present study was aimed at identifying causative hub genes within modules formed by co-expression and protein-protein interaction (PPI) networks, followed by Bayesian network (BN) construction in the liver transcriptome of starved zebrafish. To this end, the GSE11107 and GSE112272 datasets from the GEO databases were downloaded and meta-analyzed using the MetaDE package, an add-on R package. Differentially expressed genes (DEGs) were identified based upon expression intensity N(µ = 0.2, σ2 = 0.4). Reconstruction of BNs was performed by the bnlearn R package on genes within modules using STRINGdb and CEMiTool. ndufs5 (shared among PPI, BN and COEX), rps26, rpl10, sdhc (shared between PPI and BN), ndufa6, ndufa10, ndufb8 (shared between PPI and COEX), skp1, atp5h, ndufb10, rpl5b, zgc:193613, zgc:123327, zgc:123178, wu:fc58f10, zgc:111986, wu:fc37b12, taldo1, wu:fb62f08, zgc:64133 and acp5a (shared between COEX and BN) were identified as causative hub genes affecting gene expression in the liver of starving zebrafish. Future work will shed light on using integrative analyses of miRNA and DNA microarrays simultaneously, and performing in silico and experimental validation of these hub-causative (CST) genes affecting starvation in zebrafish.

Genetic va riation in the na rrow-c lawed c ra yfish (Astacus lepto dactylus) po pulatio ns as assesse d by PCR-RFLP of mitochondria l COI gene.

The genetic variation and population structure of narrow-clawed crayfish (Astacus leptodactylus) was examined by means of polymerase chain reaction (PC R) restriction fragment length polymorphism (RF LP) analysis of the cytochrome oxidase subunit I (COI) of mitochondrial DNA. A total of 194 adult specimens were collected from seven sample sites including, two in the south Caspian Sea and one each in Anzali wetland and Aras reservoir and three rivers Chafrood, Masule Rudkhan and S iah Darvishan. The PCR products were digested with 19 restriction enzymes and five enzymes revealed polymorphism patterns (DdeІ, MboІ, TaqI, RsaІ and HinfІ). Twenty eight composite haplotypes were showed with the number of haplotypes in each population sample ranging from 8 to 13. Private haplotypes were found at very low frequencies. Two regional (S iah Darvishan River and Astara) groups were clearly recognized by cluster and molecular variance model (AMOVA) analyses (P<0.0001). Each of these groups revealed dominant haplotypes while these haplotypes play less important rule in population structures of the other geographic areas. Intrapop ulatio n hap lo type (h) and nucleotide (π) diversities were high for each locality, ranging h=0.7560±0.030 and π=0.00334±0.00301, respectively. Results of this study discerned two divergent populations of narrow-clawed crayfish including S iah Darvishan River and Astara. Thus, the population structure of the narrow-clawed crayfish, as inferred from mtDN A analysis, is constituted by genetica lly separate groups that nearly reflect their geographic distribution.