Development and evaluation of the first high-throughput SNP array for common carp (Cyprinus carpio)

BACKGROUND: A large number of single nucleotide polymorphisms (SNPs) have been identified in common carp (Cyprinus carpio) but, as yet, no high-throughput genotyping platform is available for this species. C. carpio is an important aquaculture species that accounts for nearly 14% of freshwater aquaculture production worldwide. We have developed an array for C. carpio with 250,000 SNPs and evaluated its performance using samples from various strains of C. carpio. RESULTS: The SNPs used on the array were selected from two resources: the transcribed sequences from RNA-seq data of four strains of C. carpio, and the genome re-sequencing data of five strains of C. carpio. The 250,000 SNPs on the resulting array are distributed evenly across the reference C.carpio genome with an average spacing of 6.6 kb. To evaluate the SNP array, 1,072 C. carpio samples were collected and tested. Of the 250,000 SNPs on the array, 185,150 (74.06%) were found to be polymorphic sites. Genotyping accuracy was checked using genotyping data from a group of full-siblings and their parents, and over 99.8% of the qualified SNPs were found to be reliable. Analysis of the linkage disequilibrium on all samples and on three domestic C.carpio strains revealed that the latter had the longer haplotype blocks. We also evaluated our SNP array on 80 samples from eight species related to C. carpio, with from 53,526 to 71,984 polymorphic SNPs. An identity by state analysis divided all the samples into three clusters; most of the C. carpio strains formed the largest cluster. CONCLUSIONS: The Carp SNP array described here is the first high-throughput genotyping platform for C. carpio. Our evaluation of this array indicates that it will be valuable for farmed carp and for genetic and population biology studies in C. carpio and related species

Chromosome-level genome assembly of the largefin longbarbel catfish (Hemibagrus macropterus)

The largefin longbarbel catfish, Hemibagrus macropterus, is an economically important fish species in southwestern China, with males growing faster than females. This study presents a high-quality chromosome-level genome assembly of the largefin longbarbel catfish, generated by integrating Illumina short reads, PacBio HiFi long reads, and Hi-C data. The assembled genome size was 858.5 Mb, with a contig and scaffold N50 of 5.8 Mb and 28.4 Mb, respectively. A total of 656 contigs were successfully anchored to 30 pseudochromosomes with a BUSCO score of 97.7%, consistent with the number of chromosomes analyzed by karyotype. The genome contained 29.5% repeat sequences, and a predicted total of 26,613 protein-coding genes, of which 25,769 (96.8%) were functionally annotated in different databases. Evolutionary analysis showed that H. macropterus was most closely related to H. wyckioides, with a divergence time of approximately 16.3 million years. Chromosomal syntenic relationships among H. macropterus, H. wyckioides, and Pelteobagrus fulvidraco revealed a one-to-one relationship for most chromosomes, except for break, fission, and inversion of some chromosomes. The first high-quality reference genome will not only provide a valuable genetic resource for the study of sex determination mechanisms and genetic breeding of largefin longbarbel catfish, but also contribute to comparative analyses of genome and chromosome evolution within Siluriformes

Dietary Epigallocatechin-3-Gallate (EGCG) Improves Nonspecific Immune Response of Chinese Rice Field Eel (Monopterus albus)

Epigallocatechin-3-gallate (EGCG) has been recognized as a potential additive for aquafeeds due to its beneficial biological functions. In order to evaluate the potential application of EGCG in Chinese rice field eel (Monopterus albus), six isonitrogenous and isolipidic diets containing 0, 25, 50, 100, 200, and 400 mg/kg EGCG were formulated and were fed to Monopterus albus (M. albus) for 9 weeks. The results showed that M. albus fed diets containing 0 and 100 mg/kg EGCG presented higher weight again and specific growth rate than the other groups. Fish fed with 25, 50, and 400 mg/kg EGCG displayed lower whole-body lipid content. Serum aspartate aminotransferase (AST) concentration significantly decreased in EGCG treated groups with the exception of 100 mg/kg group. Hepatic catalase (CAT) activity and glutathione (GSH) concentration decreased as EGCG level increased while malondialdehyde (MDA) concentration showed an opposite trend. EGCG supplementation resulted in a promoted lysozyme (LZM) activity and immunoglobulin M (IgM) level in the liver of M. albus. Furthermore, transcription of three immune related genes including major histocompatibility complex (mhc-2α), hepcidin, and interleukin-8 (il-8) mRNAs was upregulated by EGCG treatment; while transcription of interleukin-6 (il-6) and nuclear factor kappa-B (nf-kb) genes was downregulated. Results also showed a linear relation between EGCG inclusion level and parameters of AST, CAT, GSH, MDA, LZM, IgM, and immune-related genes transcriptions. In summary, it could be suggested that EGCG supplementation enhanced the nonspecific immune response of the Chinese rice field eel. Based on the broken-line regression analysis of IgM, the optimal dietary EGCG supplementation for M. albus was estimated to be 109.81 mg/kg

Phosphorus Absorption and Excretion in Hybrid Sturgeon (<i>Huso dauricus</i><i>♀</i> X <i>Acipenser schrenckii</i><i>♂</i>) Intubated with Different Ca/P Ratios

To study the effect of Ca/P ratio on the P and Ca absorption and excretion in hybrid sturgeon (Huso dauricus♀ X Acipenser schrenckii♂), five groups of fish were intubated with 100 mg P·kg−1 BW with the Ca/P ratios of 0:1, 0.25:1, 0.5:1, 1:1, and 2:1. Plasma P concentrations were significantly elevated at Ca/P ratios below 2:1, and the highest value was obtained at Ca/P ratio of 0.5:1. Plasma Ca content was significantly increased at the highest Ca/P ratio. Urine P excretion rate in the fish intubated with Ca/P ratio of 0.5:1 was significantly higher than that of the groups with Ca/P ratios of 0:1 and 2:1. The highest urea excretion rates were observed at Ca/P ratio of 0.5:1 and 1:1. The total P excretion at 48 h post intubation reached about 30 mg·kg−1 BW, which was recorded for the group with Ca/P ratio of 0.5:1. The present study showed that P absorption efficiency was improved in hybrid sturgeon at Ca/P ratio of 0.5:1, indicating that P inclusion level in sturgeon feed can be further optimized to reduce dietary P input and lower the excessive undigested P discharge into the rearing water

Variability in the protein profiles in spermatozoa of two sturgeon species.

Conventional sperm analysis (i.e., motility and fertility) has been used to evaluate sperm quality. Understanding the quality of sperm on the molecular level in the sturgeons, Acipenser baerii and A. schrenckii, is essential for the improvement of the conservation of genetic resources and farming performance. In this study, we used the iTRAQ proteomics approach to perform proteomic profiling of spermatozoa associated with sperm quality in sturgeons (Data are available via ProteomeXchange with identifier PXD006108). The results showed 291 and 359 differentially expressed proteins in A. baerii and A. schrenckii, respectively, of which 72 were common to both species and all were upregulated in high quality compared with low quality samples. The differentially expressed proteins were mainly categorized into the generation of precursor metabolites and energy and oxidation, and they were localized to the mitochondria. Three distinguishing pathways, Arginine and proline metabolism, Pyruvate metabolism and the Citrate cycle (TCA cycle) were found to play an important role in energy metabolism, and some substrates could be used in the sperm medium for storage and cryopreservation. The quantity levels of two proteins, CKMT1 and LDHB, were verified by western blot analysis. Moreover, other potential biomarkers involved in oxidation reduction, ubiquitin-proteasome-dependent proteolysis, chaperones and binding activity were also discussed. Our study is the first to use the iTRAQ-based proteomics approach to analyse the sturgeon spermatozoa proteome, and the results that we obtained are valuable for the prediction of sperm quality and reproduction management in these threatened species

Real-time PCR confirmation of the relative expression of genes showing differential expression between the two gonad types.

<p>^a The relative-fold expression determined by Illumina transcriptome analysis.</p><p>^b The relative-fold expression validated by qRT-PCR.</p><p>O/T: The relative transcription level of genes in ovary compared to that in testis. O, Ovary; T, Testis.</p><p>Real-time PCR confirmation of the relative expression of genes showing differential expression between the two gonad types.</p

Functional annotation of unigenes of the <i>Acipenser sinensis</i> transcriptome.

<p>Functional annotation of unigenes of the <i>Acipenser sinensis</i> transcriptome.</p

Transcriptome comparison of three sturgeon species.

<p>^a Female gonad with heterogametic sex</p><p>^b Contigs for female assembly with combined reads of the ovary and the female gonad with heterogametic sex</p><p>Transcriptome comparison of three sturgeon species.</p