SNPs surpassing the suggestive significance level for muscle fat content and abdominal fat traits.

<p>SNPs surpassing the suggestive significance level for muscle fat content and abdominal fat traits.</p

Genome-Wide Association Study for Muscle Fat Content and Abdominal Fat Traits in Common Carp (<i>Cyprinus carpio</i>)

<div><p>Muscle fat content is an important phenotypic trait in fish, as it affects the nutritional, technical and sensory qualities of flesh. To identify loci and candidate genes associated with muscle fat content and abdominal fat traits, we performed a genome-wide association study (GWAS) using the common carp 250 K SNP assay in a common carp F₂ resource population. A total of 18 loci surpassing the genome-wide suggestive significance level were detected for 4 traits: fat content in dorsal muscle (MFdo), fat content in abdominal muscle (MFab), abdominal fat weight (AbFW), and AbFW as a percentage of eviscerated weight (AbFP). Among them, one SNP (carp089419) affecting both AbFW and AbFP reached the genome-wide significance level. Ten of those loci were harbored in or near known genes. Furthermore, relative expressions of 5 genes related to MFdo were compared using dorsal muscle samples with high and low phenotypic values. The results showed that 4 genes were differentially expressed between the high and low phenotypic groups. These genes are, therefore, prospective candidate genes for muscle fat content: ankyrin repeat domain 10a (<i>ankrd10a</i>), tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2 (<i>tanc2</i>), and four jointed box 1 (<i>fjx1</i>) and choline kinase alpha (<i>chka</i>). These results offer valuable insights into the complex genetic basis of fat metabolism and deposition.</p></div

Descriptive statistics of phenotypic data.

<p>Descriptive statistics of phenotypic data.</p

Relative mRNA abundance in the high and low dorsal muscle fat content groups.

<p>Relative expression levels were obtained by the 2^-ΔΔCT method; <i>18S</i> was used as normalizing controls. High group (n = 10) consisting of samples from common carp with the highest trait values and Low group (n = 10) with the lowest trait values; *, <i>P</i> < 0.05; ** <i>P</i> < 0.001.</p

Additional file 1: Table S1. of QTL variations for growth-related traits in eight distinct families of common carp (Cyprinus carpio)

Phenotypic correlations between growth-related traits in eight common. Table S2. List of suggestive (P < 0.05) and significant (P < 0.01) QTLs for body weight (BW) in eight common carp families based on half-sib analysis. Table S3. List of suggestive (P < 0.05) and significant (P < 0.01) QTLs for total length (TL) in eight common carp families based on half-sib analysis. Table S4. List of suggestive (P < 0.05) and significant (P < 0.01) QTLs for body thickness (BT) in eight common carp families based on half-sib analysis. (DOCX 123 kb

Transcriptome Analysis of Crucian Carp (<i>Carassius auratus</i>), an Important Aquaculture and Hypoxia-Tolerant Species

<div><p>The crucian carp is an important aquaculture species and a potential model to study genome evolution and physiological adaptation. However, so far the genomics and transcriptomics data available for this species are still scarce. We performed <i>de novo</i> transcriptome sequencing of four cDNA libraries representing brain, muscle, liver and kidney tissues respectively, each with six specimens. The removal of low quality reads resulted in 2.62 million raw reads, which were assembled as 127,711 unigenes, including 84,867 isotigs and 42,844 singletons. A total of 22,273 unigenes were found with significant matches to 14,449 unique proteins. Around14,398 unigenes were assigned with at least one Gene Ontology (GO) category in 84,876 total assignments, and 6,382 unigenes were found in 237 predicted KEGG pathways. The gene expression analysis revealed more genes expressed in brain, more up-regulated genes in muscle and more down-regulated genes in liver as compared with gene expression profiles of other tissues. In addition, 23 enzymes in the glycolysis/gluconeogenesis pathway were recovered. Importantly, we identified 5,784 high-quality putative SNP and 11,295 microsatellite markers which include 5,364 microsatellites with flanking sequences ≥50 bp. This study produced the most comprehensive genomic resources that have been derived from crucian carp, including thousands of genetic markers, which will not only lay a foundation for further studies on polyploidy origin and anoxic survival but will also facilitate selective breeding of this important aquaculture species.</p></div

Tuning the Coordination Microenvironment to Boost the Electrocatalytic HER Activity of M₃(C₆O₃S₃)₂

It is presently imperative to find efficient and practical catalysts for the hydrogen evolution reaction (HER) for hydrogen production with high efficiency. In this work, the catalytic HER activity of a class of two-dimensional (2D) metal–organic frameworks (MOFs), i.e., M3(C6O3S3)2 with M = Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Zr, Nb, Mo, Tc, Ru, Ta, W, and Re, is studied by using first-principles calculations. It is found that nonmetal atoms of the first coordination sphere to the central metal atom could be the active site for HER, and V3(C6O3S3)2 (ΔGH* = 0.02 eV, on V), Cr3(C6O3S3)2 (ΔGH* = −0.02 eV, on S, and ΔGH* = −0.05 eV, on O), and Cu3(C6O3S3)2 (ΔGH* = −0.03 eV, on S) are screened out as promising HER catalysts. To complete the picture of how the metal–ligand matching affects the activity, a different coordination microenvironment is considered by regulating the first coordination shell to, for example, the central V atom. It is of interest that the newly constructed moieties present high catalytic HER activity with ΔGH* almost zero, proving the significance of metal–ligand interaction. In view of these results, we propose a descriptor Δε↑↓ that correlates the local electronic structure and the catalytic HER activity. In short, our results not only identify a series of efficient HER electrocatalysts but also unravel the underneath factors that affect the activity and thus provide new insights into the rational design of catalysts for other reactions

KEGG biochemical mappings for crucian carp.

<p>KEGG biochemical mappings for crucian carp.</p

The abundance of transcripts involved in glycolysis and gluconeogenesis in four tissues.

<p>The abundance of transcripts involved in glycolysis and gluconeogenesis in four tissues.</p

Glycolysis/gluconeogenesis KEGG map populated with transcripts coding for corresponding enzymes.

<p>The enzymes identified are shown in red boxes and their abundances of transcripts in different tissues are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062308#pone-0062308-t006" target="_blank"><b>Table 6</b></a><b>.</b></p