In Silico Screening and Development of Microsatellite Markers for Genetic Analysis in Perca fluviatilis

Perca fluviatilis is an economically important species of freshwater fish. To understand the genetic structure of P. fluviatilis in China, 268 samples were collected from Wulungu Lake (WL), Jili Lake (JL), the Wulungu River (WR), and the Kalaeerqisi River (KR). These samples were then analyzed using microsatellite markers. A total of 98,425 microsatellite markers were developed based on the genomic data, and 29 polymorphic microsatellite markers were selected to analyze genetic diversity in this study. The number of alleles (Na) and observed heterozygosity (Ho) per population ranged from 4.621 (KR) to 11.172 (WL) and from 0.510 (KR) to 0.716 (JL), respectively. The results of the polymorphic information content (PIC) showed that the WL, JL, and WR populations were highly polymorphic (PIC≥ 0.5) and that the KR population was moderately polymorphic (0.25 ≤ PIC < 0.5). The genetic differentiation coefficient (Fst) among the four P. fluviatilis populations was 0.074, indicating moderate genetic differentiation among the populations in Xinjiang. The reason for the significant difference between the rivers and lakes could be the presence of a dam blocking the flow of P. fluviatilis. The development of microsatellite markers provides support for population genetics in the future. The evaluation of the genetic structure of P. fluviatilis in Xinjiang provides a reference for the reproduction and conservation of P. fluviatilis

Descriptive statistics of phenotypic data.

<p>Descriptive statistics of phenotypic data.</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

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

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

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