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

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

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

SLAF-seq: An Efficient Method of Large-Scale <em>De Novo</em> SNP Discovery and Genotyping Using High-Throughput Sequencing

<div><p>Large-scale genotyping plays an important role in genetic association studies. It has provided new opportunities for gene discovery, especially when combined with high-throughput sequencing technologies. Here, we report an efficient solution for large-scale genotyping. We call it specific-locus amplified fragment sequencing (SLAF-seq). SLAF-seq technology has several distinguishing characteristics: i) deep sequencing to ensure genotyping accuracy; ii) reduced representation strategy to reduce sequencing costs; iii) pre-designed reduced representation scheme to optimize marker efficiency; and iv) double barcode system for large populations. In this study, we tested the efficiency of SLAF-seq on rice and soybean data. Both sets of results showed strong consistency between predicted and practical SLAFs and considerable genotyping accuracy. We also report the highest density genetic map yet created for any organism without a reference genome sequence, common carp in this case, using SLAF-seq data. We detected 50,530 high-quality SLAFs with 13,291 SNPs genotyped in 211 individual carp. The genetic map contained 5,885 markers with 0.68 cM intervals on average. A comparative genomics study between common carp genetic map and zebrafish genome sequence map showed high-quality SLAF-seq genotyping results. SLAF-seq provides a high-resolution strategy for large-scale genotyping and can be generally applicable to various species and populations.</p> </div

SLAF-seq data summary for common carp F1 population.

<p>SLAF-seq data summary for common carp F1 population.</p

Pilot SLAF-seq data analysis using rice and soybeans.

<p>(a)and(b) Insert size distribution of SLAFs. SLAF length was found to cluster tightly around a mean of 430 bp, with 85% of SLAFs in the centermost 50 bp. (c) and (d)Distribution of SLAFs on the chromosomes. SLAFs were evenly distributed on the chromosomes in rice and soybeans. The gap in the middle was caused by the absence of centromere sequences. (e)and(f) Customized SLAF density design. In the rice pilot case, the density was designed using 20 kb per SLAF. In soybeans, 40 kb per SLAF was used. Both rice and soybean pilot SLAF data were found to be consistent with theoretical predictions.</p

Genetic map validation by recombination mapping.

<p>Each two rows represent a genome in a CP population including 211 progenies and 2 parents. Columns correspond to chromosomes. Red and blue shading indicate maternal or paternal haplotype, respectively. Pink shading indicates ambiguous haplotypes, and grey shading indicates missing data. Only 1.51% of the markers were found in small recombination blocks.</p

SLAF-seq flowchart.

<p>i) Pre-design scheme for SLAF selection using training data. The reduced representation design must be decided based on marker efficiency characteristics, which include random distribution throughout the genome, uniqueness in the genome, and consistent amplification efficiency among selected markers. A pilot experiment was performed to evaluate the amplification efficiency based on the pre-designed scheme. ii) SLAF-seq library construction. Genomic DNA was digested by groups of enzymesdesigned for individuals. Double barcodes were added to two round PCR reactions to discriminate each individual and to facilitate the pooling of samples for size selection, which maintained consistent fragment size among individuals. iii) Deep sequencing for the pooled RRLs with the Illumina paired-end sequencing protocol, and genotype definition and validation by software.</p