- Construction of a high-density genetic map and mapping of growth related QTLs in the grass carp (Ctenopharyngodon idellus). - Background: Grass carp (Ctenopharyngodon idellus) are important species in Asian aquaculture. - A draft genome for grass carp has already been published in 2015. - There no growth related QTLs of grass carp have been published yet.. - Even the growth trait is one of the focuses in grass carp culture.. - The total length of the consensus map is 5553.43 cM with the average marker interval of 1.92 cM. - The map has a good collinearity with both the grass carp draft genome and the zebrafish genome, and it assembled 89.91% of the draft genome to a chromosomal level. - Finally, 17 genes located in these regions were considered to be growth-related because they either had functional mutations predicted from the resequencing data of the parents.. - Conclusion: A high density genetic linkage map of grass carp was built and it assembled the draft genome to a chromosomal level. - Thirty growth related QTLs were detected. - The grass carp (Ctenopharyngodon idellus) belongs to the Cyprinidae family and is the only species of the genus Ctenopharyngodon. - As one of the most important freshwater-cultured fish, the global production of grass carp was approximately 5.8 million tons, accounting for. - Currently most studies about grass carp focused on fish immunity [2–4], nutrition [5–7], and stress resistance [8]. - A few growth-related studies in grass carp were fo- cused on the impacts of the additives, dietary, or the growth hormones [9]. - 1 Institute of Hydrobiology, the Chinese Academy of Sciences, Wuhan, China Full list of author information is available at the end of the article. - As early as in the first few years of the new century, QTL research was applied to investigate the body weight trait in rainbow trout (Oncorhynchus mykiss) [10], the first economic fish with genetic linkage mapping [11]. - In recent years, QTL studies on growth-related traits were reported in some of the main farmed species in China, e.g., common carp (Cyprinus carpio) [14] and bighead carp (Hypophthal- michthys nobilis) [15]. - However, there is no similar re- search in the grass carp as yet.. - The SNP calling and geno- typing have become feasible in grass carp since the pub- lication of the draft genome [23].. - A high-density genetic linkage map can provide a more precise localization of the loci related to target traits and mount more genomic. - The first genetic linkage map of grass carp has a low density with 279 markers [32]. - In this study, a high-density genetic linkage map was constructed as a chromosome framework for the draft genome assembling and it mounted 89.91% of the gen- ome sequences, much higher than the mounting rate (64%) of the first genetic map. - The markers were distributed over 610 supercontigs, which covered 93.47% of the grass carp draft genome. - The construction of the linkage map. - Since the ML distance was longer than the regression one, the length of linkage groups obtained were generally lon- ger than that of other maps generated throughthe regres- sion algorithm included the first grass carp genetic maps [32].. - All 6429 markers were distributed on 605 supercon- tigs with a total length of 0.81 Gb, 89.91% of the grass carp draft genome. - The 99 supercontigs, covering 642 Mb (74.39%) of the total length, were longer than the 573 Mb used previously [23]. - These SNPs showed a good macro- collinearity between grass carp and zebrafish (Fig. - Table 1 Summary statistics of the sex-averaged linkage map of grass carp. - QTL mapping of growth-related traits. - It was revealed that all of the traits showed a high correlation (p <. - qBW1b was located on LG2 (at cM), which accounted for 20.9% of the phenotypic variance (PVE). - QTL qBL5b was located on the same place as QTL qBW1b, and it accounted for 19.2% of the PVE. - The QTL with the highest LOD value was qTL14b, which was located on LG18 (at cM), accounting for 21.6% of the PVE. - The highest LOD (4.26) was found for QTL qBH15b and qBH 17, which explained 17.8% of the PVE.. - 1 The concensus genetic map and growth-related QTLs of the grass carp. - The start and end sites of the GRs were makerd by the QTL adjacent SNPs. - The endpoints of the eight GRs were located on the same supercontigs, such as qBW1a (Table 2). - The colinearity of the genetic maps and the draft genome The high-density linkage maps provide chromosomal frameworks for genome assembly validation. - 45 of the anchored supercontigs were reversed in direction compared to other supercontigs. - Most of the of supercontigs, were Table 2 The statistics of QTLs. - This is because of the lack of paren- tal linkage phase information, which can only be esti- mated by the offspring data with the introduction of. - 2 The colinearity of the genetic maps with the genome of grass carp and zebrafish. - a The colinearity of the LGs to the 99 supercontigs in the genome of grass carp. - The synteny analysis result of the LGs to zebrafish genome. - The five LGs which were located growth-related QTLs. - Table 3 The Statistic of Growth-related candidate genes with mutations. - The male, female and consensus map of grass carp were constructed through the ML algorithm and the regression algorithm was used in other fish. - The missing genotype of offspring in the SNPs would bring adverse effects to the accuracy of map dis- tances, so the means of the missing genotypes in the markers on each LGs were calculated. - In order to find out a reasonable explanation, all markers of LG5 were evaluated based on two versions of the grass carp genome: one was published online [23]. - It is well known that it is difficult to as- semble sequences (fragment seqs) generally because of the repeated sequences, DNA secondary structure and other factors. - The number of fragment seqs located in each LGs of the concensus map were counted (Fig. - The long sequencing reads and the homozygous genome made it easier to conquer the problem of the repeated regions than the published gen- ome version. - The growth-related QTL in the grass carp. - QTL mapping is one of the important applications of genetic mapping. - The current research on growth-related traits of QTL mapping is mainly concentrated on the Atlantic salmon, rainbow trout, perch, common carp and tilapia in Asia, the growth of grass carp QTL positioning characters are rarely reported. - In this study, 30 growth-related QTLs were identified by analyzing 4 growth-related phenotype data and high-density genetic linkage maps of grass carp.. - The reason for this result might be the high correlation coefficients among the 4 traits in grass carp. - The candidate genes of the growth-related QTL. - However, we did not find any intersection between the candidate genes of grass carp and the genes of the growth-related QTLs reported in salmonid fishes [38]. - different parent of the same species) have their unique alleles leading to differential growth in offsprings.. - However, some of the candidate genes in our re- search have been shown to be directly or indirectly related with the growth trait. - NOS2b protein in fish has a myristoylation consen- sus site at the extremity of the N-terminal, and is similar to mammal NOS3, which catalyze NO and mediates vas- cular endothelial growth factor (VEGF)-induced angio- genesis in coronary vessels [46]. - A high-density genetic linkage map of grass carp was built. - The map’s correctness is supported by the good collinearity with both the grass carp draft genome and the zebrafish genome, and its effectiveness is demon- strated by the mounting rate which is much higher than the first map. - A total of 30 growth related QTLs were detected, and 17 candidate genes were obtained from a cross analysis of the resequencing data from parent fishes, while the genes located on the QTLs without sep- arable or effective SNPs were excluded.. - In order to select a suitable mapping population, the fin samples of 89 grass carp parents were captured from. - 3 The number of abnormal tags in each of the LGs. - The PCR products were geno- typed through ABI3730 (ABI, USA) and the matrix of PCR band sizes of the 89 samples on all 11 SSRs were ob- tained. - Quality control was used in order to remove low-quality and non-restriction site tags (Table S6), then the parents’ data was mapped to the grass carp draft genome using SOAP2 with default values for all parameters. - Markers were screened out as the preliminary SNP tags from the progenies’ reads by two criteria: (1) the markers were genotyped successfully in at least 80% of the pro- genies. - (2) the markers were heterozygous in both of the parents.. - In order to eliminate the errors which might be intro- duced into the uniqueness of markers by any single soft- ware, the preliminary SNP tags were mapped to the grass carp genome using bowtie (v1.2) [49] and bowtie 2 (v respectively with default parameters, reads with more than 2 mismatches or Indels in any mapping were excluded. - An in- house python script was written to complete this process, in which markers with missing genotypes in some of the fish offsprings are allowed.. - The synteny analysis of grass carp draft genome and zebrafish. - During the process of the synteny analysis of zebrafish, markers located on the grass carp genetic map were mapped to the zebrafish genome (GRCz10) using bowtie and bowtie 2 with default parameters to exclude re- peated tags which can be mapped on multiple locations.. - Obtainment and analysis of parents resequencing data After the DNA sequencing libraries were constructed with an insert size of 300 bp and paired-end sequenced on an Illumina Xten sequencer, the data of the parents was obtained. - Then the filtered reads were mapped to the grass carp draft genome with BWA (version: 0.7.12). - 4 The hierachical clustering tree of the 89 grass carp parents based on SSR polymorphism. - This research was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (Grant No. - The sampling and subsequent experiments were approved by the Animal Care and Use Committee of the Institute of Hydrobiology, the Chinese Academy of Sciences.. - Identification of grass carp haemorrhage virus as a new genogroup of aquareovirus. - Evaluation of internal control genes for qRT-PCR normalization in tissues and cell culture for antiviral studies of grass carp (Ctenopharyngodon idella). - Grass carp (Ctenopharyngodon idella ) STAT3 regulates the eIF2 alpha phosphorylation through interaction with PKR. - Effect of dietary lipid level on growth, feed utilization and body composition by juvenile grass carp (Ctenopharyngodon idella). - The influence of feeding rate on growth, feed efficiency and body composition of juvenile grass carp (Ctenopharyngodon idella). - Isolation and partial characterization of pepsin-soluble collagen from the skin of grass carp (Ctenopharyngodon idella). - Expression of grass carp growth hormone in the yeast Pichia pastoris. - An ultra-high density linkage map and QTL mapping for sex and growth-related traits of common carp (Cyprinus carpio). - "A high-density genetic map and growth related QTL mapping in bighead carp (Hypophthalmichthys nobilis).". - Effects of sample size and loci number on genetic diversity in wild population of grass carp revealed by SSR. - Isolation and characterization of 25 novel EST-SNP markers in grass carp. - Detection of EST-SSRs markers and genetic structure of different populations of grass carp in Yantze River system. - "The grass carp genome database (GCGD): an online platform for genome features and annotations.". - Development and evaluation of the first high-throughput SNP array for common carp (Cyprinus carpio). - The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation. - Construction of the first high-density genetic linkage map of pikeperch (Sander lucioperca) using specific length amplified fragment (SLAF) sequencing and QTL analysis of growth-related traits. - "A consensus linkage map of the grass carp (Ctenopharyngodon idella) based on microsatellites and SNPs.". - A retrospective assessment of the accuracy of the paternity inference program CERVUS. - A microsatellite genetic map of the turbot (Scophthalmus maximus)
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