Abstract
High density genetic linkage maps are essential for QTL fine mapping, comparative genomics and high quality genome sequence assembly. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,194 SNP markers on 14,146 distinct loci for common carp based on high-throughput genotyping with the carp 250 K single nucleotide polymorphism (SNP) array in a mapping family. The genetic length of the consensus map was 10,595.94 cM with an average locus interval of 0.75 cM and an average marker interval of 0.38 cM. Comparative genomic analysis revealed high level of conserved syntenies between common carp and the closely related model species zebrafish and medaka. The genome scaffolds were anchored to the high-density linkage map, spanning 1,357 Mb of common carp reference genome. QTL mapping and association analysis identified 22 QTLs for growth-related traits and 7 QTLs for sex dimorphism. Candidate genes underlying growth-related traits were identified, including important regulators such as KISS2, IGF1, SMTLB, NPFFR1 and CPE. Candidate genes associated with sex dimorphism were also identified including 3KSR and DMRT2b. The high-density and high-resolution genetic linkage map provides an important tool for QTL fine mapping and positional cloning of economically important traits, and improving common carp genome assembly.
Highlights
High density genetic linkage maps are essential for QTL fine mapping, comparative genomics and high quality genome sequence assembly
After further filtration with more stringent condition (SNPs calling rate greater than 95% and minor allele frequency (MAF) greater than 5%), a total of 87,323 single nucleotide polymorphism (SNP) markers were retained for further analysis (Supplementary Fig. S1)
For body length (BL), we identified neuropeptide FF receptor 1 (NPFFR1) and bone morphogenetic protein 10 (BMP10) genes from QTL qBL20, which was overlapped with qBW20c on LG20
Summary
High density genetic linkage maps are essential for QTL fine mapping, comparative genomics and high quality genome sequence assembly. We constructed a high-density and high-resolution genetic linkage map with 28,194 SNP markers on 14,146 distinct loci for common carp based on highthroughput genotyping with the carp 250 K single nucleotide polymorphism (SNP) array in a mapping family. Growth-related traits have been mapped and well-studied in many teleost fishes, such as rainbow trout[31], Asian seabass[32], salmons[33]; lymphocystis disease resistant traits in Japanese flounder have been successfully mapped and applied to marker-assistant breeding[34,35]; sex-determination traits have been localized in the genetic map by QTL mapping approaches in tilapia[36], halibut[37] and smooth half tongue sole[38] and so on. We decided to use the powerful genotyping tool and construct high-density linkage genetic map for common carp
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