A genetic linkage map of common carp (Cyprinus carpio L.) was constructed using Type I and Type II microsatellite markers and a pseudo-testcross mapping strategy. The microsatellite markers were isolated from microsatellite-enriched genomic libraries and tested for their segregation in a full-sib mapping panel containing 92 individuals. A total of 161 microsatellite loci were mapped into 54 linkage groups. The total lengths of the female, male and consensus maps were 2,000, 946, and 1,852 cM, with an average marker spacing of approximately 13, 7, and 11 cM, respectively. Muscle fiber-related traits, including muscle fiber cross-section area and muscle fiber density, were mapped to the genetic map. Three QTLs for muscle fiber cross-section area and two QTLs for muscle fiber density were identified when considering both significant and suggestive QTL effects. The QTLs with largest effects for muscle fiber cross-section area and muscle fiber density were 21.9% and 18.9%, and they were located in LG3, respectively.

The adaptation of fish to low temperatures is the result of long-term evolution. Amur carp (Cyprinus carpio haematopterus) survives low temperatures (0-4°C) for six months per year. Therefore, we chose this fish as a model organism to study the mechanisms of cold-adaptive responses using high-throughput sequencing technology. This system provided an excellent model for exploring the relationship between evolutionary genomic changes and environmental adaptations. The Amur carp transcriptome was sequenced using the Illumina platform and was assembled into 163,121 cDNA contigs, with an average read length of 594 bp and an N50 length of 913 bp. A total of 162,339 coding sequences (CDSs) were identified and of 32,730 unique CDSs were annotated. Gene Ontology (GO), EuKaryotic Orthologous Groups (KOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to classify all CDSs into different functional categories. A large number of cold-responsive genes were detected in different tissues at different temperatures. A total of 9,427 microsatellites were identified and classified, with 1952 identifying in cold-responsive genes. Based on GO enrichment analysis of the cold-induced genes, “protein localization” and “protein transport” were the most highly represented biological processes. “Circadian rhythm,” “protein processing in endoplasmic reticulum,” “endocytosis,” “insulin signaling pathway,” and “lysosome” were the most highly enriched pathways for the genes induced by cold stress. Our data greatly contribute to the common carp (C. carpio) transcriptome resource, and the identification of cold-responsive genes in different tissues at different temperatures will aid in deciphering the genetic basis of ecological and environmental adaptations in this species. Based on our results, the Amur carp has evolved special strategies to survive low temperatures, and these strategies include the system-wide or tissue-specific induction of gene expression during their six-month overwintering period.

The strategies by which freshwater teleosts maintain acid-base homeostasis under alkaline stress are attractive and have been explored for a long time. In this study, a cyprinid fish that tolerates extremely alkaline environments (pH 9.6), Leuciscus waleckii, was used as a model to explore the molecular mechanisms of acid-base regulation. Using a lab-controlled alkaline challenge test and 454 sequencing, the transcriptomes of their gills and kidney were profiled and compared. mRNA profiling produced 1 826 022 reads, generated 30 606 contigs with an average length of 1022 bp, of which 19 196 were annotated successfully. Comparative analysis of the expression profiles between alkaline and freshwater L. waleckii habitats revealed approximately 4647 and 7184 genes that were differentially expressed (p < 0.05) in gills and kidney, respectively, of which 2398 and 5127 had more than twofold changes in expression. Gene ontology analysis and KEGG enrichment analysis were conducted. Comprehensive analysis found that genes involved in ion transportation, ammonia transportation, and arachidonic acid metabolism pathways changed dramatically and played important roles in acid-base homeostasis in fish under alkaline stress. These results support the existing hypotheses about candidate genes involved in acid-base regulation under alkaline stress and prompt several new hypotheses. The large transcriptome dataset collected in this study is a useful resource for the exploration of homeostasis modulation in other fish species.

No abstract