Dataset Information

Construction of Three High-Density Genetic Linkage Maps and Dynamic QTL Mapping of Growth Traits in Yellow River Carp (Cyprinus carpio haematopterus).

ABSTRACT: To provide the theoretical basis for researching growth, development, and molecular marker-assisted breeding of the economically important Yellow River carp (Cyprinus carpio haematopterus) using dynamic quantitative trait locus (QTL) mapping, we constructed three genetic linkage maps from 207 progeny using a new modified genotyping-by-sequencing method. The three maps contained 16,886, 16,548, and 7482 single nucleotide polymorphism markers, respectively, with an average interval of 0.36 cM, 0.45 cM, and 1.00 cM. We identified 148 QTLs related to four growth traits that were located on 25 chromosomes from three growth stages of Yellow River carp. A total of 32, 36, 43, and 37 QTLs were associated with body length, height, width, and weight, respectively. Among them, 47 QTLs were detected for only one growth trait in one stage, but all of the other QTLs were co-localized. Of the 14 main QTLs, 13 were located on chromosome 12, which suggests the presence of growth-related genes on this chromosome. We then detected 17 candidate genes within 50 K upstream and downstream of the 14 main QTLs. This is the first report of the dynamic QTL mapping of growth traits of Yellow River carp, and the results can be used in future studies of growth, development, and molecular-assisted breeding of this species.

SUBMITTER: Wang L

PROVIDER: S-EPMC8928983 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature

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Construction of Three High-Density Genetic Linkage Maps and Dynamic QTL Mapping of Growth Traits in Yellow River Carp (<i>Cyprinus carpio haematopterus</i>).

Wang Lei L Jia Songpeng S Zhang Yuxuan Y Jiang Shuhong S Chen Yuhan Y Chen Junping J Yu Miao M Zhang Lan L Qiao Zhigang Z Li Xuejun X

Current issues in molecular biology 20211217 3

To provide the theoretical basis for researching growth, development, and molecular marker-assisted breeding of the economically important Yellow River carp (<i>Cyprinus carpio haematopterus</i>) using dynamic quantitative trait locus (QTL) mapping, we constructed three genetic linkage maps from 207 progeny using a new modified genotyping-by-sequencing method. The three maps contained 16,886, 16,548, and 7482 single nucleotide polymorphism markers, respectively, with an average interval of 0.36 ...[more]

PMID: 34940134

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Project description:BACKGROUND:A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection for economic traits in aquaculture species. The Yangtze River common carp (Cyprinus carpio haematopterus) is one of the most important aquacultured strains in China. However, quite limited genetics and genomics resources have been developed for genetic improvement of economic traits in such strain. RESULTS:A high-resolution genetic linkage map was constructed by using 7820 2b-RAD (2b-restriction site-associated DNA) and 295 microsatellite markers in a F2 family of the Yangtze River common carp (C. c. haematopterus). The length of the map was 4586.56 cM with an average marker interval of 0.57 cM. Comparative genome mapping revealed that a high proportion (70%) of markers with disagreed chromosome location was observed between C. c. haematopterus and another common carp strain (subspecies) C. c. carpio. A clear 2:1 relationship was observed between C. c. haematopterus linkage groups (LGs) and zebrafish (Danio rerio) chromosomes. Based on the genetic map, 21 QTLs for growth-related traits were detected on 12 LGs, and contributed values of phenotypic variance explained (PVE) ranging from 16.3 to 38.6%, with LOD scores ranging from 4.02 to 11.13. A genome-wide significant QTL (LOD = 10.83) and three chromosome-wide significant QTLs (mean LOD = 4.84) for sex were mapped on LG50 and LG24, respectively. A 1.4 cM confidence interval of QTL for all growth-related traits showed conserved synteny with a 2.06 M segment on chromosome 14 of D. rerio. Five potential candidate genes were identified by blast search in this genomic region, including a well-studied multi-functional growth related gene, Apelin. CONCLUSIONS:We mapped a set of suggestive and significant QTLs for growth-related traits and sex based on a high-density genetic linkage map using SNP and microsatellite markers for Yangtze River common carp. Several candidate growth genes were also identified from the QTL regions by comparative mapping. This genetic map would provide a basis for genome assembly and comparative genomics studies, and those QTL-derived candidate genes and genetic markers are useful genomic resources for marker-assisted selection (MAS) of growth-related traits in the Yangtze River common carp.

Project description: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.

Project description:The pharmacokinetics and tissue distribution of enrofloxacin were determined in Yellow River carp (Cyprinus carpio haematopterus) reared at 20°C after single oral administration of enrofloxacin at 10 mg·kg-1 body weight (BW). Plasma, bile, and different tissue samples, including liver, kidney, gill, gut, and skin-muscle, were collected at predetermined times points. An HPLC method was developed to simultaneously determine the concentrations of enrofloxacin and its metabolite, ciprofloxacin. However, ciprofloxacin was only detectable in some liver samples with trace levels. Then the average enrofloxacin concentrations vs. time data were subjected to a non-compartmental analysis using WinNonLin 5.2 software. Multiple peaking profiles were observed in all enrofloxacin concentration-time curves. The peak concentration (Cmax) values were observed as 0.79, 1.01, 2.09, 2.85, 4.34, 10.78, and 13.07 μg·ml-1 (or g-1) in plasma, skin-muscle, gill, kidney, liver, bile, and gut, respectively, and the corresponding time to reach peak concentration (Tmax) was 8, 8, 1, 8, 1, 72, and 4 h, respectively. The values of elimination half-life (T1/2λZ ) of enrofloxacin in different tissues was in the following order: gill (291.13 h) > liver (222.29 h) > kidney (157.22 h) > plasma (129.44 h) > gut (91.47 h) > skin-muscle (87.77 h) > bile (86.22 h). The present results showed that enrofloxacin had a wide distribution in different tissues, however slow absorption and elimination in Yellow River carp. Additionally, enrofloxacin exhibited large distribution in bile, indicating that bile excretion might be the primary elimination route of enrofloxacin in Yellow River carp. A withdrawal period was calculated as 379.2 °C-day for single oral dosing of enrofloxacin at 10 mg/kg BW. Based on the calculated PK/PD indices of AUC/MIC or Cmax/MIC, the current enrofloxacin dosing regimen might have a positive therapeutic effect on the infection of Flavobacterium columnare, Aeromonas sobria, or Aeromonas hydrophila. However, the depletion study following multiple oral doses should be carried out in Yellow River carp reared at lower temperatures, and the withdrawal period should also be further calculated.

Project description:ObjectiveAs one of the most important environmental signals, photoperiod plays a crucial role in regulating the growth, metabolism, and survival of organisms. The photoperiod shifts with the transition of the seasons. The difference in photoperiod between summer and winter is the greatest under natural conditions. However, the effect of photoperiod on Huanghe carp (Cyprinus carpio haematopterus) was paid little attention. We investigated the impact of artificial manipulation of seasonal photoperiod on Huanghe carp by integrating growth performance, intestinal flora, and intestinal metabolome.MethodWe conducted an 8-week culture experiment with summer photoperiod (14 h light:10 h dark, n = 60) as the control group and winter photoperiod (10 h light:14 h dark, n = 60) based on the natural laws.ResultsWinter photoperiod provokes significant weight increases in Huanghe carp. The altered photoperiod contributed to a significant increase in triglyceride and low-density lipoprotein cholesterol levels and the gene expressions of lipid metabolism in the intestine of Huanghe carp. 16s rDNA sequencing revealed that winter photoperiod diminished intestinal flora diversity and altered the abundance. Specifically, the relative abundances of Fusobacteria and Acidobacteriota phyla were higher but Proteobacteria, Firmicutes, and Bacteroidetes phyla were reduced. Analogously, photoperiodic changes induced a significant reduction in the Pseudomonas, Vibrio, Ralstonia, Acinetobacter, and Pseudoalteromonas at the genus level. Additionally, metabolomics analysis showed more than 50% of differential metabolites were associated with phospholipids and inflammation. Microbiome and metabolome correlation analyses revealed that intestinal microbe mediated lipid metabolism alteration.ConclusionThe winter photoperiod induced intestinal flora imbalance and lipid metabolism modification, ultimately affecting the growth of Huanghe carp. This study provides new insights into the effects of seasonal photoperiodic alteration on the well-being of fish.

Dataset Information

Construction of Three High-Density Genetic Linkage Maps and Dynamic QTL Mapping of Growth Traits in Yellow River Carp (Cyprinus carpio haematopterus).

Publications

Construction of Three High-Density Genetic Linkage Maps and Dynamic QTL Mapping of Growth Traits in Yellow River Carp (<i>Cyprinus carpio haematopterus</i>).

Similar Datasets

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