| Common carp(Cyprinus carpio L.)is one of the three major aquaculture freshwater species in the world,is also one of the major freshwater farming fish in China,the global annual production of C.carpio is about 4.16 million tons(FAO,2016).China is the largest common carp fanning and consuming country in the world,with annual production of 3.36 million tons,which accounted over 80%of world production.Common carp is the aquaculture species that cultivates the most varieties and strains with a long culturing history and high output,which contributed greatly to the development of China's aquaculture industry in the past decades.The growth trait controlled by numbers of genes,is also economic trait in Common carp,which has the direct relationships with the production and affect economic benefit directly.In this study,a high-dencity,high-resolution genetic linkage map of common carp(Cyprinus carpio L.)was constructed using microsatellite and single nucleotide polymorphism(SNP)markers in a full-sib family.The quantitative trait loci(QTL)affecting total weight(TW),full length(FL),standerd length(SL),body depth(BD)and body width(BW)was fine mapped and identified.The result will supply plenty of information and laid the theoretical foundation for genetic research of growth traits in common carp,and also the theoretical and scientific basis will facilitate the further study of the growth mechanism and marker assisted selection for common carp.The results as follows:(1)A high-density,high-resolution genetic linkage map of common carp was constructed using 1116 mirosatellite markers and 4026 SNP markers in a F1 full-sib family containing 107 progeies.A total of 978 microsatellite markers and 4877 SNP markers were mapped to 50 linkage groups.The number of markers per linkage groups varied from 32 to 166 with an average of 97.54.The linkage map spans approximately 4775.903 cM,ranging in size from 47.498 cM(LG38)to 191.62 cM(LG18),with an average intermarker distance of 0.989 cM.The genome size estimate for the common carp was 4784.555 cM resulting in 97.98%coverage of the genome.This linkage map should provides a valuable tool for validating and improving the common carp whole-genome assembly and facilitates fine-scale QTL mapping for genes associated with economically important traits(2)Based on the high-density,high-resolutin linkage map,quantitative trait locus(QTL)analysis of total weight(TW),full length(FL),standerd length(SL),body depth(BD)and body width(B W)was carried out using MapQTL software.A total of 425 growth-related QTLs were detected on thirty four linkage groups(LGs)in the common carp panel.Two hundred and fifty-seven significant QTLs,explained over 10%of the phenotypic variance,were distributed among four LGs(49 QTLs on LG38,46 QTLs on LG5,40 QTLs on LG6 and 29 QTLs on LG12).Nine significant QTLs,explained over 20%of the phenotypic variance,were distributed among two LGs(4 QTLs on LG6 and 3 QTLs on LG39).Ninty-one QTLs for TW were detected,explained 8.2%-28.9%of the phenotypic variance.Seventy-two QTLs for TL were detected,explained 8.4%-28.6%of the phenotypic variance.Sixty-two QTLs for SL were detected,explained 8.4%-24.1%of the phenotypic variance.Seventy-nineQTLs for BD were detetcted,explained 8.4%-46.2%of the phenotypic variance.One hundred and twenty-one QTLs for BW were detected,explained 8.4%-40.9%of the phenotypic variance.And the QTLs were clustered in major genomic blocks across 4 LGs,most notably LG5,LG6,LG12 and LG38.MapQTL software(Version 6.0)was used to analyze the QTLs for growth traits by single marker regression analysis.Result showed sixty markers were discovered related to growth traits in common carp.Twenty-five significant markers were responsible for two or more growth traits.CC7877 was found significantly associated with TW,SL,BD and BW.Comparative to genome sequences of common carp with QTLs for growth traits,fifty candidate genes related to growth traits were detected,such as G/H(growth hormone),TGF(transforming growth factor),FGF(fibroblast growth factors),VEGF(vascular endothelial growth factor)and GHRH(growth hormone-releasing hormone),distributing among LG5,LG 12 and LG38.(3)Correlation between Genotypes of eight microsatellite loci and growth trait was analyzed and verified using Germany mirror carp(Cyprinus carpio L.)breeding population with 338 F1 samples.Thirty-three alleles and 75 genotypes were detected.The correlation was analyzed using data of body weight,body length and genotypes.The results show that HLJ343 had a significant impact on body weight and length.In addition,there were three loci,HLJ319,HLJ302 and HLJE339,and they had a significant impact on body length.This analysis reveals that the four QTL loci had correlation with body weight and length in large samples of mirror carp.(4)The genetic diversity of selective population of Germany mirror carp(Cyprinus carpio L.)was analyzed using microsatellite markers.The number of effective alleles,observed heterozygosity,expected heterozygosity and polymorphic information content were determined.The Hardy-Weinberg equilibrium was checked by ?2 Test.A total of 50 alleles were identified on 12 microsatellite loci with polymorphism from 288 samples.The average number of alleles was 4.166 7 and the average number of effective alleles was 3.076 9,the average observed heterozygosity and expected heterozygosity was 0.416 4 and 0.658 2,respectively,the average polymorphic information content was up to 0.605 6.The results show that there is a reasonable genetic diversity among the selective population.The population accorded with Hardy-Weinberg equilibrium,but the heterozygote deficit of all twelve loci was detected due to greatly artificial selection pressures.These results suggested that the level of genetic diversity of the population should be maintained and inbreeding recession in the subsequent production and selection of the German mirror carp population should be avoided.(5)Genetic potential and the correlation between markers and economic traits(such as body weight,total length,body length)of selective population of Huanghe carp(C.c.haematopterus)was analyzed using 21 microsatellite markers.The number of effective alleles,observed heterozygosity,expected heterozygosity and polymorphic information content were determined.The Hardy-Weinberg equilibrium was checked by ?2 Test.A total of 122 alleles were identified on 21 microsatellite loci with polymorphism from 56 samples.The average number of alleles was 5.8095 and the average number of effective alleles was 3.3706,the average observed heterozygosity and expected heterozygosity was 0.5893 and 0.6578 respectively,the average polymorphic information content was up to 0.6108.The results showed that there is a high genetic diversity among the selective population.The population accorded with Hardy-Weinberg equilibrium.Eight markers were discovered that had significant impact(P<0.05)on 11 economic traits(such as body weight,total length,body length,body depth).CA2203 was related with body width,head width and caudal peduncle length significantly(P<0.01),CA1603 and CA1639 was related with snout length and canal peduncle depth respectively.The result of the study would be valuable for marker-assisted breeding and selective breeding. |
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