Genetic Linkage Map And QTL Analysis Of Growth-related And Meat Quality Traits In Common Carp

Common carp (Cyprinus carpio), a member of Cyprinidae, is one of the mostimportant aquaculture species in the world with an annual global production of3.4million metric tons, accounting for nearly14%of the all freshwater aquacultureproduction, which occupy an important role in world aquaculture industry. Commoncarp is also the major culture species in China, it is the aquaculture species thatcultivates 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 pastdecades. However, the meat quality and the taste of common carp are inferior to that ofpredacious fish and sea fish. With the increase of people’s consumption level, improvingmeat quality is not only the problem for livestock but also for aquaculture industryeither. Therefore, it is quite necessary to carry out meat quality traits selecting. But fishmeat quality is a very complex trait influenced a lot by environment, feed and nutrition,etc. The traditional selection breeding is unable to effectively solve the improvement oflow heritability such as meat quality trait while marker-assisted selection (MAS) makesit possible to select this type of trait.In the molecular breeding of fish, one primary premise is to obtain the associatedgenes or QTLs with the trait. It can be considered that the molecular breeding is basedon the genetic linkage map and the QTL locus affecting trait. Since the first generationgenetic linkage map of common carp was published in2000, the molecular breeding ofcommon carp has developed fast. The third generation genetic linkage map of commoncarp has been constructed and lots of QTL results has been characterized such as growth,feed conversation rate, physiology and biochemistry, etc. The early map, however, is inlow utilization rate due to few markers, large map distance, low resolution and coveragerates of genome, and adopt dominant marker (e.g.: RAPD, AFLP, etc.) with a fewmicrosatellite markers. The thesis focuses on the following two aspects: first, toconstruct a consensus genetic map using high resolution SNP and SSR markers andintegrated it with the existing linkage map in our laboratory. then, to carry out acomparative genome analysis with zebrafish genome. Second, to identify andcomparatively analyse the QTLs affecting growth and meat quality trait such as lipaseactive level, intramuscular fat percentage, muscular protein content, ash content, etc. byfull-sib families.The results as follows: (1) A total of1536SNP and300SSR markers were genotyped in3populationscontains443progenies, linkage analysis and genetic linkage maps were constructed byindividual population respectively, and then integrated with another linkage map (68population) which have been constructed in our lab. The consensus map contained678markers (421SNPs and257SSRs) distributed on42linkage groups ranging in sizefrom3.2to201.0cM. The map spanned a genetic distance of2371.6cM and averageinterval for markers within the linkage groups was approximately6.4cM, each groupcontained3-41markers, the average interval of groups ranging from1.4to24.1cM,and the largest interval of groups ranged from1.7to43.7cM, and the average markerofall groups was16, the map cover86.7%of common carp genome.(2) The sequences of microsatellite and SNP markers on the consensus linkagemap were used for sequence similarity searches against the genomes of five model fish,the results indicated that72.9%(489/671),30.6%（205/671）,28.9%（194/671）,25.2%（169/671）and26.8%（180/671）of common carp sequences had significant matchagainst the zebrafish (Danio rerio), fugu (Takifugu rubripes), Tetraodon (Tetraodonnigroviridis), medaka (Oryzias latips) and three-spined stickleback (Gasterosteusaculeatus) genome, respectively. There were77orthologous markers common in5model fish and common carp. Based on the blast results, comparative genome mapshave been constructed between zebrafish and common carp. Apart from10loci mappedto zebrafish scaffolds that were not assigned to a specific chromosome, the remaining479loci were all present in25zebrafish chromosomes. The average number of sharedmarkers was11.4, the length of the syntenic regions in the zebrafish genome map addedup to1173.7Mb, with a range of0.04to61.37Mb. About60%of the common carplinkage groups and zebrafish chromosomes kept a high degree of linear relationship,suggesting large blocks of conserved synteny between these chromosomes in the twospecies. Additional, the most striking characteristic of the comparative mapping of thecommon carp and zebrafish genome is that each zebrafish chromosome predominatelycomprised two common carp linkage groups. Therefore, we inferred that thechromosome relationship of common carp and zebrafish is2:1.(3) Quantitative trait locus analysis of body weight, standard length, body depthand body thickness based on4populations, a total of67growth-related QTLs wereobtained,34of which were significant QTLs. In additional, the consensus map wasused to compare the distribution and variation of those QTLs among populations, Theresults shows that growth-related QTLs distributes in a cluster and the major gene is thebasis of sharing QTL among populations; the study reveals the different geneticperformances between major gene and minor gene in different populations, therefore, aconclusion has been drawn that the major gene is changing and unfixed in populations, which provides the basis for a more reasonable QTL mapping.(4) A full-sib family contains190progenies were selected as mapping panel. Ofthe1515SSR markers scanned the whole genome were tested to construct geneticlinkage map,1172successfully amplified and had polymorphism. The markers defined931(21EST-SSRs) consisted of52groups uniquely mapped positions with averageinter-marker spacing of4.6cM. The map spanned a total of4060.1cM and the coveragewas88.3%. The genetic linkage groups were established with4-39markers, with theaverage span ranged from1.8to15.2cM, and the maker density was18of each group.The length of group ranged29.1to125.4cM. The largest marker interval was6.6-45.2cM. Seven groups were less than10markers.(5) Five QTLs were identified for lipase activity level with95%linkage groupsignificant level. The confidence interval was ranged from18cM to31.6cM, and theseQTLs explained10.5-17.7%of the phenotypic variation. Comparative to genomesequences of common carp, we added40SNP markers in the largest QTL region and15markers were integrated. The average interval inter-markers was from5.3to1.8cM,meanwhile, the confidence interval was dropped to7.5cM, accounting for25.9%of thephenotypic variance and at95%genome significant level.6candidate genes wereidentified through comparing to genome sequences of zebrafish and gene annotation inthe QTL region.(6)190microsatellite markers were selected from genetic linkage map constructedin this study to genotype522progenies from8full-sib families. Half-sib based mappingstrategy was adopted to identify QTL associated with4meat quality traits aboutintramuscular fat percentage, muscle protein percentage, ash content and water content.We obtained21QTLs druing sire-based and dam-based analysis. These QTLs were4for intramuscular fat percentage,4for muscle protein percentage,8for ash content and5for water content respectively. Moreover, we conducted QTL analysis usingsignificant families, the results showed that21QTLs were really existed on linkagegroups.