QTL Mapping And Identification Of Related Molecular Markers For Growth Traits In Black Carp (Mylopharyngodon Piceus)

Black carp（Mylopharyngodon piceus）is a carnivorous fish among the bulk freshwater fish in China.In the artificial reproduction of black carp,due to the inappropriate artificial selection of the production unit,the bred black carp degenerates in terms of growth,disease resistance and other traits,resulting in a decline in the quality of germplasm,which seriously affects the sustainable development of black carp aquaculture.Therefore,in order to ensure the healthy,stable and sustainable development of black carp aquaculture,it is necessary to carry out genetic improvement and breeding of fine varieties of black carp.In this study,the first high-density genetic linkage map of black carp was constructed,and QTL mapping of body weight,body length,body width and body height was carried out for wild black carp in Hanjiang water system,and developed SNP associated with growth traits.Association analysis was performed using the developed SNP linked to growth-related QTL and phenotypic data,and dominant genotypes were found.Combined with previous studies,the reasons for the strong breeding potential of the Hanjiang population were analyzed from the perspectives of genetic diversity and historical dynamics.This study is expected to provide a reference for the future breeding of elite black carp and molecular marker-assisted breeding.The main contents are as follows:1.GBS library construction and high-throughput sequencing were performed on the Hanjiang mapping family.After a series of filtering steps,6211 SNPs with low sequence depth and missing data were remove.Finally,10,390 SNPs were finally retained for further analysis.A total of 4108 SNPs were successfully mapped into 24LGs.The average density of this map was 0.51 c M and the full length was 1708.531c M.According to the comparative genomics analysis,we found there were highly conserved synteny between the black carp and zebrafish genomes.Correlation analysis showed that there were extremely significant correlations among the four traits of body weight,body length,body width and body height.Using high-density linkage maps to mapping QTL which related to growth traits in black carp,a total of 17 QTL related to body weight,body length,body height,and body width were identified on 3 linkage groups（LG10,LG17,LG20）,explaining the phenotypes The value of variation（PVE）was between 10.9%and 15.5%.2.A Hanjiang Black carp population was reconstructed to explore the characteristics of SNP markers in the body weight QTL interval.Corresponding primers were designed according to the three molecular markers which closely linked with body weight and flanking sequence information and PCR amplification was performed.SNP typing was performed by Sanger sequencing.P_HW test was performed on the three SNP sites and the results showed that snp4197 did not conform to Hardy-Weinberg equilibrium.All genotype at the two polymorphic sites of the 288 progeny were counted,and multiple comparisons were made between different genotype at the SNP sites.The results showed that the dominant genotypes of body weight-related SNP loci snp8107and snp9562 were AG and GA,respectively.Diplotypes were constructed based on these two loci,and it was found that the diplotype composed of AA of snp8107 and GA of snp9562 had the highest average body weight,showing an advantage in body weight.The correlation analysis of body weight and body length showed that there was a very significant correlation between them.Therefore,it is possible to improve other traits by only change one of the four traits.3.The characteristics of growth-related molecular markers in different populations were explored by calculating allele frequencies,conducting genetic diversity analysis,determining base content and neutral detection.Combined with the results of previous studies,we reasoned that the molecular markers linked to the body weight QTL obtained in this study may be only associated with maximal body weight in different populations.Genetic diversity analysis was performed on three different populations of sequence fragments containing SNP loci.The results for the fragment containing snp8107 showed the haplotype diversity was 0.782 in the Hanjiang population,0.497 in the Shishou population and 0.515 in the Xiangjiang population;For the snp9562fragment haplotype diversity was 0.508 in Xiangjiang population,0.48 in Shishou population,and 0.239 in Hanjiang population.The D values of the neutral test were all greater than 0 and reach a significant level,indicating that the three populations may have experienced a bottleneck effect in history.This resulted in a large population reduction and the loss of rare alleles.Subsequently,due to the improvement of environmental factors and others,the population number was increased and gene frequencies were also changed.Combined with genetic diversity analysis and neutrality test,it is speculated that more rare alleles may be retained in the Hanjiang population when it experiences the bottleneck effect.So,the Hanjiang population has a good genetic breeding potential.