Genome-wide Association Study On Body Shape And Growth Traits Of The Yellow River Carp

The common carp(Cyprinus carpio)is one of the most important aquaculture species in the world.It has important industrial value and scientific significance.The Yellow River carp is one of the most representative subspecies.The typical characteristics of the Yellow River carp are long spindle length and delicate meat quality.However,in recent years,due to germplasm degradation and other reasons causing large difference in somatotype characters,extreme somatotype such as slender type and spindle type affect the quality and market price of the Yellow River carp,and it is urgent to carry out the study on genetic mechanism of the Yellow River carp type characters.In this study,the type and genotyping of the the Yellow River carp family were measured and genotypes were carried out.The total genome of the carp and its growth traits in the Yellow River were studied in order to find the genes related to the shape and growth traits.Morphometry includes linear measurement and geometric morphometry.The emphasis and operation of different measurement methods are different.In this study,the linear measurement method and geometric shape measurement based on ground punctuation are used to measure the shape of the body and the correlation of growth,and the advantages and disadvantages of the two methods are compared.In this study,the size and growth data of 523 the Yellow River carp samples of 13 the Yellow River carp family members fed in the same environment and fed with the same feed were collected by linear measurement and geometric shape measurement based on ground punctuation.Geometric morphometry is used to collect data from the landmark points that describe the body shape of the sample,and the data of body length,body height,body thickness,weight,eye distance and net weight are collected by linear measurement.After analyzing the ground punctuation data,20 principal components were obtained.Among them,PC1~PC3 explained the geometric shape difference of more than 50% of the sample population.PC1~PC6 explained the geometric shape difference of more than 75%of the sample population,and PC1~PC10 explained the geometric shape difference of more than 90%of the sample population.The correlation coefficients of the main components and BL/BH were different,which were 0.06379,0.47485,0.21762,0.46255,0.14542,0.44985,of which the correlation between PC1 and BL/BH was the smallest.The results of the above analysis and linear measurement are taken as body characters,and the SNP genotypes obtained by the high throughput SNP typing chip of carp are analyzed by GWAS.Then the threshold is defined according to the results of GWAS,and the genes of the upper and lower 10 K of the SNP loci above the threshold are annotated,and 1850 genes are obtained.A number of candidate genes related to body shape and growth traits were screened out through literature research,including phosphatase,Ephrin,Fibroblast growth factor-binding protein,Somatostatin receptor,Fatty acid synthase,Transforming growth factor,Insulin-like growth factor 1 receptor and Bone morphogenetic protein receptor.In addition to the genes associated with growth and development,the annotated genes include many genes related to immune,neurophylogeny,cytoskeleton,transmembrane transport,and ion channels.GO and KEGG analysis of the annotated results were used to enrich the embryo development,anatomical structure morphogenesis,ephrin receptor activity,insulin receptor,and the epidermal growth factor receptor signaling pathway,phosphatase activity,fatty acid metabolism,cell-cell junction,cell cycle,and many other pathways related to growth.These genes and pathways play an important role in cell proliferation,inhibition of cell apoptosis,growth,muscle development,cell recognition,extracellular matrix precipitation,morphogenesis,limb development and cartilage formation.We selected the most important genes from the above results and conducted PCR & Sanger sequencing for further validation.Some SNPs with significant differences in frequency were found in the two populations with large and minimal traits,some of which resulted in changes in amino acid coding.These results not only elucidate the molecular mechanism of body shape and growth traits,but also provide more support for the breeding of Yellow River carp.