Copy Number Variation And Genome-wide Association Analysis Of Color Traits Of Duck Feather

The feather colors of the poultry belong to the color traits of their skin derivatives,and is also one of the important phenotypic traits to be considered in the production of duck industry.It can not only be used as an important feature to distinguish duck varieties,and differentiate them from similar products with other appearance phenotypic traits,so that giving duck products greater market influence.At the same time,because the carcass of white feather duck after slaughtering is more beautiful,it also gives duck products stronger market competitiveness.Therefore,feather color,especially white feather,has been the focus of poultry breeding.Research on genes controlling feather color traits not only helps to understand the formation mechanism of skin colors,but also provides reference for related breeding work and improve breeding efficiency.In this study,the F2 resource population was used as the research object to analyze the copy number variation of feather color traits by whole genome re-sequencing and to construct CNV genetic map at duck whole genome level.At the same time,the genome-wide association analysis results of feather color traits based on CNV and a single SNP were combined to determine the causative CNV,SNP,and candidate genes and pathways associated with the feather color traits.The main findings of this study are as follows:1.The F2 resource group constructed with Runzhou Crested White Duck and Cherry Valley Duck as their parents,then the feather color phenotype of the F2 population was counted.Among the 308 individuals in the F2 group,there were 4 main kinds of feather color,among which there were 17 black ducks,97 white ducks,146 variegated ones,and the last 48 birds were gray.The re-sequencing results of 308 samples were detected using CNVcaller software,and a CNV genetic map at the duck genome level was constructed to help enrich the understanding of genetic variation in duck genome.The results showed that a total of 9,337 CNVRs were detected in the entire F2 population.The average length of CNVRs was 15,950 bp and the total length was 142.02 MB,accounting for approximately 12.91%of the wild duck genome.Among them,5,091 were increased,1,855 were absent,and 2,391 were compound.The number of copy number variation is positively correlated with chromosome length.CNV of the black and white populations of F2 groups were detected.As the result,A total of 6,881 CNVRs were detected in the pure black feather group.The average length of CNVRs were 18,344bp and the total length were 120.38Mb,accounting for about 10.94%of the wild duck genome,among which,3,655 were increased,1,578 were absent,and 1,648 were compound.A total of 6,539 CNVRs were detected in the pure black feather group.The average length of CNVRs were 19,138bp and the total length were 119.35 Mb,accounting for about 10.85%of the wild duck genome,among which,3,486were increased,1,622 were absent,and 1,431 were compound.Ten CNVRs were selected for qPCR verification,and the results showed that the accuracy rate was 90%,indicating that the accuracy of the detection results was good.2.Further CNV-based genome-wide association analysis of duck feather color traits was carried out.As the re sult,there was no CNVR at significant level,but two potentially related CNV sites were found.CNV1 is located at 4,422,401-4,424,400 on chromosome 25(P=4.80E-05),with a length of 2,000bp,whose type is deletion type.Its nearby genes are VWA5A,SDR39U1 and OR4N5.CNV2 is located at 8,313,601-8,316,400 on chromosome 10(P=9.99E-05),with a length of 2,800bp.Its type is deletion type,and nearby involved genes are MUSTN1,NEK4,GLT8D1 and ITIH4.3.In order to further discover genes related to feather color,a case-control-based single SNP genome-wide association analysis was performed on duck feather color traits.As the Result,8,423 SNP were associated with significant feather correlation,among which,a total of 4,649 sites annotated to 24 genes,which includes MITF,SUCLG2,FOXP1,TAFA1,FRMD4B,LRIG1,ARL6IP5,TMF1,MAGI1,ADAMTS9,SLC25A26,LMOD3,PRICKLE2,CHL1,UBA3,PDZRN3,CADPS,PPP4R2,EOGT,PLXNA1,RYBP,CNTN4,FAM107A and ITPR1.The highest point of SNP significantly associated with white feather traits is at the site of 17,814,522(-log10(P)=27.4828)at chromosome 10,which is on the introns of the MITF gene.In the F2 population,the population was verified for the insertion of introns on the MITF gene,and the skin and hair follicle tissues of individuals with different feather colors were collected for MITF-related quantitative analysis.The results show that the MITF gene of white feather individuals in the F2 population generally has intron insertions,and the expression level of the variable splicing junctions of the exons where the MITF sequence is inserted is extremely significantly lower in the white feather individuals than in the black feather individuals.Based on the genome-wide association analysis results of the feather color traits of CNV and SNP along with the verification results in the F2 population,the MITF gene is an important gene in the occurrence of the white feather trait of duck feather color.The insertion of introns on MITF in the F2 population is related to the white feather traits of ducks.VWA5A is predicted as a candidate gene for white plume traits of duck feathers,which involved in white plume traits by regulating MITF.And MUSTN1,GLT8D1 may be an alternative gene for the color traits of duck feathers,which has some impact on the plume color formation of ducks.These results provide a certain reference for the development of molecular genetic marker-assisted breeding and genomic selection breeding on poultry,and are also conducive to the development and utilization of feather color traits in subsequent poultry breeding.