| Domestication is the largest population genetics study in the world in terms of time span and scale.During the long history of domestication,plants and animals have formed varieties with significant differences from genetic level,physiological level and phenotypic level due to the ecological environment they are in,the purpose of domestication and migration.Research on the differences between wild and domesticated species and different breeds can help resolve the genetic basis of domestication from wild to domesticated animals,help reveal the genetic basis of different phenotypes,help solve the problems encountered in molecular breeding,genetic improvement and the creation of new breeds in modern agriculture,and provide a theoretical basis for breaking through the "neck" of the seed industry.The study will provide a theoretical basis for breaking through the "neck" of the breeding industry.As one of the most widely distributed and highly cultured poultry in the world,the duck provides a rich material resource for human life.However,questions about the domestication origins of ducks,the genetic basis of colour traits,the genetic basis of meat quality,the genetic variation in feed efficiency and the genetic basis of some other specific phenotypes have not yet been resolved.In order to elucidate the genetic mechanisms underlying these questions,this study resequenced 648 ducks from 32 breeds(22 Chaohu ducks,20 Runzhou crested white ducks,20 Guangxi lesser sesame ducks,3 Gaoyou ducks,25 Ji’an red ducks,25 Jinding ducks,21 Jinyun sesame ducks,21 Liancheng white ducks,27 Longsheng cui ducks,24 Ma Wang ducks,87 Peking ducks,26 Putian black ducks,19 Putian white ducks,23 Shan sesame ducks,24 Sansui ducks,38 Shaoxing ducks,22 Taiwan brown ducks,23 Youxian ducks,22 Zhongshan ducks,5 Pakistani native ducks,4 Bangladeshi native ducks,5 Cambodian native ducks,2 Laotian native ducks,5 Vietnamese native ducks,19 hybrid offspring of Liancheng white ducks and white-kai ducks,19 Chinese Spotted-billed ducks(Anas zonorhyncha),4 Gadwall ducks(Anas strepera),6 Green-winged ducks(Anas crecca),6 Falcated Duck(Anas falcata),74 Mallards(Anas platyrhynchos),3 Pintailed ducks(Anas acuta),and 4 Muscovy ducks)and systematically analyzed the phylogenetic evolution of ducks as well as candidate regions and genetic variation mining for economically important traits,with the following main findings:1.Based on the Illumina PE150 sequencing platform,648 ducks from different breeds were re-sequenced and a total of 9.9 TB of valid sequencing data were obtained,generating an average of 15.49 Gb of data per individual,with an average sequencing depth of 12.31X and over 90%of Q20 and Q30.A total of 13,260,735 high-quality SNPs were detected after filtering by comparison with the duck reference genome(ASM874695v1),and the most comprehensive genome-wide genetic variation map of ducks(DMap1)was constructed.2.The ducks were divided into two main groups,Wild Clade I,comprising part of the mottled duck and part of the green-headed mallard,together with pintails,green-winged ducks,roan ducks and ruddy ducks,and Wild Clade II,comprising the remaining mottled ducks and the remaining green-headed mallard.Population structure,principal component analysis(PCA)and population downscaling also support the results of the phylogenetic tree.The results of the genetic parameter-based analysis showed that Pintails,Green-headed Mallards and Speckled Ducks are less separated from domestic ducks,with Green-headed Mallards and Speckled Ducks as the generally accepted origins of domestic ducks and Pintails as a possible alternative origin of domestic ducks.Gene flow analyses show long term gene penetration and mixing between all domestic ducks,but there is still some territoriality,which may be due to more than a thousand years of intra-regional inter-breeding.Previous studies have only identified the Green-headed Mallard and Spotted Duck as the ancestors of the domestic duck,but this study also found gene flow from Pintails to Pakistani and Bangladeshi native ducks.These results support the possibility of multiple origins and multiple domestication sites,not just for the Spotted and Green-headed Mallards,but also for Pintails as a possible origin of the domestic duck,or for domestication with introgression from different groups of Pintails.However,further archaeological and other evidence is needed to support this,and the time of domestication of the domestic duck is essentially the same as in the previous study,around 2500 to 3000 years.3.By detecting regions and genes that were selected for during domestication in domestic ducks relative to six species of mallard.A total of 699 domestication-mediated candidate regions containing 300 protein-coding genes were detected between Ruddy-backed and domestic ducks;388 candidate regions containing 217 protein-coding genes were identified between Green-winged and domestic ducks;282 candidate regions containing 141 proteincoding genes were identified between Ruddy-backed and domestic ducks;1179 candidate regions containing A total of 1,179 protein-coding regions containing 378 protein-coding genes were identified between the gadwall and domestic duck;1,798 protein-coding regions containing 661 protein-coding genes were identified between the pintail and domestic duck;and 1,746 protein-coding regions containing 545 protein-coding genes were identified between the green-headed mallard and domestic duck.A total of 36 domestication-mediated candidate regions containing 23 genes were identified in domestic ducks relative to all mallards.The results of KEGG and GO enrichment analyses showed that most genes were enriched in protein metabolism,neuronal and carbohydrate metabolism and synthesis pathways.4.The crested cushion trait is a characteristic trait of the Chinese crested duck.To resolve the genetic basis of the crested cushion trait,this study identified four shared candidate regions(CDRs)based on selection signal analysis of 644 re-sequenced ducks from different breeds,and 48 CDRs involving 46 genes based on selection signal analysis of the F2 resource population.A total of 8,208 SNPs involving 159 genes were identified by genome-wide association analysis(GWAS)based on the F2 resource population for the crested trait.Combining the results of selection sweep analysis and GWAS,the KEL gene was identified as a key candidate gene for the crested cushion.Based on linkage disequilibrium analysis and haplotype frequency map results,the locus in the 3’UTR region of the KEL gene can clearly separate crested and non-crested ducks.To determine the role of this gene in crested development,the transcriptome was sequenced at several key periods during crested trait development.Through differential gene expression analysis,weighted co-expression network analysis(WGCNA)and expression trend analysis,the KEL gene was found to be expressed mainly at the early stages of crested development,indicating that this gene may be a key regulatory gene in the early development of crested tissue.5.As one of the earliest domesticated traits to be selected for,in order to identify candidate variants that regulate different beak,plumage and tibia colours in ducks,GWAS analysis based on the F2 resource population in this study revealed that the MITF(white/yellow)and EDNRB2(black)genes jointly regulate the formation of various tissue colors in ducks,while the POU4F3 and MC2R genes may synergistically regulate melanin The POU4F3 and MC2R genes may synergistically regulate melanin deposition and thus influence the formation of feather,rostrum and tibial spot colors.6.In this study,GWAS analyses of feed conversion ratio(FCR),feed intake(FI),residual feed intake(RFI),body weight gain(BWG),body weight at 21 days of age(BW21)and body weight at 42 days of age(B W42)of the duck F2 resource population revealed that six traits,FCR,FI,RFI,BWG,BW21 and BW42,were significantly associated loci(-log10(P)>8.38),with a total of four significantly associated SNP loci identified for FCR,three significantly associated loci identified for FI,36 significantly associated loci identified for RFI,and six,eight and ten significantly associated SNP loci identified for BWG,BW21 and BW42 respectively.Based on locus function,haplotype and KEGG and GO enrichment analysis,three genes significantly associated with FCR were identified as EDIL3,COX7C and ERCC4,which are mainly involved in oxidative phosphorylation and other pathways;FI screened for 2 genes,OTOL1 and SI;RFI screened for LSAMP,GAP43,B3GNT8,ENSAPLG00020009332,ENSAPLG00020001335,ENSAPLG00020001335,FAM241A,RAP1GDS1,UNC5C,SUCO,and GSTT1;B WG screened for 11 genes related to TBC1,INPP5A,STK32C,PRKG1,WFDC8,RPL37,ROCK2,ENSAPLG00020001341,GSTT1 and 11 other genes;BWG screened for a total of 9 genes related to TBCl,INPP5A,STK32C,PRKG1,WFDC8,RPL37,ROCK2,HOXB3 and HOXB2;BW21 screened for a total of 10 genes,including CCDC59,PPFIA2,TBC1D4,SUSD6,PNLIPRP2,NGEF,GABRE,ENSAPLG00020002037,CBLN1 and MRPL10;BW42 screened for a total of EP300,ENSAPLG00020000057,GBE1,SPRY2,NDFIP2,BCKDHB,ENSAPLG00020011494,ILIRAP,ENSAPLG00020005166,FOXP4,MDGA2,RNLS,ENSAPLG00020010580 and ENSAPLG00020009757 and 14 other genes.The results showed that 41 SNPs were identified in duck pectoral fat,3 SNPs in duck pectoral water,5 SNPs in duck pectoral collagen and 6 SNPs in duck pectoral protein.Based on locus function,haplotype and KEGG and GO enrichment analysis,the protein content,fat content,water content and collagen content of duck pectoral muscle were screened for 3(BARHL2,COPS7B and CCDC50),3(BLM,WDR76 and EOMES),4(CAMTA1,FGD5,GRM7 and RAPGEF5)and 3(RIMS2,HNRNPU and SPTBN1)protein-coding genes.In summary,this study investigated the structure,phylogeny,domestication,gene exchange and genetic diversity of duck populations at the genome-wide level,conducted systematic analyses of some traits and economic traits,suggested that there is multiple domestication or infiltration of wild ducks into domestic ducks from different backgrounds,analysed the domestication-mediated adaptive selection of domestic ducks relative to wild ducks,identified KEL as a key candidate gene for the crested cushion,and explored candidate variants for traits such as color trait and meat quality.This study provides valuable data for obtaining high quality population genomic data,investigating the mechanism of duck domestication,exploring the unique genetic information resources of ducks,analyzing the genetic mechanism of economically important traits of ducks,and genetic improvement and exploitation of economically important traits of ducks. |
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