| Domestication is the largest genetic experiment carried out by humans so far,and the detailed analysis of its genetic basis is of great significance for testing existing genetic theories,parsing the complex associations between phenotypes and genotypes,and discovering new genetic phenomena,which in turn can serve for precise molecular breeding and genetic improvement of modern agricultural animals.At the same time,research on the genetic basis of phenotypic variation in animal domestication and artificial selection can not only help people understand how wild animals survive and reproduce in human habitats and be exploited by humans,but also help people understand the social development of human beings.In this process,the identification of genomic variation is of vital importance.With the advent of the whole-genome sequencing era,the identification of genome-wide variants has become easier,and the research on the genetic basis of phenotypic variants in animal domestication and artificial selection has also made great progress.Poultry represented by chickens and ducks is an important part of domestic animals,and their short growth cycle,high reproduction rate,and easy access to wild ancestors make them an ideal model for studying domestication and artificial selection.However,the incompleteness of the reference genomes of birds such as chickens and ducks seriously hinders the comprehensive and accurate identification of theirgenomic variation.At the same time,the limitations of sampling the wild ancestors of chickens and ducks in previous studies have also hindered the comprehensive and precise analysis and application of the genetic basis of their domestication.This study took chickens and ducks as the main research objects,and discussed in detail the need for complete reference genomes and extensive and comprehensive sampling of domestic animals and their wild ancestors in animal domestication and artificial selection studies.At the same time,the construction of a more complete chicken and duck genome will also provide a great help for their future genome research.The specific results are as follows:1.In this study,the genomes of 20 individuals from different representative chicken breeds around the world were assembled.By comparing 20 de novo assembled genomes with the chicken reference genome(GRCg6a),this study identified 159 Mb missing sequences in the chicken reference genome.At the same time,this study analyzed the published genomes of 5 ducks and also identified 33 Mb of missing sequences.The analysis of the characteristics of the missing sequences of the chicken reference genome showed that these sequences have extremely high GC,G4 motif and tandem repeat content.Further analysis found that the non-classical DNA secondary structure made these missing sequences difficult to sequence,which is an important reason for the absence of these sequences in the genome assembly.In this study,a large number of previously missing protein-coding genes and non-coding genes were identified in the missing sequences of reference genome,such as the leptin and OC-17 genes which have long been missing.These missing genes include a large number of genes associated with important biological functions.Interestingly,these missing protein coding genes have a high mutation rate.The location analysis of these sequences and genes showed that they were enriched in the subtelomere region of the chromosome and the entire microchromosome.The regional complexity of the subtelomere region may be a common feature of birds,and it is the key factor that leads to fewer genes assembled in the bird genome.2.At the same time,through the analysis of the largest-scale resequencing data of domestic chickens and their wild ancestors,red jungle fowl,this study found that the previously thought chicken domestication gene TSHR has been selected in its direct wild ancestor,gallus gallus spadiceus.A further study revealed a wide selection of genes related to nerves,reproduction,and growth during chicken domestication,especially the reproduction-related GNRH-1 gene and the neural crest-related FGFR1 gene.Using a comprehensive data set covering both domestic chickens and their wild ancestors,this study also found that domestic chickens have a higher genetic load relative to their wild ancestors,suggesting that domestic chickens have experienced "cost of domestication".Further analysis showed that high-impact single nucleotide polymorphisms(h SNPs)that cause high genetic load in domestic chickens are more likely to remain heterozygous.Meanwhile,compared with their wild ancestors,the number of h SNPs in the selected region of the domestic chicken genome is less but the frequency is higher,suggesting that selected genes tend to eliminate h SNPs from their regions and/or tend to carry fewer h SNPs in haplotypes during domestication and dispersal of domesticated species.3.By analyzing the population structure and history of mallard,indigenous duck and Pekin duck,this study revealed that domestic duck breeding has gone through two stages of domestication and improvement.Subsequent analysis of the genetic basis of domestication and artificial selection also showed that the duck domestication and improvement stage carried out extensive selection of genes related to nerves,reproduction,metabolism and development.The combination of pan-genome and selection analysis has perfected the identification of causative mutations of important phenotypic variants.Through the analysis of the genetic basis of artificial selection in the improvement stage of Pekin ducks and the genome-wide association analysis of feather color in natural populations,this study identified MITF gene,which causes the whitening of Pekin duck plumages.Further pan-genome analysis of domestic ducks identified a 6.6Kb insertion mutation in the intron of the MITF gene of Pekin ducks as a potential cause of white duck down feathers in Pekin duck.This mutation led to differences in the expression of different spliced forms of the MITF gene,and subsequently led to a chain down-regulation of the expression of genes in the melanogenesis pathway downstream of the MITF gene,thereby making the whitening of Pekin duck plumages.In summary,this study revealed the reasons for the missing of bird genes and sequences by constructing a more complete chicken and duck genome.This study also analyzed the genetic basis of domestication and artificial selection of chickens and ducks through extensive sampling.Through a more complete genome,this study reveals the potential causative mutations of key phenotypic variations in domestication and artificial selection.At the same time,the more complete reference genomes of domestic chickens and ducks established in this study will also promote a more accurate and comprehensive analysis of genetic variation by future researchers,and facilitate precision molecular breeding and genetic improvement. |
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