The Genetic Pipelines Construction And Artificial Selection Analysis In Poultry

The development of genomic technology brings revolutionary technical breakthroughs and challenges to animal breeding.However,the application of those technologies still remains a big challenge and needs to be further explored and studied.The major problems for applying genome technology to animal breeding were the short of effective,stable,and parallel genetic pipelines,and the lack of centralized repository for big genetic data.Additionally,most of the previous genome studies of poultry were solely focused on SNV,and ignored the other genetic variations,like STR,SV,transposons.Thus,the insufficient genetic variantion limited the portion of phenotypic variantion that can be explained by genetic diversity.The main process of breeding was from the native breeds to highly productive breeds.However,the previous studies were focused on the process from wild ancestors to native breeds,which limited the study of molecular genetics of breeding.And this make it difficult to make break thoughs on the application of genome selection technology.Althrough,lots of genetic markers have beed found,it is still difficult to build new technology using those markers.Thus,it is an eager problem to find theorilogial support for new breeding technology and need more exploration on the genetic mechanism of breeding.The main direction of chicken breeding were broiler and layer,which have distinct phenotypic difference.But it is still unclear how genomes response to different selection pressure.To answer those questions,we developed effective genetic pipelines for genome analysis,and studied the effect of artificial selection on genome with different breeding purposes.(1)We first used Nextflow to build packaged and high parallel pipelines for data preprocess,including data preprocess,reads alignment,SNV calling,SV calling,transposon calling,STR calling,RNA-seq,and GWAS pipelines.And we used Docker container to build cross-platform,packaged computational environment for each of the pipeline.By combining them together,we developed cross-platform and high parallel poultry genome analysis pipelines.Those pipelines enriched variant calling and integrated the most common used tools.All the source code of our pipelines were published on Github.(2)Then,we used Avian broilers,Lohmann layer,Guangyuan grey-feather indigenous fowl,Jiuyuan black-boned indigenous fowl,and Daheng broilers as our study objects,by leveraging the RAD-seq and pipelines we developed,we studied how genome would change from indigenous chicken to productively commercial broilers or layers.Wefound the chicken genomes were sensitive to the selection pressure of breeding direction.We laso found purified selection and relaxed selection play an important role in egg layer breeding and broiler breeding,respectively.Then,we further verified that HBA1 and HBB genes were under relaxed selection during geese domestication,which indicated that relaxed selection can happen to some of the genes when the whole population were under extremely strong selection.(3)To compare the genome similarity,we did IBD analysis on Avian broilers,Lohmann layer,Guangyuan grey-feather indigenous fowl,Jiuyuan black-boned indigenous fowl,and Daheng broilers.We found the W and Z chromosomes were under strong artificial selection in Lohmann layer.And there were 125 genes from chromosome Z were under significant artificial selection.We also found many small genomic block on chromosome W were under strong selection in Lohmann layer.Thus,based on our findings,here,we came up a new technology that using genomic similarity to perform individual selection in egg layer breeding.(4)To explore how poultry genomes response to the pressure of directional selection in breeding,we selected the most significantly selected genes from the above 125 genes and explored their expression pattern in the embryo of Lohmann layer,Daheng broiler,and Avian broiler.We found the expression of MEF2A?SLC16A7?tns3?TFDP2 genes were highly related to the productivity of the chicken breed,which verified the expression of genes under selection were associated with the breeding direction and level.Our results indicated the change of expression of genes was an important way for genome to response to the selection pressure of directional breeding.Additionally,we also found the pattern of embryo weight,leg muscle weight of embryo,and breast muscle of embryo were consistent with breeding direction.In our study,we have built population-level variant calling pipelines,which will support the study of population genomics.We then analized the genetic mechanisms of poultry breeding,and firstly come up the technology of genomic similarity selection.We found the poultry genomes were sensitive to directional breeding,and the change on expression level of genes was an important way for genome to response to the pressure of directional breeding.Our findings provided strong support for the further exploration of breeding mechanisms.