| "Livestock development,good breed:first",improved breeding of livestock and poultry is the core of animal husbandry,its contribution rate to the development of animal husbandry is more than 40%,and play a core position in animal husbandry.Seed industry is the strategic and basic core industry of our country.At present,the problem of seed industry has attracted the attention of the party and the government.As an important part of livestock and poultry genetic resources,local chicken was formed in thousands of years of gene drift,artificial and natural selection.There are 115 local breeds of chickens in China.The rich genetic diversity and extensive genetic basis of these breeds are indispensable materials for breeding and the basis of sustainable development of animal husbandry.Therefore,assessing local chicken genetic diversity and understanding inter-population and intra-population relationships is the first step to determine the conservation,development and utilization of livestock and poultry genetic resources.This study focused on the evaluation of genetic diversity and conservation effect of Gushi chickens.Research 1:Evaluation of conservation effect of different generations of ex situ conservation population of Gushi chickenIn this study,the genomic DNA of 60 individuals of Gushi chickens(generation 2010 and 2019)was resequenced by whole genome resequencing technology.After filtering,quality control and comparative analysis of the obtained original data,a total of 19385777 SNPs were finally used for subsequent analysis.The MAF values of SNPs in two subpopulations were significantly different in the range of low frequency(0-0.05),medium frequency(0.05-0.20)and high frequency(0.20-0.50)(P<0.001);After evaluating the conservation effect of Gushi chickens,we found that the heterozygosity and nucleotide diversity of Gushi chickens were decreased,while the number of inbred lines was increased.The phylogenetic tree analysis,principal component analysis and FST analysis showed that there was no obvious stratification among different populations,and the degree of genetic differentiation was small(FST<0.05);In addition,the results of selection signal analysis showed that 177 selected genes were screened from different generations of Gushi chicken conservation population,which were mainly enriched in the regulatory pathways of energy metabolism and signal transduction.Research 2:evaluation of conservation effect of in situ and ex situ conservation population of Gushi chickenBased on the whole genome resequencing data,the conservation effects of in situ(2019 generation)and ectopic(2019 generation)populations of Gushi chickens were compared and analyzed.A total of 19227023 SNPs in the two subpopulations passed the quality inspection.The SNP density in each subpopulation was uniform,and the MAF values of SNPs were significantly different in different frequency ranges(P<0.001).The results of genome genetic diversity evaluation showed that the genetic diversity of in situ conservation population(Ho=0.1967,He=0.1998,Pp=0.7918,AR=0.79949,PA=0.0838,π=0.0041)was higher than that of ectopic conservation population(Ho=0.1425,He=0.1453,Pp=0.4749,AR=0.4664,PA=0.0052,π=0.0029),and the degree of inbreeding was lower than that of ectopic conservation,which indicated that the effect of in situ conservation was better than that of ectopic conservation;the analysis of population structure showed that there was a stratification phenomenon and a moderate degree of genetic differentiation(FST>0.05)between the in-situ and allochtho-preserved populations;Neutral genes such as LSAMP,TAOK1,RYBA1 and KMT2D were screened in Gushi chickens and their ectopic population.They were mainly enriched in the regulation pathway of nerve transmission,protein secretion and synthesis. |
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