Genetic Characteristics Analysis Of Closed Colony In Experimental Goat And Sheep

Although experimental sheep and goat were widely used in medicine and other life science research fields,there is still a lack of examination and approval system,regulatory system and standardized quality control standards.In China,laboratory animals are all put into a strict licensing and quality management system by the government.The standardization of genetic quality control is crucial to quality control management system of experimental sheep and goat.In order to standardize the genetic quality of experimental sheep and reduce the error of experimental results,this paper referred to the research results of other experimental livestocks,determined the genetic quality of the closed colony setted by our team with DNA molecular genetic marker technology of microsatellite markers.Meanwhile,the whole genome of closed colony was also sequenced to analyse the unique genomic characteristics and gene signals.The purpose of this study was analyze the genetic diversity and genomic characteristics of the experimental sheep and goat setted by our team,and lay a foundation for the establishment of genetic quality control standard of experimental sheep and goat.（1）In order to provide data support for the germplasm resources protection,breeding improvement and establishment of genetic quality control standards of experiment sheep and goat,this study analyzed the genetic diversities and genetic structures of one purebred white goat population（Haimen goat,HM）,one closed colony population（CM）and one hybrid population from Chongming area（ZY）by microsatellite markers（SSR）method.The genetic diversity of HM,CM and ZY were detected by PCR amplification and capillary electrophoresis with 30 microsatellite markers.Different genotypes at different SSR loci and population were analyzed.In HM,CM and ZY populations,the total numbers of alleles were 205,191 and 147,respectively.The average numbers of effective alleles（Ne）were 4.012,3.812 and 3.092,the average numbers of expected heterozygosity（He）were 0.683,0.668 and 0.617,the average polymorphism information contents（PIC）were 0.647,0.630 and 0.567.The total inbreeding numbers（Fit）,mean genetic differentiation coefficients（Fst）and mean gene flows（Nm）of three populations were 0.0110,0.0507 and 4.6806.The genetic distance of ZY was closed with CM than that with HM.UPGMA analysis showed that CM and ZY were gathered together.All three populations in our study showed high heterozygosity,polymorphism and genetic variation.Purebred Haimen goat and closed colony goat showed moderate genetic differentiation,low inbreeding rate and gene exchange,which could be used for the preservation and utilization of germplasm resources.The He and Ho values of closed colony white goats ranged from 0.6～0.8,and Ho>He,met the quality requirements of closed colony population.（2）The genetic diversity of Hu sheep population was analyzed with 31microsatellite markers.Loci analysis showed that 210 alleles were amplified in the population.Shannon index（I）was 1.416,Polymorphic information content（PIC）was0.634,the observed heterozygosity（Ho）was 0.692,and the expected heterozygosity（He）was 0.68.All the locis detected by Ewens-Watterson were within the confidence interval.Population analysis showed that:Ho,he,I and PIC of ram were 0.694,0.643,1.190 and 0.564,respectively;Ho,he,I and PIC of ewe were 0.676,0.693,1.403 and0.636,respectively.Rich genetic diversity and high degree of variation were observed in this population.The analysis of bottleneck effect in Hu sheep population showed that there was no bottleneck effect in this population,the allele frequency distribution was L-shaped,the mean value of each loci was in hard-Weinberg balance and the relative size and number of gene frequency were maintained.In conclusion,the population of Shanghai Hu sheep has high genetic diversity and no bottleneck effect,which can be widely used in breeding and cross utilization of this breed.（3）The closed colony white goat（CM）was a special closed breeding group to meet the needs of experiment goat.By performing whole genome re-sequencing,this study generated 14–20 coverage sequences from 10 domestic goat breeds（population）to explore the genomic characteristics and selection signatures of the closed colony population.This study identified a total of 23,508,551 single-nucleotide polymorphisms（SNPs）and 2,830,800 insertion–deletion mutations（In Dels）after read mapping and variant calling.This study further specifically identified 1.2%SNPs（271,713）and 0.9%In Dels（24,843）unique to the CM population in comparison with the other nine goat breeds.Missense（SIFT<0.05）,frame shift,splice-site,start-loss,stop-loss,and stop-gain variants were identified in 183 protein-coding genes of the CM breed.Of the183,36 genes,including AP4E1,FSHR,COL11A2,and DYSF,are involved in phenotype ontology terms related to the nervous system,short stature,and skeletal muscle morphology.Moreover,based on genome wide F_ST and pooled heterozygosity（Hp）calculation,we further identified selection signature genes between the closed colony population and the other nine goat breeds.These genes are significantly associated with the nervous system（C2CD3,DNAJB13,UCP2,ZMYND11,CEP126,SCAPER,and TSHR）,growth（UCP2,UCP3,TSHR,FGFR1,ERLIN2,and ZNF703）,and coat color（KITLG,ASIP,AHCY,RALY,and MC1R）.Our results suggest that the closed colony population may be differentiated from other goat breeds in terms of nervous system owing to natural or artificial selection.The whole-genome analysis provides an improved understanding of genetic diversity and trait exploration for this indigenous goat closed colony population.