| Tibetan sheep live in the high altitude qinghai-tibet plateau region.The harsh ecological environment has brought up the characteristics of Tibetan sheep such as strong adaptability,high immunity and wide feeding range,which are the main production and living materials for farmers and herdsmen in the qinghai-tibet plateau region.The complex topography and climate in the alpine region make the Tibetan sheep population gradually diversified.It is difficult to classify and identify these populations based on their geographical location,appearance characteristics and production performance.The various naming style,rough division method and the lack of genetic information will all become obstacles in the promotion and breeding of Tibetan sheep.With the rapid development of genomic sequencing and genotyping technology,it is possible to identify germplasm resources of livestock and poultry varieties from genomic level.In this study,the whole genome of 20 Tibetan sheep populations(384 individuals in total)in five regions of Tibet,qinghai,gansu,yunnan and sichuan was performed based on Affymetrix Ovine SNP 600K high density chip to analyze the genetic diversity and population structure of Tibetan sheep populations.And using the population differentiation index FST to screen candidate specific SNP loci in each Tibetan sheep population.The cost of germplasm resource identification is greatly reduced,and the technology has a good promotion prospect.The results are as follows:(1)The genotyping results of 384 sample DNAs showed that the detection rate of most samples reached over 94%,and 604554 SNPs were detected.After quality control,10 individuals were removed,leaving 374 individuals and 423178 high quality SNPs.(2)Genetic diversity of Tibetan sheep was detected by using heterozygosity and inbreeding coefficients.The results showed that the Langkazi sheep in Tibet had the lowest observed heterozygosity(0.2350)and the highest inbreeding coefficient(0.2796),and qinghai Valley Tibetan sheep had the highest observed heterozygosity(0.3234)and the lowest inbreeding coefficient(0.0090).In general,the genetic diversity of Tibetan sheep in Tibet and yunnan is relatively low,while that of qinghai,gansu and sichuan is relatively high.(3)Principal component analysis(PCA),NJ Tree,and STRUCTURE were used to study the genetic relationship between Tibetan sheep populations.It was found that the Tibetan sheep in Tibet and yunnan were separately clustered into one,which maintained a certain regional specificity,and each group gathered independently.In qinghai,gansu and sichuan provinces,the sheep of valley type are highly differentiated and independent,while the sheep of grassland type gather in disorder,showing little difference in genetic distance and population structure.(4)Candidate specific SNP sites were screened for each Tibetan sheep population based on the population differentiation index FST.By detecting the distinguishing effect of principal component analysis and adjacent tree on different numbers of SNPs,the population-specific SNP set was successfully constructed for 14 Tibetan sheep populations,including Tibetan sheep populationg in Tibet and yunnan,valley-type Tibetan sheep and black Tibetan sheep in qinghai,Gongga sheep and Zhaxika sheep in sichuan.(5)Some genes related to development and immunity were found by gene annotation and enrichment analysis of candidate-specific SNP sites of Gangba sheep.ACD,HOXD12,HOXD13,ACP2 and CHRD are related to skeletal system development,and IL1R1 and IL1RL2 are involved in inflammatory response and autoimmune regulation... |
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