| The Amur tiger(Panthera tigris altaica)is an endangered species.China adopts the strategy of both in-situ protection and ex-situ protection to save the Amur tiger.The first Amur tiger reserve(Qixinglazi Nature Reserve)was established in 1980,and a 1.4065 million hectare Amur tiger and leopard national park was established in 2016 to implement in-situ protection.At the same time,in 1986,China Hengdaohezi cat breeding and breeding center was established as the national northeast tiger provenance base,focusing on the breeding and wilding experiments of northeast tiger.After continuous efforts,the number of Amur tigers has gradually recovered from 12 to 16 in the late 1990 s to 60 in 2022.However,due to the long-term blocking of gene exchange with large populations in the Far East,wild populations in China have shown signs of inbreeding,and their genetic risks have received extensive attention.If the geographical barrier problem cannot be effectively solved in the short term,the use of captive Amur tigers with a high level of genetic diversity to carry out genetic rescue of wild populations has become an important option.Before formulating a genetic rescue plan,it is necessary to compare and analyze the genetic diversity of wild and captive populations,evaluate the genetic relationship,complementarity,benefits of genetic rescue and the risk of harmful gene introduction between captive and wild individuals,so as to delineate suitable individuals in captive populations as candidate gene donors in the rescue plan.In this study,the complete mitochondrial genomes of51 captive Amur tigers and 13 wild Amur tigers in Laoyeling and Wandashan were compared and analyzed.The main results are as follows :First,the mitochondrial genome was assembled from the fecal DNA resequencing data of64 Amur tigers,with an average coverage of 100 % and an average sequencing depth of 7846.8×.A total of 41 polymorphic loci and 9 haplotypes were identified in 64 individuals,including39 polymorphic loci,7 haplotypes in captive population and 3 polymorphic loci in wild population,which were distributed on 2 haplotypes.The overall nucleotide diversity(Pi)was0.00114,of which the captive population was 0.00105 and the wild population was 0.00007.The haplotype diversity(Hd)was 0.793,of which the captive population was 0.711 and the wild population was 0.385.It indicated that the mitochondrial genetic diversity of captive populations was much higher than that of wild populations.Secondly,the mitochondrial genome of Amur tiger(NCBI serial number : KF297576.1)was used as a reference to screen SNP loci for all individuals,and a total of 493 SNP loci were screened.By software ANNOVAR annotation,all SNP loci are non-harmful mutations,and genetic risk from the mitochondrial genome can be ignored when genetic rescue is performed.Third,the haplotype network diagram and phylogenetic tree divided all Amur tigers into two major branches.The first branch consisted of only two captive haplotypes,and the second branch consisted of five captive haplotypes and two wild haplotypes.The nucleotide difference between the two branches reached 35 nucleotides,which was much larger than the intra-group difference(1-4 nucleotides).The differentiation of 7 haplotypes in the second branch is only 1-4 nucleotides,indicating that these captive individuals and wild individuals are derived from the same geographic lineage.From the perspective of the mitochondrial genome,it is suitable for genetic rescue for the next nuclear genome assessment.In conclusion,the national Amur tiger provenance base has several individuals from the same geographic lineage as the wild Amur tiger,demonstrating the considerable mitochondrial genetic diversity of the captive Amur tiger.These people are good candidates for genetic rescue from the standpoint of the mitochondrial genome.A reserve resource for reestablishing historical genetic diversity in the field,the other branch of the captive population should be tracked throughout time to ascertain its phylogeographic state and conservation importance. |
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