Analysis Of Maternal And Paternal Types Of Stud Sika Deer Based On Mitochondrial DNA And Y Chromosome Gene Fragments

Sika deer(Cervus nippon)belong to Mammalia,Artiodactyla,Cervidae and Cervus.The female have no antlers,and the male have antlers.They are important economic animals and have high ornamental value,medicinal value and edible value.China has abundant resources and long domestication history of sika deer.At present,there are six developed breeds: Shuangyang sika deer,Aodong sika deer,Siping sika deer,Dongfeng sika deer,Xingkaihu sika deer,Xifeng sika deer.There is one strain: Changbaishan sika deer.However,the degeneration of the existing breeds and interspecific hybridization are serious.The genealogical pedigree is chaotic and the genetic background is not clear.The selection of stud sika deer is mainly based on phenotypic traits,such as antler performance,age,physique appearance,genetic performance and reproductive performance,lack of data support at molecular level.In this paper,mitochondrial genome of 145 stud sika deer and AMELY,DBY,USP9 Y,SRY gene fragments on Y chromosome of 198 stud sika deer from 7 sika deer populations(Shuangyang sika deer,Aodong sika deer,Siping sika,Dongfeng sika deer,Xingkaihu sika deer,Changbaishan sika deer,Dongda sika deer)were sequenced and analyzed to study genetic diversity and find out the maternal and paternal types of stud sika deer.The purpose of this paper was to provide data support and theoretical guidance for the conservation and breeding of sika deer.Stud sika deer were 16426bp~16435bp,consisting of 13 protein coding genes,22 tRNA genes,2 rRNA genes and D-loop region.In this paper,13 protein coding genes and D-loop(non-coding region)of mitochondrial DNA were analyzed.The length of 13 protein coding genes of 145 stud sika deer were 11406 bp.267 mutation sites were found and 62 haplotypes(P1~P62)were defined.P1,P2 and P3 were dominant haplotypes,acounting for 24.13%,17.24% and 11.72%.The Hd and ? value of seven stud sika deer populations were 0.8997 and 0.00477.The length of complete D-loop of 145 stud sika deer were 988~994bp.55 mutation sites,including 9 insertion/deletions and 46 base substitutions,were found.15 haplotypes(D1~D15)were defined.D1 and D2 were dominant haplotypes,accounting for 60.00% and 17.24%.The Hd and ? value of seven stud sika deer populations were 0.6047 and 0.01308.Data based on two methods all indicated mtDNA of Chinese stud sika deer had high haplotype diversity and low nucleotide diversity.The result of NJ phylogenetic tree and population structure based on two methods all showed that stud sika deer had two maternal types: M1 and M2.The frequency of M1 and M2 were 15.86% and 84.14%.M2 was the dominant maternal type.M1 was close to red deer and M2 was far from red deer.Haplotype sequence between M1 and M2 showed big difference.All Siping stud sika deer belonged to M1 maternal type,and other stud sika deer populations were mixed by M1 and M2 maternal types.The length of AMELY,DBY,USP9 Y,SRY gene fragments on Y chromosome of 198 stud sika deer were 4775 bp.There were 8 mutation sites and AMELY,DBY,USP9 Y,SRY gene fragments had 3,2,1,1,1 mutation sites.10 haplotypes(H1,H2,H3,H4,H5,H6,H9,H11,H12,H13)were defined.H1,H2 and H3 were dominant haplotypes.H1 existed in seven stud sika deer populations,accounting for 49.47%.The frequency of H2 and H3 were 21.72% and 11.61%.H5 and H12 were unique to Dongfeng stud sika deer.H9 was the primitive haplotype.The Hd and ? value of seven stud sika deer populations were 0.69041 and 0.00034,which showed that Y chromosome of chinese stud sika had high haplotype diversity and low nucleotide diversity.The result of NJ phylogenetic tree and population sructure showed that Chinese stud sika deer had 3 paternal types: Y1,Y2 and Y3.Y1 was composed of H9.Y2 was composed of H3,H5 and H12.Y3 was composed of H1,H2,H4,H6,H11 and H13.Shuangyang and Siping stud sika deer were single paternal type,and other stud sika deer populations were multiple paternal types.Maternal types of 28 sika deer from king competition were indentified by 13 protein coding genes and D-loop region,which showed the frequency of M1 and M2 were 4.6% and 95.4%.Paternal types of 24 sika deer were indentified by AMELY,DBY,USP9 Y and SRY gene fragments on Y chromosome,which showed that they all belonged to Y3.Sika deer from king competition had high antler weight,so maternal and paternal types identification of these sika deer can provide data support and theoretical basis for Chinese sika deer at the molecular level.