Association Analysis Between Polymorphisms Of TET1 And Placental Traits In Dazu Black Goats

Litter size is an important breeding index in goat production.Improving the litter size is crucial significance to ensure the sustainable and healthy development of goat industry,increase the economic efficiency and raise the enthusiasm of peasants.Due to the low heritability(0.1～0.15)and negative maternal effect,the way to improve the litter size of ewes directly through phenotype selection has not made great progress for many years.Although people also hope to improve litter size by selecting its physiological factors such as ovulation number and uterus volume,there is a negative genetic correlation between ovulation number and embryo survival rate,so selecting uterus volume directly is difficult and the overall effect is not significant.Therefore,exploring a character with strong positive correlation and high heritability such as placenta efficiency to select breeding ewes and reserve ewes in order to improve litter size is necessary.Tet1,as a member of the dioxygenase,plays an important role in early placental development,embryo implantation,fetal growth,genomic imprinting and related signal pathways regulation.It is an important candidate gene that affects placental traits and reproductive performance,could be used as a molecular marker for assisted selection of reproductive traits.There is no report about association analysis between TET1 gene and placental traits in goats at home and abroad.This paper taking Dazu Black goats for research objects,aims to explore the polymorphisms of Tet1 gene and its effect on placental traits,and to provide scientific basis for improving reproductive performance of goats by marker assisted selection.84 Dazu black ewes were selected as experimental animals in this paper.The single nucleotide polymorphisms(SNPs)of TET1 gene were detected by pooled DNA sequencing method,and genotyped by resequencing technology.The SNPs loci associations with placental traits and a part of reproductive traits(kid number,kid birth weight,placental weight,cotyledon area,cotyledon number,placental efficiency,cotyledon density,cotyledon support efficiency)were analyzed by SAS software.The results and conclusions of this study are as follows:1.TET1 gene amplification and variable sites screeningThe published TET1 gene sequence in NCBI and Ensemble nucleic acid database(accession number:NC＿030835.1 and ENSCHIG00000009920)was used as a reference,the pooled DNA of Dazu black goats was amplified by PCR and sequenced.34 SNPs were screened.11 SNPs were identified in exon1,15 SNPs were identified in exon3,1 SNP was identified in exon6,4 SNPs were identified in exon10and 3 SNPs were identified in exon11.2.Polymorphic analysis of SNPs of TET1 geneAmong the 34 SNPs,23 were genotyped by resequencing technology.6 SNPs were found to be polymorphic in Dazu black goats(a total of 84 samples),including2 in exon1,3 in exon3 and 1 in exon11,all of which were in moderate polymorphism(0.25<PIC<0.50).H_E values of SNP＿585 and SNP＿657 were larger than the H_O values,and H_E values of SNP＿77849,SNP＿77902,SNP＿79573,SNP＿117018 were smaller than the H_O values.The?~2 test indicated that the genotypic distribution of 6SNPs in TET1 gene were deviated from Hardy-Weinberg equilibrium(P>0.05).Among the 6 SNP loci,SNP＿585,SNP＿657 and SNP＿77902 were synonymous mutations,SNP＿77849,SNP＿79573 and SNP＿117018 were missense mutations.Four tag SNPs including Snp＿585,Snp＿657,Snp＿77902,Snp＿117018 were screened by using HaploView software.A total of 7 haplotypes were constructed by using the Phase method.Among them,haplotype H＿1 has the highest frequency(47.62%).3.Association analysis between SNPs polymorphism of TET1 gene and placental traits and a part of reproductive traits in Dazu Black goatAssociation analysis results showed that SNP＿77849,SNP＿77902,SNP＿79573,SNP＿117018 were not significantly associated with placental traits and a part of reproductive traits of Dazu black goats.In SNP＿585 mutation,the C/C genotype was significantly higher than those of C/T genotype in kid number,cotyledon number,cotyledon density,was the dominant genotype(P<0.05).In SNP＿585 mutation,the G/G genotype was significantly higher than those of A/G genotype in cotyledon density(P<0.05),and there was no significant differences in other traits.In the genotype combination analysis,the GE-M1(C/C,A/A,G/G,C/C),GE-M3(C/C,G/G,A/A,A/C),GE-M5(C/C,G/G,A/G,C/C)and GE-M8(C/C,A/G,G/G,C/C)were the dominant genotype combination,their haplotypes are H＿1(CGGC),H＿2(CGAA),H＿3(CGAC)and H＿6(CAGC).The GE-M12(C/T,A/A,A/G,A/C),GE-M14(C/T,A/G,A/A,A/C)and GE-M15(C/T,A/G,G/G,C/C)were inferior genotype combination,all of which contained haplotype H＿1(TAAA).Together,the SNPs of TET1 gene which have significant effects on the placental traits in Dazu Black goats were screened.A basis for further study on placental traits of goats and then improve their reproductive performance was provided by these markers.