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The barabensis PRLR Gene Cloning and Analysis of SNPs

Author: WangDongKuan
Tutor: XuLaiXiang；XueHuiLiang；XuJinHui
School: Qufu Normal University
Course: Zoology
Keywords: Cricetulus barabensis Apodemus agrarius Kunming mouse PRLR cloning SNPs
CLC: Q78
Type: Master's thesis
Year: 2009
Downloads: 28
Quote: 1
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Abstract


The 5’end part sequence of PRLR gene in Cricetulus barabensis with the GenBank submission number of EU826030 is first cloned in this study.The results indicate that the usable length is 379bp,which contains partial 5’regulation region, complete exon 1 and some intron 1.Apodemus agrarius collected from Wucun and Kunming mouse used in laboratory are also cloned in the same region of PRLR gene. This experiment mainly analyzes the single nucleotide polymorphisms(SNPs) in three different populations of Cricetulus barabensis from Wucun、Yinan and Linqu collected in Shandong province,the comparision of polymorphism among Cricetulus barabensis、Apodemus agrarius and Kunming mouse by the use of Chromas、Clustal X、DNAman、DnaSP4.0、MEGA3.1 and other key sequence analysis softwares,in order to explore the reasons for the variation in different geographic populations of Cricetulus barabensis and the variation level among different subspecies.The aims of these experiments are to exploit reproductive characters,diffusion mechanism and geographic distubution in Cricetulus barabensis and Apodemus agrarius.On this basis,the fuctions of genetic factors in this two species can be inspected.Then there will be positive meanings not only for bandicoot managements and protections of crops and forests,but also for exposing the law of periodical fluctuations and population break out in bandicoots.1 There are 98 sequences,8 polymorphic loci and 10 haplotypes of Cricetulus barabensis.The number of sequences is from FJ712222 to FJ712231.The nucleotide homology of PRLR gene among Cricetulus barabensis,Rattus norvegicus,Mus musculus、Homo sapiens Pongo abelii,Macaca mulatta and Pan troglodytes is from 82.1%to 93.4%.The homology of exonl is from 79.8%to 91.4%.This result is similar to former reports,what’s more,it can prove that the exonl is variable.So the exonl of Cricetulus barabensis is cloned successfully.To this extent,it can be considered as an ideal marker for studing relationships among animals and genetic distance.2 The homologies of nucleotide sequences among different populations are very obvious and is close to 100%.After statistics,The percentage of polymorphism was 2.11%;The nucleotide diversity(Pi) is from 0.076%to 0.309%,The Haplotype diversity(Hd) is between 0.287 and 0.638.It is very high,indicating relatively high difference among nucleotide sequences.The average number of nucleotide differences(K) and percentage of polymorphism and Theta(per site) from S(θ_ω) of Linqu population were bigger than the other two populations.The Fixation Index(Fst) of Linqu is the biggest,while the Fst value between Wucun and Yinan is negative.As a consequence,Linqu is quite different to the other two populations.The discrepancies of these three populations may be the main reason for the above results.3 33 sequences and 10 haplotypes of Apodemus agrarius,the number of sequences is from FJ712232 to FJ712241.37 sequences and 2 haplotypes of Kunming mouse The number of sequences is FJ712242 and FJ712243 are acquired.The polymorphic sites are 10 and 1,respectively.Homologies of Apodemus agrarius is 91.8%,with the reason for different number of microsatellite A from 28bp to 41bp. The similarities of Kunming mouse are 99.99%,indicating the high homologies.4 The results of Comparision among Cricetulus barabensis,Apodemus agrarius and Kunming mouse show that the homology is 95.09%.Sequences are highly conserved from 30bp to 150bp,indicating the evolution rate is very slow,and can be used for phylogenetic analysis of the rodents;The nucleotide from 22bp to 358bp, with 19 mutation loci only occurred in Cricetulus barabensis,at the same time 6 mutations only happens in Apodemus sequence from 29bp to 355bp.There are six onversion mutations at 153bp,182bp,196bp et al and one insertion mutation at 182bp in Kunming mouse.Besides these mutations,the positions from 243bp to 246bp, 295bp,326bp are unlike each other of these three species.This result can illuminate that there are evident differences of PRLR gene in three species.The NJ tree and UPGMA tree shows that the relationship between Apodemus agrarius and Kunming mouse is more closer,with the same discipline of biological classification.

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