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The Analysis of Genetic Variation among Native Populations in China and Introduced Populations in America and Hungary of Silver Carp(Hypophthalmichthys Molitrix) by Major Histocompatibility Complex (MHC)

Author: FengWei
Tutor: LiuZhiZhi
School: Shanghai Ocean University,
Course: Hydrobiology
Keywords: Hypophthalmichthys molitrix Major histocompatibility complex nativepopulation introduced population selected population genetic variaton
CLC: S917.4
Type: Master's thesis
Year: 2012
Downloads: 24
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1. Cloning and sequencing analysis of the MHC class I α2domain geneamong native populatins in China and introduced populations inAmerica and Hungary of silver carpThe major histocompatibility complex (MHC) class I α2domain was used to studythe genetic variation among native populations (Yangtze and Amur River in China,abbreviated as YZL and AMU) and introduced populations (Danube River andMississippi River, abbreviated as DAN and MIS) of silver carp. A total106differentnucleotide sequences(GenBank accession number: JQ289925~JQ289992,JQ707784~JQ707821) were got from333clones in116individuals. The major resultswere as following:①Totally, there were231usable nucleotide loci, of which160ones were polymorphic sites, accounted for69.26%. There were32,23,27and43alleles were detected in the YZL, AMU, DAN and MIS populations, respectively. Thenucleotide/amino acid sequence similarity was52.1%~99.5%/38.1%~98.6%. Allrevealed relatively high polymorphism of MHC class I α2domain in silver carp.②Therange of mean nucleotide/amino acid sequence similarity was DAN(77.52%/67.29%)>MIS (75.82%/66.94%)>AMU(74.35%/64.44%)>YZL(73.38%/63.52%), but the nucleotide/amino acid diversity index (π/πaa) was YZL(0.2598/0.3588)> AMU (0.2542/0.3527)> MIS(0.2372/0.3269)>DAN (0.2191/0.3128).It was showed that the chinese native populations (YZL,AMU) had higher geneticvariation than that of introduced populations (DAN, MIS).③The AMOVAresults,based on the amino acid sequences, indicated that there existed significantly genetic differentiation whether among the four populations or between native andintroduced populations (P<0.05).④According to the NJ tree based on the amino acidaverage genetic distance, AMU firstly clustered with DAN, then joined to MIS, finallyclustered to YZL, which showed that the relatively less close relationship between YZLand MIS.⑤The ω values of non-synonimous/synonymous nucleotide substitution inpeptide binding region (PBR) were AMU (1.4413)>YZL(1.3621)> DAN(1.3370)>MIS(1.2913)>1, and nine positive selected sites were detected in the PBRby the M2a and M8model in the CODEML program, indicating positive selectionpressure on the MHC class I α2domain in the four populations of silver carp with thehigher selection pressure on Chinese native populations.2. The polymorphism analysis of MHC class I gene among wildpopulations in Yangtze River and selected populaton of silver carp2.1Cloning and sequencing analysis for MHC I α2domain gene of silver carpamong wild populations in Yangtze River and selected population in Huanxinaquaculture farmThe major histocompatibility complex (MHC) class I α2domain was used toanalyse the genetic variation among two wild populations in Yangtze River (Shishouand Hanjiang, abbreviated as SS and HJ) and one selected population (Huanxin,abbreviated as HX) of silver carp. A total of57different nucleotide sequences(GenBank accession number: JQ289925~JQ289945, JQ289948, JQ289953, JQ289958,JQ289965, JQ289967, JQ289975, JQ289979, JQ289985, JQ707798~JQ707801andJQ707822~JQ707845) were got from156clones in52individuals. The main resultsshowed:①There were231/77usable nucleotide/amino acid loci, of which147(63.64%)/59(76.62%) polymorphic sites, respectively.21,13and34alleles weredetected in the SS, HJ and HX population. The nucleotide/amino acid sequencesimilarity was53.60%~99.50%/39.40%~98.60%. It all indicated relatively highpolymorphism of MHC class I α2domain gene in the three populations of silver carp.②The average nucleotide/amino acid sequence similarities within population were73.60%~74.52%/64.27%~65.25%, and the number of nucleotide/amino acid polymorphic sites in HJ population (122/50) was less than those of SS (138/57) and HX(137/56) populations. The nucleotide/amino acid diversity index (π/πaa) were SS(0.2611/0.3623)> HX (0.2587/0.3540)> HJ (0.2482/0.3420). Apparently, the geneticdiversity was still relatively high in HX population.③Based on amino acid sequences,the AMOVA results indicated that there were no significantly differentiation among thethree populations (P>0.05).④. In the NJ tree based on amino acid average genenticdistance, HJ clustered with HX firstly, and then joined to SS.⑤The ratio ofnon-synonimous/synonymous substitutions (ω=dN/dS) in peptide binding region (PBR)were SS(1.6525)> HJ(1.4182)> HX(1.3607)>1, and seven positive selected sitedwere detected in the PBR by the M2a and M8model in CODEML program, indicatingpositive selection pressure on the MHC class I α2domain in the three populations ofsilver carp with the least positive selection pressure on the HX population.2.2Polymorphism analysis for MHC class I gene of sliver carp between Jianli wildpopulation and Huanxin selected populationTwo pairs of special primers were designed to amplify α1, α2and α3domain ofMHC class I gene in silver carp. A total52different nucleotide sequences were obtainedfrom78clones in26individuals. The nucleotides were819~825bp in length andencoding273~275amino acid. The52nucleotide sequences encoded44differentalleles which could be defined as14main type and44subtype (GenBank accessionnumber: JQ707846~JQ707889). The main results were:①There were441(53.45%)/187(67.75%) polymorphic sites in the825/276usable nucleotide/amino acid sites.There existed154/62,179/73and108/52polymorphic sites in α1, α2and α3domain,respectively.②The mean nucleotide/amino acid sequence similarities were81.43%/72.45%. The ranges of similarity for α1, α2and α3domain were54.00%~100%/41.30%~100%,55.90%~100%/47.30%~100%and84.20%~100%/77.4%~100%, respectively. These results indicated relatively high polymorphism ofMHC class I gene in silver carp and the α3domain was more conserved than α1and α2domain.③The average nucleotide/amino acid sequence similarity within populationwas JL(81.80%/74.05%)>HX(74.62%/69.53%), but the number of nucleotide/aminoacid polymorphic sites(S/Saa)and nucleotide/amino acid diversity index (π/πaa) wasHX> JL. It proved that the genetic diversity of HX population was higher than that ofJL population.④Based on amino acid sequences, the AMOVA results indicated that there was no significantly differentiation between the two populations (P>0.05).⑤The average ω value (1.0120~3.1357) in PBR of α1,α2domain was larger than1. Inaddition, the ω value in PBR of α2domain of JL population (3.1357) was about2.4times of that in HX population (1.3331) and fifthteen positive selected sites weredetected in PBR of MHC I gene by CODEML program. These results indicated higherpositive selection pressure on the JL population than that of HX population.

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CLC: > Agricultural Sciences > Aquaculture, fisheries > Aquatic basic science > Aquatic Biology > Aquatic Zoology
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