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Study On Nucleotide Diversity, Molecular Evolution, PCR-RFLP And Genetic Effect Of Porcine Growth Hormone Gene

Posted on:2005-11-17Degree:DoctorType:Dissertation
Country:ChinaCandidate:S R ShuaiFull Text:PDF
GTID:1103360125461883Subject:Animal breeding and genetics and breeding
Abstract/Summary:PDF Full Text Request
In this thesis, full sequence of porcine growth hormone (pGH) gene of 271 samples including 11 breeds (8 native breeds and 3 foreign breeds) was amplified by PCR. The amplification products; of 61 samples were sequenced. Bst XI, ApaI, Hhal and MspI polymorphisms of 21(1 samples were detected. The polymorphisms of 61 sequences were analyzed by BioEdit( versions.0.6), DNAStar, DNAsp4.0, Areliquin2.0, Mega 2.1 and PAUP4.0(beta 10). Genetic effects of different RFLP genotypes or band-types on some important production performance were analyzed by SAS Ver 8.0.Comparison with the sequence reported by Vize et al. in 1987, the sequence of amplified pGH gene was 2107 bp including five exons and four introns. 1957 bp fragment from 64 to 2021 could be confirmed correctly. DNA polymorphism analysis showed that there were abundant Haplotype diversity and Nucleotide diversity in pGH gene. 82 mutation sites were detected, and 10 out of them were in exon regions. The number of transition was more than transversion among mutation sites. All mutation sites were neutral mutation. The polymorphism characteristic of pGH gene was different among porcine breeds.The analysis of nucleotide composition showed that GC content (over 61%) is abundant in pGH gene, and the GC content of coding regions was more than noncoding regions of 5'and 3'ends. In the ceding regions, the GC was abundant at the 1st (60.2%) and 3rd (85.5%) site of codon, and the GC was infrequent at the 2nd (41.1%) site. The GC content of codon site in growth hormone gene was different among human beings and different animal species. The analysis of codon usage indicated that the usage of synonymous codon was very biased, and the biased sorts were different among animal species.The analysis of amino acid mutation sites showed that exon 2 was the highest mutation region of pGH gene compared with other exons. 7 out of 10 mutation sites were in exon 2, and 6 out of 7 sites were nonsynonymous. There was a nonsynonymous site in exon 4, too. These amino acid mutation sites existed in difference among different porcine breeds, and which may be the molecular base to influence growth rat of different porcine breeds.The composition analysis of amino acid indicated that the content of 20 kinds of amino acid were unbalanced The most was leucine (L, 13.76%) and the least was tryptophan (W, 0.92%). According to the polarity, the content of polarity amino acid was higher than no polarity amino acid in all animals' growth hormone gene. There were 5 cysteines in mammalian growth hormone gene and only 4 cysteines existed in chicken's growth hormone gene. The primary structure characters were different among animal species. Which indicated that the receptor site of mammalian growth hormone was different from poultry.The analysis of linkage disequilibrium and recombination showed that, the mutation frequency, change direction, linkage disequilibrium sites and minimum number of recombination events in exon regions of pGH gene were different among porcine breeds. Theanalysis of synonymous (Ks) and nonsynonymous (Ka) substitution showed that Ks were higher than Ka. It proved that the mutation of exon regions existed in strong purifying selection. The molecular evolution trees of growth hormone gene showed that the evolution speed of pGH gene was different in different regions. Exon regions were more conservative than intron regions. Neijiang pig, Chenghua pig and Yanan pig lay in a same evolution branch, it was different from other branches of pig.Being digested with Apa I, the amplified 2107bp DNA segment showed 5 restriction enzyme sites, 4 alleles (A, B, C and D) and 6 genotypes (AA, AC, BC, CC, CD and DD). The distribution of 4 alleles and 7 genotypes had significant difference among porcine breeds (P< 0.05). Being digested with BstXl, the polymorphisms were only existed in native porcine breeds and no polymorphisms in Landrace and Yorkshire pigs. Hha I digestion revealed ten band-types. The distributions of the band-types among some porcine breeds were different significantly. Band...
Keywords/Search Tags:pigs, growth hormone gene, nucleotide polymorphisms, amino acid polymorphisms, molecular evolution, PCR-RFLP, genetic effect
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