中国产绒山羊品种父系与母系起源的分子特征及遗传分化
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摘要
试验对中国部分产绒山羊品种完整的SRY基因编码区、线粒体DNA (mtDNA) D-loop区和细胞色素b (Cyt b)基因进行了测序,并结合GenBank中野山羊序列进行了遗传多样性及系统发育关系分析,以期为中国绒山羊品种遗传资源的保护和利用提供科学依据,本论文内容概述如下。
试验成功克隆了雄性产绒山羊个体SRY基因整个编码区,其长度为723bp,共编码240个氨基酸。中国产绒山羊SRY基因的HMG-box区长度为231bp,位于编码区的第190位核苷酸与第420位核苷酸之间,共编码H64-A140的77个氨基酸;不同物种间SRY基因编码区序列比较分析结果支持了SRY基因在进化中高度保守的观点;通过PCR产物纯化、克隆测序的方法测定了中国11个产绒山羊品种150个个体的mtDNA D-loop区全序列,共检测到144个变异位点,群体遗传多样性丰富。基于序列的失配分布和Fu’s Fs中性检验表明,中国产绒山羊群体在历史上可能发生过群体扩张事件。基于PCR产物纯化回收、克隆测序的方法测定了中国产绒山羊线粒体Cyt b基因全序列,结果显示其全长为1140bp,编码379个氨基酸和一个终止密码子;中国产绒山羊mtDNA Cyt b基因共检测到21个变异位点,共定义了26种单倍型。基于11个中国产绒山羊品种mtDNA D-loop和Cyt b基因全序列定义的单倍型,结合GenBank中野山羊mtDNA D-loop和Cyt b基因序列,构建的系统发育树和中介网络图结果均显示,中国产绒山羊与捻角型野山羊(Capra falconeri)的母系关系密切,提示中国产绒山羊很可能起源于捻角型野山羊(Capra falconeri),但中国产绒山羊品种间系统分化不明显,呈现弱的遗传结构。
China has the richest cashmere goat genetic resources in the word. The origin of cashmere goats has long been considered a valuable research field in goat evolution. Many Chinese researchers have done much work on the origin of Chinese indigenoug goat breeds. But we have little knowledge on the origin, genetic differentiation, and breed genetic status of Chinese indigenous cashmere goats. In the present work, the complete control (D-loop) region and Cyt b gene of mitochondrial DNA and SRY gene coding region were sequenced in Chinese cashmere goat breeds, and were analyzed by combining the corresponding sequences of wild goats available in GenBank, in order to search for genetic markers on Y chrosome and mt DNA genome, and investigate deeply the molecular characterization of male and female origin in Chinese cashmere goat breeds, as well as, illuminate the quality characteristic of Chinese cashmere goat breeds from molecular level.These results will provide scientific basis for the genetic resource protection and utilization of Chinese cashmere goats. The conclusions are as follows in this work.
(1) The fragment of SRY gene containing entire encoding region of male cashmere goat was cloned with a pair of designed primers based on the sequence of goat SRY gene sequence from GenBank. The results are as follows. The entire coding region of China cashmere goat SRY gene was 723 bp in length, encoding a peptide with 240 amino acid residues, and it contains the HMG-box with 231bp between position 190 and 420, encoding 77 amino acid residues (H64-A140). We analyzed the first structure and predicted the secondary structure and the three-dimensional structure of SRY protein, as well as, the component of SRY amino acid, characterization, structure domain and three-dimensional structure of SRY protein were also analyzed in the present work. The results showed that SRY proteinw of cashmere goats are hydrophilic without signal peptide and transmembrane region, and they have some characteristics of regulator proteins. They have three helixes and their space structure is the shape of“L”, as same as the known human SRY protein. The corresponding nucleotide sequences in GenBank of goat, sheep, cattle, yak, water buffalo, forest musk deer, alpine musk deer, sika deer, hog deer, red deer, moose, white-lipped deer, elk, and pig had identities of 100%, 97.0%, 89.2%, 89.2%, 88.3%, 87.1%, 86.9%, 86.1%, 86.3%, 86.3%, 86.4%, 86.1%, 86.5% and 67.4%, and the deduced amino acid sequences had identities of 100%, 95.4%, 83.3%, 83.3%, 82.5%, 80.0%, 79.1%, 77.5%, 77.9%, 77.9%, 79.5%, 78.3%, 78.7%, and 55.7%, respectively, with the cashmere goat. These results supported well the viewpoint that SRY gene is rather conservative in evolution of species. The clustering based on the sequences of encoding region and deduced amino acid of SRY gene among species is generally in agreement with the classic taxonomic relationship. Therefore, SRY gene coding region might be useful in the construction of phylogenetic tree among different species.
(2) Based on the method of purified PCR products sequencing, complete sequence of mitochondrial DNA (mtDNA) D-loop region was sequenced in 150 individuals from 11 China cashmere goat breeds. The complete sequence of mtDNA D-loop region is 1,212 or 1,213 bp in length. 144 sites were polymorphic (11.88% in 1,213) with 120 parsimony informative polymorphic sites, 24 singleton polymorphic sites and one insertion/deletion in 1075 sites. High number of nucleotide difference, nucleotide diversity and haplotype diversity were manifested in analyzed cashmere goat populations. All sequence polymorphic sites defined 94 haplotypes. Many breeds had its unique haplotypes, and the distributions and frequencies were unequilibrium either among breeds or within breeds. The average number of nucleotide differences, haplotype diversity, and nucleotide diversity of different breed range from 9.448 to 20.385, from 0.886 to 0.982, and from 0.0079 to 0.0172, respectively, indicating there is a rich genetic diversities in China cashmere goat breeds. The curve of nucleotide mismatch distributions in 11 China cashmere goat breeds took on a near unimodal, and the Fu’s Fs neutrality test was significant (Fs= -23.9175, P<0.01) indicating that China cashmere goats might undergo expansions.
(3) The complete sequence of Cyt b gene, which is a encoding protein gene, was sequenced in 55 individuals from 11 China cashmere goat breeds based on the method of purified PCR products sequencing. The complete sequence was 1140 bp in length that coded 379 amino acids and one termination. 21 sites were polymorphic with 15 parsimony informative polymorphic sites and 6 singleton polymorphic sites. The mutations of 6 sites including site 190, 287, 743, 728, 905 and 111 caused the amino acid changes. All sequence polymorphic sites defined 26 haplotypes. The haplotype frequencies, haplotype diversity and average number of nucleotide differences of different breeds range from 0.200 to 1.000, from 0.000 to 1.000, and from 0.000 to 3.200, respectively. Rich adenine presented in the 1st codons, while the 2nd had rich thymine. The base composition showed more bias at 3rd codon with the lowest guanine content (average only 4%). There was an obvious bias in codon usage of Cyt b gene.
(4) Phylogenetic trees of NJ, ME and UPGMA method and median-joining network map were constructed based on the haplotypes defined from the sequences of mtDNA D-loop with wild goat sequences from GenBank. The results showed that there was a close genetic relationship between China cashmere goat and Capra falconeri, suggesting China cashmere goats might origin from Capra falconeri, while there no obvious divergence among China cashmere goats. The Kimura 2-parameter distances, number of nucleotide differences, number of nuc. subs. per site, and FST value between breeds range from 0.00916 to 0.01677, 10.95111 to 19.87662, 0.00904 to 0.01640, -0.02054 to 0.13538, respectively. On the whole, the result of NJ phylogenetic trees based on genetic distances of Kimura 2-parameter and Dxy of mtDNA D-loop sequences were in accordance with geographical relationship of main producing region for these cashmere breeds. But, for a few breeds, the multidimensional scaling plot of pairwise FST values constructed by SPSS software were not in accordance with geographical relationship of main producing region, indicating a weak geographical structure among breeds. The hierarchica components of mtDNA D-loop variation computed under the analysis of molecular variance (AMOVA) framework showed that smaller percentage existed among breeds (5.48%), while 94.16% within breeds with significant differences (P<0.001), indicating there were no significant divergence and weak genetic structure among breeds. The clustering and median-joining network based on the sequences of Cyt b gene were generally in agreement with that of mtDNA D-loop sequences.
试验成功克隆了雄性产绒山羊个体SRY基因整个编码区,其长度为723bp,共编码240个氨基酸。中国产绒山羊SRY基因的HMG-box区长度为231bp,位于编码区的第190位核苷酸与第420位核苷酸之间,共编码H64-A140的77个氨基酸;不同物种间SRY基因编码区序列比较分析结果支持了SRY基因在进化中高度保守的观点;通过PCR产物纯化、克隆测序的方法测定了中国11个产绒山羊品种150个个体的mtDNA D-loop区全序列,共检测到144个变异位点,群体遗传多样性丰富。基于序列的失配分布和Fu’s Fs中性检验表明,中国产绒山羊群体在历史上可能发生过群体扩张事件。基于PCR产物纯化回收、克隆测序的方法测定了中国产绒山羊线粒体Cyt b基因全序列,结果显示其全长为1140bp,编码379个氨基酸和一个终止密码子;中国产绒山羊mtDNA Cyt b基因共检测到21个变异位点,共定义了26种单倍型。基于11个中国产绒山羊品种mtDNA D-loop和Cyt b基因全序列定义的单倍型,结合GenBank中野山羊mtDNA D-loop和Cyt b基因序列,构建的系统发育树和中介网络图结果均显示,中国产绒山羊与捻角型野山羊(Capra falconeri)的母系关系密切,提示中国产绒山羊很可能起源于捻角型野山羊(Capra falconeri),但中国产绒山羊品种间系统分化不明显,呈现弱的遗传结构。
China has the richest cashmere goat genetic resources in the word. The origin of cashmere goats has long been considered a valuable research field in goat evolution. Many Chinese researchers have done much work on the origin of Chinese indigenoug goat breeds. But we have little knowledge on the origin, genetic differentiation, and breed genetic status of Chinese indigenous cashmere goats. In the present work, the complete control (D-loop) region and Cyt b gene of mitochondrial DNA and SRY gene coding region were sequenced in Chinese cashmere goat breeds, and were analyzed by combining the corresponding sequences of wild goats available in GenBank, in order to search for genetic markers on Y chrosome and mt DNA genome, and investigate deeply the molecular characterization of male and female origin in Chinese cashmere goat breeds, as well as, illuminate the quality characteristic of Chinese cashmere goat breeds from molecular level.These results will provide scientific basis for the genetic resource protection and utilization of Chinese cashmere goats. The conclusions are as follows in this work.
(1) The fragment of SRY gene containing entire encoding region of male cashmere goat was cloned with a pair of designed primers based on the sequence of goat SRY gene sequence from GenBank. The results are as follows. The entire coding region of China cashmere goat SRY gene was 723 bp in length, encoding a peptide with 240 amino acid residues, and it contains the HMG-box with 231bp between position 190 and 420, encoding 77 amino acid residues (H64-A140). We analyzed the first structure and predicted the secondary structure and the three-dimensional structure of SRY protein, as well as, the component of SRY amino acid, characterization, structure domain and three-dimensional structure of SRY protein were also analyzed in the present work. The results showed that SRY proteinw of cashmere goats are hydrophilic without signal peptide and transmembrane region, and they have some characteristics of regulator proteins. They have three helixes and their space structure is the shape of“L”, as same as the known human SRY protein. The corresponding nucleotide sequences in GenBank of goat, sheep, cattle, yak, water buffalo, forest musk deer, alpine musk deer, sika deer, hog deer, red deer, moose, white-lipped deer, elk, and pig had identities of 100%, 97.0%, 89.2%, 89.2%, 88.3%, 87.1%, 86.9%, 86.1%, 86.3%, 86.3%, 86.4%, 86.1%, 86.5% and 67.4%, and the deduced amino acid sequences had identities of 100%, 95.4%, 83.3%, 83.3%, 82.5%, 80.0%, 79.1%, 77.5%, 77.9%, 77.9%, 79.5%, 78.3%, 78.7%, and 55.7%, respectively, with the cashmere goat. These results supported well the viewpoint that SRY gene is rather conservative in evolution of species. The clustering based on the sequences of encoding region and deduced amino acid of SRY gene among species is generally in agreement with the classic taxonomic relationship. Therefore, SRY gene coding region might be useful in the construction of phylogenetic tree among different species.
(2) Based on the method of purified PCR products sequencing, complete sequence of mitochondrial DNA (mtDNA) D-loop region was sequenced in 150 individuals from 11 China cashmere goat breeds. The complete sequence of mtDNA D-loop region is 1,212 or 1,213 bp in length. 144 sites were polymorphic (11.88% in 1,213) with 120 parsimony informative polymorphic sites, 24 singleton polymorphic sites and one insertion/deletion in 1075 sites. High number of nucleotide difference, nucleotide diversity and haplotype diversity were manifested in analyzed cashmere goat populations. All sequence polymorphic sites defined 94 haplotypes. Many breeds had its unique haplotypes, and the distributions and frequencies were unequilibrium either among breeds or within breeds. The average number of nucleotide differences, haplotype diversity, and nucleotide diversity of different breed range from 9.448 to 20.385, from 0.886 to 0.982, and from 0.0079 to 0.0172, respectively, indicating there is a rich genetic diversities in China cashmere goat breeds. The curve of nucleotide mismatch distributions in 11 China cashmere goat breeds took on a near unimodal, and the Fu’s Fs neutrality test was significant (Fs= -23.9175, P<0.01) indicating that China cashmere goats might undergo expansions.
(3) The complete sequence of Cyt b gene, which is a encoding protein gene, was sequenced in 55 individuals from 11 China cashmere goat breeds based on the method of purified PCR products sequencing. The complete sequence was 1140 bp in length that coded 379 amino acids and one termination. 21 sites were polymorphic with 15 parsimony informative polymorphic sites and 6 singleton polymorphic sites. The mutations of 6 sites including site 190, 287, 743, 728, 905 and 111 caused the amino acid changes. All sequence polymorphic sites defined 26 haplotypes. The haplotype frequencies, haplotype diversity and average number of nucleotide differences of different breeds range from 0.200 to 1.000, from 0.000 to 1.000, and from 0.000 to 3.200, respectively. Rich adenine presented in the 1st codons, while the 2nd had rich thymine. The base composition showed more bias at 3rd codon with the lowest guanine content (average only 4%). There was an obvious bias in codon usage of Cyt b gene.
(4) Phylogenetic trees of NJ, ME and UPGMA method and median-joining network map were constructed based on the haplotypes defined from the sequences of mtDNA D-loop with wild goat sequences from GenBank. The results showed that there was a close genetic relationship between China cashmere goat and Capra falconeri, suggesting China cashmere goats might origin from Capra falconeri, while there no obvious divergence among China cashmere goats. The Kimura 2-parameter distances, number of nucleotide differences, number of nuc. subs. per site, and FST value between breeds range from 0.00916 to 0.01677, 10.95111 to 19.87662, 0.00904 to 0.01640, -0.02054 to 0.13538, respectively. On the whole, the result of NJ phylogenetic trees based on genetic distances of Kimura 2-parameter and Dxy of mtDNA D-loop sequences were in accordance with geographical relationship of main producing region for these cashmere breeds. But, for a few breeds, the multidimensional scaling plot of pairwise FST values constructed by SPSS software were not in accordance with geographical relationship of main producing region, indicating a weak geographical structure among breeds. The hierarchica components of mtDNA D-loop variation computed under the analysis of molecular variance (AMOVA) framework showed that smaller percentage existed among breeds (5.48%), while 94.16% within breeds with significant differences (P<0.001), indicating there were no significant divergence and weak genetic structure among breeds. The clustering and median-joining network based on the sequences of Cyt b gene were generally in agreement with that of mtDNA D-loop sequences.
引文
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