家鹅线粒体DNA tRNApro和tRNAthr基因序列与结构分析

采用PCR和DNA测序技术测定了6个中国家鹅品种和2个欧洲鹅品种25个个体线粒体tRNApro(69 bp)和tRNAthr(68 bp)基因的完整序列,通过对家鹅线粒体基因组的研究,首次报道了家鹅线粒体tRNApro和tRNAthr基因的结构,对鸿雁、灰雁、白额雁(Anser albifrons,序列号为AF363031)雁属种间tRNApro和tRNAthr基因的二级结构及序列的变异特征进行了分析,并通过家鸡(Gallus gallus domesticus,序列号为NC001323)与鸿雁家鹅间tRNApro和tRNAthr基因二级结构的比较,初步进行了鸡形目与雁形目两个目间tRNApro和tRNAthr基因二级结构及序列变异的分析.结果表明:家鹅tRNApro和tRNAthr基因均可折叠成标准的三叶草形二级结构; 2个tRNA基因三叶草结构的氨基酸臂、反密码子环在鸿雁、灰雁和白额雁种间以及鸡形目与雁形目两个目间没有变异,具有高度的保守性.本研究的结果将为进一步探讨家鹅线粒体DNA tRNApro和tRNAthr基因序列与结构、功能的关系奠定基础.所测的序列已登录GenBank数据库,序列号为AY427800～AY427805和AY427812～AY427814.     

暗纹东方鲀线粒体COI及其侧翼tRNA基因的克隆与序列分析

以暗纹东方鲀(Takifugu fasciatus)肝脏的线粒体DNA为模板,按照红鳍东方鲀线粒体DNA序列设计合成特异引物进行PCR扩增,克隆并测定了线粒体细胞色素氧化酶I亚基（COI）及其侧翼tRNA基因的全序列,结果显示,克隆了暗纹东方鲀COI基因1546bp及其5′端上游的tRNATyr基因和3′端下游的tRNASer基因序列共1766bp。用DNA分析软件对暗纹东方鲀与GenBank中10个目13种鱼类的COI序列进行比较分析,显示暗纹东方鲀与这些鱼类的COI基因具有较高的同源性,与同属红鳍东方鲀的同源性最高为97.6%,与同目不同科的矛尾翻车鲀和翻车鲀的同源性为76.5%和75.4%。根据暗纹东方鲀与其他13种鱼的COI基因序列同源性所建立的进化树,与传统的分类地位基本吻合。推定的这二种tRNA的二级结构都具有典型的三叶草型结构。     

鹅的起源分化和相关雁类的分子系统发生研究

运用线粒体DNA的限制性片段长度多态性(mtDNA RFLP)技术和随机扩增多态DNA(RAPD)技术对中国鹅的4个品种、欧洲鹅的2个品种以及2种野雁--鸿雁(Anser cygnoides)和灰雁(Anser anser)的遗传变异进行了分析,探讨了中国鹅和欧洲鹅的起源、分化及相关雁类的系统发生关系.     

北京鸭线粒体基因组全序列测定和分析

线粒体DNA作为遗传标记,已在家鸡(Gallus gallus)和家鹅(Anser anser)的研究中取得了重大进展,而对家鸭(Anas platyrhychos domesticus)的研究却很少.本研究参照近源物种线粒体基因组序列设计15对引物,通过PCR扩增、测序、拼接,获得北京鸭(A.platyrhychos)线粒体基因组全序列,初步分析其特点和各基因的定位.结果显示,北京鸭线粒体基因组全长16 604 bp,碱基组成为29.19%A、22.20%T、15.80%G、32.81%C,包含13个蛋白质编码基因、2个rRNA基因、22个tRNA基因和1个非编码控制区(D-loop),基因组成及排列顺序与其他鸟类相似.基于线粒体D-loop区全序列,用N-J法构建了7种雁形目鸟类系统进化树,结果表明,北京鸭与绿头鸭(A.platyrhychos)系统进化关系较近.     

基于线粒体DNA D-loop区序列的我国灰鹅遗传多样性和起源分析

为了探究我国灰鹅品种的遗传多样性和系统进化,运用DNA测序技术测定了我国13个灰鹅品种mtDNAD-loop区521bp序列。结果表明:这13个灰鹅品种521bpD-loop区序列的T、C、A和G碱基含量分别为23.8%、29.0%、32.3%和15.0%;平均单倍型多样度和核苷酸多样度分别为0.19245和0.00036;13个灰鹅种间变异大于种内变异,且均未出现群体扩张现象;共享单倍型和系统进化树分析表明,伊犁鹅起源于灰雁(Anser anser),其余12个灰鹅品种起源于鸿雁(A.cygnoides)。     

短额负蝗线粒体基因组及其lrRNA和srRNA二级结构分析

采用长距PCR扩增及保守引物步移法测定并注释了短额负蝗的线粒体基因组全序列。结果表明,短额负蝗的线粒体基因组全长15558bp,A T含量为74.3%,37个基因位置与飞蝗的一致,基因间隔序列共计11处64bp,间隔长度从1～16bp不等;有15对基因间存在51bp重叠,重叠碱基数在1～8bp之间。13个蛋白质编码基因中找到6种可能的起始密码子,有12个基因在基因3'端能找到完全的TAA或TAG终止密码子,只有ND5基因终止密码子为不完整的TA。除tRNASer(AGN)外,其余21个tRNA基因的二级结构均属典型的三叶草结构。tRNASer(AGN)的DHU臂缺失,在相应的位置上只形成一个环。预测的lrRNA二级结构总共有6个结构域(结构域Ⅲ缺失),49个茎环结构。预测的srRNA的二级结构包含3个结构域,33个茎环结构。A T丰富区中存在一个被认为与复制及转录起始有关的Ploy(T)(T-stretch)结构。     

家鹅品种细胞色素b基因序列分析及其系统发育关系

测定了15个中国家鹅和2个欧洲家鹅品种44个个体线粒体细胞色素b基因全序列（1143 bp）,并结合GenBank中的野生种白额雁序列比较分析表明,检测到31个可变位点和4种单倍型,没有发现缺失或插入,核苷酸多样度和单倍型多样度分别为0.00648和0.45,密码子第三位点G碱基的含量较低（14.2%）,A、T和C的含量极相似,第一、二位点的偏倚度（0.057和0.223）低于第三位点（0.492）,转换数明显高于颠换数(Ts/Tv＝9.5～19),密码子第三位点的转换数最高。系统发育分析结果支持中国家鹅的两个不同起源学说。     

短额负蝗线粒体基因组及其lrRNA和srRNA二级结构分析

采用长距PCR扩增及保守引物步移法测定并注释了短额负蝗的线粒体基因组全序列。结果表明，短额负蝗的线粒体基因组全长15 558 bp，A+T含量为74.3%，37个基因位置与飞蝗的一致，基因间隔序列共计11处64 bp，间隔长度从1～16 bp不等；有15对基因间存在51 bp重叠，重叠碱基数在1～8 bp之间。13个蛋白质编码基因中找到6种可能的起始密码子，有12个基因在基因3＇端能找到完全的TAA或TAG终止密码子，只有ND5基因终止密码子为不完整的TA。除tRNA^Ser（AGN）外，其余21个tRNA基因的二级结构均属典型的三叶草结构。tRNA^Ser（AGN）的DHU臂缺失，在相应的位置上只形成一个环。预测的lrRNA二级结构总共有6个结构域（结构域Ⅲ缺失），49个茎环结构。预测的srRNA的二级结构包含3个结构域，33个茎环结构。A+T丰富区中存在一个被认为与复制及转录起始有关的Ploy（T）（T-stretch）结构。     

长江中下游湿地大型水鸟种群动态和幼鸟比例研究

迁徙水鸟保护对生物多样性保护具有重要意义。开展水鸟种群数量和幼鸟比例监测,对科学评估其种群变化趋势、制定长期保护策略具有重要价值。长江中下游湿地是东亚-澳大利西亚迁徙路线上重要的水鸟越冬区之一。本研究采用野外同步调查等方法对该区域87个湿地的亟需保护和具有代表性的10种大型越冬水鸟,其中雁形目6种,分别是鸿雁Anser cygnoides、豆雁A.fabalis、灰雁A.grus、白额雁A.albifrons、小白额雁A.erythropus和小天鹅Cygnus columbianus;鹤形目4种,分别是白鹤Leucogeranus leucogeranus、白枕鹤Antigone vipio、灰鹤Grus grus和白头鹤G.monacha,进行了长期监测(2003—2019年冬季),并结合相关文献,评估其种群变化趋势、幼鸟比例和死亡率。研究结果如下：(1)2005—2019年3种水鸟(豆雁、灰雁和灰鹤)的种群数量呈上升趋势,7种水鸟(鸿雁、白额雁、小白额雁、小天鹅、白鹤、白枕鹤和白头鹤)种群数量呈下降趋势;(2)种群趋势下降组(N=7)和上升组(N=3)的幼鸟比例均值在2016—2...     

牛胚系基因中两种 JH 和 Cμ抗体基因的克隆与分析

根据NCBI GenBankTM中登录的2个牛抗体重链可变区J基因(JH)(序列号为AY158087,AY149283)的序列不同之处设计PCR引物,能从同一个体的Holstein牛基因组DNA中扩增得到与以上2个基因分别相同的序列,证明这2个JH基因的差异不是由于牛个体或品种不同引起的.提取牛脾脏总RNA,RT-PCR扩增IgM cDNA,测序结果显示:序列号为AY149283的JH基因中第六外显子JH6是一个功能基因,它可以编码牛IgM的部分CDR3区和完整的FR4区,从2种IgM cDNA克隆的测序结果可以看出,其恒定区序列分别与序列号为U63637和AY230207的2种抗体重链恒定区μ基因(Cμ)cDNA序列相同.PCR扩增JH-Cμ序列,测序结果表明:序列号为AY158087的JH基因是同以上2种Cμ基因分别串连在一起的(序列号分别为AY230207和U63637).以上结果证明:序列号为U63637和AY230207的2个Cμ基因分别与AY149283的JH基因串联在一起,都能够参与牛IgM的产生,它们与AY158087的JH基因共同存在于同一个体Holstein牛胚系基因中.     

Mitochondrial DNA Cleavage Patterns Distinguish Independent Origin of Chinese Domestic Geese and Western Domestic Geese

It has generally been assumed, based on morphology, that Chinese domestic goose breeds were derived from the swan goose (Anser cygnoides) and that European and American breeds were derived from the graylag goose (Anser anser). To test the validity of this assumption, we investigated the mtDNA cleavage patterns of 16 Chinese breeds and 2 European breeds as well as hybrids produced between a Chinese breed and a European breed. After 224 mtDNAs, isolated from the Chinese and European breeds, were digested by 19 restriction endonucleases, variations of the cleavage patterns were observed for four enzymes (EcoRV, HaeII, HincII, and KpnI). All Chinese breeds and their maternal hybrids except the Yili breed showed an identical haplotype, named haplotype I or the Chinese haplotype; the European breeds and the Yili breed showed another haplotype, named haplotype II or the western haplotype. None of the haplotype found in the Chinese type was detectable in the western type and vice versa. The two haplotypes were found to differ from each other at 8.0% of the sites surveyed and with a 0.72% sequence divergence. Using 2% substitution per million years calibrated from the genera Anser and Branta, the two domestic geese haplotypes were estimated to have diverged approximately 360,000 years ago, well outside the 3000-6000 years in domestic history. Our findings provide the first molecular genetic evidence to support the dual origin assumption of domestic geese in the world. Meanwhile, the four mtDNA restriction fragment length polymorphisms can be used as maternal genetic markers to distinguish the two types of domestic geese.     

The cytogenetics of domestic geese

Hybrids were produced between an African male and several Pilgrim female domestic geese. Partial karyotypes revealed a difference in the fourth largest pair of autosomal chromosomes. This chromosome pair was metacentric in the African, submetacentric in the Pilgrim, and heteromorphic in the hybrids. A similar difference between the putative wild ancestors of the African and Pilgrim breeds has been reported by others. These findings provide cytological evidence to support the traditional opinion that the African breed was derived from the Asiatic swan goose (Anser cygnoides) and the Pilgrim breed was derived from the European greylag goose (Anser anser).     

The Origin of the White Roman Goose

In order to avoid interference from nuclear copies of mitochondrial DNA (numts), mtDNA of the white Roman goose (domestic goose) was extracted from liver mitochondria. The mtDNA control region was amplified using a long PCR strategy and then sequenced. Neighbor-joining, maximum parsimony, and maximum-likelihood approaches were implemented using the 1,177 bp mtDNA control region sequences to compute the phylogenetic relationships of the domestic goose with other geese. The resulting identity values for the white Roman geese were 99.1% (1,166/1,177) with western graylag geese and 98.8% (1,163/1,177) with eastern graylag geese. In molecular phylogenetic trees, the white Roman goose was grouped in the graylag lineage, indicating that the white Roman goose came from the graylag goose (Anser anser). Thus, the scientific name of the white Roman goose should be Anser anser ‘White Roman.’     

Relationship between wild greylag and European domestic geese based on mitochondrial DNA

The origins of the European domestic goose are uncertain. The available information comes from archaeological findings and historical literature, but genetic evidence has hitherto been scarce. The domestic goose in Europe is derived from the greylag goose (Anser anser), but it is not known where the initial domestication took place and which of the two subspecies of greylag goose was ancestral. We aimed to determine the amount and geographical distribution of genetic diversity in modern populations of greylag geese as well as in different breeds of the domestic goose to make inferences about goose domestication. We studied DNA sequence variation in the mitochondrial control region of greylag geese from multiple populations across Europe and western Asia as well as specimens of domestic geese representing 18 modern breeds and individuals not belonging to any recognised breed. Our results show notable differences in genetic diversity between different greylag goose populations and the presence of six mitochondrial haplogroups which show a degree of geographical partitioning. The genetic diversity of the domestic goose is low, with 84% of sampled individuals having one of two major closely related haplotypes, suggesting that modern European domestic geese may derive from a narrow genetic base. The site of domestication remains unresolved, but domestic geese in Turkey were unusually diverse, indicating the importance of further sampling in the vicinity of the eastern Mediterranean and the Near East. There appears to be past or ongoing hybridisation between greylags and domestic geese in particular areas, consistent with field observations.     

中国主要家鹅品种的遗传分化研究

利用PCR和DNA测序技术扩增了15个中国家鹅品种线粒体DNA控制区部分序列（1042bp）。研究结果表明：伊犁鹅与14个品种间的核苷酸分歧度最高,为3．805％～4．067％;不同品种内核苷酸多样度表现出较大的差异,为0～0．116％。除伊犁鹅外的14个家鹅品种中,豁眼鹅与其他品种间的核苷酸分歧度为0．211％～0．272％,明显高于其他品种间的0～0．094％。中国家鹅品种的遗传分化格局与地理分布有关,豁眼鹅的分歧时间较早,遗传漂变是导致豁眼鹅遗传分化的主要因素（Nm=0．02～0．54）,基因流则是另外13个家鹅品种间遗传分化不明显的主要因素（Nm=12．0～65．33）．     

鸿雁卵、家鹅卵主要物理性状的比较研究

通过对鸿雁卵和家鹅卵的主要物理性状指标的测定、计算,获得它们的蛋型指数,蛋壳厚度,蛋白、蛋黄和蛋壳在总重量中各自所占比例等实际指标,经统计分析分别得出了蛋重和蛋黄重,蛋重与壳比例,蛋壳厚度与壳的比例等几对性状之间的相对系数。结果表明：家鹅卵重量大于鸿雁卵,鸿雁卵蛋壳厚度大于家鹅卵,而两者的其他物理性状的变化规律基本一致。     

Genetic structure among greater white‐fronted goose populations of the Pacific Flyway

An understanding of the genetic structure of populations in the wild is essential for long‐term conservation and stewardship in the face of environmental change. Knowledge of the present‐day distribution of genetic lineages (phylogeography) of a species is especially important for organisms that are exploited or utilize habitats that may be jeopardized by human intervention, including climate change. Here, we describe mitochondrial (mtDNA) and nuclear genetic (microsatellite) diversity among three populations of a migratory bird, the greater white‐fronted goose (Anser albifrons), which breeds discontinuously in western and southwestern Alaska and winters in the Pacific Flyway of North America. Significant genetic structure was evident at both marker types. All three populations were differentiated for mtDNA, whereas microsatellite analysis only differentiated geese from the Cook Inlet Basin. In sexual reproducing species, nonrandom mate selection, when occurring in concert with fine‐scale resource partitioning, can lead to phenotypic and genetic divergence as we observed in our study. If mate selection does not occur at the time of reproduction, which is not uncommon in long‐lived organisms, then mechanisms influencing the true availability of potential mates may be obscured, and the degree of genetic and phenotypic diversity may appear incongruous with presumed patterns of gene flow. Previous investigations revealed population‐specific behavioral, temporal, and spatial mechanisms that likely influence the amount of gene flow measured among greater white‐fronted goose populations. The degree of observed genetic structuring aligns well with our current understanding of population differences pertaining to seasonal movements, social structure, pairing behavior, and resource partitioning.     

Genetic diversity of swan goose (Anser cygnoides L.) in Russia: Analysis of the mitochondrial DNA control region polymorphism

Using to analysis of hypervariable fragment polymorphism in the control region of mitochondrial DNA(268 bp), the genetic variability of Swan goose Anser cygnoides L., included in the first category of endangered species in the Russian Red Book, has been investigated. Samples from the two main groups nesting in Russia—the Far Eastern group (Khabarovsk krai, n = 38) and the Dauric group (Chita region, n = 10) were examined. Eleven haplotypes were described. The genetic diversity of Swan geese was low comparable with that observed in some other globally endangered Eurasian goose species. Nucleotide and haplotype diversity of goose from Khabarovsk krai was 0.0031 and 0.65, respectively; in those from Chita region, 0.0041 and 0.80; and for in total group, 0.0074 and 0.77, respectively. No identical haplotypes in Swan goose from Far Eastern and Daurical groups have been demonstrated. However, the small sample size does not allow us to make final conclusions on the degree of genetic differentiation between these groups.