贵州黎平黄牛线粒体DNA D-loop区全序列初步分析

为了解贵州黎平黄牛的遗传多样性及遗传背景,我们测定了20头黄牛的线粒体DNA D-loop区序列。结果检测到8种单倍型,其中4种为普通牛血统的单倍型,4种为瘤牛血统的单倍型,表明黎平黄牛同时受普通牛和瘤牛的影响。该研究对于黎平黄牛的保种及持续利用有着重要的理论指导意义。     

Phylogenetic relationships of German heavy draught horse breeds inferred from mitochondrial DNA D-loop variation

Summary We analysed a 610-bp mitochondrial (mt)DNA D-loop fragment in a sample of German draught horse breeds and compared the polymorphic sites with sequences from Arabian, Hanoverian, Exmoor, Icelandic, Sorraia and Przewalski's Horses as well as with Suffolk, Shire and Belgian horses. In a total of 65 horses, 70 polymorphic sites representing 47 haplotypes were observed. The average percentage of polymorphic sites was 11.5% for the mtDNA fragment analysed. In the nine different draught horse breeds including South German, Mecklenburg, Saxon Thuringa coldblood, Rhenisch German, Schleswig Draught Horse, Black Forest Horse, Shire, Suffolk and Belgian, 61 polymorphic sites and 24 haplotypes were found. The phylogenetic analysis failed to show monophyletic groups for the draught horses. The analysis indicated that the draught horse populations investigated consist of diverse genetic groups with respect to their maternal lineage.     

3种鼢鼠线粒体DNA控制区结构及其系统发育分析

采用PCR 产物直接测序法测定了3种鼢鼠Mospalax spp.18个个体的线粒体控制区(Control region)核苷酸全序列,并进行了结构分析。通过与仓鼠亚科其他啮齿动物的控制区序列进行比较,将鼢鼠的控制区分为终止序列区、中央保守区和保守序列区3个区域。同时识别了鼢鼠中一系列保守序列,并给出了它们的一般形式。选用普通田鼠Microtus rossiaemeridionalis、褐家鼠Rattus norvegicus、小家鼠Mus musculus、鼹鼠Nannospalax ehrenbergi为外类群,采用NJ和UPGMA法构建分子系统发育树。结果显示：鼢鼠中控制区基因适于系统发育分析,根据分子系统学、形态学的结果初步认为高原鼢鼠M.baileyi和甘肃鼢鼠M.cansus达到了种级地位。     

浙江6个地方猪种的mtDNA控制区多态性分析

本研究对淳安花猪等6个浙江地方猪种的116条mtDNA序列进行了多态性分析,参照猪群为长白猪和皖南花猪。结果显示,浙江地方猪种581 bp mtDNA控制区序列中共存在14个变异位点,群体的核苷酸多样度Pi值为0.00403±0.00036;单倍型多样度Hd值为0.835±0.018。地方猪的单倍型从Hap_5至Hap_19共15种,而长白猪为Hap_1至Hap_4。淳安花猪和皖南花猪的单倍型频率均以Hap_8为主(0.680和0.833);嘉兴黑猪以Hap_5(0.625)为主;嵊县花猪和碧湖猪均以Hap_6为主(0.500和0.375);岔路黑猪以Hap_5、Hap_8居多(0.429和0.429);金华猪有11种单倍型,频率最高的是Hap_5(0.241)。NJ系统发生树中,浙江地方猪种大致可分为5支(编号A~E),其中,淳安花猪主要出现在E支,个体数占淳安花猪样本数的68.0%(17/25);C支全为金华猪,个体数占金华猪样本数的29.3%(17/58);D支金华猪个体数占金华猪样本数的24.1%(14/58)。本研究结果表明,浙江地方猪种的mtDNA多态性较为丰富,且与长白猪在基因序列上存在明显差别。地方猪种的单倍型组成和频率与其地理分布及品种的形成特点有密切关系。     

达乌尔黄鼠线粒体Cyt b基因序列特征及其系统进化分析

在甘肃省天祝藏族自治县采集12只达乌尔黄鼠(Spermophilus dauricus),PCR产物直接测序获得Cyt b基因1140bp序列,采用Clustal X 1.84、MEGA 6.0、Dna SP 5.0等生物信息学软件进行了序列特征和系统地位分析。结果显示,达乌尔黄鼠Cyt b基因含116个多态信息位点,群体中多态位点类型有转换、颠换,Cyt b基因T,C,A,G碱基含量分别为33.7%,25.9%,27.6%,12.9%。基于Kimura双参数的遗传距离显示,属内种间大黄鼠(Spermophilus major)与新疆黄鼠(Spermophilus fulvus)间遗传距离最小(0.034),高加索黄鼠(Spermophilus musicus)与达乌尔黄鼠最大(0.172),达乌尔黄鼠群体内遗传距离为0.140,种群分化较大,基于NJ法构建的系统进化树符合传统分类标准,研究为达乌尔黄鼠Cyt b基因标记的种群遗传学应用提供了参考。     

Analysis of mitochondrial DNA protein-coding region in the Yeso Sika deer (Cervus nippon yesoensis)

In the present study, mitochondrial DNA sequences of the Yeso Sika deer (Cervus nippon yesoensis) were studied. Specifically, protein‐coding genes as mitochondrial NADH dehydrogenase subunits (ND1, ND2, ND3, ND4L, ND4, ND5 and ND6), cytochrome c oxidase subunits (CO I and CO III), ATP synthase subunits (ATPase8 and ATPase6) and cytochrome b. Also, phylogenetic analyses on eight mammalian species were performed, including the Muntjac deer (Muntiacus reevesi). The rate of amino‐acid substitution was lowest (3.74%) between Yeso Sika deer and Muntjac deer, and the values between Yeso Sika deer and other species (sheep, cattle, horse, pig, mouse, human and chimpanzee) were 6.63%, 7.30%, 12.55%, 13.03%, 23.59%, 24.82% and 25.04%, respectively. Among them, the highest value of divergence was recognized in ATPase8, and the second structure of ATPase8 showed a difference between the Yeso Sika deer and Muntjac deer as a result of the substitution of 34His→Tyr and 49Thr→Ile. In addition, we identified a substitution of an amino‐acid sequence (19Thr→Ala) between the Yeso Sika deer and Yakushima Sika deer (C. n. yakushimae). From these results, ATPase8 was also a variable region in Cervidae.     

Phylogeography of North African Amietophrynus xeros estimated from mitochondrial DNA sequences

Amietophrynus xeros was sequenced for part of the 16S rRNA mitochondrial region to assess genetic diversity between populations from Niger, Mali, Senegal, Mauritania and Tanzania. Although populations are currently unconnected, diversity within the Sahel region was relatively low, indicating that the species only expanded into this region relatively recently, perhaps after the last glacial maximum. Diversity was higher between samples from Tanzania. Some individuals of two species from previously published studies, A. garmani and A. gutturalis, share haplotypes with A. xeros, but this is likely to be due to error, possibly misidentifica-tion. Similar errors appear to exist in published studies of other North African Amietophrynusspecies such as A. regularis.     

贵州威宁黄牛线粒体DNA D-loop区全序列分析

为了解贵州威宁黄牛的遗传多样性及遗传背景，测定了19个个体的线粒体DNAD-loop区全序列。威宁黄牛D-loop区全序列中，A＋T平均含量为61．4％，G＋C含量为38．6％。经比对，共检测到威宁黄牛D-loop区8种单倍型，核苷酸多态位点45个，其中7种为普通牛血统的单倍型，1种为瘤牛血统的单倍型，表明威宁黄牛同时受到普通牛和瘤牛的影响。在威宁黄牛19个个体中，其单倍型多样度为0．715，核苷酸歧异度（π值）为2．415％，表明威宁黄牛品种的遗传多样性丰富。     

新批准的西南地区5个山羊遗传资源mtDNA D-loop遗传多样性与亲缘关系研究

为了研究新批准的西南地区5个山羊遗传资源的遗传多样性及其与其他羊种的亲缘关系,试验利用设计的引物对山羊的mtDNA D-loop序列进行了PCR扩增和测序,对序列数据进行了核苷酸多样性、单倍型和亲缘关系分析。结果表明:在西南地区新批准的5个山羊遗传资源中,大足黑山羊、黔北麻羊和酉州乌羊平均多态位点数比较接近,均高于渝东黑山羊和贵州黑山羊;大足黑山羊、黔北麻羊和酉州乌羊遗传多样性高于贵州黑山羊和渝东黑山羊;从亲缘关系来看,渝东黑山羊与板角山羊和南江黄羊亲缘关系较近,酉州乌羊与板角山羊亲缘关系最近,贵州3个羊种(贵州白山羊、贵州黑山羊和黔北麻羊)遗传距离近,大足黑山羊与乐至黑山羊遗传距离较近。说明渝东黑山羊和贵州黑山羊遗传多样性较低,需要加强遗传资源的保护和提纯;新批准的5个山羊遗传资源的遗传距离和亲缘关系与其所处的地理位置存在密切关系。     

Constant transmission of mitochondrial DNA in intergeneric cloned embryos reconstructed from swamp buffalo fibroblasts and bovine ooplasm

Although interspecies/intergeneric somatic cell nuclear transfer (iSCNT) has been proposed as a tool to produce offspring of endangered species, conflict between donor nucleus and recipient cytoplasm in iSCNT embryos has been identified as an impediment to implementation for agricultural production. To investigate the nuclear–mitochondrial interactions on the developmental potential of iSCNT embryos, we analyzed the mtDNA copy numbers in iSCNT embryos reconstructed with water buffalo (swamp type) fibroblasts and bovine enucleated oocytes (buffalo iSCNT). As controls, SCNT embryos were derived from bovine fibroblasts (bovine SCNT). Buffalo iSCNT and bovine SCNT embryos showed similar rates of cleavage and development to the 8‐cell stage (P > 0.05). However, buffalo iSCNT embryos did not develop beyond the 16‐cell stage. Both bovine and buffalo mtDNA content in buffalo iSCNT embryos was stable throughout the nuclear transfer process, and arrested at the 8‐ to 16‐cell stage (P > 0.05). In bovine SCNT embryos that developed to the blastocyst stage, mtDNA copy number was increased (P < 0.05). In conclusion, both the donor cell and recipient cytoplast mtDNAs of buffalo iSCNT embryos were identified and maintained through the iSCNT process until the 8–16‐cell stage. In addition, the copy number of mtDNA per embryo was a useful monitor to investigate nuclear–mitochondrial interactions.     

草原红牛及其杂交群体中微卫星DNA多态性研究

选用草原红牛及其与利木赞牛的杂交后代66头作为试验牛群体,提取血液及肝脏基因组DNA,设计8对微卫星引物进行PCR扩增,从分子水平上对草原红牛及其杂交群体8个位点的遗传多态性进行微卫星分析。结果表明,在草原红牛中,ETH225、IDVGA2、IDVGA46和IDVGA44等位基因数分别为5、4、3和4,多态信息含量(PIC)分别为0．5420、0．6736、0．5218和0．5750,这4个位点均为高度多态。而另4个位点BM2113、BM1824、IDVGA55和TGLA44等位基因数分别,2、2、2和5,多态信息含量分别为0．3698、0．3604、0．3538和0．4708,属于中度多态性位点。在杂交牛群体中,BM2113、ETH225、IDVGA2、IDVGA46、ID- VGA44、BM1824、IDVGA55和TGLA44这8个位点的等位基因数分别为4、5、4、4、5、4、4和6,多态信息含量(PIC)分别为0．6432、0．5943、0．6593、0．5794、0．7259、0．6121、0．6120和0．6204,杂合度为0．7034,均属于高度多态性位点。这些微卫星位点作为遗传标记应用于草原红牛遗传育种研究之中是可行的。     

3个鸡群体中4个微卫星DNA多态性及其与杂种优势的关系

利用4个微卫星标记（ADL101、MCW020、ADL183、ADL298）对玫瑰冠鸡、新罗曼鸡和安卡红鸡的等位基因频率、群体多态信息含量、有效等位基因数、杂合度和遗传距离进行了遗传检测,并测定了玫瑰冠鸡与安卡红鸡及新罗曼鸡的杂交效果。结果表明,4个微卫星标记在玫瑰冠鸡、安卡红鸡和新罗曼鸡3个群体中存在多态性,可以用于鸡遗传多样性的评估;从不同的群体来看,安卡红肉鸡遗传变异程度最大,而玫瑰冠鸡的遗传变异程度相对较小;玫瑰冠鸡与安卡红鸡的遗传距离大于其与新罗曼鸡的遗传距离,玫瑰冠鸡与安卡红鸡的杂种优势高于与新罗曼鸡的杂种优势,与实际杂种优势测定结果相符。     

甘南州蕨麻猪mtDNA D-环序列的起源及遗传多样性分析

为了研究甘南州蕨麻猪mtDNA D-环序列起源与遗传多样性,利用文献报道的1对引物对蕨麻猪mtDNA D-环序列进行PCR扩增及测序,对所得数据进行单倍型、遗传多样性、系统发育树和网络关系分析.分析结果显示,135头蕨麻猪mtDNA D-环序列表现出3种长度变异,其中4个序列长度为1 199 bp,3个序列长度是1 319 bp,127个序列长度为1 219 bp.对127个长度为1 219 bp的序列进行分析,发现83个单倍型.单倍型比例、单倍型多样度、核苷酸多样度和平均核苷酸差异数在卡加曼蕨麻猪最高,而在夏河蕨麻猪为最低.系统发育树和网络关系分析均将83个单倍型分为2个分支,说明蕨麻猪具有2个母系起源.与其他猪种mtDNA D-环序列比较,蕨麻猪与东南沿海野猪有较近的亲缘关系,没有发现东亚与东南亚野猪对蕨麻猪的起源有贡献的证据.     

The validity of different zokor species and the genus Eospalax inferred from mitochondrial gene sequences

To help resolve the systematic position of Myospalacine (zokors) and to clarify the phylogenetic relationships among zokor species, complete mitochondrial 12S rRNA and cytochrome b gene sequences were determined for seven zokor species from China. Phylogenetic relationships among all extant zokors, except the Siberian zokor (Myospalax myospalax) and Smith's zokor (Eospalax smithi), were reconstructed with the Chinese bamboo rat (Rhizomys sinensis) as an outgroup. Our results support the generic status of Eospalax and also support the validity of the specific status of Eospalax cansus, Eospalax baileyi and Eospalax rufescens.     

Complete nucleotide sequence of mitochondrial DNA in White Leghorn and White Plymouth Rock chickens

Among the chicken breeds, White Leghorn (WL) and White Plymouth Rock (WR) are major breeds and have different history in their establishments. Whole mitochondrial DNA of the breeds were sequenced in order to elucidate the genetic relationship between the breeds. The lengths of the two WL and two WR mitochondrial DNA were found to be 16 788 and 16 785 base pairs, respectively. When the DNA sequences were compared, the similarity was found to be 99.96% (six nucleotide differences). In addition, the present study conformed the existence of an extra nucleotide ‘C’ in NADH dehydrogenase subunit 3 (ND3) of the chicken mitochondrial DNA, which has been consistently observed in Galliformes.     

The Eurasian Steppe is an important goat propagation route: A phylogeographic analysis using mitochondrial DNA and Y‐chromosome sequences of Kazakhstani goats

Goats (Capra hircus) were domesticated in the Fertile Crescent and propagated all over the world. The Silk Road through the Eurasian Steppe belt is a possible propagation route for domestic goats to Central Asia. Kazakhstan is in close geographical proximity to domestication centers and covers the majority of the Eurasian Steppe belt. In this study, we examined the genetic diversity and phylogeographic structure of Kazakhstani goats. The mtDNA sequences of 141 Kazakhstani goats were categorized into haplogroups A, C, and D, of which haplogroup A was predominant (97%), whereas haplogroups C and D were detected at low frequencies (1.4% each). The Kazakhstani haplotypes C were thzen categorized into Asian mtDNA type. Sequence analysis of the SRY gene on the Y‐chromosome in 67 male Kazakhstani goats revealed two haplotypes: Y1A (64%) and Y2A (36%). Analysis of the distribution of mtDNA haplogroups and SRY haplotypes from Eurasia and Africa demonstrated genetic similarity among animals from Kazakhstan, Mongolia, and Northwest China located on the Eurasian Steppe belt. These phylogeographic results suggested that the Eurasian Steppe belt was an important propagation route for goats to Central Asia.     

Defect of the mitochondrial DNA hypervariable region as a risk factor for canine mammary tumour

The aim of this study was to identify mutations in the hypervariable region of mitochondrial DNA in canine mammary tumours and to determine their association with the process of neoplastic transformation. A total of 93 biological samples, including blood as well as normal and neoplastic tissue samples from 31 dogs with diagnosed malignant canine mammary tumours were analysed. DNA extraction, amplification and sequencing of the D‐loop as well as bioinformatic and statistical analyses were performed. In the mitochondrial D‐loop sequence, 26 polymorphic loci and 5 mutations were identified. For the first time, D‐loop length heteroplasmy was detected in dogs with mammary tumours. The malignancy grade exerted no effect on the presence of nucleotide changes. A statistically significant association between the presence of mutations and polymorphisms and the size of dogs was demonstrated. The 100% frequency of length heteroplasmy may imply that this is a hotspot mutation of canine mammary tumour.     

波尔山羊和山西省地方山羊品种微卫星DNA多态性分析及群体间杂种优势预测

（方法）利用5个微卫星标记对山西省5个山羊品种遗传多态性进行分析,（目的）以预测波尔山羊与地方山羊品种的杂种优势,为山西省肉用山羊新品种培育及波尔山羊在山西省合理杂交利用提供理论依据。（结果）5个山羊品种共检测到70．0个等位基因,各位点的等位基因数在9．0～21．0之间;经群体遗传统计分析,5个山羊品种平均有效等位基因数4．94～6．05个,平均多态信息含量0．7053～0．7982,平均基因杂合度0．7592～0．8316。5个山羊品种间遗传分化系数0．0607;波尔山羊与吕梁黑山羊的标准遗传距离最大（0．5083）,其余依次为阳城白山羊（0．4474）、洪洞奶山羊（0．4332）、黎城大青羊（0．3301）。（结论）5个微卫星位点均为高度多态位点,可用于5个山羊品种遗传多样性评估;5个山羊品种在5个微卫星位点多态性丰富,遗传变异大,品种间遗传分化小。据品种间遗传距离推测,波尔山羊与吕梁黑山羊的杂种优势最大,与阳城白山羊和洪洞奶山羊的杂种优势次之,与黎城大青羊的杂种优势最小。     

基于RAPD和SSR分子标记的家蚕部分实用品种多态性及其亲缘关系分析

分子标记是生物系统进化和亲缘关系分析的重要手段。利用RAPD和SSR标记对12个家蚕实用品种的基因组DNA进行多态性分析和聚类分析。采用21条RAPD引物对12个品种的基因组DNA扩增产生的清晰稳定条带数为196条,其中多态性片段143条,多态位点比例72.96%,品种间的遗传距离在0.157～0.352之间。采用32条SSR引物对12个品种的基因组DNA扩增产生的片段数为86条,其中多态性带80条,多态性位点比例93.02%,遗传距离在0.214～0.600之间。对12个家蚕品种的2种分子标记的单独聚类结果表现出一定差异,但均把12个品种分为中系、日系两大类,其中7532和湘晖、871和57B的亲缘关系较近,而传统分类于中系品种东34却聚类于日系,但又独立于其余6个日系品种。结合RAPD标记和SSR标记的12个品种间的遗传距离与聚类结果,更能准确地从分子水平上反映品种间的亲缘关系及其来源,是家蚕杂交育种亲本选择的依据。     

Lineages differentiation and population structure of the light‐vented bulbul Pycnonotus sinensis in China based on mitochondrial DNA and microsatellite analysis

The light‐vented bulbul Pycnonotus sinensis is a small resident passerine that is found widely in central and south China, North Vietnam, and some East Asian islands, including Hainan, Taiwan and the Ryukyu Islands. Its subspecies status has been under considerable debate. A total of 10 subspecies have been proposed, but only 4 are widely recognized, including 1 continental taxon, P. s. sinensis, and 3 insular subspecies: P. s. hainanus, P. s. formosae and P. s. orii. Two mitochondrial DNA genes and 9 microsatellite loci were used to investigate the genetic divergence of this species, to identify the evolutionary status of 2 insular subspecies (P. s. hainanus and P. s. formosae) and to uncover probable historical causes that shaped them. The results reveal that P. s. formosae has diverged significantly from the other 2 subspecies because of a substantial time of isolation for populations on Taiwan Island. There was no significant genetic differentiation between P. s. sinensis and P. s. hainanus. The notable morphological difference in P. s. hainanus might be attributed to a rapid, recent adaptation to the tropical environment of Hainan Island. The low genetic divergence between P. s. sinensis and P. s. hainanus might result from a recent divergence or gene flow between them. Two insular subspecies of light‐vented bulbul populations might have diverged recently from their continental relatives through a complex evolution history owing to island isolation, ecological isolation, and possibly even hybridization. Both P. s. hainanus and P. s. formosae should be considered important conservation units because of their morphological and genetic distinctiveness.