家养动物线粒体DNA最新研究进展

线粒体DNA多态性研究对于了解家养动物的驯化历史十分重要.本文对家猪、黄牛、水牛、马、驴、绵羊、山羊与家鸡的线粒体DNA多态性最新研究进展作了总结.通过mtDNA D-loop研究,发现家养动物都是通过野生动物多次驯化而来,可能有多个驯化地点,表现出复杂的驯化历史.     

Mitochondrial diversity of native pigs in the mainland South and South-east Asian countries and its relationships between local wild boars

In this study, we analyzed DNA sequence of mitochondrial DNA (mtDNA) control regions on the 130 native domestic pigs and eight wild boars in the mainland South and South-east Asian countries including Bhutan, Cambodia, Laos, Myanmar, and Vietnam. Forty-four haplotypes were found in the 138 individuals, 41 were in the domestic and four were in wild boars. Only one haplotype was shared by domestic and wild population in Bhutan. In other cases, mtDNA of wild boars did not show close affinity to that of the domestic pigs in the same location, indicating that the native domestic pigs in these countries did not originate in the present habitat. Phylogenetic analyzes of mtDNA haplotypes recapitulated several major clusters identified in other studies, but 11 haplotypes were grouped in a new cluster we named MTSEA. In most cases, more than one lineage group were present in a sampling station, indicating that the present indigenous domestic pigs may have multiple origins. The MTSEA haplotypes were present in relatively high frequencies in domestic pigs in the mountainous area of mainland South-east Asia (Cambodia and Laos), with a few found in Myanmar and Bhutan. The distributions of MTSEA haplotypes are in great conformity with the distribution of present-day Mon-Khmer language and indicated the existence of yet another independent domestication. The D2 haplotypes that distribute high frequency (almost 100%) throughout the Chinese breeds were dominant in Bhutan, Myanmar, and Vietnam. These results suggest an existence of human-mediated dispersal of domestic pigs from north to the south during the historical expansion of Sino-Tibetan and Tai peoples. The D3 haplotypes previously reported in north India were found in sympatric domestic and wild pigs in Bhutan. The D3 haplotype is an important proof of independent domestication event and/or great gene flow between wild and domestic pigs in the foot of Himalaya.     

Genetic diversity of Chinese domestic goat based on the mitochondrial DNA sequence variation

The aim of this study was to characterize the genetic diversity of domestic goat in China. For this purpose, we determined the sequence of the mitochondrial DNA (mtDNA) control region in 72 individuals of the Yangtze River delta white goat, and reanalysed 723 published samples from 31 breeds/populations across China. All goat haplotypes were classified into four haplogroups (A–D) previously described. The phylogenetic pattern that emerged from the mtDNA control region sequence was confirmed by the analysis of the entire cytochrome b sequence of eight goats representative of the four haplogroups. It appeared that in Chinese domestic goat, haplogroups A and B were dominant and distributed in nearly all breeds/populations, while haplogroups C and D were only found in seven breeds/populations. Four breeds/populations contained all four haplogroups. When grouping the breeds/populations into five geographic groups based on their geographic distributions and ecological conditions, the southern pasturing area had the highest diversity whereas the northern farming area had the lowest diversity. 84.29% and 11.37% of the genetic variation were distributed within breeds and among breeds within the ecologically geographical areas, respectively; only 4% of genetic variation was observed among the five geographic areas. We speculate that the traditional seasonal pastoralism, the annual long-distance migrations that occurred in the past, and the commercial trade would account for the observed pattern by having favoured gene flows.     

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.     

中国9个家驴品种mtDNA D-loop部分序列分析与系统进化研究

本研究利用Dnasp4.10软件对中国9个家驴品种162个个体的mtDNA D-loop区385bp进行遗传多样性分析,共检测到32种单倍型35个核苷酸多态位点,其单倍型多样度为0.8137～0.9722,核苷酸多样度为0.0182～0.0270,表明我国家驴的遗传多态性丰富;利用MEGA3.1软件采用邻接法与3个努比亚野驴、3个索马里野驴和6个亚洲野驴的序列构建NJ系统发育树,并进行系统进化分析。结果表明:我国家驴的母系起源是非洲野驴中的努比亚野驴和索马里野驴,亚洲野驴不是中国家驴的母系祖先。     

Mitochondrial DNA diversity and the origin of Chinese indigenous sheep

Large-scale mitochondrial DNA (mtDNA) D-loop sequences data from previous studies were investigated to obtain genetic information which contributes to a better understanding of the genetic diversity and history of modern sheep. In this study, we analyzed mtDNA D-loop sequences of 963 individuals from 16 Chinese indigenous breeds that distributed seven geographic regions. Phylogenetic analysis showed that all three previously defined haplogroups A, B, and C were found in all breeds among different regions except in Southwest China mountainous region, which had only the A and B haplogroups. The weak phylogeographic structure was observed among Chinese indigenous sheep breeds distribution regions and this could be attributable to long-term strong gene flow among regions induced by the human migration, commercial trade, and extensive transport of sheep. The estimation of demographic parameters from mismatch analyses showed that haplogroups A and B had at least one demographic expansion of indigenous sheep in China.     

中国家驴mtDNA D-loop 遗传多样性与起源研究

对我国12个家驴品种126个个体（包括引用26个个体）的mtDNA D-loop区399 bp进行分析,共检测到36种单倍型37个多态位点,其单倍型多样度为0.466 7-0.977 8,核苷酸多样度为0.001 2-0.028 5,表明我国家驴的遗传多态性丰富。与3条努比亚野驴、3条索马里野驴和6条亚洲野驴的序列构建NJ系统发育树,首次证明我国家驴的母系起源为非洲野驴中的索马里驴和努比亚驴,亚洲野驴不是中国家驴的祖先。本文还讨论了我国家驴可能的迁徙路线。     

The phylogenetic status of typical Chinese native pigs: analyzed by Asian and European pig mitochondrial genome sequences

China is one of the most diverse countries, which have developed 88 indigenous pig breeds. Several studies showed that pigs were independently domesticated in multiple regions of the world. The purpose of this study was to investigate the origin and evolution of Chinese pigs using complete mitochondrial genomic sequences (mtDNA) from Asian and European domestic pigs and wild boars. Thirty primer pairs were designed to determine the mtDNA sequences of Xiang pig, Large White, Lantang, Jinhua and Pietrain. The phylogenetic status of Chinese native pigs was investigated by comparing the mtDNA sequences of complete coding regions and D-loop regions respectively amongst Asian breeds, European breeds and wild boars. The analyzed results by two cluster methods contributed to the same conclusion that all pigs were classified into two major groups, European clade and Asian clade. It revealed that Chinese pigs were only recently diverged from each other and distinctly different from European pigs. Berkshire was clustered with Asian pigs and Chinese pigs were involved in the development of Berkshire breeding. The Malaysian wild boar had distant genetic relationship with European and Asian pigs. Jinhua and Lanyu pigs had more nucleotide diversity with Chinese pigs although they all belonged to the Asian major clade. Chinese domestic pigs were clustered with wild boars in Yangtze River region and South China.     

中国水牛的遗传多样性与起源分化

中国水牛资源丰富,主体上为沼泽型水牛,主要分布于我国的热带和亚热带地区其在我国南方地区的农业生产中发挥着重要作用.与其他家养动物相比,中国水牛的遗学研究起步较晚.已有的研究结果表明,中国沼泽型水牛的染色体数为2n=48,其与河流传型水牛的杂种后代群体存在染色体数的多态性;早期的血液蛋白与同工酶座位的遗传检测显示,中国水牛各地方类群间遗传差异小,遗传关系较近;而近年微卫星 DNA 标记和 mtDNA标记检测结果显示,其群体遗传多样性较为丰富,且存在一定的遗传分化.考古发现及近年的分子遗传学研究揭示沼泽型和河流型水牛是在不同的地点独立驯化而来,中国可能是沼泽型水牛最初驯化之地.     

Interpopulation and intrapopulation maternal lineage genetics of the Lanyu pig (Sus scrofa) by analysis of mitochondrial cytochrome b and control region sequences

The Lanyu pig is an indigenous breed from the Lanyu Islet, which is southeast of Taiwan. Two herds of Lanyu pigs were introduced from the Lanyu Islet into Taiwan in 1975 and 1980. The current population of conserved Lanyu pigs consists of only 44 animals with unknown genetic lineage. The Lanyu pig possesses a distinct maternal genetic lineage remote from Asian and European pigs. The present study aimed to understand the phylogenetic relationship among conserved Lanyu, Asian, and European type pigs based on the cytochrome b coding gene, to ascertain the maternal lineage and genetic diversity within the conserved Lanyu pigs, and to address whether genetic introgression from exotic or Formosan wild pigs had occurred in the conserved Lanyu pigs. Entire mitochondrial genomes of both types of Lanyu pig comprised 2 ribosomal RNA, 22 transfer RNA, and 13 protein-coding genes. Only 2 haplotypes of the mitochondrial DNA (mtDNA) control region and cytochrome b were identified in the conserved Lanyu pig herds. When maximum likelihood trees were constructed, the Type I Lanyu mitochondrial genes formed a unique clade with a large pairwise distance of both cytochrome b and the control region from Asian and European type breeds, Formosan wild pigs, and exotic breeds. Significant loss of genetic diversity of mtDNA within the conserved Lanyu pigs was demonstrated by low haplotype and nucleotide diversities, supported by Fu and Li's D* neutrality test (1.44055; P < 0.05). The mtDNA control region sequences of extant pigs in the Lanyu Islet, however, showed high haplotype and nucleotide diversity, and clustered with exotic pigs. These results indicate no maternal lineage mtD-NA gene introgression from Formosan wild pigs and introduced exotic pigs to conserved Type I Lanyu pigs, and a severe loss of heterozygosity of mtDNA in conserved Lanyu pigs. The remaining extant pigs on the Lanyu Islet have been introgressed with exotic breeds. Strategies for future conservation of native Lanyu pigs are now even more urgent and important.     

Genetic variation in domestic and wild elk (Cervus elaphus)

Elk (Cervus elaphus) have recently been established as domestic livestock derived from extant wild populations and may provide insights into changes in genetic variation during domestication. We compared genetic variation at 10 microsatellite DNA loci and the mitochondrial DNA D-loop in 2 herds of domestic elk in Alaska and Canada and wild elk from 8 locations in western North America and Asia. Average individual heterozygosity was 0.55 in domestic elk and 0.47 in wild elk, average number of alleles per locus was 4.1 in domestic elk and 3.9 in wild elk, and 4 mitochondrial DNA haplotypes were observed in domestic elk and 3 in wild elk. Levels of genetic variation were not significantly different among the domestic elk and wild elk we analyzed. Our results are consistent with other studies showing that genetic variation can be maintained in domestic and wild populations of elk and other deer with appropriate management.     

Genetic profile and serosurvey for virus infections of Japanese wild boars in Shikoku Island

To estimate the genetic background of Japanese wild boars inhibiting the 4 prefectures of Shikoku Island (Kagawa, Tokushima, Kouchi and Ehime), we examined haplotypes of mitochondrial DNA (mtDNA) and genotypes of the nuclear glucosephosphate isomerase-processed pseudogene (GPIP) in 189 wild boars. Of the 8 different mtDNA haplotypes (J5, J10, J12, J13, J15, J19, J20 and E33) detected in Shikoku Island, the first to be identified were J19 and J20 (of Japanese wild boar lineage) and E33 (of European domestic pig lineage). The presence of haplotype E33 indicates local crossbreeding between wild boar and escaped domestic pigs and/or crossbred Inobuta. Four kinds of the GPIP genotypes were detected from 189 wild baors in Shikoku Island, but no European GPIP alleles were found. In 113 wild boars, no antibodies against Classical Swine Fever or Aujeszky's disease were detected, suggesting that they had not been exposed to those pathogens.     

Biochemical constituents in domestic and wild horses I. Serum proteins, electrolytes and metabolites

Serum chemical determinations were made in groups of domestic and wild horses under various conditions of restraint and captivity. Results obtained differed very little from normal horse values, but did vary between groups. In general, few differences between males and females within groups were seen, but recently captured wild horses varied from domestic horses and wild horses held in captivity. The stress of capture and confinement was thought to have affected some of the measured parameters.     

中国矮马与普氏野马的亲缘关系

产于中国西南山地的矮马是一种珍贵的资源,它的优良品质可以与原产于设得兰群岛的欧洲矮马媲美。本文研究了产自广西德保的中国矮马骨骼标本,通过与欧洲矮马的对比,发现它们之间的头骨、颊齿和肢骨上都 存在较大的差异,显然亲缘关系较远。而中国矮马与普氏野马的头骨的比例上却相当一致,头骨在马属的系统演化中具有非常重要的意义,因此,这一结果证明中国矮马与普氏野马有密切的亲缘关系。尽管从汉代起中国已广泛引入西方马种     

Biochemische Polymorphismen und Haupt-mtDNA-Haplo-typen bei Bergschafrassen und Waldschafen als Beitrag zur Abstammung der Hausschafe

Biochemical polymorphisms and major mtDNA haplotypes in Bergschaf breeds and Waldschaf as contribution to descent of domestic sheep Morphological similarities between domestic sheep and certain subspecies of Ovis ammon L. 1758 are not necessarily proof of the domestication of a specific subspecies, as crossbreeding of foreign wild sheep populations of different genetic origin with domestic sheep could have led to observed similarities. The maternal inherited mitochondrial genome offers the opportunity to trace modern domestic sheep breeds across numerous generations to presumptive wild ancestors regardless of domestication induced morphological changes and crossbreeding, etc. An investigation based on haplotype specific HinfI – mtDNA fragments and protein polymorphisms in different mountain sheep breeds thought to represent maternal descendants of the Torfschaf as well as in the Waldschaf breed, which belongs to the Zaupel group, were used to help clarify if the major European mtDNA haplotype B was associated with the Torfschaf (Ovis aries palustris RÜTIMEYER 1862), the oldest domesticated sheep in Europe. Samples derived from Steinschaf of the Slovenian and Bavarian type, white and brown varieties of Bergschaf, Brillenschafe from Bavaria and Villnösserschafe showed haplotype B. A single investigated ram of the Bergamasker breed was of the same haplotype. mtDNA haplotype A was detected in more than 50% of the Waldschaf animals. This demonstrates that not all sheep breeds derived from Zaupelschaf are descendants of the same wild ancestor. Within haemoglobin (HBB) the variants HBB^A and HBB^B occur in a well balanced pattern in all breeds investigated, while the frequency of HBB^A was high (0.857) in the brown Bergschaf. Steinschafe of Bavarian type were polymorphic at the CA2‐locus and Waldschafe at the GC‐locus. At the transferrin locus, differences in the occurrence and frequency of the different alleles could be demonstrated between populations. Relationships between Torfschaf, Kupferschaf, Steinschaf, Zaupelschaf, Bergamasker and European Mouflon are discussed. It is likely that the domesticated ancestors of most European sheep can be traced from the Torfschaf to an as yet unknown wild sheep (Ovis ammon) subspecies in Asia.     

Genetic diversity of Bangladeshi native chickens based on complete sequence of mitochondrial DNA D-loop region

ABSTRACT

1. The aim of this study was to explore genetic diversity and possible origin of Bangladeshi (BD) native chickens. The complete mtDNA D-loop region was sequenced in 60 chickens representing five populations; naked neck, full feathered, Aseel, Hilly and autosomal dwarf. The 61 reference sequences representing different domestic chicken clades in China, India, Laos, Indonesia, Myanmar, and other Eurasian regions were included. The mtDNA D-loop sequence polymorphism and maternal origin of five BD populations were analysed.

2. A total of 35 polymorphic sites, and 21 haplotypes were detected in 60 mtDNA D-loop sequences. The haplotype and nucleotide diversity of the five populations were 0.921 ± 0.018 and 0.0061 ± 0.0019, respectively. Both mtDNA network and phylogenetic analysis indicated four clades (four haplogroups) in BD populations (21 haplotypes) along with 61 reference haplotypes. Clade E contained the most individuals (20) and haplotypes (11) of BD chickens, followed by clade D (17, 6), clade C (12, 2) and clade F (11, 2), respectively.

3. The higher number of unique haplotypes found in Yunnan, China, suggested that the origin of BD chickens was in this region. The haplotypes from different haplogroups were introduced in Bangladeshi chickens from India, China and Myanmar. The phylogenetic tree showed a close relationship of BD chickens with the clusters from India, China, Myanmar and Laos, and indicated the dispersion of BD chickens from these sources. The phylogenetic information revealed high genetic diversity of BD chickens because of their origin from different lineages with high genetic variation and distance, which was determined from four cluster and neighbour-joining trees.

4. In conclusion, BD populations had high genetic diversity. The mtDNA network profiles and phylogenetic trees showed multiple maternal origins of BD chickens from India, China, Myanmar and Laos.     

家猪起源的研究进展

家猪作为重要的家养动物,它的起源、驯化、扩散是依赖于人类的活动与迁移而实现的。研究家猪的起源和驯化具有重要的意义。本文介绍了家猪和野猪的特点,以及家猪起源和驯化的考古学发现,并着重综述了家猪驯化的分子生物学证据的研究进展。     

The novel polymorphism of the beta 3-adrenergic receptor gene and its distribution in domestic pigs and wild boars in Asia

The beta 3‐adrenergic receptor (ADRB3) is a G protein‐coupled receptor that is involved in regulating energy homeostasis. We have studied DNA sequences of porcine ADRB3 to find candidate genetic polymorphisms for economically important growth and performance traits in pigs. Five novel haplotypes derived from the three In/dels and 44 SNPs were identified among domestic pigs and wild boars. Three of them encode non‐synonymous amino acid sequences by five missense polymorphisms and a frameshift by a thymine insertion. The amino acid polymorphic sites were distributed as follows: one substitution was in extracellular loop 1, three substitutions were in intracellular loop3 and one substitution and the deletion of two amino acids were at the carboxyl‐terminal. There was no polymorphism in the transmembrane domains. In addition, we surveyed the allelic frequency of the thymine insertion that cause frameshift in South‐east Asian local pigs, including some commercial breeds and wild boars. This thymine insertion was distributed widely in the domestic pigs and wild boars. The frequencies of this allele were relatively low in Western improved breeds, while they were very common in Asian breeds and wild boars in Asia. This result indicates that this insertion originally occurred in ancient Asian wild boars and then circulated among Asian domestic pigs. This allele also spread over Western breeds, probably through the introgression of Asian pigs into European stocks during the 18th and 19th centuries.     

Genetic diversity and structure of the West Balkan Pramenka sheep types as revealed by microsatellite and mitochondrial DNA analysis

Several different phenotypes of the native Pramenka sheep have been developed in the Balkan region for different environmental and socio‐cultural conditions. Animals from seven West Balkan Pramenka sheep types were analysed for 15 microsatellite markers and for mitochondrial DNA (mtDNA) and the results were used to assess genetic variation within and among the types and to infer the genetic population structure of the Pramenka sheep. Mean expected heterozygosity and allelic richness over the microsatellite loci and sheep types were 0.78 and 7.9, respectively. A Bayesian statistical method for estimating hidden genetic structure suggested that a core of the largest panmictic population was formed by Serbian, Kosovan, Bosnian, Montenegrin and Albanian types, while Croatian and Macedonian types comprised two other main populations, respectively. Mitochondrial DNA analysis revealed two mtDNA haplogroups in the Pramenka sheep, B and A, with a frequency of 93.7% and 6.3%, respectively. A total of 60 mtDNA haplotypes were found in 64 animals sequenced, and the mean nucleotide and haplotypic diversities over the types were 0.013 and 0.945, respectively. Molecular analysis suggests that the West Balkan Pramenka sheep types have their origins in two distinct maternal lineages of domestic sheep and different Pramenka phenotypes tend to form few panmictic populations. The Pramenka sheep represents a valuable resource of genetic diversity in sheep.     

我国当地野生草坪地被植物的研究进展

从资源调查、生态生物学特性、引种驯化、坪用特性等方面对我国当地野生草坪地被植物的研究现状进行了阐述,对我国今后城市草坪绿化的趋势进行了分析,并为合理开发利用当地野生草坪地被植物提出了建议.