Genetic relationships among Chinese and American isolates of Phytophthora sojae assessed by RAPD markers

The genetic diversity of three geographic populations of Phytophthora sojae from China and the United States was determined using random amplified polymorphic DNA （RAPD）. The purpose was to explore genetic relationships among Chinese and American isolates of the organism. 21 random primers were selected among 200 random primers screened. A total of 223 reproducible RAPD fragments were scored among 111 individuals, of which 199 （89.23%） were polymorphic. Analysis of genetic variation showed that there existed higher genetic variation in the United States population in comparison to the Chinese populations. Nei＇s genetic identity and principal component analysis indicated that the populations of Fujian and United States are closer to each other than to Heilongjiang populations. Shannon-Wiener diversity index revealed that the United States populations have a higher genetic di- versity than that of Chinese populations. These data are in support of the hypothesis that P. sojae in the United States might not have been introduced from China.     

The genetic diversity of cen-tral and peripheral popula-tions of ratlike hamster(Cricetulus triton)

The impact of habitat fragmentation and isolation on the genetic diversity of populations has attracted much attention in studies of meta-population and conservation biology. In this work, using the randomly amplified polymorphic DNA (RAPD) technique, we studied the genetic diversity of central, peripheral and peninsular populations of ratlike hamster, which were collected in five locations of the North China Plain and its surrounding areas, in 1999. The study revealed that, ⅰ) the genetic diversity of central population of Raoyang County＞the sub-central populations of Gu'an County and Taikang County＞the peripheral population of Shunyi District＞the peninsular population of Mentougou District; ⅱ) the genetic diversities of the five populations were positively correlated to the nearest distances to the peripheral line of population distribution; ⅲ) there were significant differences of gene frequencies of some RAPD fragments among the five populations. More RAPD fragments disappeared in peripheral populations than in central or sub-central populations. The frequencies of two RAPD fragments were correlated to the latitude. This study clearly indicated that the variation of the genetic diversities of the five populations was caused by edge effect and frag- mentation through the enhanced inbreeding and genetic drift, and thus supported the view that habitat fragmentation and related edge effect reduce the population genetic diversity.     

Phenotypic and genetic variation between two populations of the Chinese yellow pond turtle, Mauremys mutica （Cantor, 1842）

Mauremys mutica (Cantor, 1842) is an endangered species in China. Main phenotypic variations in body color, body weight, body shape, clutch size, egg size, and hatchling size were revealed between the southern and northern populations. Both populations have the phenomenon of "larger male" sexual size dimorphism (SSD), especially in the southern population. Furthermore, genetic variations between the two populations were analyzed by RAPD band patterns of 30 random individuals in each population. The average genetic distance was 0.299±0.108 among the samples of two populations. The average genetic distance between southern and northern populations was 0.305±0.046. Cluster analysis indicated that all the individuals from the southern and northern populations were clustered among themselves to form two distinct clades. A total of 20 population-specific RAPD fragments were scored from 16 primers, and could be used as RAPD markers for distinguishing the southern and the northern population. Based on the nucleotide sequences of two RAPD markers, two pairs of SCAR primers (SC1-S and SC2-S) were designed, which could be used as SCAR markers for the southern population. According to the significant phenotypic and genetic variations, we suggested that the northern population and southern population might be considered as two separate taxa, the "northern taxon" and the "southern taxon", and the conservation should be respectively conducted on the two taxa.     

Molecular phylogenetic status of Siberian roe deer （Capreolus pygargus） based on mitochondrial cytochrome b from Jeju Island in Korea

In order to elucidate the genetic diversity and taxonomic status of Siberian roe deer （Capreolus pygar- gus） from the Korean peninsula, partial sequences of the mitochondrial cytochrome b gene were analyzed. We col- lected 57 roe deer samples from Mainland and Jeju Island between July 2004 and June 2009. A total of 50 sequences （1,070 bp） were obtained, and seven haplotypes were defined. Five haplotypes were found from Mainland, and two were discovered from Jeju Island. The genetic diver- sity was lower in the Jeju Island population than in the Mainland population. In addition, both the consensus neighbor-joining tree and maximum parsimony tree showed an identical topology between the Mainland and Jeju Island clades. Based on the results, two subspecies of the Korean roe deer were confirmed. Siberian roe deer in Jeju Island showed a distinct difference in the cytochrome b gene compared with other Siberian roe deer, being aunique native species inhabiting only Jeju Island in Korea. Because Siberian roe deer in Jeju Island can be classified at subspecies level, the new subspecies in Jeju was named Capreolus pygargus jejuensis in this study. For this new subspecies, reasonable conservation and management effort is needed in the future.     

Genetic diversity of Tricholoma matsutake in Yunnan Province

To investigate the genetic diversity of Tricholoma matsutake,we studied ITS and IGS1 sequences and PCR polymorphism of a retrotransposon in 56 fruit bodies collected from 13 counties of 9 regions in Yunnan Province. We found one and three haplotypes based on ITS and IGS1 sequences,respectively. Moreover,there was no significant difference in PCR polymorphism of the retrotransposon among different populations. Compared with Jilin Province(China) and Japanese populations,although Yun-nan was highly homogenous to Japanese populations,low genetic diversity of T. matsutake in Yunnan did not support the view that this species originated from Yunnan.     

Genetic diversity of Chinese summer soybean germplasm revealed by SSR markers

There are abundant soybean germplasm in China. In order to assess genetic diversity of Chinese summer soybean germplasm, 158 Chinese summer soybean accessions from the primary core collection of G max were used to analyze genetic variation at 67 SSR loci. A total of 460 alleles were detected, in which 414 and 419 alleles occurred in the 80 Huanghuai and the 78 Southern summer accessions, respectively. The average number of alleles per locus was 6.9 for all the summer accessions, and 6.2 for both Huanghuai and Southern summer accessions. Marker diversity (D) per locus ranged from 0.414 to 0.905 with an average of 0.735 for all the summer accessions, from 0.387 to 0.886 with an average of 0.708 for the Huanghuai summer accessions, and from 0.189 to 0.884 with an average of 0.687 for the Southern summer accessions. The Huanghuai and Southern summer germplasm were different in the specific alleles, allelic-frequencies and pairwise genetic similarities. UPGMA cluster analysis based on the similarity data clearly separated the Huanghuai from Southern summer soybean accessions, suggesting that they were different gene pools. The results indicate that Chinese Huanghuai and Southern summer soybean germplasm can be used to enlarge genetic basis for developing elite summer soybean cultivars by exchanging their germplasm.     

Microsatellite polymorphisms of Sichuan golden monkeys

Previous study using protein electrophoresis shows no polymorphism in 44 nuclear loci of Sichuan golden monkey （Rhinopithecus roxellana）, which limits our understandings of its population genetic patterns in the nuclear genome. In order to obtain sufficient information, we scanned 14 microsatellite loci in a sample of 32 individuals from its three major habitats （Minshan, Qinling and Shennongjia）. A considerable amount of polymorphisms were detected. The average heterozygosities in the local populations were all above 0.5. The differentiations among local populations were significant. There was evidence of geneflow among subpopulations, but geneflow between Qinling and Shennongjia local populations was the weakest. Minshan and Qinling populations might have gone through recent bottlenecks. The estimation of the ratio of the effective population sizes among local populations was close to that from census sizes. Comparisons to available mitochondria data suggested that R. roxellana＇s social structures played an important role in shaping its population genetic patterns. Our study showed that the polymorphism level of R. roxellana was no higher than other endangered species; therefore, measures should be taken to preserve genetic diversity of this species.     

Population Genetic Structure and Genetic Differentiation of the Pufferfish Takifugu Rubripes and Takifugu Pseudommus Revealed by RAPD Analysis

RAPD analysis is used to assay the population genetic structure and genetic differentiation of pufferfish T.rubripes and T.pseudommus.One hundred and twenty fragments are aplified with 21 random sequence 10-mer primers.The proportion of polymorphic fragments of T.rubripes populations from the coast of China(TRC),the coast of Japan(TRJ),general population of T.rubripes both from China and Japan(TRCJ),and the population of T.pseudommus are 31.7%,33.3%,35.0%and 39.2% respectively.The mean expected heterozygosities of the four populations are 0.116,0.125,0.126,and 0.144,respectively.Low genetic distances(ranging from 0.0118 to 0.0309)and Fst estimates(0.020 to 0.024) among the populations indicated that there is no significant differentiation between T.rubripes and T.pseudommus and suggested that only one species is involved.     

High genetic diversity in population of <Emphasis Type="Italic">Lepturichthys fimbriata</Emphasis> from the Yangtze River revealed by microsatellite DNA analysis

Lepturichthys fimbriata (Günther) is one of the benthic and rock-attached fish species that is typically found in torrential flows of the upper reaches of the Yangtze River in China. Several dams in the Yangtze River (the Ertan Dam, the Three Gorges Dam, the Gezhouba Dam, the Xiluodu Dam and the Xiangjiaba Dam (the latter two dams are under construction)) may have significant effects on the habitat and spawning behaviors of L. fimbriata, and could ultimately threaten the survival of this fish. We studied the population genetic diversity of L. fimbriata samples collected at three sites within the Yangtze River and one of its tributaries, the Yalong River. Genetic diversity patterns were determined by analyzing genetic data from 14 polymorphic microsatellite loci isolated in Jinshaia sinensis (Sauvage et Dabry). A high genetic diversity among these L. fimbriata local populations was indicat- ed by the number of microsatellite alleles (A) and the expected heterozygosity. No reductions of genetic diversity in any L. fimbriata population were observed. However, significant population differentiations were observed among three local populations by pairwise comparisons (P<0.001). We deduced that L. fimbriata local populations were not small ones. In addition, the habitat behaviors of rock-attachment and possible residence of L. fimbriata could account for the genetic differences found in local populations.     

Genetic diversity in Penaeus chinensis shrimp as revealed by RAPD technique

The random amplified polymorphic DNA analysis was used to estimate genetic diversity in one successively cultivated stock and three wild stocks of Penaeus chinensis shrimp, two of which were collected from the spawning and wintering grounds in the west coast of Korean Peninsula, and one from the feeding ground in the China coast of the Yellow Sea. A random primer kit was employed to scan the genomic DNA in 20 individuals of each index stock. A total of 110 reproducible RAPD markers were obtained, 68.2 % of which showed a sound eonformability within all the individuals detected, implying that the genetic variability in P. chinensis is relatively low. The proportions of polymorphic loci among these four stocks ranged from 20% to 33.3%, while the degrees of genetic polymorphisms varied from 0.0093 to 0.0307. The genetic variability of inter-stocks was higher than that of intra-stock. The genetic diversity in different stocks differed from each other; that is, a less genetic differentiation in the spawning and wintering stocks from the west coast of Korean Peninsula was revealed and their genetic diversities were higher than that of the spawning stock in the Bohai Sea and the China coast of the Yellow Sea. As detected, the genetic diversity in the successively cultivated stock was the lowest among these four stocks. Through genetic distance analysis between a random pair of individuals, a dendrogram of the above-mentioned four stocks was constructed by unweighted pair group method with arithmetic mean. The results based on cluster analysis well fitted with the geographical distribution of P. chinensis in the Bohai and Yellow Seas.     

GENETIC DIVERSITY AMONG CHINESE SIKA DEER (CERVUS NIPPON) POPULATIONS AND RELATIONSHIPS BETWEEN CHINESE AND JAPANESE SIKA DEER

SIKA DEER,CERVUS NIPPON,WAS HISTORICALLY WIDE-SPREAD THROUGHOUT NORTHEASTERN ASIA,FROM THE USSURI REGION TO VIETNAM,INCLUDING THE KOREAN PENINSULA,MAINLAND CHINA AND TAIWAN,AND THE JAPANESE ARCHI-PELAGO,AND UP TO13SUBSPECIES HAVE BEEN DESCRIBED[1].THE FOS…     

梅花鹿抗病毒蛋白的生物信息学分析

通过在线生物软件分析梅花鹿四种抗病毒蛋白A3Z2、BST-2A、BST-2B和SAMHD1蛋白的生物信息学特性。从转录组中获得四种蛋白的基因序列,应用Prot Param、Protscale、SOPMA、TMHMM、Target P、Signal P、Motif Scan、Interproscan以及BLAST等在线软件分析蛋白的理化性质、二级结构、穿膜域、结构域等等。首次获得了四种抗病毒因子的基因和蛋白序列,梅花鹿A3Z2基因编码393个氨基酸,相对分子质量为47.59 k Da,碱性,不稳定性亲水蛋白,无信号肽和跨膜结构域,胞内定位,具有糖基化和磷酸化位点,两个胞嘧啶脱氨酶结构域。梅花鹿BST-2A和2B基因编码159个氨基酸,相对分子质量为17.69 k Da和18.12 k Da,酸性,不稳定性亲水蛋白,无信号肽,BST-2A有两个跨膜结构域,BST-2B有一个跨膜结构域,膜定位,具有糖基化和磷酸化位点。梅花鹿SAMHD1基因编码613个氨基酸,相对分子质量为70.51 k Da,碱性,不稳定性亲水蛋白,无信号肽和跨膜结构域,胞内定位,具有磷酸化位点,d NTP磷酸水解酶活性结构域。梅花鹿A3Z2、BST-2A、BST-2B和SAMHD1蛋白具有潜在的抗病毒能力。     

江西桃红岭国家级自然保护区梅花鹿种群生存力分析

梅花鹿华南亚种(Cervus nipponkopschi)是我国Ⅰ级重点保护野生动物。目前仅分布于江西、浙江、安徽等狭窄的区域内,形成多个孤立种群。根据梅花鹿种群的相关参数,借助漩涡模型Vortex 9.99,以江西桃红岭国家级自然保护区梅花鹿种群为研究对象,对其梅花鹿种群在1983年后100 a内的动态及敏感性进行了模拟分析。模型结果表明,在自然情况下,该种群在100 a内灭绝概率为0。第1阶段(1983-1998年)种群数量从60只快速增长至226只,第2阶段(1998-2011年)种群数量从226只增长到341只,第3阶段(2011-2083年)种群数量维持在352只左右,年均增长率分别为9.25%、3.32%、0.04%。虽然高死亡率、灾害延缓了种群增长的速度,近亲繁殖导致近100 a内基因杂合率下降了7.46%,但这些因素并没有显著影响桃红岭梅花鹿种群近100 a内的命运。在不考虑其它条件的情况下,环境容纳量对梅花鹿种群遗传多样性损失具有明显的影响,是限制该梅花鹿种群发展的重要因素。因此,改善生境质量,提高环境容纳量是促进该梅花鹿种群增长的有效途径。有计划的火烧、植被矮化以及开辟生境走廊,可以有效地改善鹿类环境容纳量,是当前梅花鹿保护亟待开展的工作。同时,应进一步提高当地社区居民的保护意识,杜绝偷猎盗猎,降低人类生产经营活动对梅花鹿的影响。     

中国梅花鹿地理分布的变迁

在综合化石记录、历史文献和野外资料的基础上对我国梅花鹿地理分布的变迁进行了探讨.早更新世,梅花鹿分布于华北区和台湾;中更新世至全新世,向北扩展到蒙新区的东部、东北区以及朝鲜、苏联西伯利亚东南部,向南经华中区的东部分布到广西和越南北部,另有一支经东部滨海平原迁移到了日本.川西高原的四川亚种是由华北区向西南延伸的一支演化而来.梅花鹿是适应性很强的林缘动物,其分布区急剧地缩减与晚更新世至全新世青藏高原的强烈抬升有关,更主要地是受冰期后人为活动的影响.     

植被对桃红岭保护区梅花鹿分布的影响

植被是草食动物生存的必要条件。为了解植被状况对梅花鹿分布的影响,笔者在2008年梅花鹿发情期对桃红岭保护区核心区、缓冲区和实验区内的18个点进行了调查。结果显示,植被状况直接决定梅花鹿的分布,草丛和灌草丛的植被类型适合梅花鹿生存,乔木和乔灌木不适合梅花鹿活动。保护区应制定合理的植被规划,为梅花鹿生存提供适宜的环境。     

东北梅花鹿肠道纤维素降解微生物的分离筛选

食草动物依赖胃肠道微生物分解利用天然木质纤维素物质。为获得高效纤维素降解菌，本文将东北梅花鹿粪便样品，经过研磨，重悬于羧甲基纤维素钠（CMC-Na）作为唯一碳源的富集培养基中，进行富集培养和筛选，用革兰氏碘液染色显示纤维素水解圈，通过纤维素水解圈直径（D）和菌落直径（d）比值，初步判断纤维素降解菌降解纤维素能力．筛选出106株纤维素降解微生物，包括72株细菌、22株真菌和12株放线菌．细菌16S rDNA和真菌ITS序列测序结果显示，这些纤维素降解菌主要集中分布于变形菌门（Proteobacteria）、厚壁菌门（Firmicutes）、放线菌门（Actinobacteria）和子囊菌门（Ascomycota）．本文提供了一种快速有效的反刍动物肠道纤维素降解微生物的筛选方法，为东北梅花鹿肠道微生物高通量测序结果提供实验数据支持．      

梅花鹿鹿茸软骨细胞和间充质干细胞永生化细胞株的构建及鉴定

分离梅花鹿鹿茸软骨细胞和间充质干细胞,使用SV40 LT抗原慢病毒载体建立永生化软骨细胞和间充质干细胞系并鉴定。将含有SV40 LT基因片段的慢病毒载体,转染人胚肾细胞293T获得包装后的病毒粒子,感染鹿茸软骨细胞及间充质干细胞,连续传代培养,通过形态观察、细胞增殖、real-time PCR、甲苯胺蓝染色法和流式细胞术等方法检测SV40 LT抗原表达以及细胞性质。实验所建立的永生化鹿茸软骨细胞系与间充质干细胞系能够稳定传代并具有较强的体外增值活性。RT-PCR检测到SV40T抗原的表达,通过甲苯胺蓝染色法和流式细胞术鉴定所得细胞系具有原代细胞的基本性质。成功获得永生化的软骨细胞与间充质干细胞系,为后续鹿茸生长及发育研究奠定了基础。     

基于MHCⅡ类B基因的凹耳臭蛙(Odorrana tormota)种群遗传分化模式

利用II类MHC基因单基因座位Odto-A作为分子标记,对皖南山区凹耳臭蛙6个种群的遗传多样性和遗传分化进行研究.结果显示,皖南凹耳臭蛙总的基因多样性为0.812,核苷酸多样性为0.018.局域种群单倍型多样性变化范围为0.531-0.864,香溪种群单倍型多样性最高,最低的是漳河种群.与线粒体cyt b基因所揭示的单倍型多样性差别不大,但B基因的核苷酸多样性较之线粒体cyt b基因的高达一个数量级.暗示MHC基因丰富的核苷酸多态性可能与其病原体抗性多样性密切相关.分子变异分析结果显示,皖南山区凹耳臭蛙种群MHC II类B基因遗传变异主要来源于种群内,种群间发生了显著的遗传分化(Fst=0.05644,P=0.00391).成对种群间的遗传分化分析结果显示,直线距离最近的浮溪和香溪种群间也发生了显著的遗传分化,暗示这两个种群经历了不同的选择压力.受平衡选择的作用,MHC基因与基于中性分子标记所揭示的遗传格局不同,基于MHC基因的种群遗传分化与水系和直线地理距离均没有明显的相关性,而与种群所经历的选择压力密切相关.结果表明皖南凹耳臭蛙不同局域种群所经历的环境病原体的选择压力存在时空变异.