三个黄颡鱼群体遗传多样性及亲缘关系的微卫星标记分析

利用微卫星标记技术对3个黄颡鱼群体(W S、TE和QF)的遗传多样性及亲缘关系进行研究。通过筛选的30个引物对3个黄颡鱼群体基因组DNA的扩增,获得了19个有效引物,其中有6个微卫星位点具有多态性,并计算出了3个黄颡鱼群体间的遗传相似系数和遗传距离,TE和QF群体间的遗传相似系数最大(0.8736),遗传距离最小(0.1790);W S和QF群体间的遗传相似系数最小(0.7284),遗传距离最大(0.2768)。同时运用聚类分析(UPGMA)的方法建立了3个黄颡鱼群体的系统发生树。     

利用微卫星标记分析东平湖黄颡鱼的遗传多样性

采用27对鲤微卫星引物对山东东平湖黄颡鱼进行全基因组扫描,结果有19对引物能获得稳定的扩增条带,其中有6个微卫星位点具有多态性。对这6个位点的扩增产物进行分析,结果显示:6个位点共检测到22个等位基因,每个位点的等位基因数从2个到6个不等;平均基因纯合率为41.67%,平均多态信息含量(PIC)为0.488,平均杂合度为0.5833。这表明东平湖黄颡鱼种群结构合理,群体遗传多样性较丰富,种质资源处于安全状态。     

三个野生群体日本囊对虾遗传多样性的SSR分析

为了解野生种群日本囊对虾遗传分化和改良遗传育种,用SSR技术对福建厦门(XM)、广东湛江(ZJ)、广西北海(BH)3个地区野生日本囊对虾进行遗传多样性的研究。采用了10对微卫星引物对3个野生种群进行分析,10个微卫星位点在3个种群中均表现为高度的多态性,每个位点平均检测到3.87个等位基因;平均多态信息含量为0.5893;3个群体的观测杂合度分别为0.6243、0.5704、0.4661,全部群体观测杂合度平均为0.5536;期望杂合度分别为0.7193、0.6189、0.6226,全部群体平均期望杂合度为0.6536。这说明3个野生种群在10个微卫星位点上均具有丰富的遗传多样性。基于Nei's遗传距离的聚类分析显示厦门群体和湛江群体的遗传距离较近。     

长江中下游黄鳝遗传多样性的微卫星分析

为了解我国长江中下游地区野生黄鳝(Monopterus albus)的种质资源现状,利用黄鳝微卫星分子标记分析我国长江中下游4个黄鳝野生群体(湖北群体、安徽群体、江苏群体和浙江群体)的遗传多样性水平.通过磁珠富集法获得50个黄鳝徽卫星序列,设计并合成了30对微卫星引物,经筛选得到8对多态性稳定的引物,均为高度多态位点.每对引物扩增得到等位基因数12 -26,平均等位基因数17.4个群体的平均多态信息含量分别为0.804、0.864、0.824和0.736,平均等位基因数分别为9.13、11.00、9.00和7.25,平均期望杂合度分别为0.865、0.918、0.882和0.813,表明4个黄鳝群体遗传多样性丰富,其中安徽群体遗传多样性水平最高,浙江群体相对较低.4个群体间遗传分化指数(FsT)为0.031 2-0.096 5,6.28％的遗传变异存在于群体间,表明4个群体间存在一定的遗传分化.聚类分析显示,浙江群体与安徽群体先聚在一起,再与江苏群体聚为一支,湖北群体单独聚为一支.     

稀有鮈鲫近交系微卫星多态性分析

利用17对微卫星引物对稀有鮈鲫（Gobiocypris rarus）野生群体和近交系F20和F22进行了遗传分析。结果表明在野生群体中17个微卫星位点均为多态位点,但在F20中仅有6个多态位点,F22中则仅有4个多态位点。在野生群体中共检测到64个等位基因,F20、F22分别为26、21个。近交系的平均基因纯合率均较高,其中F20为86.18%,F22达91.96%,而野生群体平均基因纯合率为46.84%。近交系平均杂合度和平均多态信息含量均较野生群体低。在近交系F20和F22中,群体间遗传相似性指数最大,其遗传距离最小,说明二者之间的亲缘关系最近。HAN系遗传多样性明显降低,已具有较高的遗传纯度。     

长江中上游两个鲢群体遗传变异的微卫星分析

对长江中上游2个鲢群体使用39个微卫星标记进行了遗传多样性分析, 计算并统计了平均观测等位基因数、平均有效等位基因数、多态信息含量、遗传杂合度、Hardy-Weinberg平衡偏离指数、遗传相似系数、遗传距离等遗传参数。结果表明: 万州鲢和监利鲢群体所检测微卫星位点的平均观测等位基因数分别为6.128和4.974; 平均有效等位基因数分别为4.107和3.395; 多态位点百分率分别为100和94.87; 39个微卫星标记共有等位基因259个, 173个等位基因为两群体所共有; 多态微卫星位点的PIC在0.077~0.865之间变动,平均为0.617; 两群体所检测位点平均观测杂合度为0.834和0.775, 平均期望杂合度为0.713和0.623; 两个群体间的遗传相似系数为0.618, 群体间的遗传距离为0.482。结果显示长江中上游两个鲢群体间存在显著遗传分化, 应隶属于不同的种群。     

宽口光唇鱼微卫星位点的筛选与特征分析

通过FIASCO法(Fast Isolation by AFLP Sequences Containing Repeats)筛选宽口光唇鱼Acrossocheilus monticola(Günter)基因组微卫星位点,利用生物素标记的寡核苷酸探针(AC)8、(CT)8、(GGT)8、(GATA)8和(GATT)7首次成功构建宽口光唇鱼基因组微卫星富集文库。从文库中共筛选495个克隆测序,成功设计163对微卫星引物,经PCR扩增检测,获得了18个多态性微卫星标记。利用这18对多态性引物,分析了赤水河赤水市宽口光唇鱼种群的遗传多样性,数据显示:18对多态性微卫星引物的等位基因数为8～31个,平均等位基因数为19.6个,平均期望杂合度为0.8701,平均观测杂合度为0.8312,其中引物Am07、Am35、Am47、Am69、Am78和Am127显著偏离哈迪温伯格平衡(P<0.05),以上数据表明赤水河赤水市宽口光唇鱼种群的遗传多样性水平较高。筛选的微卫星标记对于宽口光唇鱼的遗传背景分析和生物种质资源的保护有重要作用。     

湘江野鲤养殖群体和自然群体遗传多样性的微卫星分析

采用微卫星技术,用17对微卫星引物对湘江野鲤养殖群体和自然群体的的遗传多样性进行分析.结果表明:有15对引物扩增出清晰的条带,其中13对引物在群体间呈现多态性;2个群体中,13对多态性引物分别扩增等位基因2～12个,共90个,其中35个等位基因为2群体共有,55个等位基因具有群体特异性,引物平均等位基因数为6.92个,等位基因频率为0.0667～0.8333;养殖群体和自然群体的平均遗传杂合度和平均多态信息含量分别为0.5688、0.5152,0.5860、0.5347;2个群体间遗传相似性指数为0.6762,遗传距离为0.3238,表明湘江野鲤养殖和自然群体遗传多样性均较为丰富,2个群体间遗传变异程度较高.     

雄性普通黄颡鱼与所保护受精卵间的亲缘关系分析

父母通过保护自己的子代来确保其繁殖的成功率.在普通黄颡鱼(Pelteobagrus fulvidraco)中,雄性普通黄颡鱼具有筑巢产卵保护后代的习性,其所保护的子代与其是否有亲缘关系是有待探讨的问题.本文利用10对微卫星分子标记鉴定12窝普通黄颡鱼受精卵与护卵鱼之间的亲缘关系,并对子代的遗传多样性进行分析.在单亲鉴定中,累积非父排除概率为0.9986,平均父权相对机会(RCP)在99.989%-99.999%之间,每个子代在10个微卫星位点上的累积PI值在2006.73-604464.07之间.同时在亲权鉴定分析中,发现3窝卵子的等位基因来自2个母亲,说明雄性黄颡鱼可以和2条雌性黄颡鱼发生交配;在遗传多样性分析中,黄颡鱼子代的平均等位基因数为11.7, 无偏观测杂合度值(Ho)在0.2473-0.9866之间,多态信息含量(PIC)值0.7096-0.8993之间.通过亲权鉴定分析,可以确认看护受精卵的雄性普通黄颡鱼与受精卵间的亲子关系.     

梅花鹿3个种群遗传多样性的微卫星标记分析

利用16个微卫星标记对黑龙江省部分地区(兴凯湖农场、大庆市银浪牧场、五大连池大庆农场鹿苑)的3个梅花鹿(Cervus nippon)群体进行了遗传多样性检测.统计了3个鹿群的等位基因组成、平均有效等位基因数(Ne)、平均遗传杂合度(h)和多态信息含量(PIC).结果表明,除5个位点外,其余11个微卫星位点均表现出不同的多态信息含量,其中高度多态位点5个,中度多态位点4个.这说明本研究所选用的微卫星位点可较准确地评估3个梅花鹿群体的遗传多样性,并为今后相关研究筛选出了有价值的引物.3个梅花鹿群体的平均h在0.454～0.636之间变动,其中兴凯湖梅花鹿群体最高,为0.636,具有较大的遗传潜力.     

Genomic evidence for the population genetic differentiation of Misgurnus anguillicaudatus in the Yangtze River basin of China

Misgurnus anguillicaudatus, an important aquatic species, is mainly distributed in the Yangtze River basin. To reveal the population genetic structure of M. anguillicaudatus distributed in the Yangtze River basin, genotyping by sequencing (GBS) technique was employed to detect the genome wide genetic variations of M. anguillicaudatus. A total of 30.03 Gb raw data were yielded from 70 samples collected from 15 geographic sites located in the Yangtze River basin. Subsequently, 2092 high quality SNPs were genotyped across these samples and used for a series of genetic analysis. The results of genetic analysis showed that high levels of genetic diversity were observed and the populations from upper reaches (UR) were significantly differentiated from the middle and lower reaches (MLR) of Yangtze River basin. Meanwhile, no significant isolation by distance was detected among the populations. Ecological factors (e.g. complicated topography and climatic environment) and anthropogenic factors (e.g. aquaculture and agriculture cultivation) might account for the genetic disconnectivity between UR and MLR populations. This study provided valuable genetic data for the future breeding program and also for the conversation and scientific utilization of those abundant genetic resources stored in the Yangtze River basin.     

Genetic diversity and differentiation of Daphnia galeata in the middle and lower reaches of the Yangtze River,China

Mitochondrial 16S rDNA and CO I gene were used as molecular markers for the analysis of the genetic diversity and differentiation of Daphnia galeata populations in nine water bodies in the middle and lower reaches of the Yangtze River. In the combined 16S rDNA and CO I gene sequences, 54 variable sites and 44 haplotypes were observed among 219 individuals belonging to nine D. galeata populations. Average haplotype diversity and nucleotide diversity were, respectively, 0.72% and 0.56%. The F‐statistics (F_ST) value of the D. galeata populations was 0.149. According to the results of the neutral test, D. galeata in the middle and lower reaches of the Yangtze River had experienced a bottleneck effect in the history. Molecular variance analysis indicated that the genetic differentiation of the D. galeata populations mainly occurred within populations (85.09%). Greater genetic differentiations of D. galeata among individuals within populations appeared in the populations from the Huaihe River basin, whereas smaller genetic differentiations occurred in the populations from the middle reaches of the Yangtze River. Strong gene flows were all observed between Group I (four populations from the middle reaches of the Yangtze River) and Group ΙΙ (three populations from the middle and lower reaches of the Yangtze River), and Group ΙΙΙ (two populations from the Huaihe River basin). The effective migration rates (M) were 851.49 from Group I to Group ΙΙ and 685.96 from Group I to Group ΙΙΙ, respectively. However, no significant relationship was observed between the genetic differentiation and geographical distance of the nine populations (r = .137, p > .05). Results suggested that the genetic differentiation of D. galeata in the water bodies in the middle and lower reaches of the Yangtze River resulted mainly from geographical isolation.     

长江水系钱草鱼遗传结构及变异性的RAPD研究

采用随机扩增多态性DNA（RAPD）技术对长江中游的湖北嘉鱼与江西瑞昌两个地理群体和中游的汉江和湘江两大水系的鲢和草鱼的群体进行了遗传学研究。发现长江水系链的遗传变异要高于草鱼,与现今生物量成反比的反常现象。鲢遗传多样性从大到小的分布是嘉鱼→湘江→瑞昌→汉江。草鱼遗传多样性从大到小的分布是瑞昌→汉江→湘江→嘉鱼,鲢和草鱼的遗传多样性地理分布并不一致。遗传分化指数Gst分别为12.3%和17.5%,表明鲢和草鱼的四个地理群体的遗传分化度较低,可能与地理较近和基因交流频繁有关。     

Genetic variation of the Chinese longsnout catfish Leiocassis longirostris in the Yangtze River revealed using mitochondrial DNA cytochrome b sequences

The mitochondrial DNA cytochrome b of 132 Leiocassis longirostris collected from 12 localities in the upper to lower reaches of the Yangtze River were amplified and partially sequenced using the PCR technique. The results showed that 27 nucleotide sites were variable along 817 bp length of homologous sequence (3.3%), base substitutions happened mostly at the third codon position. A total of 22 haplotypes were identified, which were characterized with moderate haplotype diversity (h = 0.5417 ± 0.0519), but low nucleotide diversity (π = 0.0019 ± 0.0012). Median-joining network analysis revealed star-shaped patterns with one common central haplotype (H3), whereas mismatch distribution analysis found that the Chinese longsnout catfish fitted a smooth unimodal distribution, which suggested that this species underwent population expansion following bottlenecks and/or they originated from a small number of founding individuals. The time that the total population of Chinese longsnout catfish in the Yangtze River expanded was estimated 169,000–337,000 years before present. The analysis of molecular variance (AMOVA) and phylogenetic reconstructions did not detect significant geographic structure between different river sections, especially between above and below the Gezhouba Dam and the Three Gorges Dam, which suggested that these recently developed dams might have not significantly resulted in population genetic differentiation in the Chinese longsnout catfish.     

Genetic variation at mtDNA and microsatellite loci in Chinese longsnout catfish (<Emphasis Type="Italic">Leiocassis longirostris</Emphasis>)

Genetic variability and population structure of the Chinese longsnout catfish Leiocassis longirostris Günther in the Yangtze River was examined with mitochondrial control region sequences and nuclear microsatellite markers. A 705-bp segment of the mitochondrial DNA control region was sequenced from 132 samples, which identified a total of 61 haplotypes. The Chinese longsnout catfish in the Yangtze River was characterized with high haplotype diversity (h = 0.9770 ± 0.0041) but low nucleotide diversity (π = 0.0081 ± 0.0043). Median-joining network analysis revealed a star-shaped pattern and mismatch distribution analysis found a smooth unimodal distribution, which suggested that this species in the Yangtze River underwent a population expansion following bottlenecks and/or they originated from a small size of founding population. It was estimated that the possible time of population expansion was 139,000–435,000 years before present, a time period in the middle Pleistocene. The analysis of molecular variance and phylogenetic reconstructions did not detect significant geographic structure between different river sections. This pattern of genetic variation was further evidenced with nuclear microsatellite markers. The genetic differentiation between above and below the Gezhouba Dam and Three Gorges Dam is very small at mitochondrial and nuclear levels, which suggested that these recently developed dams might have not significantly resulted in population genetic fragmentation in the Chinese longsnout catfish. However, the potential exacerbation of genetic structuring by the dams should not be overlooked in the future.     

长江经济带快速城镇化对耕地保护的影响

长江经济带建设作为我国三大发展战略之一,在快速推进城市化的同时,对耕地资源的影响是不容忽视的。土地快速城镇化对耕地的大量侵占是我国城市化面临的突出问题,而近些年长江流域及长江经济带的快速发展对耕地资源的影响尚缺乏全面系统的分析。基于中分遥感数据,将覆盖长江经济带与长江流域范围的156个地级市作为研究目标,从自然区位(上、中、下游)与城市规模(人口规模)相结合的角度分析了2000—2015年城镇化对耕地的影响,结果表明:(1) 2000—2015年,长江流域及长江经济带人工表面增加56.80%,耕地减少17.09%。其中,下游人工表面增加幅度最为明显,耕地减少也是最多的;(2)随着时间推移,长江流域及长江经济带城镇化对耕地的压力逐渐减弱,十五年间人工表面增长率从2733.75 km~2/a提高至2985.87 km~2/a,而耕地减少的速度从4439.94 km~2/a降低到3940.91 km~2/a,并且有大量旱田向水田转变;(3)位于不同流域且规模不同的城市,其人工表面的增加幅度以及对耕地的影响存在明显差异。例如,长江下游的中等城市人工表面15年间增加最多(增幅385.88%),同时耕地也损失最多;中游的大城市的人工表面增速最快,而上游则是巨大型城市,这种现象说明长江流域存在发展不协调的问题。长江流域及经济带未来城市优化布局不仅要充分考虑耕地保护问题,还要均衡不同规模城市的扩张速度,以及进一步提高开发用地的利用效率。     

Population genetic structure and evolutionary history of grass carp <Emphasis Type="Italic">Ctenopharyngodon idella</Emphasis> in the Yangtze River,China

Ample studies have been conducted to investigate the population genetic structure of grass carp Ctenopharyngodon idella in the Yangtze River, China. However, samples from the upper reaches were not included. In this study, we collected samples from the entire river, including three locations in the upper reaches: Yibin, Banan and Yunyang, two locations in the middle reaches: Shishou and Ruichang and one location in the lower reaches: Hanjiang, and sequenced three mitochondrial coding genes (ND5, ND6 and Cytb) and one control region (i.e., the D-loop). Nineteen haplotypes were observed in grass carp of the Yangtze River through the analysis of combined sequence data sets (around 4428 bp). Haplotype diversity indices (0.6000 ∼ 0.9333) and nucleotide diversity indices (0.0002 ∼ 0.0020) demonstrated low genetic diversity in the Yangtze grass carp. The analysis of molecular variance and the fixation index (F _ST = 0.0202) revealed insignificant genetic difference between samples from different reaches. Two monophyletic lineages of haplotypes were identified, with the lineage A experiencing potential expansion events. Along with previous findings, this study provides a better understanding of genetic diversity and variation of grass carp in the Yangtze River and will be served as an important baseline to evaluate the long-term impact of the Three Gorges Dam and other hydroelectric facilities on fish biodiversity.     

长江流域鱼类物种多样性大尺度格局研究

作者以长江流域鱼类编目数据库为基础数据,研究了长江流域鱼类物种多样性的大尺度格局。长江流域内共记录了鱼类378种(亚种),隶属于14目32科144属。其中淡水鱼338种(亚种),以鲤形目为主,达到269种(亚种),洄游鱼类11种,河口鱼类29种;流域内特有种和受威胁物种分别有162种(亚种)和69种(亚种)。根据鱼类分布特点,按水系将长江流域分为19个区域,除了江源区和金沙江中上游外,物种数和G-F多样性指数上游高于中下游,但各区域内差异不大,然而特有种比例从上游到下游随海拔降低而逐渐降低。利用Jaccard物种相似性系数对19个区域进行聚类分析,将整个流域分成三部分:(1)江源区和金沙江中上游,地理上属于青藏高原东南部波状平原部分和横断山区,(2)上游其他流域,地理上属于川西高原、云贵高原、四川盆地及秦巴山区,(3)中下游流域,地理上属于淮阳山地、江南丘陵和长江中下游平原,基本反映了流域内自然地理环境及我国大陆地势三级台阶变化的特点。     

中国栽培稻遗传多样性中心和起源研究

本研究对中国栽培稻6个地理分布群的700份古老地方栽培品种进行9个多态性等位酶基因位点的遗传多样性分析.结果表明籼稻和粳稻的平均基因多样性均以云南最大,淮河上游次之,黄河以北最小.中国栽培稻有3个遗传多样性中心:云南,长江中游-淮河上游,华南.长江中游-淮河上游可能是中国栽培稻的起源中心.结合考古学资料及前人的工作,认为云南不是中国栽培稻的起源中心,而可能是中国起源中心衍生的一个次生中心并受到南亚中心的强烈影响.