摘要
本研究采用富集文库——菌落原位杂交法和PCR扫描法筛选了11对玉筋鱼和14对松江鲈的微卫星分子标记,并利用开发的微卫星分子标记评价了这两种海洋鱼类的群体遗传结构和遗传多样性等指标。综合分析了影响海洋鱼类遗传多样性和地理格局的因素以及物种自身生活史特征对其遗传结构影响。主要研究结果如下:
1.两种海洋鱼类微卫星标记的筛选和评价
(1)玉筋鱼微卫星标记的筛选及评价
首先,利用HaeⅢ酶对玉筋鱼基因组进行酶切,经过膜富集(AC)n和(AG)n后构建了玉筋鱼的微卫星富集文库。运用菌落原位杂交的方法,使用(AC)n和(AG)n为探针经过杂交后,筛选得到阳性克隆,经测序共获得了108个玉筋鱼的微卫星序列。在对玉筋鱼微卫星序列设计的31对引物中,11对可以扩增出清晰的微卫星条带。利用36个个体对能够扩增清晰微卫星条带的位点进行主要遗传学参数的估算,结果显示11对引物具有高多态性。多态性标记中,扩增出的等位基因数目从8到29个不等,观测杂合度和期望杂合度分别为0.441到0.886和0.818到0.965。这些标记的开发为后续的玉筋鱼种群遗传学研究做好了准备。
(2)松江鲈微卫星标记的筛选及评价
不同于玉筋鱼微卫星标记的筛选,在构建松江鲈部分基因组文库后,我们采用PCR扫描法筛选了松江鲈的微卫星序列。在设计的18对松江鲈微卫星标记中,有14对引物在文登29个个体中得到了较为清晰的、能够准确判断的扩增条带。随机抽取部分样本进行2~3次的重复实验表明,微卫星的扩增结果稳定、重复性高。读取全部基因型,14个位点获得了113个等位基因,其中有5个位点仅获得了2个等位基因。不同的引物获得的等位基因数为2~13个不等,观测和期望杂合度在0.682到1.000和0.853到0.953之间。
2.玉筋鱼遗传多样性及分子系统地理格局
玉筋鱼是西北太平洋的重要的经济种类,在玉筋鱼渔业区的渔业捕捞中占有比较高的比重。我们利用微卫星分子标记评估了其种群遗传多样性和系统地理格局。基于8对微卫星标记和16个玉筋鱼群体共计318个玉筋鱼个体的研究结果发现,玉筋鱼存在两个独立的自由交配组。在混合模型下,大连、青岛、相岛、香川、爱知、濑户内海、鹿岛、大津、仙台小个体、深辅大部分个体被分配于一号自由交配群;陆奥湾、仙台大个体、青森、石狩湾、礼文岛、宗古个体的大部分个体被分配于二号自由交配群。基于微卫星分子标记的遗传多样性研究发现玉筋鱼个群体个位点均具有较高的遗传多样性水平。综合大量微卫星研究结果,海洋鱼类通常表现出较高的遗传多样性水平,可能是由于海洋鱼类巨大的群体数量与微卫星DNA高的突变速率。
3.松江鲈鱼遗传瓶颈及种群评估
松江鲈是一种溯河洄游鱼类。由于环境污染和人类的过度捕捞,在中国的东南海域松江鲈鱼迅速的减少或几近消失。松江鲈鱼的科学管理和可持续的开采已经迫在眉睫。我们利用微卫星标记研究了6个松江鲈地理群体的遗传多样性和遗传结构。研究结果显示,多态信息含量(PIC)值在0.683-0.928之间,期望杂合度在0.763(C79-E)~0.970(E95-E)之间,观测杂合度(HO)在0.333(C44-E)~1.000(C46-E、C44-QTJ)之间变化。文登和荣成天鹅湖有比较小的有效群体大小,在4000以下,其余群体的都在4000以上。利用BOTTLENECK软件进行Mode shift测试发现天鹅湖与钱塘江群体均显示瓶颈事件的发生。
通过9个微卫星位点等位基因频率计算6个松江鲈群体间遗传分化指数在0.0131(丹东和秦皇岛)和0.0467(日本有明海与杭州钱塘江)之间变化。基于分子标记的个体分配模式显示,日本有明海群体95%以上个体被分配于一号自由交配群;钱塘江、丹东、秦皇岛和文登大部分个体(>93%)被分配于二号自由交配群;天鹅湖群体则表现为两类基因型混杂的现象,其中43.7%的为红色类型的基因型,56.3%的为绿色类型的基因型。松江鲈营淡水生活,降河产卵,产卵场一般位于潮间带,距离沿岸1~2km处。这些生物学特征和地理分布会限制松江鲈鱼群体间的交流。
MicrosatelliteDNA markers for Sand lance (Ammodytes personatus) and roughskinsculpin (Trachidermus fasciatus) were isolated developed by enrichmentlibraries-colony hybridization and PCR screening. Population structure and geneticdiversity were using these microsatelliteDNA markers in the two species.
1. Isolation and characterization of microsatellite markers for two marine fishes
(1) Isolation and characterization of microsatellite markers for Sand lance (A.personatus)
Microsatellite enrichment library of Sand lance (A. personatus) was constructed,which was digested by HaeⅢ. The primers flanking31microsatellites isolated fromthe genomic library enriched for (AC)nand (AG)nwere designed in the Sand lance (A.personatus). Eleven primer pairs provided clear and polymorphic amplificationproducts. Based on characterization with36Sand lance individuals, the number ofalleles ranged from8to29. The values of HOand HEvaried from0.441to0.886and0.818to0.965, respectively. These markers are therefore potentially useful for studiesof the population genetics of the species.
(2) Isolation and characterization of microsatellite markers for roughskin sculpin (T.fasciatus)
Different from Sand lance (A. personatus), PCR screening after genomic libraryenriched constructed were used to develop14novel polymorphic and informativemicrosatellite markers for the roughskin sculpin (T. fasciatus). We characterized theseloci by genotyping29individuals in Wendeng population. A total of113alleles werefound. The number of alleles ranged from2to13across the14microsatellite loci. The values of HOand HEvaried from0.682to1.000and0.853to0.953, respectively.
2. Molecular phylogeography and Genetic diversity for sand lance (A. personatus)
The Japanese sand lance A. personatus is a common and commercially importantspecies in northwestern Pacific. Sand lance, A. personatus, usually constitutes a highproportion of the fish biomass in the regions where they occur. Microsatellite DNAmarkers were used to estimate the population structure and demographic history ofSand lance. Two high distinct lineages were detected in318individuals from16populations across the range of the species based on sequence variations ofmicrosatellite. The majority of individuals of the Dalian(Dl)、 Qingdao(Qd)、Fukuoka(Fuku)、Kagawa (Kag)、Ise Bay (Ise)、Hyogo (Hy)、Kashima(Kas)、Otsuko(Ot)、Sendai Bay Small (Ss)、Fukaura Kuka populations of sand lance were assignedto an inferred cluster, and above the93%of the individuals of the fourpopulations(Mutsu Bay (Mu)、Sendai Bay Large (Sl)、Hachinohe (Ha)、Ishikari Bay(Ish)、Rebun Island (Re)、Cape Soya (Ca) of sand lance were assigned to the other.Pleistocene coastal glaciations might have divergent in the Sea of Japan and Pacificcostal waters of Japanese Island, during the low sea level. Two major ecologicalgroups of sand lance may be accomplished since then. The high genetic diversity wasfound for sand lance based on microsatellite DNA markers. The large effectivepopulation size coupled with the high mutation rate may be responsible for the highgenetic diversity.
3. Bottleneck effect and population estimate for roughskin sculpin (T. fasciatus)
Roughskin sculpin (T. fasciatus) is a Catadromous species. The distribution area ofthe species in China has been reduced greatly and almost disappears completely alongthe sea areas in the east and the south caused by environmental pollution andover-catching. It is urgent for scientific management for sustainable exploitation. Toexamine population genetic diversity and structure of T. fasciatus, samples from fivedifferent locations of China and Ariake population in Japan were analyzed by usingmicrosatellite technology. The Polymorphism Information Content (PIC) were high(PIC=0.683-0.928). The expected heterozygosities ranged from0.763(C79-E) to0.970(E95-E). The observed heterozygosities varied from (HO)0.333(C44-E) to 1.000(C46-E、C44-QTJ). An effective population size reduction (bottle effect) isdetected in Te and Qt by Mode shift test. The effective population size of Wd and Tepopulation was below4000, and smaller than other populations.
High significant genetic differentiations were found among6populations byscanning9microsatellite loci variations. The pairwise FSTvalues ranged from0.0131to0.0467. The majority of individuals (>95%) of the Ariake populations of roughskinsculpin were assigned to an inferred cluster, and above the93%of the individuals ofthe four populations of roughskin sculpin were assigned to the other. Current and itslife cycle might restrict the gene flows between populations.
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