团头鲂3个选育群体遗传潜力的微卫星分析

为从遗传多样性的角度了解团头鲂(Megalobrama amblycephala)3个选育群体的遗传潜力,该研究以团头鲂"浦江1号"选育奠基群体(F_0)为对照组,采用14个多态性转录组微卫星标记评估了团头鲂3个选育群体的遗传多样性,分析其遗传潜力。结果显示,3个选育群体平均每个位点的等位基因数(A)为7.928 6~8.785 7,有效等位基因数(A_E)为4.409 4~4.878 4,观察杂合度(H_O)为0.491 1~0.574 4,期望杂合度(HE)为0.741 3~0.751 8,多态信息含量(PIC)为0.691 2~0.705 2,近交系数(FIS)为0.229~0.352。3个选育群体的遗传多样性水平(AE、HE)均高于F0群体,但不存在显著差异(P0.05)。3个选育群体的有效群体大小(N_e)为11.0~29.3,在近期可能经历过遗传瓶颈。3个选育群体间D_A、D_(SW)遗传距离分别为0.175 4~0.358 8、0.804 7~1.054 4。该结果表明,3个选育群体的遗传多样性较高,遗传潜力较大,但因有效群体数量较少和瓶颈效应的影响,存在杂合度下降和近交衰退的风险,今后需采取科学措施来保护选育群体的遗传潜力。     

驯养、选育条件下尼罗罗非鱼群体的选择压力分析

家养动物是研究长期人工选择对动物基因组产生选择效应机制的独特对象,尼罗罗非鱼(Oreochromis niloticus)是一种受人工干预(驯养、选育)历史较短的优良养殖对象,可作为研究新近发生的人工干预对动物基因组产生影响的遗传机制的良好模型。本研究以1个尼罗罗非鱼埃及野生群体为对照组,以4个"新吉富"罗非鱼选育系群体、2个企业自主选育群体和5个驯养群体为实验组,采用3种模型分析方法(岛屿模型、分级岛屿模型和贝叶斯似然法),在12个微卫星位点上进行F_(ST)-离群值点检测(F_(ST)-outlier test)。结果显示,在本研究所分析的12个微卫星位点中,4个"新吉富"罗非鱼选育系群体在2个微卫星位点(OMO043,OMO114)受到了显著的正向选择压力(P0.01),2个企业自主选育群体在另外2个微卫星位点(OMO049,OMO100)受到显著的正向选择压力(P0.01),而5个驯养群体只在1个微卫星位点(OMO013)受到了显著的正向选择压力(P0.01)。由此可见,选育群体受到的正向选择位点数明显多于驯养群体,选育群体与驯养群体受到正向选择的位点各异,不同选育群体间受到正向选择的位点也各不相同。本研究结果表明,不同的人工干预途径从不同的方向上对尼罗罗非鱼基因组产生了影响。     

罗非鱼性别相关微卫星标记的初步筛选

为分析罗非鱼群体的遗传多样性以及筛选与罗非鱼性别相关的微卫星标记。应用24对微卫星引物,使用常规PCR及聚丙烯酰胺凝胶电泳的方法在两个尼罗罗非鱼(Oreochromis niloticus)群体和两个奥利亚罗非鱼(O.aureus)群体中初步筛选到UNH931、GM128、GM201、GM258、GM597以及UNH898共6个与性别相关的微卫星标记。然后使用降落PCR以及毛细管电泳的方法在两个尼罗罗非鱼群体、两个奥利亚罗非鱼群体以及ZY 1、WY 1、YY 1和YY 2型罗非鱼群体中进一步扩增这6个微卫星标记,统计各群体的遗传多样性参数:6个微卫星标记在上述群体共297个样本中检测到95个等位基因,其大小在97~302 bp之间,各位点在各群体等位基因数在1~13个之间,各群体平均观测等位基因数为2.167~9.333,平均有效等位基因数为1.624~4.966,平均观测杂合度为0.324~0.983,平均期望杂合度为0.329~0.782,平均多态信息含量为0.275~0.753;两个尼罗罗非鱼群体、WY 1和YY 2群体达到高度多态(PIC>0.5),两个奥利亚罗非鱼群体、ZY 1和YY 1群体为中度多态(0.25相似文献   

罗非鱼“粤闽1号”及其繁育群体的遗传多样性和遗传关系分析

罗非鱼“粤闽1号”是用尼罗罗非鱼(Oreochromis niloticus)和奥利亚罗非鱼(O. aureus)培育的全雄罗非鱼新品种。采用同工酶电泳技术和线粒体DNA控制区序列分析方法,对罗非鱼“粤闽1号”及其繁育群体的遗传多样性、遗传结构及群体之间的遗传关系进行研究。同工酶电泳结果显示,酯酶(EST)和乳酸脱氢酶(LDH)的酶谱具有组织和群体特异性。肌肉和脾脏中的EST表达量极低,而肝脏中的EST表达量较高,LDH在3种组织中均有较高表达,但酶谱存在差异。在罗非鱼“粤闽1号”及其繁育群体中,共检测到10条EST酶带和5条LDH酶带,多态性位点比例(P)为12.50%~71.43%,平均观测杂合度(Ho)为0.0417~0.6143,Hardy-Weinberg遗传偏离指数(D)为?0.2347~0.9072。线粒体DNA控制区序列分析结果显示,mtDNA D-loop区的碱基组成无显著差异,均呈现出A+T碱基偏向性(63.39%)。在罗非鱼“粤闽1号”及其繁育群体中,共发现20种单倍型,核苷酸多样性指数(Pi)为0~0.0519,奥尼罗非鱼雌鱼(WY1)、尼罗罗非鱼雌鱼(XX)、尼罗罗非鱼雄鱼(XY)和罗非鱼“粤闽1号”(XY2)群体的Pi值(0.0440~0.0519)明显高于超雄尼罗罗非鱼(YY1)、超雄奥尼罗非鱼(YY2)和奥利亚罗非鱼雌鱼(WZ)群体的Pi值(0~0.0009)。各群体之间的遗传分化指数(FST)为?0.0115~0.9963,XY2与WY1群体之间、XX与XY群体之间以及WZ和YY2群体之间的遗传分化不显著(FST<0.05, P>0.05)。XY2群体与尼罗罗非鱼群体(XX群体和XY群体)和奥利亚罗非鱼群体(WZ群体)之间的平均遗传距离分别为0.0639和0.0695。在NJ系统进化树中,XX、XY、YY1和XY2群体聚为一支,WY1、WZ和YY2群体聚为另一支。本研究揭示了罗非鱼“粤闽1号”的生化和分子遗传特征,为其种质鉴定、繁育群体的构建和优良性状的稳定遗传提供理论基础。     

团头鲂野生、驯养、选育3类遗传生态群体遗传变异的线粒体DNA分析

通过对线粒体DNA控制区和COⅠ基因序列的联合分析,研究了团头鲂(Megalobrama amblycephala)3类遗传生态群体(包含4个野生群体、2个驯养群体、1个选育良种"浦江1号"群体)的遗传多样性和遗传分化情况.结果表明:(1)在所分析的7个群体中,共确定了64种单倍型,群体间无共享单倍型.(2)4个野生群体内线粒体DNA的单倍型多样度(Hd)在0.857～0.943之间,核苷酸变异位点数在31～40之间,核苷酸多样性指数(π)在0.275%～0.461%之间,平均核苷酸差异数(K)的范围为4.043～6.800;2个驯养群体的相应参数变化范围分别为0.714～0.800、18～21、0.122%～0.175%、1.800～2.586,均低于野生群体;选育群体的相应参数分别为0.843、23、0.193%、2.843,低于4个野生群体,但高于2个驯养群体.以上4种多样性参数在7个群体中的变化趋势一致.(3)7个群体之间的平均遗传距离在0.000 6～0.003 5之间,遗传分化指数(FST)在0.010 9～0.133 1之间.4个野生群体间FST值差异不显著(P＞0.05),而2个驯养群体间FST值差异显著(P＜0.05),它们与选育群体间的FST值差异也显著(P＜0.05).以上结果表明,生存环境的殊异(敞开的天然水体,封闭的驯养池塘)和人工选择(严格有序的科学选育)对种群遗传结构影响巨大,导致鱼类不同遗传生态类型群体间产生遗传变异和遗传分化.     

吉富品系尼罗罗非鱼抗病性状分子标记筛选及遗传多样性分析

文章采用微卫星标记技术,对吉富品系尼罗罗非鱼(GIFT strain Oreochromis niloticus)抗病群体和易感病群体进行了遗传差异分析。结果显示:在30个微卫星位点中20个能扩增出多态性高、重复性好和扩增条带清晰;抗病群体和易感病群体的平均等位基因数分别为2.5和2.4个;观测杂合度和期望杂合度分别为0.476和0.453,0.44和0.457;多态信息含量PIC分别为0.359和0.379;UNH845和UNH189位点在抗病群体中偏离Hardy-Weinberg平衡(P0.05),GM180位点在易感病群体偏离Hardy-Weinberg平衡,两个群体间的遗传距离和遗传分化指数0.055和0.054。此外GM251和GM462位点的差异等位基因片段(135bp和198bp)与抗病性状存在一定的连锁关系。以上结果表明,吉富品系尼罗罗非鱼抗病群体与易感病群体之间的遗传多样性差异不明显,筛选出2个与抗病性状相关的微卫星标记,为开展吉富品系尼罗罗非鱼抗病品种分子标记辅助选育奠定了基础。     

菲律宾蛤仔人工选育群体与野生群体的遗传多样性分析

本研究利用10对微卫星标记对菲律宾蛤仔(Ruditapes philippinarum)人工选育群体与野生群体进行遗传多样性分析。结果表明,每个位点的等位基因数为3~12个,期望杂合度范围为0.307~0.757,观测杂合度范围0.208~0.583。等位基因丰富度AR的大小范围是3.0~10.7,PCR扩增产物片段大小在178~390 bp,共得到63个等位基因,平均等位基因数范围从4.4(白蛤)到5.1(龙王塘野生群体),野生群体等位基因丰富度最大(5.278),白蛤群体的等位基因丰富度最小(4.267)。哈迪–温伯格检验发现4个群体和10对微卫星的40个组合中,有21个组合显著偏离哈迪–温伯格平衡状态。Kruskal-Wallis检验表明各个群体间的平均等位基因丰富度无显著差异。4个群体遗传分化系数F_(st)在0.086~0.180,遗传分化最大的是白斑马蛤群体与龙王塘野生群体(F_(st)=0.180),遗传分化最小的是白蛤群体和海洋橙群体(F_(st)=0.086)。人工选育群体表现为中度分化水平(F_(st):0.086~0.113);龙王塘野生群体与人工选育群体表现为较大分化水平(F_(st):0.134~0.180)。结果表明,人工选育群体的遗传多样性仍然比较高,但连续的选育对群体的遗传多样性和遗传分化有一定程度的影响。     

中国明对虾人工选育群体与野生群体遗传多样性的SSR分析

利用微卫星标记技术分析了中国明对虾(Fenneropenaeus chinensis)野生群体(Wild Population,WP)和"黄海2号"第10代选育群体(Breeding Population,BP)的遗传多样性,以检测累代人工选育对中国明对虾群体遗传结构的影响。结果显示,15个微卫星位点共检测到462个等位基因,微卫星位点等位基因数(N_a)和有效等位基因数(N_e)分别为3~44个和2~29个,多态信息含量(PIC)为0.518~0.964。野生群体和选育群体的平均观测杂合度分别为0.852和0.810,15个微卫星位点的等位基因频率在2个群体发生了显著的变化。通过计算P值确定位点Hardy-Weinberg平衡偏离情况,Fis结果显示,共有11个群体位点表现为杂合子过剩,Shannon指数(H)分别为2.786和2.399。2个群体的N_ei′s无偏遗传距离(u D)和无偏遗传相似度(u I)分别为0.177和0.838,遗传分化指数为0.017(P=0.001),表明群体发生了弱遗传分化。遗传变异来源分析显示,只有7.50%的变异来自于群体间,其余遗传变异均来自于个体间。结果表明,人工选育的中国明对虾"黄海2号"第10代群体具有较高的遗传多样性,仍具有很大的选育潜力,可以继续作为选育材料。     

基于简化基因组测序的中国明对虾3个选育世代遗传多样性分析

本研究基于简化基因组测序(2b-RAD)技术,对中国明对虾(Fenneropenaeus chinensis) “黄海2号” 2015~2017年3个连续选育世代(G9~G11)的亲本群体、共649个个体进行了简化基因组测序,并对这3个亲本群体进行了遗传结构和遗传多样性分析。实验在3个选育世代中共获得66985个SNP位点。遗传分析的结果显示,G9~G11平均核苷酸多样性(Pi)分别为0.1439、0.1587和0.1674,平均观测杂合度(Ho)分别为0.1388、0.1515和0.1609,多态信息含量(PIC)分别为0.1241、0.1360和0.1430。G9~G11亲本群体的遗传多样性整体呈现一定的上升趋势,但差异不显著。F检验显示, 3个世代总的Fst值为0.0061,G9~G11相邻世代群体间遗传分化程度较弱(G9~G10为0.0029, G10~G11为0.0026),表明相邻世代的遗传距离逐渐减小。3个世代间基因交流充分,基因流为62.91~94.63。本研究表明,人工定向选育工作的推进对中国明对虾选育群体遗传多样性和遗传结构产生了一定的影响：在固定的选择压力下(4%~5%),亲本群体的遗传多样性并无降低的趋势,中国明对虾选育群体遗传分化小,遗传结构趋向稳定。研究结果为进一步制定中国明对虾选育计划提供基础遗传数据和科学的理论指导。     

海南省6个养殖罗非鱼群体遗传差异的微卫星分析

利用筛选的20对微卫星引物对海南省6个养殖罗非鱼群体进行遗传多样性研究,分析各群体内的遗传变异和各群体间的遗传关系,比较不同群体的等位基因数、有效等位基因数、观测杂合度、期望杂合度、Shannon’s多态性指数、平均多态性信息含量等遗传参数,并利用遗传距离构建6个罗非鱼群体的系统聚类图。结果表明:1)6个罗非鱼群体等位基因数为68个,平均等位基因数为1.992 2~2.255 8,平均观测杂合度为0.572 5~0.745 0,平均期望杂合度为0.469 2~0.532 3,Shannon’s多样性指数为0.719 3~0.848 6,多态信息含量为0.25PIC0.50,其中莫桑比克罗非鱼的遗传多样性指数最高,奥尼罗非鱼最低。2)采用邻接法(NJ)对6个罗非鱼群体进行聚类分析,表明6个罗非鱼群体分为2大支,吉富罗非鱼、尼罗罗非鱼、红罗非鱼、莫桑比克罗非鱼聚为一大支,其中吉富罗非鱼和尼罗罗非鱼聚为一小支,红罗非鱼与莫桑比克罗非鱼聚为一小支;奥尼罗非鱼和泰奥罗非鱼聚为一支。综上所述,海南省6个养殖罗非鱼群体的遗传多样性较高,但不同群体之间存在差异;尼罗罗非鱼与泰奥罗非鱼亲缘关系最远,吉富罗非鱼与尼罗罗非鱼亲缘关系最近。     

尼罗罗非鱼8个养殖群体线粒体控制区遗传多样性和遗传关系分析

 利用线粒体DNA控制区部分序列对中国8个尼罗罗非鱼 (Oreochromis niloticus) 养殖群体(埃及、吉拉达、美国、鹭业、吉诺玛、宝路、广东、新吉富)的遗传多样性和相互间遗传关系进行了分析。在所分析的237个样本中, 可归结为15种单倍型, 其中单倍型BL1为宝路(BL)、埃及(EGY)、吉拉达(GLD)、吉诺玛(GNM)和鹭业(LY) 5个群体所共享, 但没有一个单倍型为所有群体共享。8个群体内的核苷酸多态位点数(S)在4~83, 平均核苷酸差异数(K)的范围为0.50~37.26, 单倍型多样性(h)为0.190 8~0.802 3, 核苷酸多样性(π)为0.000 8~0.056 9。AMOVA分析与群体间两两比较的遗传分化指数(F_ST)表明, 这些罗非鱼群体存在显著的遗传分化与差异(P<0.01)。利用Kimura two-parameter模型分析的系统发育关系表明: 宝路、广东和新吉富3个群体亲缘关系较近, 它们聚为一大支; 埃及、美国、吉拉达、鹭业、吉诺玛这5个群体聚为另一大支。单倍型网络(NETWORK)结果显示, 8个群体并没有明显的谱系分化。本研究结果旨为尼罗罗非鱼种质资源的聚合利用奠定基础。

     

Genetic diversity and differentiation of Nile tilapia (Oreochromis niloticus) revealed by DNA microsatellites

To assess the genetic diversity of Nile tilapia Oreochromis niloticus, a total of 250 fish from five Egyptian populations were genotyped using six microsatellite markers. Heterozygosity and Wright's F‐statistics (F_IS, F_ST, and F_IT) were calculated to determine the genetic variation within and between these populations. Observed heterozygosities were in the range of 0.4 (Burullus) to 0.96 (Qena), with F_IS values ranging from 0.082 to 0.282. The mean F_ST showed that approximately 96.5% of the genetic variation was within‐population and 3.5% was among populations. Standard genetic distances were used to classify the five populations into two major groups. The deeper lotic river Nile populations of Assuit and Cairo formed one group and the shallow less lotic Delta lakes populations of Manzalla and Burullus formed the second group, with the upstream Nile Qena population being an outgroup. The findings from the current study help understanding of the broad‐scale population structuring of the Nile tilapia (O. niloticus) allowing the population groupings identified to act as potential sources of genetic variation. These populations could be included in future Marker‐Assisted‐Selection programs for economically desired production traits.     

Genetic diversity and structure of domesticated strains of red sea bream,Pagrus major,inferred from microsatellite DNA markers

The genetic diversity and structure of nine domesticated strains of red sea bream used in a private hatchery were studied and compared to a wild population. A total of 313 individuals were genotyped at eight microsatellite loci. Average number of alleles per locus ranged from 5.5 to 9.4 in domesticated strains, but that of the wild population was 28.4. Heterozygosity of domesticated strains (ranged 0.697–0.804) was also lower compared to the wild population (0.952). Estimated Ne also decreased in all domesticated strains (ranged 10.3–126.0) compared to the wild population (1422.5). The UPGMA tree and 3‐D FCA showed that there were two main clusters containing domesticated strains, and the wild population was at the middle of both of the domesticated clusters. The STRUCTURE analysis also supported the phylogenetic analysis, and revealed three sub‐clusters in the domesticated strains. Pairwise F_ST revealed that all domesticated strains were statistically different from the wild population, and also the differentiation between domesticated strains was all statistically significant. Information on genetic diversity and structure of domesticated strains of red sea bream obtained in this study will be useful for future broodstock management and selective breeding programmes.     

Survey of genetic variation at three microsatellite loci in captive populations of endangered Japanese minnow <Emphasis Type="Italic">Aphyocypris chinensis</Emphasis> with implications for reduction of inbreeding

The Japanese population of the cyprinid minnow Aphyocypris chinensis is nearing extinction in the wild. The genetic diversity of three microsatellite loci in five captive populations was investigated, and an effective breeding strategy to reduce inbreeding from pairwise relatedness (R _xy ) between each captive line is discussed. The average number of alleles ranged 2.33–4.67 and the average heterozygosity ranged 0.283–0.602. The pairwise relatedness observed in most combinations showed a significant decrease between the populations. It is suggested that exchange of individuals between different breeding lines should effectively stop inbreeding. Studies show that the effective population size (N _e ) estimated from the number of parental individuals was 8.54 in one captive population, which is insufficient to maintain genetic diversity. It is recommended that more parental individuals should be used, and to exchange fish in a rotating mating mode between institutions participating in captive breeding of A. chinensis.     

Genetic diversity of Nile tilapia populations revealed by randomly amplified polymorphic DNA (RAPD)

Genetic diversity of the Nile tilapia Oreochromis niloticus collected from the river Nile (Cairo, Assuit and Qena) and two Delta lakes (Burullus and Manzalla) in Egypt was examined by the analysis of randomly amplified polymorphic DNA (RAPD). Of 25 primers examined,21 primers produced 230 RAPD bands. The percentage of polymorphic bands in Manzalla (29.4%) and Burullus (24%) populations was low compared with Assuit (30.54%), Cairo (33.5%) and Qena (44.84%) populations. The highest percentage of polymorphic bands was observed in the Qena population,suggesting a greater potential for use in breeding programs. The molecular phylogenetic tree constructed by unweighted pair‐group method of analysis shows Manzalla and Burullus populations strongly linked and separate from the Assuit and Cairo populations, with Qena population as outgroup. The data serve as a baseline analysis of the current genetic diversity found among O. niloticus populations in Egypt.     

基于SSR-seq技术评估中间球海胆多代选育群体和普通养殖群体的遗传多样性

为明确不同选育群体中间球海胆的遗传多样性和遗传结构,利用SSR-seq技术和15个微卫星位点,对1个家系选育群体(FP)、1个群体选育群体(IP)和1个未经选育的普通养殖群体(CP)的遗传多样性及遗传结构进行了分析。结果显示,15个微卫星位点共检测出112个等位基因,FP、IP、CP 3个群体的平均观测等位基因数(N_a)分别为5.077、5.133和6.133个,平均有效等位基因(N_e)分别为2.816、2.873和3.638个,平均观测杂合度(H_o)分别为0.522、0.441和0.501,平均期望杂合度(H_e)分别为0.595、0.599和0.667,平均多态性信息含量(PIC)分别为0.546、0.543和0.623。家系选育群体(FP) H_e与H_o的差值(0.073)低于IP (0.158)和CP (0.166),平均固定指数(F)(0.115)低于IP (0.248)和CP (0.246)。3个群体间遗传分化系数(F_st)介...     

Genetic relatedness and differentiation of hatchery populations of Asian seabass (Lates calcarifer) (Bloch, 1790) broodstock in Thailand inferred from microsatellite genetic markers

After more than 20 years of hatchery production of Asian seabass in Thailand, genetic information is still lacking for effective genetic management and a selective breeding programme. This study aimed to evaluate genetic status of existing hatchery populations and genetic consequences of a selective breeding attempt. We examined genetic relatedness in seven hatchery samples, including a selectively bred population (RACF‐F1), compared with three wild samples using 11 microsatellite loci. Genetic diversity and relatedness values within most hatchery samples, except for RACF‐F1, did not differ from those of wild populations (P > 0.05). RACF‐F1 had the lowest allelic diversity and effective population size (A_r = 6.99; N_e = 7.8) and highest relatedness values (mean r_xy = 0.075–0.204). Pairwise Φ_ST values, principal component analysis and model‐based cluster analyses revealed three genetically distinct hatchery groups: Eastern Thailand (CHN, RACF, NSCF and SKCF), Southern Thailand (NICA) and the Andaman Sea (STCF). Results suggest that exiting domestic populations capture reasonable amount of genetic variation and can be useful for a base population for genetic improvement programmes. In addition, given the rapid increase in relatedness that we observed in one selectively bred population, we recommend using selection methods and hatchery practices that reduce variability in family contribution in the subsequent generations.