Inbreeding depression and heterosis in various quantitative traits of the guppy, Poecilia reticulata

The present study examines the effects of inbreeding and crossing on various quantitative traits in the guppy, Poecilia reticulata. Effects of inbreeding and crossing were examined in six quantitative traits; body length at birth, survival at day 120, undwarf rate at day 120, body length at day 120, salinity tolerance and high temperature tolerance. Full-sib matings revealed that the amount of inbreeding depression varied from −1.0% to 24.6% among the traits and a significant decrease in survival at day 120 and salinity tolerance was observed. This result indicates that inbreeding reduces the performance for some of the quantitative traits but not all. On the other hand, crosses between genetically different strains showed that the amount of heterosis varied from −1.3% to 42.2% among the six quantitative traits and a significant increase in survival at day 120 and salinity tolerance was observed. The relationship between the amount of inbreeding depression and heterosis supports the theory that the phenomenon of heterosis is the reverse of inbreeding depression, indicating that the traits which have decreased by inbreeding can be recovered by means of crossing.     

Genetic relationship between broodstocks of olive flounder, Paralichthys olivaceus (Temminck and Schlegel) using microsatellite markers

For the first generation of a selective breeding programme, it is important to minimize the possibility of inbreeding. This mostly occurs by mating between closely related individuals, while proper mating can provide an opportunity to establish the base families with wide genetic variation from which selection for subsequent generations can be more effective. Genotyping with microsatellite‐based DNA markers can help us determine the genetic distances between the base populations. The genetic markers further facilitate the identification of the correct parents of the offspring (parentage assignments) reared together with many other families after hatching. We established a genetic analysis system with microsatellite DNA markers and analysed the genetic distances of three farmed stocks and a group of fish collected from wild populations using eight microsatellite markers. The averaged heterozygosity of the farming stocks was 0.826 and that of the wild population was 0.868. The hatchery strains had an average of 8.6 alleles per marker, which was less than a wild population that carried an average of 14.3 alleles per marker. Significant Hardy–Weinberg disequilibrium (HWDE) was observed in two farming stocks (P<0.05). Despite relatively low inbreeding coefficiency of the hatchery populations, the frequency of a few alleles was highly represented over others. It suggests that the hatchery stocks to some extent have experienced inbreeding or they originated from closely related individuals. We will develop a selective program using the DNA markers and will widen the usage of the DNA‐based genetic analysis system to other fish species.     

青石斑鱼微卫星标记的筛选及群体多态性分析

微卫星DNA,又称短串联重复序列(STR)或简单序列重复(SSR),是广泛存在于真核生物基因组中的简单重复DNA片段,一般每个重复单位仅1～6个碱基,重复数为10～20次,其中动物体中以双核苷酸(CA/GT)n最为常见。根据微卫星DNA核心序列两端的保守序列设计引物     

Genetic variability in meiotic gynogenetic muskellunge,Esox masquinongy (Mitchell), estimated from segregation of microsatellite alleles

Muskellunge, Esox masquinongy, is an important recreational freshwater fish native to North America. Since muskellunge populations are often maintained through stocking efforts, advances in muskellunge reproductive technologies are of direct relevance to fishery enhancement. We evaluated the efficiency of inbreeding through induced meiotic diploid gynogenesis. Eggs from six female muskellunge were manually stripped and activated using ultra violet‐irradiated yellow perch, Perca flavescens, sperm. Hydrostatic pressure shocking regimes (48 263 kPa) were then applied to the eggs to prevent second polar body expulsion producing unambiguous meiotic gynogens. Six female dams and samples of 12–20 of their gynogenetic progeny were genotyped at seven polymorphic microsatellite loci. Chromosomal recombination frequencies of microsatellite loci based on retention of heterozygosity among gynogens ranged from 0.043 to 0.839 (0.576 ± 0.237). There were no statistical differences in recombination frequency among females at any of the loci. The average inbreeding coefficient (F‐value) ranged from 0.581 to 0.979, equivalent to three to fourteen generations of full‐sibling crosses respectively. The average F‐value overall was 0.712, equivalent to between five and six generations of full‐sibling crosses. Centromere map distances of the seven microsatellite loci ranged from 2.15 to 41.95 cM and meiotic gynogenesis was useful in eliminating heterozygosity at loci proximal to the centromere, but not distal. Since the age at maturity of female muskellunge is approximately 5 years, gynogenesis may pose an expeditious alternative to traditional breeding strategies for creation of homozygous pedigrees for some loci that may be outcrossed to introduce positive heterozygosity effects in the offspring.     

剑尾鱼RW-H近交系的遗传结构分析

筛选31条随机引物对剑尾鱼的第8代近交RW-H系A、B、C3窝共11尾剑尾鱼个体基因组DNA进行RAPD扩增，计算近交系个体间及不同窝间的相似系数及遗传距离。结果筛选的31条引物共扩增出383条带，扩增片段的大小在0．2～3kb。其中多态性带30条，多态性带频率在0～58．33％，平均为7．83％。近交系剑尾鱼不同个体拥有相同条带的比率较高。计算得到近交系的平均相似系数(S)为0．9829(0．9716～0．9960)，平均等位基因频率(q)为0．8692，最低平均杂合率(H)为0．1308。同时，用5个微卫星标记对非选育剑尾鱼和近交系RW-H系的基因组进行分析，检测等位基因的个数和大小，结果5个微卫星座位在非选育剑尾鱼中显示为多态，而在近交系RW-H系除1个位点出现等位基因外，其余均为纯合子，计算得到近交系的平均遗传相似系数为0．9345，两种方法均证明近交RW-H系第8代剑尾鱼有较高的遗传纯合度。     

云斑尖塘鳢微卫星分子标记的筛选与检测

用磁珠富集法分离云斑尖塘鳢的微卫星序列,由所获得的1032个克隆中筛选出146个阳性克隆,经测序81个含有微卫星序列,52个为完美型,27个为非完美型,2个为复合型,其中43个微卫星序列重复次数在10以上。所获得的云斑尖塘鳢微卫星序列中除探针中使用的CA重复单元和GA重复单元外,还有TAC等其他类型的重复单元。设计合成38对微卫星引物,其中29对引物可稳定扩增出条带,使用这些引物对云斑尖塘鳢48个个体进行检测显示:观测杂合度平均值为0.63,期望杂合度平均值为0.43。29对引物中1对引物表现为单态,7对表现为高度多态,14对表现为中度多态,7对表现为低度多态,多态性较为丰富,说明本研究开发的绝大部分微卫星分子标记较为理想。     

长江刀鲚选育群体转录组EST-SSR的分布特征分析

本研究利用MISA软件挖掘长江刀鲚(Coilia ectenes)肌肉和肝脏转录组中的微卫星标记,为刀鲚选育群体的种质资源评估和分子标记辅助育种奠定基础。结果显示,从71869条Unigenes中共获得33896条重复单元长度为1~6碱基的微卫星序列;刀鲚转录组中不同类型微卫星的重复基序具有不同的分布特征,其中,单核苷酸重复、二核苷酸重复和三核苷酸重复为主要的微卫星重复类型,分别占总微卫星数目的34.94%、49.47%和13.34%;不同微卫星重复类型的优势重复基序亦有所不同,其中,A/T为单核苷酸重复基序的优势重复基序占86.25%,AC/GT为二核苷酸重复基序的为优势重复基序占75.25%,AGG/CCT为三核苷酸重复基序的优势重复基序占28.57%;不同微卫星重复基序核苷酸的数量和重复次数亦有所不同,重复次数伴随着重复单元中核苷酸数量的增加而呈现降低的趋势;从100对四核苷酸重复的SSR引物中筛选获得了16对多态性微卫星标记,并以此为基础,对长江刀鲚选育群体(F3)的遗传学特征进行了初步评估,结果显示,长江刀鲚选育群体F3的平均有效等位基因数(Ne)、平均观测杂合度(Ho)、平均期望杂合度(He)和Shannon多样性指数I分别为1.7580、0.3414、0.3977和0.6278。以上结果表明,基于刀鲚转录组数据批量开发微卫星是切实可行的,所开发的多态性微卫星标记能够应用于长江刀鲚选育群体的遗传背景评估和进一步的遗传育种研究。     

人工雌核发育鲢近交F2微卫星DNA变异分析

采用17对鲢微卫星引物,以野生鲢、养殖鲢、雄鲤作对照对人工雌核发育鲢近交F2及其亲本进行了微卫星分析。结果表明:人工雌核发育鲢近交F2、养殖鲢和野生鲢群体的平均等位基因数范围为2.1～4.0;平均观测杂合度范围为0.2762～0.9588;期望杂合度范围为0.2774～0.7360;遗传多样性指数范围为0.4500～1.2258,人工雌核鲢近交F2为0.4500,显著低于养殖鲢(1.0273)和野生鲢(1.2258),揭示人工雌核发育鲢近交F2遗传多样性水平较低,纯合度较高。从遗传距离来看,人工雌核发育鲢近交F2与对照群体之间的遗传距离都要大于野生鲢与养殖鲢群体之间遗传距离,表明人工雌核发育鲢近交F2发生了一定程度的遗传分化。     

利用微卫星DNA多态性预测鸡的杂种优势

利用4个微卫星标记(ADL101、MCW020、ADL183、ADL298)对玫瑰冠鸡、新罗曼鸡和安卡红鸡的等位基因频率、群体多态信息含量、有效等位基因数、杂合度和遗传距离进行了遗传检测,并测定了玫瑰冠鸡与安卡红鸡及新罗曼鸡的杂交效果。结果表明:4个微卫星标记在玫瑰冠鸡、安卡红鸡和新罗曼鸡3个群体中存在多态性,可以用于鸡遗传多样性的评估;从不同的群体来看,安卡红肉鸡遗传变异程度最大,而玫瑰冠鸡的遗传变异程度相对较小;玫瑰冠鸡与安卡红鸡的遗传距离大于与新罗曼鸡,玫瑰冠鸡与安卡红鸡的杂种优势高于与新罗曼鸡,与实际杂种优势测定结果相符。     

长江草鱼多态微卫星位点的分离及后备亲鱼的遗传多样性分析

本研究采用磁珠富集法分离了10对具有多态性的草鱼(Ctenopharyngodon idellus)微卫星位点,并对140条长江野生草鱼组成的后备亲鱼群体的遗传结构进行了分析。结果显示:本试验得到的草鱼微卫星序列主要是以2个碱基为重复单位、重复次数在5～22之间的多重复单元,重复次数在10次以上的微卫星序列较易得到多态性;77个微卫星座位中,完美型、非完美型和混合型微卫星标记所占的比例分别为87.01%、2.60%和10.39%;群体遗传分析显示,10个多态性微卫星座位中,除了GC39座位外,其它座位都符合哈迪-温伯格平衡,适用于草鱼群体的遗传结构分析;每个座位检测到3～8个等位基因,平均有效等位基因数为3.9302,多态信息含量在0.4129～0.8107之间变动,平均为0.6678,除了GC78座位为中度多态外,其他9个座位均为高度多态。基因分化系数、Shannon指数、平均观测杂合度和平均期望杂合度的平均值分别为0.3457、1.4262、0.9511和0.7193,表明该群体的遗传多样性比较丰富。     

河川沙塘鳢3个不同地理群体杂交F_1代生长性能及遗传多样性

选取来自浙江建德、安徽当涂、江苏太湖3个不同地理群体的河川沙塘鳢,采用3×3完全双列杂交方式进行配组,对9个组合F1子代的生长性状及遗传多样性进行比较分析。通过对2月龄和4月龄F1子代的生长性状进行对比分析发现,建德(♂)×当涂(♀)杂交组合的全长增加率、质量增加率分别为42.58%、190.79%,建德×当涂(正反交)组合的全长杂交优势率、体质量杂交优势率分别为17.88%、66.75%,均高于其他组合。不同地理群体间的杂交F1子代的全长增加率、质量增加率、杂交优势率均高于同一地理群体间的自繁F1子代。采用8个微卫星引物分析获得9个组合F1子代的遗传分化指数平均值为0.195,表明9个组合子代间存在遗传差异与分化,其期望杂合度为0.1493~0.7971,观测杂合度为0.1562~1.0000。双列杂交子代的杂合度和遗传多样性高于自繁子代,其中建德(♂)×当涂(♀)组合的等位基因数、多态信息含量值分别为3.9和0.486,均高于其他组合。综合生长性能和遗传多样性,初步选择建德(♂)×当涂(♀)为最佳杂交组合。     

我国泥鳅微卫星遗传多样性初步分析

用6个微卫星标记分析了安徽(AH)、甘肃(GS)、广东(GD)、广西(GX)、黑龙江(HLJ)、江苏(JS)和重庆(CQ)7个泥鳅(Misgurnus anguillicaudatus)群体的遗传多样性。这6个微卫星摘自泥鳅微卫星连锁图谱,不存在连锁不平衡,在HLJ群体中处于哈代-温伯格平衡,适用遗传多样性分析。六个微卫星共检测到69个等位基因,每位点7到16个不等,有效等位基因数(Ne)3.0-5.5个,观察杂合度在0.202和0.408之间,而期望杂合度在0.673和0.820之间,揭示的多样性信息含量(PIC)在0.643和0.796之间。这些数据显示7个泥鳅群体遗传多样性丰富。群体间遗传分化系数(Fst)达到0.499,49.9%的变异可归于群体间差异,而Fis在0.167和0.421之间,表明泥鳅群体存在较明显的近交或斑块化分布。聚类分析显示AH、GD、HLJ和JS聚成一个分支,而CQ、GS 和GX聚为另一个分支。这表明我国泥鳅呈现东西向梯度分布并在南北向可能存在扰动。这些发现将有助于我国泥鳅资源的有效管理和合理利用。     

Microsatellite marker isolation and cultured strain identification in <Emphasis Type="Italic">Carassius auratus gibelio</Emphasis>

Microsatellites have become the preferred molecular markers for strain selection and genetic breeding in fish. In this study a total of 105 microsatellites were isolated and identified in gibel carp (Carassius auratus gibelio) by microsatellite sequence searches in GenBank and other databases and by screening and sequencing of positive clones from the genomic library enriched for AG and GATA repeats. Moreover, nineteen microsatellites were randomly selected to design locus-specific primer pairs, and these were successfully used to identify and discriminate different cultured strains of gibel carp including strains A, D, L, and F. Three different types of microsatellite pattern were distinguished by the number and length of fragments amplified from the 19 primer pairs, and some microsatellite primer pairs were found to produce different microsatellite patterns among strains and strain-specific fragments. In addition, some duplicated alleles were also detected in two microsatellite patterns. Therefore, the current study provides direct molecular markers to discriminate among different cultured strains for selective breeding and aquaculture practice of gibel carp.     

中国明对虾单个家系中与生长性状相关微卫星标记的初步筛选

以1个人工授精获得的中国明对虾(Fenneropenaeus chinensis)F2家系为材料,对其中80尾中国明对虾进行正态分布检验,选择19个稳定扩增的微卫星位点对每一个体进行扩增和基因分型,分析家系遗传信息.利用最小二乘法对微卫星位点与中国明对虾体长、全长、体质量性状进行关联性分析.采用SPSS 11.5软件作微卫星分子标记与经济性状的方差分析,考察各微卫星位点对体长、全长、体质量3个经济性状的影响程度.结果表明,中国明对虾体长、全长、体质量3个性状均呈正态分布(P＞0.05);相关分析得到,19个微卫星位点中RS0683和FC019两个微卫星位点与体长、全长、体质量呈显著相关(P＜0.05);同时对差异显著的位点进行不同基因型间经济性状的多重比较,RS0683标记座位AA基因型在体长、全长、体质量的表型效应上极显著高于AB、BB基因型(P＜0.01),表明该标记位点基因型AA与3种经济性状正相关;FC019标记座位的AA基因型体长、全长、体质量显著低于AB、BC基因型(P＜0.05),表明该标记位点基因型AA与3种经济性状呈负相关.     

鲤鱼的遗传连锁图谱（初报）

建立了鲤鱼的遗传连锁图谱。图谱有ＲＡＰＤ分子标记５６个,鲤鱼的ＳＳＬＰ标记２６个,鲤鱼ＳＳＬＰ标记１９个,斑马鱼的ＳＳＬＰ分子标记７０个,鲤鱼基因标记９１个,共有标记２６２个;图谱有５０个连锁组,连锁图给出鲤鱼的基因组大小在５７８９ＣＭ左右。     

牙鲆回交、全同胞近交及其亲本家系的微卫星研究

应用10对微卫星引物对2007年建立的抗病家系之一(将其定义为亲本家系)及其回交家系和全同胞近交家系进行分析,结果发现10个位点的等位基因数为1.7～3.0,平均等位基因数为2.3,有效等位基因数为1.553 2～2.887 8,平均有效等位基因数为2.054 1,杂合度观测值为0.307 0～0.664 8,平均杂合度观测值为0.487 0,无偏期望杂合度值为0.200 0～0.606 8,平均无偏期望杂合度值为0.606 8,多态信息含量为0.233 4～0.579 4,平均多态信息含量为0.399 5,3个家系均为中度多态,多态信息含量从大到小依次为:亲本家系、回交家系、全同胞近交家系,其中Poli194TUF位点在全同胞近交家系中发生纯合.家系间的遗传分化系数为0.067 1,表明遗传变异有6.71%来自于家系间,家系间分化较低.根据家系间的遗传距离,利用UPGMA法进行聚类,亲本家系和全同胞近交家系聚为一类.全同胞近交家系纯化基因速率较快,适合牙鲆品系的快速建立.     

中国和匈牙利白斑狗鱼群体遗传变异的微卫星标记分析

本研究应用18个微卫星分子标记,对白斑狗鱼(Esox lucius L.)3个中国新疆群体(乌伦古湖、吉力湖和6号湖)和1个匈牙利巴拉顿湖群体的遗传结构进行了分析.结果表明,3个中国白斑狗鱼群体的平均等位基因丰富度(AR)、平均观测杂合度(Ho)和平均期望杂合度(HE)均显著低于匈牙利巴拉顿湖群体(P＜0.05),而匈牙利群体的平均近交系数(FIS)高于中国群体;经SMM和TPM模型检测,匈牙利白斑狗鱼群体存在显著的遗传瓶颈信号(P＜0.001);AMOVA和群体两两比较的FST值表明,中国与匈牙利白斑狗鱼的遗传分化十分显著(P＜0.01);NJ树、主成分分析(PCA)进一步证实中国白斑狗鱼与匈牙利白斑狗鱼群体间存在显著的遗传差异和分化.此外,贝叶斯遗传聚类结果表明,中国新疆6号湖白斑狗鱼群体极可能来源于乌伦古湖,而非吉力湖.     

Application of microsatellite DNA parentage markers in the swimming crab Portunus trituberculatus

Microsatellites have been a powerful genetic tool in determining pedigree relationships among individuals. A microsatellite marker suite can be used to reliably assign parentage in the Portunus trituberculatus selective breeding programs. Thirty published microsatellites were screened for their suitability to be included in a DNA parentage marker suite. Nineteen microsatellite markers that exhibited significant stutter, poor allele resolution, null allele, and significant deviation from Mendelian expectations were eliminated from the marker suite, and the left eleven markers were ranked by PIC. Six most polymorphic markers with mean He?=?0.928 and PIC?=?0.901 from the original eleven were further assessed for the efficiency of pedigree identification. Total predicted power of the markers to exclude false parents was higher than 99%. Both simulations and real data analysis confirmed the high statistical power of six microsatellites suite in parentage exclusion, which permit us to trace back all offspring to single pairs of parents.     

Development of Microsatellite Markers in Sea Perch,Lateolabrax Japonicus,from Codominant Amplified Fragment Length Polymorphism Bands

A fast and cost‐effective protocol to develop candidate microsatellite markers from sea perch, Lateolabrax japonicus, was described here. Ten suites of codominant bands that contained seven microsatellites were discovered in this marine fish, in which no microsatellite development was reported previously. All the seven microsatellites were found to be polymorphic among tested 20 individuals of sea perch. Five of the above seven loci conformed to Hardy–Weinberg equilibrium (HWE) as determined by using the Markov‐Chain method implemented, the other two loci significantly deviated from HWE, both of them showed a large heterozygote excess (H_E). Out of 21 possible pair‐wise comparisons among the seven loci applied to sea perch, none showed significant linkage disequilibrium (LD) (P > 0.008). Five additional fish species assessed for cross‐species amplification revealed that some of the loci appear to be applicable in close‐related species.     

Effects of intraspecific hybridisation between two hatchery‐reared strains of Atlantic salmon,Salmo salar,on juvenile survival and fitness‐related traits

Intraspecific hybridisation may result in hybrid offspring exhibiting superior (heterosis) or inferior (outbreeding depression) fitness relative to their parental populations. As both have been demonstrated in salmonids, consequences of interbreeding between divergent populations are relevant to their conservation. Atlantic salmon Salmo salar L. were extirpated from Lake Ontario by the late 19th Century due to anthropogenic causes. Multiple allopatric populations of hatchery‐reared Atlantic salmon are being stocked in an effort to re‐establish a self‐sustaining population. This study evaluated whether interbreeding between Sebago Lake (Maine) and LaHave River (Nova Scotia) individuals will result in heterosis or outbreeding depression in juveniles. This was accomplished through full‐factorial 2 × 2 mating crosses between the strains and comparing multiple fitness‐related traits between the cross types. Hybrid juveniles displayed no signs of outbreeding depression nor heterosis. Further studies on comparative fitness of backcross and F₂ hybrids are recommended to assess potential consequences for this and similar restoration efforts.