Genetic characterization of four strains of Nile tilapia (Oreochromis niloticus L.) using microsatellite markers

Four domesticated strains of Nile tilapia (Oreochromis niloticus L.) were genetically characterized using 14 microsatellite markers and 64 animals per strain. Two strains, Chitralada (AIT) and International Development Research Centers (IDRC) were obtained from the AIT institute, Bangkok, Thailand. The GIFT strain (5th generation) came from NAGRI, Thailand, and the GÖTT strain was supplied by the University of Göttingen, Germany. The average numbers of alleles per marker were 5.0 (GÖTT), 5.4 (AIT), 5.6 (IDRC) and 7.5 (GIFT). Private alleles were found at all markers with the exception of two. No fixation of alleles was found at any marker. Population differentiation, F_ST, was 0.178 (great genetic differentiation) and confirmed grouping of the animals in strains. The expected level of heterozygosity ranged from 0.624 to 0.711, but the observed level of heterozygosity significantly deviated from the expected level in three strains. This was probably because of small population size. Moderate to great genetic differentiation was found between strains. A phylogenetic tree reflected the strains known histories. Application of the Weitzman approach showed that all strains have added value for the total genetic diversity and thus should be retained.     

Microsatellite DNA markers for genetic mapping in Oreochromis niloticus

The isolation of seven tri-, and 133 di-nucleotide microsatellite markers from a tilapia, Oreochromis niloticus , is described. An efficient methodology for isolating large numbers of such markers and their potential applications in applied aquaculture and evolutionary genetics are discussed.     

Effect of melatonin on GnIH precursor gene expression in Nile tilapia,Oreochromis niloticus

Sexual maturation and gonadal development of fish is greatly influenced by photic information, an external environmental factor, and melatonin mediates this information to regulate gonadotropin (GTH) secretion and gonadal activation. The relationship between gonadotropin inhibiting hormone (GnIH) and melatonin in fish, however, has not been studied to date. Here, the GnIH expression pattern and daily change of melatonin levels were compared to each other in mature tilapia (body length 16.1 ± 0.2 cm, body weight 77.7 ± 3.43 g), and the effect of melatonin injection on GnIH gene expression was investigated. GnIH gene expression increased at night when the secretion of melatonin increased, whereas gene expression decreased during the day when melatonin secretion decreased. Injecting tilapia intraperitoneally with melatonin increased GnIH gene expression and decreased the expression of gonadotropin releasing hormone (GnRH) and GTH. Furthermore, the injection decreased the 11-KT concentration in male tilapia. These results indicate that melatonin is likely to suppress the hypothalamus-pituitary-gonad (HPG) axis via the action of GnIH in this species.     

Evaluation of the genetic variability of 23 bovine microsatellite markers in four Belgian cattle breeds

The polymorphism of 23 microsatellites in the four main cattle breeds in Belgium (Holstein Friesian, Belgian Blue, Belgian Red Pied and East Flemish) was analysed. Heterozygosity, polymorphism information content, the effective number of alleles, exclusion probability and the probability of genotypic identity for two random individuals were calculated for all microsatellites and all breeds. The Belgian Blue breed is generally a little less polymorphic in comparison with the other three breeds. Estimates of the genetic distances between these breeds confirmed the widely accepted proposition that the Belgian Blue is the most genetically distinct of these breeds. The three other breeds are likely to become one population, given current breeding strategies. Exclusion probabilities in parentage control cases are >0·9999 in all four breeds when all 23 microsatellites are used and >0·98 with only the two most polymorphic multiplexes.     

Assessment of genetic diversity of coffee leaf rust pathogen Hemileia vastatrix using SRAP markers

Coffee leaf rust caused by the fungus Hemileia vastatrix (Berk and Br.) is a major disease occurring in coffee plantations. Although the rust fungus exists in different physiological races, the genetic difference between them is meagrely understood. In this study, genetic diversity of 14 identified and two unidentified leaf rust races was determined by sequence‐related amplified polymorphism (SRAP) markers. Of 48 SRAP primer pairs tested, 35 primers are polymorphic and generated 347 distinct scorable fragments. The number of fragments ranged from 4 to 18 with a mean of 9.97 fragments per primer combination. Of the total 347 amplified fragments, 185 fragments (53.31%) are polymorphic with an average of 5.41 fragments per primer combination. The average resolving power (Rp) and the average polymorphism information content (PIC) of the 35 SRAP primer combinations were 13.60 and 0.356, respectively. Of 35 SRAP primer pairs, 15 primer pairs were more informative and generated 25 unique fragments, which are useful for race discrimination. The study demonstrated the existence of genetic variability among various leaf rust races and this information will be helpful in coffee breeding programmes.     

Isolation and characterization of fourteen polymorphic microsatellite markers in the viperine snake Natrix maura

Nineteen polymorphic microsatellite loci were identified and developed for Natrix maura. Polymorphism was assessed for 120 individuals sampled across four sampling sites from the French Pyrenees Mountains. The number of alleles per locus ranged from 3 to 15, and expected heterozygosity per locus ranged from 0.227 to 0.863. We tested for deviation from Hardy–Weinberg equilibrium and linkage disequilibrium and assessed the presence of null alleles for all loci, resulting in a selection of 14 high‐quality polymorphic markers. These markers will be extremely useful in identifying fine‐scale genetic structures and providing insight into conservation management plans of this species.     

Fine‐scale population structure of Collichtys lucidus populations inferred from microsatellite markers

The spinyhead croaker Collichthys lucidus (Richardson) is a small sciaenid species distributed along the inshore waters of northwestern Pacific Ocean, and now has been listed as Key Protected Commercial Sources of Aquatic Animals and Plants in China. To delineate stock boundaries and inform conservation policy for its management, samples were collected from eight locations across the Chinese coastal waters and analyzed at nine microsatellite loci. C. lucidus populations showed low genetic diversity (expected heterozygosity = 0.445–0.542; observed heterozygosity = 0.392–0.539; Polymorphism Information Content = 0.268–0.684). Strong genetic fdifferentiation (F_st = 0.065–0.510, all significant after Bonferroni correction) among all populations and high levels of self‐recruitment (89.2%–91.5%) were observed, which suggested limited genetic exchange for this species. Clustering results of discriminant analysis of principal components and STRUCTURE found strong support for obvious genetic clusters (populations FZ, XM and SZ vs. populations SH, YRE, ZS, WZ and ND). The results of the present study not only supported the phylogeographic pattern of north‐south differentiation, but also suggested that C. lucidus populations may be predominantly sustained by self‐replenishment rather than by recruitment from distant populations.     

Evaluation of the genetic variability of 13 microsatellite markers in native Indian pigs

We analysed polymorphism of 13 microsatellites in two Indian domesticated pig types (North Indian and Northeast Indian). Heterozygosity, polymorphism information content, and probability of identity of two random individuals were calculated for all microsatellites in both types. The number of alleles observed at a locus varied between five and 12. The evaluated microsatellites exhibited a very high heterozygosity and polymorphism information content. The probability of identity of two random individuals from different populations taking into account all the 13 microsatellites was as low as 3.51 × 10^-19. On the basis of these results, we propose that these microsatellite markers may be used with reliability for studying the genetic diversity and for identification of individuals in Indian pig types.     

Characterization of polymorphic microsatellite markers for a coniferous shrub Juniperus sabina (Cupressaceae)

Juniperus sabina L. is an evergreen coniferous shrub, with a widespread distribution in Asia and Europe. It is one of the key species for restoration of the ecosystem in desertification areas. In the present study, we isolated and characterized eight microsatellite loci of this species. The number of alleles per locus ranged from two to 27, with observed heterozygosity values ranging from 0.256 to 0.744 and expected heterozygosity from 0.276 to 0.939. The markers developed in this study could be useful for population genetics studies of J. sabina.     

Circadian Rhythms of Locomotor Activity in the Nile Tilapia Oreochromis niloticus

Behavioral rhythms of the Nile tilapia were investigated to better characterize its circadian system. To do so, the locomotor activity patterns of both male and female tilapia reared under a 12:12 h light-dark (LD) cycle were studied, as well as in males the existence of endogenous rhythmicity under free-running conditions (DD and 45 min LD pulses). When exposed to an LD cycle, the daily pattern of activity differed between individuals: some fish were diurnal, some nocturnal, and a few displayed an arrhythmic pattern. This variability would be typical of the plastic circadian system of fish. Moreover, reproductive events clearly affected the behavioral rhythms of female tilapia, a mouth-brooder teleost species. Under DD, 50% (6 of 12) of male fish showed circadian rhythms with an average period (τ) of 24.1±0.2 h, whereas under the 45 min LD pulses, 58% (7 of 12) of the fish exhibited free-running activity rhythms with an average τ of 23.9±0.5 h. However, interestingly in this case, activity was always confined to the dark phase. Furthermore, when the LD cycle was reversed, a third of the fish showed gradual resynchronization to the new phase, taking 7–10 days to be completely re-entrained. Taken together, these results suggest the existence of an endogenous circadian oscillator that controls the expression of locomotor activity rhythms in the Nile tilapia, although its anatomical localization remains unknown.     

Effects of exogenous melatonin on the reproductive activities of Nile tilapia,Oreochromis niloticus

Gonadal development and sexual maturation of fish are often related to photic conditions. We attempted to utilise the direct application of melatonin to elicit similar effects in the absence of photoperiod manipulation. We found no significant differences in somatic growth between melatonin-treated groups and controls, indicating that melatonin administration did not negatively affect the growth of the experimental fish. Treatment with low-dose melatonin (0.3 mg/kg BW) resulted in a decrease in spawning frequency, number of spawned eggs and gonadosomatic index in female tilapia. In male tilapia, low-dose melatonin was associated with a decrease in sperm count, spermatocrit and spermatozoa activity index, implying that exogenous melatonin might mimic the effects of shortened light photoperiod, which suppresses reproductive activity in this species. These results suggest the possibility that an optimised dose of melatonin treatment could be used to control the spawning behaviour of this species.     

Genetic diversity and differentiation of Chinese domestic buffalo based on 30 microsatellite markers

To determine genetic diversity and evolutionary relationships among Chinese buffalo populations, 18 indigenous swamp buffalo populations and two introduced river buffalo breeds were genotyped for 30 microsatellite loci. The mean number of alleles across the 30 loci was 8.13, and the expected heterozygosity ranged from 0.517 (Yanjin) to 0.609 (Dehong). Although there was abundant genetic variation, genetic differentiation between Chinese buffalo populations was low, with only 2.8% of the total genetic variance among populations. The genetic differentiation pattern and genetic relationships among Chinese buffalo populations were consistent with their geographic distribution. The Dehong population was discerned as a distinct indigenous population, but suffered genetic admixture with river buffalo. The remaining populations were divided into four major clusters, i.e. the Upper and Middle Reaches of Yangtze Valley cluster (Guizhou, Guizhoubai, Yanjin, Fuling, Enshi and Jianghan), the Lower Reaches of Yangtze Valley cluster (Haizi, Shanqu and Dongliu), the South China cluster (Fuan and Xinfeng) and the Southwest China cluster (Xinglong, Xilin, Diandongnan and Dechang).     

利用30个微卫星标记分析长江中下游鲢群体的遗传多样性

摘要: 利用30对微卫星分子标记对长江中下游5个鲢群体进行了遗传多样性分析。结果表明: 在30个基因座中, 共检测到144个等位基因, 每个座位检测到的等位基因数为1～10个, 其中有25个座位具有多态性, 多态位点百分率为83.33,5个群体的平均等位基因数A为4.0/4.1, 平均有效等位基因数Ne为2.4445～2.6332, 平均观察杂合度Ho为0.3233～0.3511, 平均期望杂合度He为0.4421～0.4704, 平均多态信息含量PIC为0.4068～0.4286。对数据进行F-检验, Fst值表明群体间的遗传分化程度中等, 并对基因型进行了基于Hardy-Weinberg平衡的卡方检验, 所得P值说明5个群体均一定程度上偏离了平衡。5个群体间的遗传相似系数为0.8466～0.9146,遗传距离为0.0893～0.1665, 并根据Nei氏标准遗传距离用UPGMA方法对5个鲢群体进行亲缘关系聚类。     

Higher genetic diversity on mountain tops: the role of historical and contemporary processes in shaping genetic variation in the bank vole

Glacial phases during the Pleistocene caused remarkable changes in species range distributions, with inevitable genetic consequences. Specifically, during interglacial phases, when the ice melted and new habitats became suitable again, species could recolonize regions that were previously covered by ice, such as high latitudes and elevations. Based on theoretical models and empirical data, a decrease in genetic variation is predicted along recolonization routes as a result of the consecutive founder effects that characterize the recolonization process. In the present study, we assessed the relative importance of historical and contemporary processes in shaping genetic diversity and differentiation of bank vole (Myodes glareolus) populations at different elevations in the Swiss Alps. By contrast to expectations, we found that genetic variation increased with elevation. Estimates of recent migration rates and a contrasting pattern of genetic differentiation observed at the mitochondrial cytochrome b gene and nuclear microsatellites support the hypothesis that higher genetic diversity at high elevation results from contemporary gene flow. Although historical recolonization processes can have marked effects on the genetic structure of populations, the present study provides an example where contemporary processes along an environmental gradient can reverse predicted patterns of genetic variation.     

Characterizing genic and nongenic molecular markers: comparison of microsatellites and SNPs

The implications of transitioning to single nucleotide polymorphism (SNPs) from microsatellite markers (MSs) have been investigated in a number of population genetics studies, but the effect of genomic location on the amount of information each type of marker reveals has not been explored in detail. We developed novel SNP markers flanking 1 kb regions of 13 genic (within gene or <1 kb away from gene) and 13 nongenic (>10 kb from annotated gene) MSs in the threespine stickleback genome to obtain comparable data for both types of markers. We analysed patterns of genetic diversity and divergence on various geographic scales after converting the SNP loci within each genomic region into haplotypes. Marker type (SNP haplotype or MS) and location (genic or nongenic) significantly affected most estimates of population diversity and divergence. Between‐lineage divergence was significantly higher in SNP haplotypes (genic and nongenic), however, within‐lineage divergence was similar between marker types. Most divergence and diversity measures were uncorrelated between markers, except for population differentiation which was correlated between MSs and SNP haplotypes (both genic and nongenic). Broad‐scale population structure and assignment were similarly resolved by both marker types, however, only the MSs were able to delimit fine‐scale population structuring, particularly when genic and nongenic markers were combined. These results demonstrate that estimates of genetic variability and differentiation among populations can be strongly influenced by marker type, their genomic location in relation to genes and by the interaction of these two factors. This highlights the importance of having an awareness of the inherent strengths and limitations associated with different molecular tools to select the most appropriate methods for accurately addressing various ecological and evolutionary questions.     

Deleterious impacts of heat stress on steroidogenesis markers,immunity status and ovarian tissue of Nile tilapia (Oreochromis niloticus)

The water temperature of aquacultures is a primary factor of fish welfare, reproductive patterns, and immunity. To elucidate the molecular and biological processes of the temperature modulation of reproduction and immunity, female Nile tilapia (190 ± 10g) were allocated into five groups following acclimatization (150 females, three replicates, each n = 10). Each group was subjected to various temperatures (28 °C, 30 °C, 32 °C, 34 °C, and 37 °C), the group at 28 °C representing the control. Their serum levels of estradiol, cortisol, and vitellogenin were measured as well as serum triiodothyronine (T3) hormone, thyroxine (T4) hormone, and non-specific immunity (phagocytic and lysozyme activity). In addition, steroidogenic acute regulatory protein (STAR), vitellogenin gene receptor, and heat shock protein 70 (HSP70) gene expression were evaluated. The serum levels of estradiol, cortisol, and vitellogenin markedly declined (P < 0.05) in fish group at higher temperatures. In addition to T3, T4 was significantly affected (P < 0.05) in the control group. The expressions of the STAR gene (steroidogenesis) and vitellogenin receptors were also considerably down-regulated. The histopathological photomicrograph of fish subjected to high water temperature revealed injuries in ovary tissues, demonstrating its harmful effects. The experimental results verified the possible role of water temperature as a main stressor on Nile tilapia’ physiology through modulation of steroidogenesis-related gene expression and immunity.     

Effect of water temperature,feeding frequency,and protein percent in the diet on water quality,growth and behavior of Nile tilapia Oreochromis niloticus (Linnaeus, 1758)

This study evaluated how water temperature (26, 28, and 30°C), number of meals per day (one or two meals), and protein percent in diet (20, 25 and 30%) impact growth performance, biometric indices, and feeding behavior of Nile tilapia, Oreochromis niloticus. Fish were randomly allocated into 18 equal replicate groups. Higher final body weight was observed in fish reared at 30°C and fed one meal per day containing 30% crude protein. Better weight gain, weight gain %, feed conversion ratio, specific growth rate, and condition factor were recorded in fish reared at 26°C and fed one meal per day containing 30% protein. The best length weight relationship was obtained in fish reared at 26°C and fed one meal per day containing 30% crude protein. Shorter feeding duration and duration of appetite inhibition latency were recorded in fish reared at 30°C, fed one meal per day, and given a diet containing 30% protein. The highest proactivity was recorded in fish reared at 30°C, received one meal per day, and with 25% crude protein in their diet. Conclusively, rearing Nile tilapia at 26–30°C with a lower feeding frequency (one meal/day) and a 30% crude protein diet achieved better performance and feeding behavior.     

Assessing the geographic scale of genetic population management with microsatellites and introns in the clam Ruditapes decussatus

The clam Ruditapes decussatus is commercially important in southwestern Europe, suffering from population decline and hybridization with exotic Manila clam (R. philippinarum). Previous studies with intronic markers showed a genetic subdivision of the species in three races (Atlantic, West Mediterranean, and Adriatic‐Aegean). However, detailed population genetic studies to help management of the main production areas in the southwest of Europe are missing. We have analyzed eight Atlantic and two Mediterranean populations from the Spanish coasts using 14 microsatellites and six intronic markers. Microsatellites confirmed the Atlantic and West Mediterranean races detected with introns and showed that genetic variability was higher in Mediterranean than in Atlantic populations. Both marker types showed that genetic differentiation of Atlantic populations was low and indicated that populations could be managed at the regional level in the case of Cantabrian and Gulf of Cadiz areas, but not in the case of Rias Baixas and the Mediterranean. This study shows the interest of including different types of markers in studies of genetic population structure of marine organisms.