Grass Carp Populations Research Articles

Growth performance and selection signatures revealed by whole-genome resequencing in genetically selected grass carp (Ctenopharyngodon idella)

Grass carp (Ctenopharyngodon idella) is a highly productive freshwater fish species that is widely cultivated worldwide, contributing substantial economic value to the aquaculture industry annually. Recently, a breeding program for grass carp has progressed to the fourth generation (F4) after four consecutive generations of family selection. To further assess the growth performance of the genetically selected grass carp F4, a 90-day consecutive growth comparison experiment was conducted between the selected population and a wild base population. The results showed that the selected grass carp F4 had better growth performance. Whole-genome resequencing of both wild and selected populations of grass carp yielded a total of 4,354,416 high-quality single nucleotide polymorphisms (SNPs). Parameters of genetic diversity including observed heterozygosity (Ho), expected heterozygosity (He), nucleotide diversity (π), and polymorphic information content (PIC) were slightly decreased in the selected population compared to the wild population. The fixation index (Fst) indicated a low level of genetic differentiation (Fst = 0.021). Selection signatures analysis identified a total of 173 candidate selected regions with a cumulative size of 23.75 Mb, and 912 candidate genes including igf-1r, igfbp-2, igfbp-5 and itga6. This study provides valuable insights into the growth performance and the genetic basis of selection signatures in the process of grass carp selective breeding, and offers guidance for future breeding programs.

A Review of Grass Carp and Related Species Literature on Diet, Behavior, Toxicology, and Physiology Focused on Informing Development of Controls for Invasive Grass Carp Populations in North America

Grass carp (Ctenopharyngodon idella) are globally important in aquaculture and aquatic vegetation control. However, escaped grass carp have established invasive populations. A targeted keyword search was performed on a carp (order: Cypriniformes) literature database maintained by the U.S. Geological Survey to identify literature relevant to grass carp. Additional sources cited in reviewed documents and provided by numerous reviewers were also included. There were three focus areas designed to provide support for invasive grass carp management: (1) diet and behavior; (2) physiological constraints, toxicity, and biology; and (3) gut physiology. Each focus area provides information to guide development of potential pathways for invasive grass carp control. Information from other carp species was used to fill in gaps where grass carp information was lacking and provide additional, potential research directions. Diet-related information included food selection and aquacultural diet formulations. Behavioral information included stimuli and non-physical barriers to attract, repel, or stop movement. Physiological constraints, toxicology, reproductive control, and biological control provide a research review for control options. Gut physiology and related control pathways provide knowledge to improve toxin or pathogen delivery. This review provides a basis for developing approaches and research for controlling invasive grass carp populations, aquaculture, and native population management.

Whole-genome resequencing reveals genetic diversity and signatures of selection in mono-female grass carp (Ctenopharyngodon idella)

Grass carp (Ctenopharyngodon idella) is an important aquaculture species in China even in the world, and the production of mono-female population can effectively increase its yield as its females grow faster than males. Assessing the genetic basis of mono-female population is of great importance for breeding and culture, and the detection of signature of selection may shed light on genes and mutations associated with important phenotypic traits. In this study, whole-genome resequencing technology was employed to detect the genetic variation in wild populations of grass carp from the Yangtze River and the Pearl River, as well as in a mono-female population based on combining gynogenesis with sex-reversal breeding method. A total of 9,510,648 informative single nucleotide polymorphisms (SNPs) were identified across the three populations. The mean observed heterozygosity (Ho) and mean expected heterozygosity (He) of SNPs were calculated to be 0.2139 and 0.2894, 0.2313 and 0.2888, and 0.2523 and 0.2418 in the Yangtze River, Pearl River and mono-female population, respectively. The genetic distance between the mono-female population and the wild populations indicated that there was a moderate genetic differentiation between the three populations. Furthermore, analysis of run of homozygosity (ROH) revealed that the mono-female population exhibited a lower level of genomic inbreeding (inbreed coefficient = 0.075) compared to higher levels in the Yangtze River (inbreeding coefficient = 0.2410) and Pearl River populations (inbreed coefficient = 0.1894). Short ROHs were more frequently observed in the mono-female population, while long ROHs were more common in the Yangtze River and the Pearl River populations, providing insight into the population history of grass carp. Using the Yangtze River and Pearl River populations as references, 646 and 594 genes with hypothesized selection signature were identified by selective sweeps in the mono-female population, respectively. These genes were involved in 25 KEGG pathways associated with some important traits, such as growth (esm1 and zbed1), reproduction (ccnb1 and ptpn13), development (grin1a, mcc and brd2) and immune response (npr2, psmb9a, psmb8, tap2 and h2a). These results will be helpful for the molecular marker-assisted breeding and development conservation strategies of grass carp germplasm resources.

Mitochondrial diversity and population structure of grass carp (Ctenopharyngodon idella) in the Pearl River after anthropogenic release

The grass carp Ctenopharyngodon idella is a commercially relevant carp species with a long-term artificial release history in China. To date, several genetic diversity studies have been performed on the Yangtze River C. idella populations, but similar reports were sparse for the Pearl River populations. Here, our study explored the genetic diversity patterns and population structure of the Pearl River C. idella populations after human intervention using two mitochondrial loci. Phylogenetic analyses demonstrated that grass carp populations in the Pearl River exhibited two maternal genetic lineages. Haplotype networks demonstrated that most main Pearl River haplotypes were shared with those of the Yangtze River samples. No genetic structure was detected among the Pearl populations and low level of population differentiation was observed between individual Yangtze River populations and the Pearl River populations. These findings might be attributed to the high dispersal ability of grass carp, as well as anthropogenic release. Moreover, the nucleotide diversity of the Pearl River populations was higher than that of the Yangtze River, indicating that artificial release programs might have significant effects on the genetic diversity of the Pearl River populations. Taken together, our findings demonstrated artificial release programs may have influenced the Pearl River grass carp populations and provide important knowledge that may guide the future management of grass carp in the Pearl River.

Different resistance potential to reovirus in grass carp (Ctenopharyngodon idella) populations and their immune characteristics

Our aim was to verify whether genes in the coagulation complement and cytokine interaction pathways are crucial to the resistance to grass carp hemorrhagic disease in grass carps (Ctenopharyngodon idella). To evaluate this, we acquired male grass carps with grass carp reovirus (GCRV) resistance, F1 generation, ordinary male fish, control F1 progenies (hybridized ordinary fish), and barbel chub (Squaliobarbus curriculus) as a positive control. We compared the expression variation of 13 immune factors in different tissues using real-time fluorescent quantitative PCR. Our results showed that the expression of the transforming growth factor-β3, nerve growth factor receptor, coagulation factor D, chemokine receptor XCR1, profibrinolysin, γ-globulin of complement component 1, complement component 2, and complement component 5 in the different tissues of the barbel chub were significantly higher than those in the grass carps populations under normal conditions. Except for a limited number of genes, their expression exhibited significant differences. There was no significant difference in these genes among grass carp populations with different GCRV resistance. These results indicate that the high gene expression in the coagulation complement and cytokine interaction pathways may be the main reason for the strong resistance of barbel chub to GCRV. However, high gene expression was not a factor affecting GCRV resistance between grass carp populations.

Use of Environmental DNA to Detect Grass Carp Spawning Events

The timing and location of spawning events are important data for managers seeking to control invasive grass carp populations. Ichthyoplankton tows for grass carp eggs and larvae can be used to detect spawning events; however, these samples can be highly debris-laden, and are expensive and laborious to process. An alternative method, environmental DNA (eDNA) technology, has proven effective in determining the presence of aquatic species. The objectives of this project were to assess the use of eDNA collections and quantitative eDNA analysis to assess the potential spawning of grass carp in five reservoir tributaries, and to compare those results to the more traditional method of ichthyoplankton tows. Grass carp eDNA was detected in 56% of sampling occasions and was detected in all five rivers. Concentrations of grass carp eDNA were orders of magnitude higher in June, corresponding to elevated discharge and egg presence. Grass carp environmental DNA flux (copies/h) was lower when no eggs were present and was higher when velocities and discharge increased and eggs were present. There was a positive relationship between grass carp eDNA flux and egg flux. Our results support the further development of eDNA analysis as a method to detect the spawning events of grass carp or other rheophilic spawners.

Population structure, demographic history and local adaptation of the grass carp

BackgroundGenetic diversity within a species reflects population evolution, ecology, and ability to adapt. Genome-wide population surveys of both natural and introduced populations provide insights into genetic diversity, the evolutionary processes and the genetic basis underlying local adaptation. Grass carp is the most important freshwater foodfish species for food and water weed control. However, there is as yet no overall picture on genetic variations and population structure of this species, which is important for its aquaculture.ResultsWe used 43,310 SNPs to infer the population structure, evidence of local adaptation and sources of introduction. The overall genetic differentiation of this species was low. The native populations were differentiated into three genetic clusters, corresponding to the Yangtze, Pearl and Heilongjiang River Systems, respectively. The populations in Malaysia, India and Nepal were introduced from both the Yangtze and Pearl River Systems. Loci and genes involved in putative local selection for native locations were identified. Evidence of both positive and balancing selection was found in the introduced locations. Genes associated with loci under putative selection were involved in many biological functions. Outlier loci were grouped into clusters as genomic islands within some specific genomic regions, which likely agrees with the divergence hitchhiking scenario of divergence-with-gene-flow.ConclusionsThis study, for the first time, sheds novel insights on the population differentiation of the grass carp, genetics of its strong ability in adaption to diverse environments and sources of some introduced grass carp populations. Our data also suggests that the natural populations of the grass carp have been affected by the aquaculture besides neutral and adaptive forces.

A multiplex microsatellite PCR method for evaluating genetic diversity in grass carp (Ctenopharyngodon idellus)

Grass carp is one of the most important cultured fishes all over the world. The genetic diversity of grass carp plays an important role whatever in selective breeding progress or ecological conservation purposes. However, some genetic diversity researches were not accuracy and cannot be compared with each other due to different molecular markers, sample size and detection methods. In this study, we constructed five multiplex PCR assays contained 20 microsatellites with highly polymorphism and heterozygosity for evaluating genetic information of grass carp. We used nine cultured populations consisting of 507 individuals to detect stability of the five multiplex PCR assays. The results showed that the number of alleles (Na), effective number of alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He) and polymorphism information content (PIC) of the 20 microsatellite loci were relative high compared with the genetic diversity parameters of microsatellite loci developed by other researchers. Six loci were significantly deviated from Hardy-Weinberg equilibrium (P < 0.01). And with exception of the Shaoguan, Indian and Nepal cultured population, all other cultured populations showed very high genetic diversity. Through the test of grass carp populations, we developed an effective and accurate multiplex SSR-PCR assays that can be as statistical powerful tool for detecting genetic information of grass carp.

Site-specific water quality criteria for lethal/sublethal protection of freshwater fish exposed to zinc in southern Taiwan

There were considerable concerns about the zinc (Zn) pollution caused by electroplating, chemical, and computer-related high-tech industrial discharges in Kaohsiung Rivers situated at south Taiwan. There is, however, a lack of site-specific water chemistry based toxicity assessment and little is known about the sublethal toxicity on freshwater fish. This study proposes an integrated framework to link experimental and mechanistic model-based data analysis of lethal and sublethal Zn toxicities for grass carp (Ctenopharyn odon idellus) populations for providing the site-specific Zn water quality threshold in Kaohsiung Rivers. A biotic ligand model (BLM) that relates toxicity impairment of physiological active sites impacted by Zn species was used to elucidate the site-specific water chemistry affecting the bioavailability and biological response of grass carp exposed to Zn. Results indicated that 96-h LC50 for mortality and 28-d EC50 for growth inhibition were 474.7 ± 1.3 (mean ± SE) and 149 ± 23.5 μg L−1, respectively. Here the BLM-based predicted steady-state LC50s for mortality were 2110.7, 818.2, 1303.6, 563.3, and 497.1 μg L−1, whereas measured steady-state EC50s for growth inhibition were 726.8, 326.2, 373.4, 193.9, and 170.5 μg L−1 for the Agongdian, Houling, Love, Fengshan, and Gaoping Rivers, respectively. A positive correlation between Mg2+ and EC50 values were found in both acute (r = 0.94, p < 0.01) and chronic (r = 0.97, p < 0.01) Zn exposures. This study suggests that the use of site-specific water chemistry data and ecophysiological traits would enhance the predictive capacities to assess the potential effect of metal toxicity posed to aquatic organisms.

Confronting species distribution model predictions with species functional traits.

Species distribution models are valuable tools in studies of biogeography, ecology, and climate change and have been used to inform conservation and ecosystem management. However, species distribution models typically incorporate only climatic variables and species presence data. Model development or validation rarely considers functional components of species traits or other types of biological data. We implemented a species distribution model (Maxent) to predict global climate habitat suitability for Grass Carp (Ctenopharyngodon idella). We then tested the relationship between the degree of climate habitat suitability predicted by Maxent and the individual growth rates of both wild (N=17) and stocked (N=51) Grass Carp populations using correlation analysis. The Grass Carp Maxent model accurately reflected the global occurrence data (AUC=0.904). Observations of Grass Carp growth rate covered six continents and ranged from 0.19 to 20.1gday(-1). Species distribution model predictions were correlated (r=0.5, 95% CI (0.03, 0.79)) with observed growth rates for wild Grass Carp populations but were not correlated (r=-0.26, 95% CI (-0.5, 0.012)) with stocked populations. Further, a review of the literature indicates that the few studies for other species that have previously assessed the relationship between the degree of predicted climate habitat suitability and species functional traits have also discovered significant relationships. Thus, species distribution models may provide inferences beyond just where a species may occur, providing a useful tool to understand the linkage between species distributions and underlying biological mechanisms.

Long‐Term Population Response of Triploid Grass Carp Stocked in Piedmont and Coastal Plain Reservoirs to Control Hydrilla

AbstractThe triploid Grass Carp Ctenopharyngodon idella has been used to control hydrilla Hydrilla verticillata infestations in southern U.S. reservoirs for several decades. After eliminating hydrilla in the water column, Grass Carp must be maintained in sufficient densities to control hydrilla regrowth from the tuber banks in the hydrosoil. We monitored the long‐term response of triploid Grass Carp populations that had eliminated hydrilla within the water column in two Piedmont (Lake Norman and Mountain Island Lake, North Carolina) and two Coastal Plain reservoirs (the Santee Cooper system comprising Lakes Marion and Moultrie, as well as the connecting canal in South Carolina). Triploid Grass Carp stocked in Lake Norman and Mountain Island Lake exhibited both slow growth and erratic, but potentially high, mortality. Due to erratic survival in the two Piedmont reservoirs, we could not estimate mortality using a catch curve. Fish stocked into the Santee Cooper system not only grew larger and faster, they also persisted (i.e., significant numbers of age‐16–21 fish were collected during sampling in 2011). We hypothesize that Piedmont reservoirs without hydrilla in the water column and with little naturally occurring aquatic vegetation have a very low carrying capacity for triploid Grass Carp. Consistent, long‐term survival of triploid Grass Carp in the Santee Cooper system may be due to available food provided by hydrilla regrowth in the water column, floating vegetation, and less‐palatable, native, submersed vegetation. Hydrilla management in systems with residual plant food could involve estimating an average mortality rate and maintaining enough fish (i.e., about one fish per four hectares of surface area) to control hydrilla regrowth. In Piedmont reservoirs, possible management alternatives could include maintenance stockings based upon (1) yearling stocking rates that were successful in the past, (2) stockings determined from indirect measures of mortality such as from von Bertalanffy growth equation parameters, or (3) stockings derived from measures or indices of abundance such as counts conducted at night by bowfishers.Received January 28, 2014; accepted April 20, 2014

Genetic variability and relationships among six grass carp Ctenopharyngodon idella populations in China estimated using EST-SNP Markers

The grass carp, which is one of the most important farmed fish species in China, is widely distributed in different river basins. In this study, 21 single nucleotide polymorphism markers, developed in the grass carp expressed sequence tag database, were used with the snapshot genotyping method to analyze the genetic structure of six grass carp populations (SS, JL, HH, YJ, NX, and FS) from the Yangtze River and the Pearl River. The effective numbers of alleles (Ne) of the six grass carp populations was 1.7680–1.8038, the observed heterozygosity (Ho) was 0.5938–0.6305, the expected heterozygosity (He) was 0.4420–0.4443, and the polymorphic information content (PIC) was 0.3241–0.3403. The PIC, Ne, and He of the JL population were the highest among all populations, whereas those of the YJ population were the lowest. The NJ tree analysis based on genetic distance of the grass carp populations revealed that the six populations clustered into two branches: the SS, JL, and HH populations clustered first into one branch, which then clustered with YJ population; the FS and NX populations constituted a separate branch. The established genetic structures and phylogenetic relationships of some of the grass carp populations of the Yangtze River and Pearl River may lay the foundation for selecting core breeding populations.

Genetic variation analysis of wild populations of grass carp (Cteno-pharyngodon idella) using microsatellite markers

Twelve microsatellites were used to analyze the genetic diversity and genetic structure of eight wild populations of grass carp, among which six populations from Yangtze River (Hanjiang, Wujian, Jiujiang, Shishou, Mudong, and Wanzhou), one population from Pearl River and Heilongjiang River for each, Zhaoqing, and Nenjiang, respectively. Twelve markers showed highly polymorphic and all the eight populations contained high genetic variations. The variations of six populations of Yangtze River and Zhaoqing population of Pearl River were higher than Nenjiang population of Heilongjiang River. Bottleneck analysis revealed that four populations (Zhaoqing, Nenjiang, Mudong, and Wangzhou) had experienced a recent genetic bottleneck, and the effective population size was reduced. Pairwise FST and AMOVA analysis detected significant genetic difference among populations. The pairwise population genetic distances and the UPGMA tree demonstrated that the genetic distances between six populations of Yangtze River and Zhaoqing population were closer and clustered together earlier, as compared to those populations with Nenjiang population. The genetic structure simulation analysis suggested that there were five logic populations of all individuals. The genetic structures of Zhaoqing and Nenjiang populations were shown with independent separation, but the genetic structures of populations from Yangtze River were shown with fuzzy distribution. The high diversity was found in the wild grass carp from three major watersheds in China, which would supply a basis for future genetic improvement. However, the bottleneck effect of some populations should be taken into account in the practical breeding programs.

Genetic analysis of grass carp populations from three major water-sheds based on 26 microsatellite markers

Grass carp(Ctenopharyngodon idellus) are economically important in China,though wild populations have been in serious decline throughout the region.We used microsatellite markers to evaluate the genetic diver-sity amongst grass carp from four populations in three watersheds(Yangtze River,Pearl River,and Heilongjiang River).We selected 26 microsatellite markers and calculated heterozygosity,polymorphism information content(PIC),valid allele number,allele frequency,genetic distance,genetic similarity coefficient,and Hardy-Weinberg balance deflection index.There was a high degree of polymorphism within the markers in all three watersheds.The mean polymorphism information content(PIC) ranged from 0.581 3 to 0.638 6.Each microsatellite locus had 2-11 alleles(mean: 5.46).We identified a total of 154 alleles from all four populations,with a mean number of valid alleles of 3.455 6.The heterozygosity was between 0.711 4 and 0.804 5.FST and AMOVA analysis across all populations and loci suggested that there was low level of divergence amongst the four populations(FST=0.031 73).The Jianli population and the Hanjiang population were grouped in one cluster,which was clustered with the Pearl River population.The Heilongjiang population was grouped in a separated cluster.Our results suggest that there is a high level of genetic diversity among grass carp from the three watersheds,and no obvious differentiation.Our results may be used to better manage the fishery for conservation of locally adapted populations.

Microsatellite genetic diversity and differentiation of native and introduced grass carp populations in three continents

Grass carp (Ctenopharyngodon idella), a freshwater species native to China, has been introduced to about 100 countries/regions and poses both biological and environmental challenges to the receiving ecosystems. In this study, we analyzed genetic variation in grass carp from three introduced river systems (Mississippi River Basin in US, Danube River in Hungary, and Tone River in Japan) as well as its native ranges (Yangtze, Pearl, and Amur Rivers) in China using 21 novel microsatellite loci. The allelic richness, observed heterozygosity, and within-population gene diversity were found to be lower in the introduced populations than in the native populations, presumably due to the small founder population size of the former. Significant genetic differentiation was found between all pairwise populations from different rivers. Both principal component analysis and Bayesian clustering analysis revealed obvious genetic distinction between the native and introduced populations. Interestingly, genetic bottlenecks were detected in the Hungarian and Japanese grass carp populations, but not in the North American population, suggesting that the Mississippi River Basin grass carp has experienced rapid population expansion with potential genetic diversification during the half-century since its introduction. Consequently, the combined forces of the founder effect, introduction history, and rapid population expansion help explaining the observed patterns of genetic diversity within and among both native and introduced populations of the grass carp.

Mitochondrial DNA Dosage Effects in Triploid Grass Carp

AbstractThe grass carp Ctenopharyngodon idella is used widely in aquaculture for aquatic weed control. Historically, concern about the proliferative growth of nonnative diploid grass carp populations led to development of the hydrostatic pressure shock technique for the production of sterile triploids. Despite the success of this technique in accomplishing management goals, little is known about the cellular physiology of triploids. In particular, few studies have explored whether the induction of triploidy via hydrostatic pressure shock affects mitochondrial DNA (mtDNA) copy number in addition to that of chromosomal DNA. While the nuclear DNA (nDNA): mtDNA ratio is conserved in polyploid yeast, there are few data suggesting that vertebrate polyploids have nDNA: mtDNA ratios consistent with those of their diploid counterparts. In this study, two novel quantitative polymerase chain reaction assays were used to explore gene copy number in the nuclear and mitochondrial genome of diploid and triploid grass carp and to determine whether nuclear–mitochondrial copy number differences can be exploited to determine the ploidy of individual fish. The results of this study suggest that the ratio of mtDNA to overall cellular DNA is conserved in vertebrate polyploids and that real‐time assays of mtDNA copy number are not a feasible alternative to current methodologies for identifying triploid grass carp.

Analysis of genetic variation in grass carp ( Ctenopharyngodon idellus) from native and colonized regions using ISSR markers

The grass carp ( Ctenopharyngodon idella), a freshwater species native to China, have been introduced in more than 100 countries. In this paper, inter simple sequence repeat (ISSR) markers were used to evaluate genetic variation within and among grass carp populations sampled from its native (China) and colonized habitats (USA, Hungary, and Japan). Twenty-two ISSR primers were used to generate 207 bands, of which 82 (39.61 %) were polymorphic. The highest genetic diversity was observed in the Yangtze River population, whereas the lowest diversity was found in the Tone River population (Japan). Compared with colonized populations, the native populations possess approximately twice as much genetic diversity. The AMOVA analysis showed a relatively high level of genetic variation within populations. Significant genetic differences were revealed both among the native populations and between pooled native and colonized populations.

GRASS CARP (&lt;I&gt;CTENOPHARYNGODON IDELLUS&lt;/I&gt;) GENETIC STRUCTURE ANALYSIS AMONG NATIVE POPULATIONS IN CHINA AND INTRODUCED POPULATIONS IN USA, EUROPE AND JAPAN BASED ON MITOCHONDRIAL SEQUENCE

Grass carp (Ctenopharyngodon idellus) is one of the most important freshwater species in aquaculture. Meanwhile,the grass carp is originally distributes in China,and then it has been introduced into more than 100 countries for aquatic weed control and aquaculture since 1960s. In the past five decades,the grass carps have been adapted to the local environment and developed local groups. However,the genetic variation among the grass carps in native and introduced regions,as well the genetic phylogeny,is not clear. Meanwhile,there is no available literature to clarify which river systems in China are the most likely origins of colonized populations in introduced regions. In this study,partial sequences of the mitochondrial D-Loop (764bp),COII+tRNA (719bp) were analyzed from native (the Yangtze,Amur and Pearl Rivers in China) and introduced (the Danube River in Hungary,the Mississippi River in USA and the Tonegawa River in Japan) populations of the grass carp. The data of the two mtDNA fragments showed no competitive with the ILD (Incongruence Length Difference) test (p=0.42),and they could combine together as one data. The results indicated that there were the total of 32 haplotypes in all specimens,and 5 haplotypes were shared,all other haplotypes were singletons. In the 5 shared haplotypes,one was found in all populations,one in Amur River and Pearl River,two in China and Hungary,and the last one was found only in China. The genetic variation in the native populations was higher than that in the colonized populations. In the native populations,the genetic diversity ordered as the Pearl Rivers (π=0.0042) Yangtze River (π=0.0028) Amur River (π=0.0013). In the introduced populations,the genetic diversity ordered as the Danube River (π=0.0019) Mississippi River (π=0.0010) Tonegawa River (π=0.0001). The analysis of AMOVA using Arlequin 3.01 indicated that the variation mostly existed within populations (77.27%),but it was very low contribution from the sampling regions (0.38%). The pairwise FST values demonstrated that there was a significant differentiation in most pairwise populations. The Tajima's D values were significant negative in the populations of the Amur River and Mississippi River (was marginable significance in Tonegawa River),which demonstrating the recent population expansion in their histories,and were positive in the other populations. Base on the software TCS 1.21,the haplotype network showed that the Yangtze River population would be the most original and then expanded to other rivers. Based on the base composition,transition/transversion values from the software MEGA4,the gene flow among populations using the software Migrate-2.4.3 showed that the Danube River population and the Tonegawa River population might have two origins from China,namely the Yangtze and Amur River,the Mississippi River population might have three origins,the Yangtze,Amur and Pearl Rivers. The gene flow gave a sign that all grass carp populations would be derived from the Yangtze River,which is agreement with the results of the haplotype network.

Effects of Sample Size and Loci Number on Genetic Diversity in Wild Population of Grass Carp Revealed by SSR

Sample collection and marker selection are of primary importance in population genetic studies, and can greatly influence the analysis and interpretation of the data obtained. Microsatellite DNA sequences are the most revealing DNA markers available so far for inferring population structure and have been widely employed in genetic studies of populations．Nevertheless，few studies have specifically examined the effects of sample size and loci number on various genetic diversity measures in population genetic work using these markers．Here，we examined this issue using experimental data from an analysis of genetic diversity of wild populations of grass carp at 45 polymorphic microsatellite loci. The following genetic diversity measures were studied: number of alleles per locus (N_a), effective number of allele per loci (N_e)，observed hererozygosity (H_o) and expected heterozygosity (H_e)．We also tried to infer the theoretical minimum sample size and loci number needed for population genetic studies with microsatellite loci. The results are as follows: (1) N_a and Mean number of allele over loci (MNA) are significantly affected by sample size. It increase according to the raise of the sample size, only when the sample size exceeds 40 it tends to be stable. The significant correlation between sample size and N_a was observed and the correlation curve is Y=3.8403+0.6376, r²=0.967．However, there is no significant correlation between the mean value of N_e, H_o, H_eand the sample size. Mean value of H_o, H_e fluctuate with the raise of the sample size, only when the sample size exceeds 40 it manifest a stable trend. (2) Evaluating of different genetic parameters with the makers of different polymorphism information content, a significantly different result were acquired. When PIC>0.5, N_a, N_e, H_o, H_e were 3.6, 1.5934, 0.2824, 0.3540, While PIC<0.5, N_a, N_e, H_o, H_e were 9.5, 5.9209, 0.8497, 0.8242 respectively. Accordingly, marker selecting strategy has much greater impact on evaluation of genetic diversity. (3) According to the rise of loci number, the value of genetic parameter could be divided into three stages: ① Descending stage: loci number between 0&#8722;5, values of N_a, N_e, H_o, H_e indicated descending trend. ② Loci number between 5&#8722;10, values of N_a, N_e, H_o, H_e demonstrate ascending trend. ③ When loci number exceeded 15 values of N_a, N_e, H_e tend to be stable, while only when loci number exceeded 25 the value of H_o tend to be stable. Analysis above proved that not only the sample size and loci number but also the polymorphism information of microsatellite markers have significant effect on the estimation of population genetic diversity. So, we suggested that when microsatellite markers were used to estimate genetic diversity of population the minimum loci number and sample size are needed to exceed 25 and 40, respectively. Moreover, the conclusion above has been used to evaluate the genetic diversity of wild population of grass carp, values of the parameter were N_a=7.26、N_e =4.21、H_o=0.73、H_e=0.68, which demonstrated that has a relatively high diversity, a totally different conclusion from the former studies. Therefore, further researches are necessary for the evaluation of genetic diversity of geographically different population of grass carp.

Genetic structure analyses of different populations of grass carp (Ctenopharyngodon idella) using the TRAP technique

AbstractTarget region amplified polymorphism (TRAP) was used to compare genetic structures among three populations of grass carp (Ctenopharyngodon idella) – one wild and two cultured populations. Seven out of 15 primer combinations produced good amplification patterns and provided 103 amplified loci from the three populations. Numbers of polymorphic loci in the wild population were higher, indicating a decrease in genetic polymorphism in the two cultured populations. Compared with the wild population, only 39.98% loci gene frequency remained unchanged in the cultured samples, showing a genetic structure change in cultured populations. The genetic distances between wild and cultured populations were 0.0421 and 0.0809. With primer combination Ga5-800-E5, we detected a region in the electrophoretic pattern in which the number of amplified loci apparently decreased in cultured populations. These results establish a good scientific basis for developing molecular markers that can help in distinguishing wild from cultured populations.