Allozyme genetic analysis in hatchery strains and wild blue shrimp, Penaeus (Litopenaeus) stylirostris (Stimpson), from the Gulf of California

We conducted a population genetic analysis of Penaeus stylirostris to describe the genetic variability in two wild samples (Guaymas and Peñasco) and in two cultivated strains (A and B), and to determine the relationship among samples. Seventeen enzymatic systems and general proteins were used to visualize 31 loci. Of the 31 loci, 11 polymorphic loci (35%) were detected in all the organisms, with an average heterozygosity of 0.10 and an average of 1.8 per locus. There were no significant differences among the four samples of observed heterozygosity or percentage of polymorphic loci. According to Hardy–Weinberg, both cultivated strains showed disequilibrium in more loci than the wild samples. Guaymas showed linkage disequilibrium in five pairs of polymorphic loci, Peñasco samples in two pairs, A in seven pairs, and B in nine pairs. Peñasco and both cultivated lineages showed evidence of recent reductions in their effective populations size. Based on the comparisons of F_st values, and the distribution of the allelic frequencies, the cultivated strains were significantly different from the two wild populations. There is evidence that strain B originated from A and the discrepancies between the strains are probably the result of genetic drift and a founder effect.     

Genetic characterization of naturalized populations of brown trout Salmo trutta L. in southern Chile using allozyme and microsatellite markers

This study describes the genetic structure of five naturalized populations of brown trout in southern Chile using allozyme and microsatellite markers to establish levels of intra‐ and interpopulation genetic variability and divergence. Fourteen enzymatic systems were used comprising 20 loci and three microsatellite loci specific to brown trout. The genetic variability values (allozymes, P=20–35%, average=27%, H_O=0.118–0.160, average=0.141; microsatellites, P=33.3–100%, average=66.66%, H_O=0.202–0.274, average=0.229) are similar to values described in other naturalized populations of brown trout present in Chile, but higher than those observed in European populations of this species. Values of total genetic diversity (H_T) (allozymes=0.1216 and microsatellites=0.3504) and relative genetic divergence (G_ST) (allozymes=9.5% and microsatellites=15%) were also similar to the results obtained in previous studies of Chilean populations of brown trout. These values, when compared with those obtained in Europe, proved to be similar for H_T but lower for G_ST. The low interpopulational genetic differentiation was in accordance with the small genetic distance observed between the populations analysed (D Nei=0.004–0.025). On the other hand, the high frequency of one of the two alternative alleles of the phylogeographic marker locus LDH‐5* in the populations analysed (LDH‐5*90>0.84) would indicate a European origin, in particular Atlantic as opposed to Mediterranean, for the brown trout introduced into Chile. The high levels of genetic variability suggest a mixed origin for the naturalized brown trout in Chile, which could have originated either before or during the introduction process. Nevertheless, the low level of genetic differentiation between populations could reflect the short lapse of time in evolutionary terms, during which populations introduced into Chile have been exposed to different evolutionary forces, and which has not been sufficiently long to produce greater genetic differentiation between populations.     

High allozyme variation and genetic similarity of two populations of commercial penaeids, Penaeus brevirostris (Kingsley) and P. vannamei (Boone), from the Gulf of California

Genetic resources assessment is considered as the starting point for population management in both fisheries and aquaculture. In this study, we have obtained genetic variability measures of two commercial penaeid shrimp species, Penaeus brevirostris (Kingsley) and P. vannamei (Boone), from the Gulf of California by means of starch electrophoresis analysis of 16 enzymatic systems, plus total protein. Thirty-two loci were resolved, which revealed polymorphism values (P₉₅) of 15.63% in P. brevirostris and 25.00% in P. vannamei. Unbiased expected heterozygosity (H_e) was 0.076 and 0.105 respectively. These are high genetic variability figures, taking into account the previously low genetic variability, assessed by means of allozyme variation, reported in several penaeid species around the world. Nei’s genetic similarity between the two species is 0.891.     

利用微卫星标记对文蛤4个壳色花纹品系的遗传分析

利用9个微卫星位点对文蛤红壳(RS)、黑斑(BS)、细纹(TC)、暗纹(DF)4个壳色花纹品系共120个个体进行遗传差异分析。结果共检测到105个等位基因,每个位点平均观察等位基因数为11.7个,其中WG07位点等位基因数最多(21个),WG11位点最少(7个)。每个品系均具有特异等位基因类型,不同品系中相同微卫星位点的等位基因分布规律不同。4个文蛤品系的观测杂合度、期望杂合度和多态信息含量变异范围分别为0.110～1.000、0.486～0.867、0.433～0.834,均属高度多态性位点。Hardy-Weinberg平衡的卡方检测发现,大多数位点偏离平衡状态;聚类分析表明,4个品系间存在较明显的遗传差异,TC品系与其它品系的遗传距离最大,DF品系和RS品系的遗传距离相对较小。     

Genetic variation of wild and cultured populations of the Kuruma prawn Marsupenaeus japonicus (Bate 1888) using microsatellites

The microsatellite DNA technique was used to detect the genetic variations between wild and cultured populations of Kuruma prawn Marsupenaeus japonicus Bate 1888. All the six microsatellite loci screened in this study showed high polymorphism for their PIC (0.6701–0.8989), which was much more than the standard value of 0.5. A total of 73 alleles were observed over six loci from 93 shrimps. The mean number of allele locus ranged from 9.83 (cultured) to 11.83 (wild). The number of effective alleles varied from 6.86 (cultured) to 8.58 (wild). The average of observed heterozygosity (H_o) of populations varied from 0.6935 (cultured) to 0.7370 (wild), and that of expected heterozygosity (He) was 0.8169 (wild) and 0.8209 (cultured). Tests of Hardy–Weinberg showed that these loci deviated significantly or highly significantly in one or both populations. Compared with the wild population, the cultured population showed little reduction in genetic variation. The total number of alleles (71, 59) was not significantly (P=0.296) different between wild and cultured populations. The paired‐samples t test of observed heterozygosity and expected heterozygosity implied that there was no significant difference (P=0.572 and 0.891 respectively) between wild and cultured populations. However, some rare allele loss might have occurred in the cultured population. A total of 14 unique alleles were found in the wild population, but only two unique alleles were observed in the cultured population. Therefore, there is a need to monitor genetic variability of cultured population, and to improve the hatchery program for the conservation of wild Kuruma prawn resources.     

利用微卫星荧光多重PCR技术分析壳白长牡蛎3代人工选育群体的遗传多样性

为了探讨壳白长牡蛎人工选育对群体遗传变异的影响,实验利用4个多重PCR组合共10个微卫星标记分析了连续3代壳白长牡蛎人工选育群体和野生群体及基础群体的遗传多样性。结果发现,6个群体的平均等位基因数量为7.2~12.6,等位基因丰度为6.8~11.0,期望和观测杂合度分别为0.672~0.769和0.486~0.542;与野生群体相比,3代选育群体的平均等位基因数显著降低,但平均期望杂合度并无显著差异。哈迪—温伯格平衡检验结果显示,在60个群体—位点组合中有39个群体—位点组合显著偏离哈迪—温伯格平衡,近交系数F_(is)范围为0.215~0.342。群体间遗传分化指数F_(st)范围为0.005~0.076,处于中—低等的遗传分化水平。研究表明,虽然连续选育对群体的遗传多样性和遗传分化造成了一定程度的影响,但人工选育群体依然表现为较高的遗传多样性,仍可以一定的选择压力对选育群体进行人工选育。     

Evolution of introduced Chinook salmon (Oncorhynchus tshawytscha) in Lake Huron: emergence of population genetic structure in less than 10 generations

Abstract – Population genetic structure was detected in Chinook salmon Oncorhynchus tshawytscha in their non‐native range of Lake Huron using microsatellite DNA. All Chinook salmon in this system descend from Green River, Washington cohorts, originally transplanted to Michigan hatcheries in the late 1960s. We tested for population genetic differentiation of age 0 fish collected from 13 rivers and two hatcheries in 2007. The amount of genetic differentiation among collection sites was low but statistically significant, with F_ST values ranging from 0.036 to 0.133 and R_ST values ranging from 0.008 to 0.157 for specific loci. Based on pairwise F_ST and R_ST values and Bayesian cluster analysis, the Maitland River population in the Main Basin of Lake Huron was genetically distinct from the remaining collection sites. Based on analysis of bycatch data from commercial gill net fisheries, Chinook salmon likely colonised the Main Basin by 1975 (10 generations ago) and the North Channel and southern Georgian Bay regions by 1980 (eight generations ago). Thus, population genetic structure has emerged in Lake Huron Chinook salmon in <10 generations.     

Allozyme variation of hatchery and river populations of rohu (Labeo rohita, Hamilton) in Bangladesh

The genetic variations of rohu (Labeo rohita, Hamilton) sampled from five hatchery populations (Arabpur, Brahmaputra, Comilla, Kishorganj and Natore) and three major river populations (the Halda, the Jamuna and the Padma) were analysed by allozyme electrophoresis. Ten enzymes encoded by 11 loci were screened, and six were polymorphic. Alleles at three loci (Est‐1^*, Gpi‐1^* and Gpi‐2^*) proved variable for hatchery and river populations, and the Mdh‐2^* locus exhibited heterozygous genotypes for river populations only. Polymorphic loci per population (27.3±5.3%), heterozygous loci per individual (15.5±1.2%) and relative gene diversity (0.27±0.08) in river populations were higher than those for hatchery populations (25.5±1.8%, 10.7±1.6% and 0.25±0.01 respectively). Also, the observed heterozygosity (Ho) and expected heterozygosity (He) (0.09±0.03 and 0.14±0.04 respectively) in river populations were higher than those in hatchery populations (0.08±0.01 and 0.11±0.01 respectively). The lower levels of genetic variability in hatchery populations suggested the occurrence of inbreeding and/or genetic drift. The pairwise population differentiation (F_ST) values showed a lower level of genetic differentiation between hatchery and river population pairs. The unweighted pair‐group method with arithmetic mean dendrogram of Nei's genetic distances showed a relationship between the genetic distance and geographic distance. The populations were clustered into three groups: the Padma in one group, the Halda in second group and the Jamuna, including five hatcheries, in the third group. Highly diversified rohu individuals were observed in the Padma and Halda Rivers, whereas less genetically variable individuals were found in the Jamuna River and five hatcheries. These findings can be useful for rohu hatchery propagation to enhance the sustainable aquaculture production.     

Microsatellite analysis in domesticated and wild Atlantic salmon (Salmo salar L.): allelic diversity and identification of individuals

Samples of wild and domesticated salmon in Norway were genotyped at 12 microsatellite loci to compare allelic variability and investigate the potential of microsatellite markers for identification of individuals. The following loci were amplified: Ssa20, Ssa62NVH, Ssa71NVH, Ssa90NVH, Ssa103NVH, Ssa105NVH, SsaF43; Ssa20.19; Ssa13.37; SsOSL85; Ssa197; Ssa28. All domesticated strain samples displayed reduced variability compared to wild salmon. On average 58% of the allelic richness observed within the four wild stocks were present in the samples taken from domesticated strains. No systematic differences in heterozygosity were observed between samples representing the two groups.

Pairwise genetic distances, as estimated by Fst values and Nei [1978] was 2–8 times higher among domesticated strains than among wild strains. Among the wild stocks, the highest genetic distances were observed between the river Neiden, located in northern Norway, and the other wild stocks located in the southwest of Norway.

Assignment tests indicated that the wild and domesticated salmon could be distinguished with high precision. Less than 4% of domesticated salmon were misassigned as wild salmon, and less than 3% of wild fish were misassigned as domesticated salmon. Fish from individual domesticated strains were identified with similarly high precision. Assignment to wild salmon stocks was less accurate, with the exception of the sample taken from the river Neiden, for which 93% of the individuals were correctly assigned.     

The effects of the 1983 El Niño on Oregon's Coho (Oncorhynchus kisutch) and Chinook (O. tshawytscha) Salmon

The 1983 El Niño event off the Pacific Coast of North America resulted in increased adult mortality and decreased average size for Oregon's coho and chinook salmon. Actual return of adult coho salmon to the Oregon Production Area in 1983 was only 42% of the pre-season prediction. Coho smolts entering the ocean in the spring of 1983 also survived poorly, resulting in low adult returns again in 1984. Abundance of chinook stocks in southern Oregon was also reduced, as was abundance of Columbia River chinook stocks that show localized ocean distribution. Northerly migrating chinook stocks from the Columbia River showed little or no decline in abundance. The average weight of coho and chinook salmon landed in 1983 by Oregon's commercial troll fishery was the lowest recorded since statistics were first recorded in 1952. Comparison of the length-weight relationship for these fish indicated coho and chinook were in poorer condition in 1983 than in non-El Niño years. Because adult coho salmon returned to hatcheries at a smaller size, the fecundity (eggs per female) in 1983 was reduced from the 1978–1982 average by 24% at coastal hatcheries and by 27% at Columbia River hatcheries. The fecundity of chinook salmon was unchanged at most hatcheries.     

Genetic variation measured by microsatellites among three strains of domesticated rainbow trout (Oncorhynchus mykiss, Walbaum)

Genetic variation fuels selective change in natural and captive populations. In establishing a broodstock for selective improvement, the level of genetic diversity is an important consideration because it provides an indication of the scope for selective progress. Three domesticated strains of rainbow trout, Oncorhynchus mykiss (Walbaum), were examined at nine polymorphic microsatellite loci to assess detectable levels of allelic diversity and heterozygosity within and differentiation among the strains. A total of 126 alleles were observed to segregate into unique multilocus genotypes for each of the 152 individuals assayed. There was an average heterozygosity of 71.5% at these nine loci, and an average of 14 alleles at a locus. Each locus was represented by alleles unique to at least two of the three strains. Deviations from Hardy–Weinberg expectations of genotype frequencies were detected in each strain. Subsequent analysis indicated sub‐structuring within strains leading to Wahlund effects that caused these deviations. Significant differences in genotype frequencies and pairwise F_ST values demonstrated that all strains were unique. The overall F_ST of 0.089 provides additional evidence of unique genetic diversity present in each strain, and agrees well with the degree of genetic variation found in rainbow trout across broad geographical ranges. The genetic diversity contributed by each population suggests that there is greater scope for selective improvement of numerous traits within a synthetic strain combining these three strains than within any individual strain.     

Genetic differentiation of wild and hatchery Oujiang color common carp: potential application to the identification of escapees

The escape or release of cultured and domesticated organisms into the wild poses a threat to the genetic integrity of natural populations. Based on data from 17 microsatellite loci, the genetic differentiation between wild and hatchery Oujiang color common carp Cyprinus carpio var. color was investigated, and its potential application for identifying the escapees of hatchery strains was assessed using Bayesian genetic assignment. No significant differences were observed between pooled hatchery and pooled wild populations in terms of allelic richness (A _R), observed heterozygosity (H _O), and inbreeding coefficient (F _IS). Analysis of molecular variance and pairwise F _ST comparisons suggested significant genetic differentiation between hatchery strains and between hatchery and wild populations, which was further confirmed by principal components analysis and Bayesian clustering analysis. Bayesian genetic alignment showed high self-assignment accuracy (ranging from 86.0 to 96.0%) in the original populations, demonstrating the ability of this technique to identify hatchery Oujiang color common carp escapees in the wild population.     

When low genetic variability in feral and hatchery-reared tilapia becomes a vicious circle: Oreochromis niloticus from Oaxaca, Mexico

Several tilapia species in Mexican reservoirs have been used as food source for more than 40 years but little effort has been devoted to the conservation and genetic selection of those species. Our objective was to evaluate genetic variability in feral (n = 59) and hatchery-produced (n = 58) Oreochromis niloticus stocked in the Benito Juarez dam. Allozyme analyses for 13 enzymatic systems and general proteins yielded 27 genetic loci. Seventeen loci were polymorphic in at least one sample. The observed heterozygosity was lower than expected and the imbalance in the Hardy–Weinberg equilibrium in almost all loci was caused by heterozygote deficiency. The inbreeding coefficient was 84%. Although the evidence suggests moderate genetic differentiation, it is probable that a great proportion of the source of hatchery organisms is from feral organisms. According to our results, management of the hatchery strain is inadequate, therefore other breeding strategies are needed to increase the genetic variability of O. niloticus from Oaxaca.     

Allozymic variation and differentiation in naturalized populations of rainbow trout, Oncorhynchus mykiss (Walbaum), from southern Chile

An allozyme survey was conducted in three naturalized populations of rainbow trout, Oncorhynchus mykiss (Walbaum), from rivers in two Andean lakes of southern Chile. The analysis was based on 32 presumed loci, 10 of which were variable, and revealed that the mean percentage of polymorphic loci (P= 21.8%; range = 15.6-28.1%), the mean number of alleles per locus (n=1.26; range = 1.2-1.3) and the mean observed heterozygosity (H_O=7.0%; range = 6.0-8.2%) are high, although within the range reported for rainbow trout. Although the mean genetic distance between the samples was low (D = 0.003), and only 5.2% of the total observed genetic variation can be accounted by interpopulation differences (F_ST= 0.052), eight out of 10 polymorphic loci exhibited significant allelic heterogeneity. Some loci, notably EST-1*, IDHP-3,4*, MEP-1* and PGM-1*, showed considerable discriminatory capacity among the samples. Rainbow trout has a longer history in Chilean waters since salmonid introduction started earlier this century. Under current intensive farming practices, the preliminary information provided in the present paper is likely to be helpful in setting up a baseline for further characterization and/or monitoring of naturalized populations.     

Parentage Determination and Effective Population Size Estimation in Mass Spawning Pacific Oyster,Crassostrea gigas,Based on Microsatellite Analysis

Seven high polymorphic microsatellite loci were used to determine the pedigrees in a mass spawning of Pacific oyster, Crassostrea gigas, and to estimate the genetic variability between broodstock and offspring. Parental assignment was performed on a total of 155 individuals, including 141 offspring, 8 candidate mothers, and 6 candidate fathers. The assignment results of real offspring were generally in agreement with simulation with a success rate over 99% using only six of these loci. The allelic diversity and observed heterozygosity (H_o) exhibited similarity between parents and offspring populations, but the expected heterozygosity (H_e) had a significant decrease in offspring. Although all the males and females contributed to the next generation, the variances of reproductive success and unequal sex ratio resulted in a decline in effective population size (N_e = 11.42). The inbreeding rate of this small‐scale, mass spawning population was estimated at approximately 16.5% per generation. This gave us an insight that when designing breeding programs based on mass spawning for future oyster cultivation generations, the higher inbreeding and lower effective population size should be considered.     

Ceratomyxa shasta genotypes cause differential mortality in their salmonid hosts

Ceratomyxa shasta is a myxozoan parasite of salmonid fish. In natural communities, distinct genotypes of the parasite are associated with different salmonid hosts. To test the hypothesis that genotypes of C. shasta cause differential mortality, the polychaete host was experimentally infected with different parasite genotypes. Genotype I was obtained from Chinook salmon, Oncorhynchus tshawytscha, and genotype II from either coho salmon, O. kisutch, or rainbow trout, O. mykiss, We then challenged four salmonid strains: Chinook and coho salmon that occur in sympatry with the parasite and allopatric Chinook salmon and rainbow trout. Parasite genotype I caused mortality only in Chinook strains, although mortality in the allopatric strain also occurred from exposure to genotype II. A second experiment demonstrated that genotype II could be separated into two biotypes based on differential mortality in rainbow trout and coho salmon. These differential patterns of mortality as a result of infection by certain genotypes of C. shasta support field observations and suggest a co‐evolutionary relationship between these parasites and their hosts.     

Genetic diversity in a Tasmanian hatchery population of Atlantic salmon (Salmo salar L.) compared with its Canadian progenitor population

The level of genetic diversity in a cultured Atlantic salmon (Salmo salar) population from Tasmania, Australia was examined at 11 microsatellite loci and compared with that in its progenitor population from the River Philip in Nova Scotia, Canada. The reference progenitor population consisted of archived scales collected from wild River Philip salmon in 1971 and 1972, not long after salmon from this river were imported into Australia in the mid‐1960s. The Tasmanian hatchery stock had a significant reduction in the mean number of alleles (31–43%) and mean allelic richness (28–39%) across all microsatellite loci compared with the wild Canadian population. Mean heterozygosity levels remained unchanged. Estimates of per‐generation effective population sizes for the Tasmanian population, based on allele frequency temporal variance with the wild progenitor population, ranged from 102–207 individuals and reflected hatchery records.     

Genestic differences between successive year classes of two strains of reared rainbow trout, Oncorhynchus mykiss (Walbaum)

The genetic composition of consecutive year classes of two farmed rainbow trout, Oncorhynchus mykiss (Walbaum), strains was assessed, using starch gel electrophoresis of 11 enzymes encoded by a minimum of 23 loci, many of which have been shown to be polymorphic in previous studies. Angle frequencies at the majority of polymorphic loci varied significantly between year classes of each strain. Several alleles which were present at low frequency in the 1900 year classes, were absent in the samples from the 1991 cohorts. However, mean heterozygosity per locus (H) did not differ significantly between year classes of either strain, illustrating that allelic diversity is a more sensitive indicator of loss of genetic variability than mean heterozygosity. This heterogeneity between cohorts is probably due either to broodstock maintenance practices such as the use of insufficient numbers of spawners, or, in the case of one strain, to bottlenecking caused by selection for late maturation and increased growth rate. Genetic monitoring of all year classes of reared strains is suggested, if insufficient breeding and distribution records are available from egg producers. Such records are often unavailable in commercial situations.     

Development of Gene‐derived SNP Markers and Their Application for the Assessment of Genetic Diversity in Wild and Cultured Populations in Sea Cucumber,Apostichopus japonicus

The Apostichopus japonicus is a valuable aquaculture species in China. In this study, 51 single nucleotide polymorphisms (SNPs) were identified from expressed sequence tags of sea cucumber using high‐resolution melting. The average observed heterozygosity (Ho) and expected heterozygosity (He) were 0.2462 and 0.2897, respectively. Thirty‐two of these loci were used for estimating the genetic similarity and variation between the five hatchery stocks from China and two wild stocks from Japan. No significant differences in Ho or He were observed between the wild and hatchery populations. The pairwise Fst (which ranged from 0.0119 to 0.0236) and the genetic identity (which varied from 0.9802 to 0.9915) showed no significant differentiation between the wild and cultured stocks. The analysis of molecular variance indicated the source of variation was at the level of “within the populations.” The information on the genetic variation and differentiation in cultured and wild populations of A. japonicus obtained in this study is useful for setting up suitable guidelines for founding and maintaining of cultured stocks and for future genetic improvement by selective breeding.