The consequences of differential family survival rates and equalizing maternal contributions on the effective population size (Ne) of cultured silver‐lipped pearl oysters,Pinctada maxima

The effective population size (N_e) is a critical gauge of how efficiently an aquaculture operation is capturing or maintaining genetic diversity and can govern the long‐term success of genetic selection programmes. In communally reared pearl oysters (Pinctada maxima), high variance in family sizes is a significant contributor towards low N_e and its severity may be compounded by differential survival rates of individual families. To determine the effect of variable survival on N_e in cultured P. maxima, families from two commercial populations were analysed using DNA parentage analyses to monitor survival and changes in relative contributions. Significant shifts in relative contributions were observed between 72 days and 18 months of age in both commercial cohorts (P<0.001). Survival rates were found to be highly variable among families (ranging from 2.5% to 49.5%) when reared in a common environment. Additionally, we investigated whether equalizing maternal family sizes before communal rearing will reduce family size variance, and increase N_e, compared with stocking at naturally produced proportions. Family equalization (E) significantly improved N_e (P=0.013) compared with rearing at natural (N) proportions (E: N_e=7.18±0.34; N: N_e=5.60±0.15); however, this practice may unintentionally magnify negative influences of poor performing families if survival is correlated with other commercially important traits. It is concluded that highly variable family survival will affect N_e in communally reared P. maxima, and the practice of equalizing family sizes in order to maximize N_e may only become consistently beneficial once further progress is made towards understanding, and then reducing variation in family survival rates.     

Japanese chum salmon stock enhancement: current perspective and future challenges

This study reviews the present status of the Japanese chum salmon Oncorhynchus keta stock enhancement program and considers the ecological sustainability of wild populations while providing fishery production, exemplified by the hatchery-based Kitami region set net fishery. The return rate and the number of returns have been historically high in the Sea of Okhotsk, but have decreased in other regions since 2005. Natural spawning of chum salmon occurred in at least 160 rivers in Hokkaido. The genetic diversity of Japanese chum salmon was similar to or higher than that of other Pacific Rim populations. Numbers of alleles were high at microsatellite loci, but the loss of rare haplotypes was observed in all populations. The estimated N _e /N ratio for the Kitami region was >0.15 % including hatchery and wild fish under the present high fishing pressure. Four regional populations were inferred in Hokkaido, however, genetic differentiation was weak and some river-populations were nested. Substantial changes in run timing were observed, but it has recovered gradually owing to the recent practice of escapement. Our analyses highlight the importance of juvenile quality and the vital roles of escapements in enhanced and non-enhanced rivers. New research is needed to minimize the genetic risks associated with hatchery programs.     

基于SSR-seq技术评估中间球海胆多代选育群体和普通养殖群体的遗传多样性

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

Genetic dynamics of a small population system: a model applicable to interactions between hatchery and wild fish

Straying between wild anadromous salmon populations is a natural process, and it is likely that the amount of gene migration from straying fish results from and reflects coadaptation between local populations. In contrast, introgression from cultured or transplanted fish may be disruptive. Data used to describe the genetic structure of populations usually come from biochemical genetic traits which may not reflect the strong selection that affects life-history characteristics. Simulations of a simple model of populations which included selection, genetic exchange and gene sampling error were conducted to examine the influences of these processes on population structure within the system. Results of these simulations indicate that data from loci not influenced by natural selection may provide a very different picture of population structure than data from loci subject to dispersive selection. Even relatively small decreases in average population fitness (0.0075) that accompany relatively weak selection can produce divergence between populations in the presence of local immigration rates of between 1 and 10%. Because of natural or anthropogenic causes, many population systems may not be in genetic equilibrium. Estimates from these simulations of parameters such as N_e, G_ST, N_em, and the G-statistic for heterogeneity, which are used to describe population genetic structure, may differ substantially from equilibrium values and from expectations for neutral loci. Statistically significant divergence between populations can occur even in the presence of 10 immigrants per generation. Results of simulations provide a means to examine potential results of introgression of alien fish into natural populations; but without knowing the extent of gene migration which occurs among wild populations and the magnitude of loss in average fitness of populations which results from introgression, it is not possible to predict what the impact will be.     

基于线粒体控制区的许氏平鲉养殖群体与野生群体比较研究

为研究许氏平鲉养殖群体与野生群体遗传结构及遗传多样性状况,采用PCR扩增获得许氏平鲉线粒体DNA控制区高变区片段,并对其进行比对分析。结果显示,在长度为451 bp的线粒体控制区片段中,养殖群体单倍型多样度(0.540±0.067~0.815±0.021)明显低于野生群体(0.883±0.053~0.944±0.028),而核苷酸多样度(0.001±0.001~0.007±0.004)与野生群体(0.004±0.003~0.007±0.004)相差不大,遗传多样性水平均较低。在52个单倍型中,养殖群体仅占12个,且有6个单倍型与野生群体共享。群体间遗传分化指数和AMOVA分析结果显示,养殖群体和野生群体之间以及养殖群体之间的遗传分化较大,而野生群体间遗传变异较小,组群间的遗传分化较小且不显著(ΦCT=-0.013;P0.05)。单倍型最小跨度树和NJ系统发育树均未检测到明显的谱系结构。     

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。     

Evaluation of genetic characteristics of wild and cultured populations of the Japanese pearl oyster <Emphasis Type="Italic">Pinctada fucata martensii</Emphasis> by using AFLP markers

Genetic characteristics of four wild (Mie, Fukui, Shimane and Nagasaki) and five cultured populations (selectively bred for 12 years with an origin of Ehime population) of the Japanese pearl oyster, Pinctada fucata martensii, were evaluated by using AFLP markers. Six primer pairs generated 1019 loci in total, among which 45.2–55.1 % was polymorphic among populations. Although there was no significant difference in gene diversity between wild (0.170–0.174) and cultured (0.158–0.173) populations, genetic relatedness in cultured populations (0.316–0.450) was about three times higher than that in wild populations (0.110–0.165). In addition, genetic differentiation was about twenty times larger in cultured populations (Nei’s distance: 0.0111) than in wild populations (Nei’s distance: 0.0005). These results mean that selective breeding can cause marked inbreeding as well as large genetic differentiation among cultured populations in a short period. On the other hand, it was suggested that genetic homogenization in the wild, probably due to a large-scale transport of cultured oysters, had progressed in the sea around Japan. In conclusion, it is necessary to prevent inbreeding by the reconsideration of the style of selective breeding in cultured populations, while the escape of gametes or spats of cultured strains in the wild should be avoided for the preservation of genetic characteristics in native populations of P. f. martensii.     

Genetic structure of brown trout,Salmo trutta,populations from differently sized tributaries of Lake Mjøsa in south‐east Norway

This study was based on genotyping eight microsatellite loci of 463 brown trout, Salmo trutta L., sampled in nine differently sized tributaries in three areas on the eastern shore of Lake Mjøsa, south‐eastern Norway. The populations were genetically structured, and Mantel's test showed that genetic distance correlated positively with geographical distance. Temporal differentiation F_ST over a 2‐year period was estimated in five streams and was non‐significant after Bonferroni correction. Effective population size N_e was positively correlated with the habitat length available from the lake (0.3–22 km) and negatively with the number of full sib pairs in the sample. There was no correlation between N_e and genetic diversity, and private alleles were recorded in three medium‐sized streams, but not in the largest two. The importance of small spawning and nursery streams for the maintenance of genetic diversity of brown trout was demonstrated.     

Genetic diversity of cultured and wild populations of the giant freshwater prawn Macrobrachium rosenbergii (de Man, 1879) based on microsatellite analysis

Freshwater prawn (Macrobrachium rosenbergii) culture in the Western Hemisphere is primarily, if not entirely, derived from 36 individual prawns originally introduced to Hawaii from Malaysia in 1965 and 1966. Little information is available regarding genetic variation within and among cultured prawn stocks worldwide. The goal of the current study was to characterize genetic diversity in various prawn populations with emphasis on those cultured in North America. Five microsatellite loci were screened to estimate genetic diversity in two wild (Myanmar and India‐wild) and seven cultured (Hawaii‐1, Hawaii‐2, India‐cultured, Israel, Kentucky, Mississippi and Texas) populations. Average allelic richness ranged from 3.96 (Israel) to 20.45 (Myanmar). Average expected heterozygosity ranged from 0.580 (Israel) to 0.935 (Myanmar). Many of the cultured populations exhibited reduced genetic diversity when compared with the Myanmar and the India‐cultured populations. Significant deficiency in heterozygotes was detected in the India‐cultured, Mississippi and Kentucky populations (overall F_is estimated of 0.053, 0.067 and 0.108 respectively) reflecting moderate levels of inbreeding. Overall estimate of fixation index (F_st = 0.1569) revealed moderately high levels of differentiation among the populations. Outcome of this study provide a baseline assessment of genetic diversity in some available strains that will be useful for the development of breeding programmes.     

Comprehensive assessment of the genetic diversity and population structure of cultured populations of golden pompano, <Emphasis Type="Italic">Trachinotus ovatus</Emphasis> (Linnaeus, 1758), by microsatellites

Golden pompano, Trachinotus ovatus, belongs to the family Carangidae. Within one decade, this species has rapidly become one of the most important cultured marine fish species in South China. However, the lack of a comprehensive genetic diversity assessment hinders the conservation of natural resources and management of cultured populations. Thus, we sampled one wild population and six cultured populations of golden pompano, which represented the whole cultured population, to assess the genetic diversity and population structure. The level of genetic diversity was low compared with those of other cultured fish, as the values of allelic richness, number of effective alleles and expected heterozygosity in the combined whole sample were 3.709, 2.592, and 0.591, respectively. These populations were little differentiated (Fst?=?0.02091, p value?=?0.00), and the whole sample did not show an explicit population structure at the individual level. The effective population size in each cultured population was small and in the whole sample was acceptable for a closed selection system. The pedigree reconstruction showed no evidence of artificial disturbance in mating. This general survey of cultured golden pompano populations showed the common characteristics of domestication with wild inputs. However, the low level of and potential decrease in genetic diversity should receive close attention in future breeding programs. In addition, we recommend wide surveys of natural resources and the establishment of closed breeding systems to increase genetic gain.     

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

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

利用高通量测序开发的熊本牡蛎微卫星标记评价野生和养殖群体的遗传多样性及通用性

利用高通量测序的方法,从熊本牡蛎基因组中开发了20对具有多态性的微卫星标记,通过微卫星标记位点比较了野生群体和养殖群体的遗传多样性。野生群体中,所有位点共扩增出330个等位基因,等位基因数(N_a)范围为6～39,平均等位基因数为16.500 0;有效等位基因数(N_e)范围为1.352 9～33.361 7,平均值9.517 2;观测杂合度(H_o)范围为0.200 0～1.000 0,平均值0.671 5;期望杂合度(H_e)范围为0.265 6～0.987 7,平均值0.832 1;ShannonWeiner指数(Ⅰ)范围为0.648 3～3.585 8,平均值2.276 9;多态信息含量(PIC)范围为0.254 5～0.969 2,平均值0.803 5,共有16个位点符合Hardy-Weinberg平衡。养殖群体中,N_a平均值为10.250 0,N_e平均值为5.843 4,H_o平均值为0.639 1,H_e平均值为0.763 6,I平均值为1.791 4,PIC平均值为0.720 7。结果显示,熊本牡蛎养殖群体的遗传多样性低于野生群体,但仍然维持在高度多态水平。研究表明,在熊本牡蛎人工繁育过程中,使用大数量的亲本进行繁育,可有效防止选育群体的遗传多样性降低,但人工选育对选育群体的遗传多样性也产生了一定的影响。另外,分析了这些引物在近缘种葡萄牙牡蛎、长牡蛎、香港牡蛎、有明牡蛎、僧帽牡蛎、咬齿牡蛎以及舌骨牡蛎中的通用性情况,发现XB1-6、XB1-39和XB1-45 3个位点在8个物种中均能扩增出目的条带,XB1-41仅能在熊本牡蛎中扩增出目的条带。     

白梭吻鲈3个群体的遗传结构比较

为了加强良种选育工作,切实做好亲本遗传管理,防止近交衰退的发生,利用20个微卫星分子标记对白梭吻鲈(Sander lucioperca)新疆野生群体及山东和苏州2个养殖群体的遗传结构进行检测。结果表明,20个微卫星标记中18个有扩增产物,14个呈现多态性;每个位点的等位基因数为2~6个,平均等位基因数为3.6个,3个群体的平均等位基因数为2.57~3.36,平均观测杂合度为0.5085~0.5621,平均多态性信息含量为0.3931~0.4764,表明3个白梭吻鲈群体的遗传多样性处于中等偏低水平,遗传多样性大小为:新疆群体苏州群体山东群体。群体的Fst为0.1798,表明群体间有一定的遗传分化。在白梭吻鲈人工繁殖与养殖过程中,必须加强亲本遗传结构监测并维持一定数量的亲本规模,以利于其产业的持续发展。     

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.     

Genetic diversity status of Pacific white shrimp (<Emphasis Type="Italic">Litopenaeus vannamei</Emphasis>) using SSR markers in Iran

Genetic diversity is vital for the maintenance of genetic pool in cultured shrimps. In order to estimate the current status of genetic diversity in Litopenaeus vannamei shrimp in Iran, as an exotic species, a total of 45 individuals from Amiri and Gorgeaj farms in Jask port of Hormozgan province and one hatchery in Gomishan city of Golestan province, were detected using four microsatellite loci. The number of alleles per locus was 5–10, and the mean effective number of alleles (N _e) across populations and loci ranged from 4.834 to 5.148. The overall mean observed heterozygosity (H _o) ranged from 0.450 to 0.479, which was lower than the expected one (0.789–0.794). There was nothing remarkable about any of the allele frequencies across populations or loci. The mean inbreeding coefficient (F _IS) and pairwise genetic differentiation (F _ST) among populations were 41.6 % and 0.133, respectively. The three studied populations departed from Hardy–Weinberg equilibrium (HWE). Analysis of molecular variance revealed 14 % variability among and 86 % within populations. However, considering departing from HWE and the high F _IS and F, the moderate pairwise F _ST values, importance of introducing genetically diverse broodstock and monitoring to control inbreeding is discussed.     

Genetic Variability in Eight Cultured and Two Wild Populations of Japanese Flounder,Paralichthys olivaceus,Based on the Mitochondrial DNA Control Region

To examine the present population genetic diversity and variability of Japanese flounder, a 394‐bp hypervariable fragment of mtDNA control region was sequenced. A total of 215 individuals from two wild and eight cultured populations were analyzed. The 91 variable sites defined 61 haplotypes and 12 of them were shared. Six single base pair insertion/deletions were detected. The haplotype diversity (h), the nucleotide diversity (π), and mean number of pairwise differences (k) in cultured populations (h = 0.443–0.844; π = 0.010–0.030; k = 3.745–11.838) were obviously lower than those in the wild populations (h = 0.987–0.988; π = 0.032; k = 12.443–12.718). Fixation index (F_st) and analysis of molecular variance (AMOVA) revealed that significant genetic differentiation mainly existed among cultured populations. The results of the exact test of population differentiation (nondifferentiation exact P values) rejected a panmictic mtDNA gene pool in all cultured populations. The results of this study indicated that genetic diversity of cultured Japanese flounder populations in China had significantly declined due to farm propagation and an increase in broodstock number should increase genetic diversity in cultured Japanese flounder base on the genetic theory.     

Changes in growth characteristics of the small abalone Haliotis diversicolor (Reeve, 1846) after one decade in a closed culture system: a comparison with wild populations

Small abalone Haliotis diversicolor (Reeve, 1846) is one of the smallest commercial abalone in the world. The successful application of artificial propagation and mass seed production techniques since the 1980s have resulted in the establishment of well-developed culture systems for small abalone in Taiwan. In the study reported here, we estimated the growth of a population of small abalone after a decade in a closed culture system and its growth characteristics with those of wild populations reported in previous studies. The von Bertalanffy growth equations of the shell length (L) and body weight (W) of cultured abalone were L _t  = 71.73 (1 ? e^{?0.84 (t?0.16)}) and W _t  = 47.70 (1 ? e^{?0.84 (t?0.16)})^3.180, respectively. The instantaneous rate of change for weight had an inflection point at the age of 1.54 years, indicating that cultured abalones reach their apex of body growth around this age. Compared with the wild populations, the cultured population exhibits a significantly smaller maximal shell length (L _∞) and a significantly larger growth coefficient (k). Based on our results, it appears that the artificial culture of generations of small albalone for one decade or more in a closed system could be one of the major factors causing the observed minimization of size in the cultured abalone; this may be an adaptation in which growth is traded off for the larger k.     

Genetic monitoring of broodstocks of the marine shrimp Litopenaeus vannamei in a closed rearing system in Pernambuco,Brazil

Loss of genetic variability can be detrimental to a population's survival traits and fitness. These effects are likely to be maximized in shrimp closed broodstock rearing systems where post‐larvae are often produced from crosses of breeders collected from an associated grow‐out farm after mass selection. Longtime broodstock management in closed systems is also expected to lead to reduction in or even complete eradication of genetic variability. The present work aimed at monitoring the genetic variability of a Litopenaeus vannamei hatchery in the state of Pernambuco (Brazil), during three successive replacements, using microsatellite markers. No significant genetic diversity losses have been observed through the values of mean heterozygosity (H_o=0.460 and H_e=0.660 in the first sample; H_o=0.420 and H_e=0.620 in the second sample; and H_o=0.600 and H_e=0.660 in the third sample). However, some alleles appear to have been lost after three replacements. The diversity level was considered to be high and is comparable to those reported for wild populations, suggesting that the original imported founder stock of Brazilian L. vannamei is likely to have had a high genetic diversity, possibly due to multiple origins.     

草鱼野生与选育群体遗传变异微卫星分析

为探究经过2个选育世代后选育群体遗传多样性和遗传结构的变化,实验采用多重PCR技术对4个野生草鱼群体(邗江、九江、石首、吴江)和2个选育群体(F1和F2)进行了微卫星序列遗传变异分析。结果显示,6个草鱼群体遗传多样性水平较高,2个选育群体除了平均等位基因数外,其他遗传多样性参数均小于4个野生群体。哈迪—温伯格平衡(Hardy-Weinberg equilibrium)检测显示,在120个群体—位点组合中有62个位点显著偏离哈迪—温伯格平衡,62个群体—位点组合中只有11个组合其近交系数值为负值,其余的51个组合的Fis均为正值。6个草鱼群体AMOVA分析结果显示,3.75%的变异来自于群体间,96.25%的变异来自于群体内,整体的遗传分化指数值为0.038。进一步分析各个群体间Fst,只有石首群体与F1、F2群体之间的Fst大于0.05,处于中等分化,其余群体间分化程度较低,且F2群体与4个野生群体之间Fst比F1群体与4个野生群体之间的Fst大。奈氏标准遗传距离分析结果显示,2个选育群体与野生群体之间的遗传距离大于野生群体之间的遗传距离。基于Dn建立的UPGMA系统发育树得出了相同的结果,即2个选育群体与野生群体之间的亲缘关系比4个野生群体之间的亲缘关系要远。研究表明,经过2个世代选育后,相比4个野生群体,2个选育群体遗传多样性虽有部分下降,但仍处于较高的水平,2个选育群体的遗传结构已发生变化,但其遗传分化程度尚不明显。本研究结果为制定出更加完善有效的选育方案提供了重要参考。     

Conservation genetics of the Mary River turtle (Elusor macrurus) in natural and captive populations

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