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1.
Genomic selection is more and more popular in animal and plant breeding industries all around the world, as it can be applied early in life without impacting selection candidates. The objective of this study was to bring the advantages of genomic selection to scallop breeding. Two different genomic selection tools MixP and gsbay were applied on genomic evaluation of simulated data and Zhikong scallop (Chlamys farreri) field data. The data were compared with genomic best linear unbiased prediction (GBLUP) method which has been applied widely. Our results showed that both MixP and gsbay could accurately estimate single-nucleotide polymorphism (SNP) marker effects, and thereby could be applied for the analysis of genomic estimated breeding values (GEBV). In simulated data from different scenarios, the accuracy of GEBV acquired was ranged from 0.20 to 0.78 by MixP; it was ranged from 0.21 to 0.67 by gsbay; and it was ranged from 0.21 to 0.61 by GBLUP. Estimations made by MixP and gsbay were expected to be more reliable than those estimated by GBLUP. Predictions made by gsbay were more robust, while with MixP the computation is much faster, especially in dealing with large-scale data. These results suggested that both algorithms implemented by MixP and gsbay are feasible to carry out genomic selection in scallop breeding, and more genotype data will be necessary to produce genomic estimated breeding values with a higher accuracy for the industry. 相似文献
2.
Genomic selection(GS)can be used to accelerate genetic improvement by shortening the selection interval.The successful application of GS depends largely on the accuracy of the prediction of genomic estimated breeding value(GEBV).This study is a fi rst attempt to understand the practicality of GS in Litopenaeus vannamei and aims to evaluate models for GS on growth traits.The performance of GS models in L.vannamei was evaluated in a population consisting of 205 individuals,which were genotyped for 6 359 single nucleotide polymorphism(SNP)markers by specifi c length amplifi ed fragment sequencing(SLAF-seq)and phenotyped for body length and body weight.Three GS models(RR-BLUP,Bayes A,and Bayesian LASSO)were used to obtain the GEBV,and their predictive ability was assessed by the reliability of the GEBV and the bias of the predicted phenotypes.The mean reliability of the GEBVs for body length and body weight predicted by the dif ferent models was 0.296 and 0.411,respectively.For each trait,the performances of the three models were very similar to each other with respect to predictability.The regression coeffi cients estimated by the three models were close to one,suggesting near to zero bias for the predictions.Therefore,when GS was applied in a L.vannamei population for the studied scenarios,all three models appeared practicable.Further analyses suggested that improved estimation of the genomic prediction could be realized by increasing the size of the training population as well as the density of SNPs. 相似文献
3.
《中国海洋湖沼学报》2020,(2)
Hypoxia,a frequent occurring threat in coastal regions,often results in mass mortalities of marine organisms and brings a serious ecological problem.The commercially important Zhikong scallop Chlamys farreri is being under such a threat as the risks of eutrophication and hypoxia have risen in their culture areas.However,little information has been known concerning their tolerance to hypoxia and their strategy for survival.In the present study,a 20-day experiment was conducted to determine the ef fects of hypoxia on the survival,behavior,and metabolism of Zhikong scallop.With the LC_(50) for dissolved oxygen(DO) being estimated as 1.8 mg/L,the survival of Zhikong scallop can be greatly challenged even under the moderate hypoxic condition of around 2.0 mg/L DO.The survival rate ranged from 69% to 59% when DO dropped from 3.0 to 2.0 mg/L,and it was further reduced to 47% at 1.5 mg/L DO.In hypoxic conditions,the scallops became significantly active,which may be explained as escape attempts to avoid hypoxic water.To save energy,Zhikong scallop would depress their respiration.However,when DO dropped from 3.0 to 2.0 mg/L,the oxygen consumption rate hardly changed.The upregulation of lactate dehydrogenase activity and the unrepressed phosphofructokinase activity,which often result in the unbalanced cellular homeostasis and energy budget,may account for the observed increase in the mortality rate of Zhikong scallops.In general,Zhikong scallop is sensitive to hypoxia events,though possible escape attempts,depressed respiration,and oxaloacetate-pathway may increase their survival chance. 相似文献
4.
Selection for growth performance of tank-reared Pacific white shrimp, Litopenaeus vannamei 总被引：1，自引：0，他引：1
Seven growth-related traits were measured to assess the selection response and genetic parameters of the growth of Pacific white shrimp, Litopenaeus vannamei, which had been domesticated in tanks for more than four generations. Phenotypic and genetic parameters were evaluated and fitted to an animal model. Realized response was measured from the difference between the mean growth rates of selected and control families. Realized heritability was determined from the ratio of the selection responses and selection differentials. The animal model heritability estimate over generations was 0.44±0.09 for body weight (BW), and ranged from 0.21±0.08 to 0.37±0.06 for size traits. Genetic correlations of phenotypic traits were more variable (0.51–0.97), although correlations among various traits were high (>0.83). Across generations, BW and size traits increased, while selection response and heritability gradually decreased. Selection responses were 12.28%-23.35% for harvest weight and 3.58%–13.53% for size traits. Heritability estimates ranged from 0.34±0.09 to 0.48±0.15 for harvest weight and 0.17±0.01–0.38±0.11 for size traits. All phenotypic and genetic parameters differed between various treatments. To conclude, the results demonstrated a potential for mass selection of growth traits in L. vannamei. A breeding scheme could use this information to integrate the effectiveness constituent traits into an index to achieve genetic progress. 相似文献
5.
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6.
《中国海洋湖沼学报》2017,(1)
The kuruma prawn, Marsupenaeus japonicus, is one of the most cultivated and consumed species of shrimp. However, very few molecular genetic/genomic resources are publically available for it. Thus, the characterization and distribution of simple sequence repeats(SSRs) remains ambiguous and the use of SSR markers in genomic studies and marker-assisted selection is limited. The goal of this study is to characterize and develop genome-wide SSR markers in M. japonicus by genome survey sequencing for application in comparative genomics and breeding. A total of 326 945 perfect SSRs were identified, among which dinucleotide repeats were the most frequent class(44.08%), followed by mononucleotides(29.67%), trinucleotides(18.96%), tetranucleotides(5.66%), hexanucleotides(1.07%), and pentanucleotides(0.56%). In total, 151 541 SSR loci primers were successfully designed. A subset of 30 SSR primer pairs were synthesized and tested in 42 individuals from a wild population, of which 27 loci(90.0%) were successfully amplified with specific products and 24(80.0%) were polymorphic. For the amplified polymorphic loci, the alleles ranged from 5 to 17(with an average of 9.63), and the average PIC value was 0.796. A total of 58 256 SSR-containing sequences had significant Gene Ontology annotation; these are good functional molecular marker candidates for association studies and comparative genomic analysis. The newly identified SSRs significantly contribute to the M. japonicus genomic resources and will facilitate a number of genetic and genomic studies, including high density linkage mapping, genome-wide association analysis, marker-aided selection, comparative genomics analysis, population genetics, and evolution. 相似文献
7.
8.
《中国海洋大学学报(英文版)》2016,(3)
Gene-centromere mapping is an essential prerequisite for understanding the composition and structure of genomes. Half-tetrad analysis is a powerful tool for mapping genes and understanding chromosomal behavior during meiosis. The Japanese scallop(Patinopecten yessoensis), a cold-tolerant species inhabiting the northwestern Pacific coast, is a commercially important marine bivalve in Asian countries. In this study, inheritance of 32 informative microsatellite loci was examined in 70-h D-shaped larvae of three induced meiogynogenetic diploid families of P. yessoensis for centromere mapping using half-tetrad analysis. The ratio of gynogenetic diploids was proven to be 100%, 100% and 96% in the three families, respectively. Inheritance analysis in the control crosses showed that 51 of the 53 genotypic ratios observed were in accordance with Mendelian expectations at the 5% level after Bonferroni correction. Seven of the 32 microsatellite loci showed the existence of null alleles in control crosses. The second division segregation frequency(y) of the microsatellite loci ranged from 0.07 to 0.85 with a mean of 0.38, suggesting the existence of positive interference after a single chiasma formation in some chromosomes in the scallop. Microsatellite-centromere distances ranged from 4 c M to 42 c M under the assumption of complete interference. Information on the positions of centromeres in relation to the microsatellite loci will represent a contribution towards the assembly of genetic maps in the commercially important scallop species. 相似文献
9.
Two Large-insert genomic bacterial artificial chromosome （BAC） libraries of Zhikong scallop Chlamys farreri were constructed to promote our genetic and genomic research. High-quality megabase-sized DNA was isolated from the adductor muscle of the scallop and partially digested by BamH I and Mbo I, respectively. The BamH I library consisted of 53 760 clones while the Mbo I library consisted of 7 680clones. Approximately 96 % of the clones in BamH I library contained nuclear DNA inserts in average size of 100 kb, providing a coverage of 5.3 haploid genome equivalents. Similarly, the Mbo I library with an average insert of 145 kb and no insert-empty clones, thus providing a genome coverage of 1.1 haploid genome equivalents. 相似文献
10.
The kuruma prawn, Marsupenaeus japonicus, is one of the most cultivated and consumed species of shrimp. However, very few molecular genetic/genomic resources are publically available for it. Thus, the characterization and distribution of simple sequence repeats (SSRs) remains ambiguous and the use of SSR markers in genomic studies and marker-assisted selection is limited. The goal of this study is to characterize and develop genome-wide SSR markers in M. japonicus by genome survey sequencing for application in comparative genomics and breeding. A total of 326 945 perfect SSRs were identified, among which dinucleotide repeats were the most frequent class (44.08%), followed by mononucleotides (29.67%), trinucleotides (18.96%), tetranucleotides (5.66%), hexanucleotides (1.07%), and pentanucleotides (0.56%). In total, 151 541 SSR loci primers were successfully designed. A subset of 30 SSR primer pairs were synthesized and tested in 42 individuals from a wild population, of which 27 loci (90.0%) were successfully amplified with specific products and 24 (80.0%) were polymorphic. For the amplified polymorphic loci, the alleles ranged from 5 to 17 (with an average of 9.63), and the average PIC value was 0.796. A total of 58 256 SSR-containing sequences had significant Gene Ontology annotation; these are good functional molecular marker candidates for association studies and comparative genomic analysis. The newly identified SSRs significantly contribute to the M. japonicus genomic resources and will facilitate a number of genetic and genomic studies, including high density linkage mapping, genome-wide association analysis, marker-aided selection, comparative genomics analysis, population genetics, and evolution. 相似文献
11.
Microsatellite markers have become one kind of the most important molecular tools used in various researches. A large number of microsatellite markers are required for the whole genome survey in the fields of molecular ecology, quantitative genetics and genomics. Therefore, it is extremely necessary to select several versatile, low-cost, efficient and time- and labor-saving methods to develop a large panel of microsatellite markers. In this study, we used Zhikong scallop (Chlamys farreri) as the target species to compare the efficiency of the five methods derived from three strategies for microsatellite marker development. The results showed that the strategy of constructing small insert genomic DNA library resulted in poor efficiency, while the microsatellite-enriched strategy highly improved the isolation efficiency. Although the mining public database strategy is time- and cost-saving, it is difficult to obtain a large number of microsatellite markers, mainly due to the limited sequence data of non-model species deposited in public databases. Based on the results in this study, we recommend two methods, microsatellite-enriched library construction method and FIASCO-colony hybridization method, for large-scale microsatellite marker development. Both methods were derived from the mi-crosatellite-enriched strategy. The experimental results obtained from Zhikong scallop also provide the reference for microsatellite marker development in other species with large genomes. 相似文献
12.
准确认识三江源植被生产力月度尺度的时空格局变化,对三江源畜牧业生产以及生态保护政策制定具有重要意义,可稳定获取的重访周期为4 d的16 m分辨率GF-1/WFV数据使中等空间分辨率的月度NPP产品生产成为可能。本文建立了一套以GF-1/WFV为基本数据源的中等空间分辨率草地月度NPP估算技术方法,并评估了其在三江源地区应用的可行性。在黄河源区玛多县的实验表明以GF-1/WFV为基础,以MODIS13Q1数据为补充,可以获得覆盖全区的中等空间分辨率月度NDVI数据,据其反演得到的草地NPP,地面验证精度在70%以上,优于MODIS NPP产品精度,且能更为详细地反映草地生产力变化的空间差异,在青海三江源地区利用GF-1/WFV数据生产中等空间分辨率的草地月度NPP产品是可行的。 相似文献
13.
Development of 101 novel EST-derived single nucleotide polymorphism markers for Zhikong scallop (Chlamys farreri) 总被引：1，自引：0，他引：1
Zhikong scallop(Chlamys farreri) is an important maricultured species in China.Many researches on this species,such as population genetics and QTL fine-mapping,need a large number of molecular markers.In this study,based on the expressed sequence tags(EST),a total of 300 putative single nucleotide polymorphisms(SNPs) were selected and validated using high resolution melting(HRM) technology with unlabeled probe.Of them,101(33.7%) were found to be polymorphic in 48 individuals from 4 populations.Further evaluation with 48 individuals from Qingdao population showed that all the polymorphic loci had two alleles with the minor allele frequency ranged from 0.046 to 0.500.The observed and expected heterozygosities ranged from 0.000 to 0.925 and from 0.089 to 0.505,respectively.Fifteen loci deviated significantly from Hardy-Weinberg equilibrium and significant linkage disequilibrate was detected in one pair of markers.BLASTx gave significant hits for 72 of the 101 polymorphic SNP-containing ESTs.Thirty four polymorphic SNP loci were predicted to be non-synonymous substitutions as they caused either the change of codons(33 SNPs) or pretermination of translation(1 SNP).The markers developed can be used for the population studies and genetic improvement on Zhikong scallop. 相似文献
14.
联合GRACE卫星轨道及距离变率数据反演地球重力场方法研究 总被引：2，自引：1，他引：1
基于动力学法,研究联合GRACE卫星精密轨道及距离变率数据反演地球重力场的方法,该方法可对重力位系数及卫星初始状态误差同时进行有效校正。通过对各观测值模拟不同的随机误差,研究了不同精度观测值联合反演所能达到的精度,以及用相同精度的观测值进行联合反演时不同采样率对反演结果的影响,模拟计算结果表明：联合反演模式下,当距离变率精度为1 μm/s,卫星位置精度为2~3 cm,速度精度为0.1~0.5 mm/s时,加速度计精度为(1.0×10 -10~1.0×10-9 m/s 2比较适合;将距离变率精度由1 um/s提高到0.1 um/s时,反演精度可获得相应提高;在观测值精度一定的情况下,联合反演算法宜采用5 s采样率。 相似文献
15.
人工神经网络和决策树模型在滑坡易发性分析中的性能对比 总被引：1，自引：0，他引：1
机器学习模型广泛应用于区域性滑坡易发性分析。模型的选择关系到评价结果的可信度、准确率和稳定性。现有滑坡易发性分析模型对比研究侧重模型的预测精度。模型的稳定性和数据量敏感性对机器学习模型的性能评估同样非常重要。本文以福建省南平市蔡源流域为研究区,以四川省绵阳市北川县为验证区,从预测精度、稳定性和数据量敏感性3个方面深入对比BP（Back Propagation）人工神经网络模型和CART（Classification and Regression Tree）决策树模型在滑坡易发性分析中的效果,主要结论如下:① 在逐渐增加一定数量训练样本的过程中,BP人工神经网络模型预测精度的增长率更高。在蔡源流域内,当训练样本数量增加10 000时,BP人工神经网络模型的预测精度上升5.22%,CART决策树模型的预测精度上升2.11%。② BP人工神经网络的预测精度高于CART决策树模型,且较为稳定。在100组数据集上,BP人工神经网络模型验证集预测精度的均值和验证集滑坡样本预测精度的均值分别为81.60%和84.86%,高于CART决策树模型的72.97%和76.59%。与此同时,BP人工神经网络模型对应预测精度的标准差分别是0.32%和0.37%,小于CART决策树模型的0.35%和0.67%。③ BP人工神经网络模型分析的滑坡易发区相比CART决策树模型,更接近实际滑坡的空间分布。最后,北川县的验证实验也出现了相同的现象。 相似文献
16.
17.
APPROACH TO THE REGIONALIZATION OF AGRICULTURAL—PASTURALIZATION AROUND CHANGSHAN ISLANDS IN NORTHERN YELLOW SEA 总被引：1，自引：1，他引：0
Based on the data of resources,environment and foundation of production,applying principal compo-nents-clustering quantitative analysis,this article divides the maritime space of Changshan Islands into three regions of agricultural-pasturalization,providing a scientific basis for the rational distribution of marine cultivation.The three re-gions are as follows:1)The region of an agricultural-pasturalization in the northern part of maritime space.It includes Da Wangjia and Shicheng islans.The main production is cultivation of prawn and mollusks in sea beach,float raft culture of mussel in shallow sea and scallop ,and breeding of sea cucumber in submarine.2)The region of agricultur-al-pasturalization in the middle western part of maritime space.It includes Da Changshan and Guanglu islands and west-ern part of Xiao Chengshan Island.The man production is folat raft culture of mussel and scallop in shallow sea,and breed-ing of sea cucumber in submarine.3)The region of agricultural-pasturlization of the southeastem part of maritime space.It includes the eastern part of Xiao Chan Island,Haiyang and Zhangzi islands.The main production is breeding of abalone,sea cucumber,algaes and fish. 相似文献
18.
在遥感图像分类过程中,进行合理的特征优选操作,将有助于提高分类器的分类效率及精度。本文以淮南地区资源三号卫星多光谱遥感影像数据为例,采用二值离散化、直方图法及F统计法3种计算方法实现mRMR（minimal-Redundancy-Maximal-Relevance）算法特征优选过程。根据3种方法所得到的特征优选结果及全部特征信息,分别采用C5.0决策树和K近邻2种分类器进行图像分类实验,并利用目视解译方法对不同方法组合的影像分类结果进行精度验证。实验结果表明,利用3种计算方法实现mRMR特征优选算法对不同分类器的影响程度不同：在分类效率方面,C5.0决策树分类器可提高36.84%,而K近邻分类器可提高72.05%;在分类精度方面,C5.0决策树分类器能保证分类精度大致不变,总体分类精度可提高0.60%,Kappa系数可提高0.80%,而K近邻分类器总体分类精度可提高4.34%,Kappa系数可提高7.90%。 相似文献
19.
The original purpose of Vessel Monitoring System(VMS) is for enforcement and control of vessel sailing. With the application of VMS in fishing vessels, more and more population dynamic studies have used VMS data to improve the accuracy of fisheries stock assessment. In this paper, we simulated the trawl trajectory under different time intervals using the cubic Hermite spline(c Hs) interpolation method based on the VMS data of 8 single otter trawl vessels(totally 36000 data items) fishing in Zhoushan fishing ground from September 2012 to December 2012, and selected the appropriate time interval. We then determined vessels’ activities(fishing or non-fishing) by comparing VMS speed data with the corresponding speeds from logbooks. The results showed that the error of simulated trajectory greatly increased with the increase of time intervals of VMS data when they were longer than 30 minutes. Comparing the speeds from VMS with those from the corresponding logbooks, we found that the vessels’ speeds were between 2.5 kn and 5.0 kn in fishing. The c Hs interpolation method is a new choice for improving the accuracy of estimation of sailing trajectory, and the VMS can be used to determine the vessels’ activities with the analysis of their trajectories and speeds. Therefore, when the fishery information is limited, VMS can be one of the important data sources for fisheries stock assessment, and more attention should be paid to its construction and application to fisheries stock assessment and management. 相似文献
20.
《中国海洋湖沼学报》2017,(3)
Ten microsatellite markers were used to analyze the levels of genetic diversity and inbreeding in a hatchery release population of Rhopilema esculentum Kishinouye(Scyphozoa: Rhizostomatidae). A total of 85 alleles were detected in 600 individuals. Within-population levels of observed( H o) and expected( H e) heterozygosity ranged from 0.152 to 0.839(mean=0.464) and from 0.235 to 0.821(mean=0.618), respectively. The polymorphism information content(PIC) of each marker ranged from 0.207 to 0.795 with an average of 0.580, indicating that the hatchery population maintained a high level of genetic diversity. Inbreeding levels were estimated in the hatchery population and the inbreeding coefficient was 0.203. This result revealed that a certain level of inbreeding occurred within the population. Meanwhile, we also determined genetic diversity at the clone level. Several polyps from the same scyphistomae were genotyped at the ten microsatellite loci and there was virtually no difference in their genotypes. Furthermore, we calculated the probabilities of exclusion. When both parents were known, the average exclusion probability of ten loci was 99.99%. Our data suggest that the ten microsatellite markers can not only be used to analyze the identity of individuals but they can also be applied to parentage identification. Our research provides a theoretical basis and technical support for genetic diversity detection and reasonable selection of R. esculentum hatchery populations. These findings support the use of releasing studies and conservation of R. esculentum germplasm resources. 相似文献