Performance Comparison of Two Efficient Genomic Selection Methods(gsbay & MixP ) Applied in Aquacultural Organisms

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 Mix P 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 Mix P 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 Mix P; 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 Mix P and gsbay were expected to be more reliable than those estimated by GBLUP. Predictions made by gsbay were more robust, while with Mix P the computation is much faster, especially in dealing with large-scale data. These results suggested that both algorithms implemented by Mix P 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.     

Predictive ability of genomic selection models for breeding value estimation on growth traits of Pacific white shrimp Litopenaeus vannamei

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.     

Genome-wide mining,characterization, and development of microsatellite markers in <Emphasis Type="Italic">Marsupenaeus japonicus</Emphasis> by genome survey sequencing

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.     

Selection for growth performance of tank-reared Pacific white shrimp, Litopenaeus vannamei

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.     

Construction of bacterial artificial chromosome libraries for Zhikong Scallop <Emphasis Type="Italic">Chlamys farreri</Emphasis>

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.     

Genome-wide mining,characterization, and development of microsatellite markers in Marsupenaeus japonicus by genome survey sequencing

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.     

Effects of hypoxia on survival,behavior,and metabolism of Zhikong scallop Chlamys farreri Jones et Preston 1904

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.     

Importance of kelp-derived organic carbon to the scallop <Emphasis Type="Italic">Chlamys farreri</Emphasis> in an integrated multi-trophic aquaculture system

Bivalves and seaweeds are important cleaners that are widely used in integrated multi-trophic aquaculture (IMTA) systems. A beneficial relationship between seaweed and bivalve in the seaweed-based IMTA system has been confirmed, but the trophic importance of seaweed-derived particulate organic materials to the co-cultured bivalve is still unclear. We evaluated the trophic importance of the kelp Saccharina japonica to the co-cultured scallop Chlamys farreri in a typical IMTA farm in Sungo Bay (Weihai, North China). The dynamics of detritus carbon in the water were monitored during the culturing period. The proportion of kelp-derived organic matter in the diet of the co-cultured scallop was assessed via the stable carbon isotope method. Results showed that the detritus carbon in the water ranged from 75.52 to 265.19 μg/L, which was 25.6% to 73.8% of total particulate organic carbon (TPOC) during the study period. The amount of detritus carbon and its proportion in the TPOC changed throughout the culture cycle of the kelp. Stable carbon isotope analysis showed that the cultured scallop obtained 14.1% to 42.8% of its tissue carbon from the kelp, and that the percentages were closely correlated with the proportion of detritus carbon in the water (F =0.993, P= 0.003). Evaluation showed that for 17 000 tons (wet weight) of annual scallop production, the kelp contributed about 139.3 tons of carbon (535.8 tons of dry mass). This confirms that cultured kelp plays a similar trophic role in IMTA systems as it does in a natural kelp bed. It is a major contributor to the detritus pool and supplies a vital food source to filter-feeding scallops in the IMTA system, especially during winter and early spring when phytoplankton are scarce.     

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CYTOLOGICAL COMPARISON OF GAMETOGENESIS OF SCALLOPS, ARGOPECTEN IRRADIANS AND CHLAMYS FARRERI

Histological characteristics of gametogenesis of two kinds of scallops, gonochoric Chinese scallop, Chlamys farreri and hermaphroditic bay scallop, Argopecten irradians were investigated in this study. Spermatogenesis in C. farreri has different developmental stages: spermatogonia, primary spermatocyte, second spermatocyte, spermatid and spermatozoon. A large number of same developmental stage spermatic cells converge at a definite area of the testis. Premeiotic, previtellogenic and vitellogenic oocytes can be found during oogenesis in C. farreri, where oocyte distribution is obviously irregular. The A. irradians gonad consists of two different parts in one individual: one part functions as testis, the other as ovary. Between these two parts is a special appearance area, where a large number of spermatic cells are bound with two layers of acellular substance with many oocytes in it.     

Development of 101 novel EST-derived single nucleotide polymorphism markers for Zhikong scallop (Chlamys farreri)

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.     

基于GF-1/WFV数据的三江源草地月度NPP反演研究

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。     

Methods Comparison for Microsatellite Marker Development： Different Isolation Methods, Different Yield Efficiency

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.     

面向土地覆盖变化信息局域精度预测的逻辑回归协变量选用的直接策略与组合策略

土地覆盖信息是地理国情监测、生态环境建模等领域的重要组成。逻辑回归方法是土地覆盖变化信息局域精度量化颇有潜力的方法之一。在逻辑回归建模中,可从待检验地图提取若干像素尺度的景观指数(如像素类别、同质性、异质性、斑块大小等),用作协变量;基于验证样本,可估计逻辑回归系数,从而进行未采样点位的的精度预测。关于协变量的选择有两种策略:一是直接使用土地覆盖变化图中的若干景观指数作为协变量(直接策略),二是使用两时相的土地覆盖图中相应的景观指数的组合作为协变量(组合策略)。基于武汉部分城区的验证结果显示,两种策略下的逻辑回归预测结果的差异不明显。因此,从提高计算效率的角度,推荐采用直接策略进行土地覆盖变化信息的局域精度预测。     

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

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。     

APPROACH TO THE REGIONALIZATION OF AGRICULTURAL—PASTURALIZATION AROUND CHANGSHAN ISLANDS IN NORTHERN YELLOW SEA

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.     

集成夜间灯光数据与Landsat TM影像的不透水面自动提取方法研究

利用多源遥感数据提取不透水面信息是一个重要的研究方向。针对以往研究中多需要人工选取不透水面样本进行模型训练的问题,本文通过整合夜间灯光遥感与Landsat TM影像中的空间和光谱信息实现了不透水面覆盖范围（Impervious Surface Area,ISA）的自动提取。首先根据夜间灯光的分布来定位ISA聚集的城市区域的位置,分别在城市区域内部和外部自动提取可靠性高的ISA及非ISA样本,然后通过迭代分类提取城市区域的ISA,再以此为样本对城市区域外部进行分类,最后将分类结果整合完成整幅影像的ISA提取流程。应用本方法对美国雪城地区的DMSP/OLS夜间灯光影像上提取了84个城市区域,提取精度大于95%。从中分别选择高ISA密度和低ISA密度的2个城市区域作为ISA提取的测试区,本文方法在城市区域内的ISA提取总体精度与kappa系数分别为88.23%和0.63;在城市区域外部为78.6%和0.54,均优于人工样本选取方法的提取精度,表明该方法能够实现精度稳定且高效的ISA自动提取。