Differences of EST-SSR and genomic-SSR markers in assessing genetic diversity in poplar

We analyzed the genetic differences of 16 poplar clones between genomic-SSR and EST-SSR markers. The statistical results show that the average number of alleles detected by genomic-SSR was 4.1, Shannon＇s index 1.0646, observed heterozygos- ity 0.4427 and expected heterozygosity 0.5523, while for the EST-SSR, the average number of alleles was 2.8, Shannon＇s index 0.6985, observed heterozygosity 0.2330 and expected heterozygosity 0.4684. Cluster analysis indicated that the EST-SSR capacity of genotypic identification was more precise than that of genomic-SSR. These resuks reveal that EST-SSR and genomic-SSR have statistically significant genetic differences in polymorphism detection and genotypic identification. These differences could provide a theoretical basis for the rational use of SSR markers in species diversity and other related research.

Inter-and Intra-specific Genetic Diversity in Diospyros Using SCoT and IRAP Markers

The genus Diospyros contains more than 500 species, among them persimmon(Diospyros kaki Thunb.) is the most economically important species. However, the inter-and intra-specific genetic diversity remains unknown due to historic cultivation, domestication and introduction in different regions of China. In this study, we investigated the genetic diversity and relationship among 268 Diospyros accessions from different regions in China using start codon-targeted(SCo T) and inter-retrotransposon-amplified polymorphism(IRAP) markers. Among 268 samples,232 accessions were D. kaki varieties and 36 were closely related species, that is, D. lotus(21), D. glaucifolia(1), D. virginiana(5), D. kaki Thunb.var. silvestris(3), D. oleifera(5) and D. deyangnsis(1). In our study, a total of 90 and 97 polymorphic alleles were obtained from nine SCo T and nine IRAP markers, respectively, and these markers displayed rich polymorphisms for evaluation of the genetic diversity among 268 samples. A study on the relationship, genetic structure and analysis of molecular variance(AMOVA) showed that inter-and intra-specific gene exchanges were frequent among/within the samples from five regions. Moreover, the genetic distance between the Southwest China(SWC) and the other regions was relatively far;the samples from North China(NC), East China(EC), South and Central China(SCC), Northwest China(NWC) regions had a relatively close relationship. The unweighted pair group method with arithmetic means(UPGMA) and population structure analysis indicated that persimmons within geographic regions were clustered together, which revealed that the samples from various regions exhibited gene exchange, and the geographical proximity of persimmons resulted in a more frequent exchange. In addition, the persimmon had a close relationship with D. kaki var. silvestris, D. deyangnsis and D. oleifera species, and exhibited a far distance with respect to D. virginiana. These SCo T and IRAP markers will be helpful for understanding of the inter-and intra-specific genetic diversity of Diospyros germplasms, which play an important role in the germplasm efficient conservation, identification and utilization for Diospyros resources.

Intra-specific genetic relationship analyses of Elaeagnus angustifolia based on RP-HPLC biochemical markers

Elaeagnus angustifolia Linn. has various ecological, medicinal and economical uses. An approach was established using RP-HPLC （reversed-phase high-performance liquid chromatography） to classify and analyse the intra-specific genetic relationships of seventeen populations of E. angustifolia, collected from the Xinjiang areas of China. Chromatograms of alcohol-soluble proteins produced by seventeen populations of E. angustifolia, were compared. Each chromatogram of alcohol-soluble proteins came from a single seed of one wild plant only. The results showed that when using a Waters Delta Pak. C 18, 5μm particle size reversed phase column （150 mm×3.9mm）, a linear gradient of 25%-60% solvent B with flow rate of 1 ml/min and run time of 67 min, the chromatography yielded optimum separation of E. angustifolia alcohol-soluble proteins. Representative peaks in each population were chosen according to peak area and occurrence in every seed. The converted data on the elution peaks of each population were different and could be used to represent those populations. GSC （genetic similarity coefficients） of 41% to 62% showed a medium degree of genetic diversity among the populations in these eco-areas. Cluster analysis showed that the seventeen populations orE. angustifolia could be divided into six clusters at the GSC=0.535 level and indicated the general and unique biochemical markers of these clusters. We suggest that E. angustifolia distribution in these eco-areas could be classified into six variable species. RP-HPLC was shown to be a rapid, repeatable and reliable method for E. angustifolia classification and identification and for analysis of genetic diversity.

Analysis of Genetic Differences among Monokaryon Strains of Flammulina velutipes Using SCoT and ISSR Markers

[Objective]This study aimed to analyze genetic differences among Flammulina velutipes monokaryon strains.[Method]Twenty F1monokaryon strains（W1-W20）of F.velutipes were separated with conventional dilution method.Fifteen SCoT primers and nine ISSR primers were screened.According to amplification results,genetic similarity coefficients among various strains were calculated using NTsys 2.10e analysis software for cluster analysis.[Result]Six primers could be use to amplify clear polymorphic bands.To be specific,a total of 327 clear DNA fragments were amplified,including 287 polymorphic bands,accounting for 87.77%of the total number of bands amplified.Based on SCoT analysis,the genetic identity（GI）among 20 strains ranged from 0.187 5 to 0.937 5;to be specific,GI between W2 and W3 and that between W11 and W12 reached the maximum of 0.9375;GI between W15 and W18 was the minimum of 0.187 5.Based on ISSR analysis,GI among 20 strains ranged from 0.250 0 to 1.000 0;to be specific,GI between W3,W4 and W9,GI between W15 and W17,and that between W16 and W19 reached the maximum of 1.000;GI between W14 and W18 was the minimum of 0.250 0.Such low genetic identity fully demonstrated great genetic differences among F.velutipes monokaryons.According to results of cluster analysis,at a similarity level of 0.55,20 F.velutipes monokaryons were significantly divided into three groups using SCoT markers;at a similarity level of 0.66,20 F.velutipes monokaryons were divided into three groups using ISSR markers.Specifically,W11,W18 and W20 were invariably divided into one group;W15 and W17 were divided into one subgroup.[Conclusion]In this study,two type of markers were used for analysis of genetic diversity among F.velutipes monokaryon strains,which provided scientific and practical basis for screening high-quality monokaryon parents of F.velutipes.

Genetic difference of Chinese horseshoe crab(Tachypleus tridentatus) in southeast coast of China based on mitochondrial COI gene analysis

Population genetic structure and historical demography of Chinese horseshoe crab (T.tridentatus)along southeast coast of China were inferred from the sequence data of mitochondrial cytochrome c oxidase subunit Ⅰ (COI) fragment.The sequence analysis for 964 bp COI fragment was conducted in 28 individuals collected from five localities:Ninghai in Zhejiang Province,Meizhou and Zhangpu in Fujian Province,Beihai of Guangxi Zhuang Autonomous Region and Danzhou of Hainan Province.Sequence variation was relatively low with a total of seven transitions observed.In all localities,Haplotype H3 was the dominant type observed among eight haplotypes defined previously,and was at the center of radiation in Median-Joining network.The prolonged star-like network suggests a signature of population expansions.The level of diversity was low in total,with haplotype diversity ( Hd) being equal to 0.765 and nucleotide diversity (π) being equal to 0.00118,respectively.The genetic structure analysis revealed the significant genetic difference between Ninghai and Danzhou populations.Both mismatch distribution analysis and Fu's Fs test provided consistent inference of historic population expansion.The low genetic diversity of horseshoe crab observed along China coast indicated that urgent measures should be taken to protect this rare marine animal.

Analysis of Genetic Difference Between Species in Lupins by AFLP

The genetic difference between species in 18 lupins (Lupinus L .) varieties including L. angus-tifolius L., L . albus L., L. pilosus Murr. was analyzed using AFLP. A total of 462 bands were observed, a-mong of which, 442 (95.7%) were polymorphic, with an average of 110.5 polymorphic bands for each AFLP primer combination. The average genetic diversity index was 0.781 in this study. The genetic difference between species was higher than that of between varieties, the average identification percentage of four AFLP primer combinations was 100% and 84.7% between species and between varieties, respectively. The cluster analysis indicated that 3 species were distinctly distinguished on the dendrogram using UPGMA method.

Modeling Dynamic Systems by Using the Nonlinear Difference Equations Based on Genetic Programming

When acquaintances of a model are little or the model is too complicate to build by using traditional time series methods, it is convenient for us to take advantage of genetic programming (GP) to build the model. Considering the complexity of nonlinear dynamic systems, this paper proposes modeling dynamic systems by using the nonlinear difference e-quation based on GP technique. First it gives the method, criteria and evaluation of modeling. Then it describes the modeling algorithm using GP. Finally two typical examples of time series are used to perform the numerical experiments. The result shows that this algorithm can successfully establish the difference equation model of dynamic systems and its predictive result is also satisfactory.

Genetic Differences of Mitten Crabs Based on RFLP Analysis on Mitochondrial Cytochrome Oxidase Subunit I(COI) Gene

The genetic differences of 15 mitten crab populations from 6 river systems in China's Mainland and 1 population from Russia were studied based on RFLP analysis of mitochondrial cytochrome oxidase subunit I （CO I）. The results showed that Tas I-RFLP pattern could be used as a genetic marker to distinguish Eriocheir hepuensis from Eriocheir sinensis, Eriocheirjaponica and Eriocheir leptognathus; genetic distances among 13 populations of Eriocheir sinensis range from 0 to 0.015, indicating that they were different geographic strains; the subspecies status of Eriocheir sinensis and Eriocheir hepuensis （population from Nanliujiang） were considered owning to their genetic distances of 0.02-0.044, indicating that genetic divergence between them was low; Eriocheir leptognathus （population from Nanpaihe, Tianjin） was the most distant taxon with genetic distances value of 0.147-0.195, which could be defined as genetic distances between species in genus Eriocheir.

Optimization of the seismic processing phase-shift plus finite-difference migration operator based on a hybrid genetic and simulated annealing algorithm

Although the phase-shift seismic processing method has characteristics of high accuracy, good stability, high efficiency, and high-dip imaging, it is not able to adapt to strong lateral velocity variation. To overcome this defect, a finite-difference method in the frequency-space domain is introduced in the migration process, because it can adapt to strong lateral velocity variation and the coefficient is optimized by a hybrid genetic and simulated annealing algorithm. The two measures improve the precision of the approximation dispersion equation. Thus, the imaging effect is improved for areas of high-dip structure and strong lateral velocity variation. The migration imaging of a 2-D SEG/EAGE salt dome model proves that a better imaging effect in these areas is achieved by optimized phase-shift migration operator plus a finite-difference method based on a hybrid genetic and simulated annealing algorithm. The method proposed in this paper is better than conventional methods in imaging of areas of high-dip angle and strong lateral velocity variation.

Optimization of a global seventh-order dissipative compact finite-difference scheme by a genetic algorithm

A global seventh-order dissipative compact finite-difference scheme is optimized in terms of time stability. The dissipative parameters appearing in the boundary closures are assumed to be different, resulting in an optimization problem with several parameters determined by applying a generic algorithm. The optimized schemes are analyzed carefully from the aspects of the eigenvalue distribution, the ε-pseudospectra, the short time behavior, and the Fourier analysis. Numerical experiments for the Euler equations are used to show the effectiveness of the final recommended scheme.

Analysis on Genetic Diversity and Isolation Mechanism by Distance of Different Ecological Type Sheep Breeds in Mon-golia Sheep Group

In the present study with Tan sheep, small-tailed Han sheep, Hu sheep, Tong sheep, and Wadi sheep, we detected the distribution of gene frequency of several microsatellite sites in different chromosomes, the result showed that： 1） Hu sheep was in the status of Hardy-Weinberg extreme disequilibrium （P 〈 0.01）, while populations including Tong sheep, small-tailed Han sheep, Tan sheep, and Wadi sheep were in Hardy-Weinberg equilibrium （P 〉 0.05）. 2） Variance analysis of the heterozygosity and poly- morphic information content at rnicrosatellite makers showed that there were not significant differences among populations as to heterozygosity and PIC （P 〉 0.05）, as to effective number of alleles there were not significant differences both among Tan sheep, Hu sheep, Tong sheep, and Wadi sheep, and between Wadi sheep and small-tailed sheep （P 〉 0.05）, but between the former three populations and the latter two populations, there were significant differences （0.01〈 P 〈0.05）. The variation levels of small-tailed Han sheep was the highest in the five populations based on microsatellite maker data, subsequently followed by Wadi sheep, Tong sheep, Tan sheep, and then Hu sheep. 3） The phylogenetic relationships of the five sheep populations in this study did not meet the mechanism of isolation by distance, and the genetic differentiation relationships among five sheep populations were not closely linearly correlative with their geography distribution. Our findings supported related records in literature： The five populations originated on different time stage from the primogenitor population and communicated genetically with each other thereafter in the process of natural and artificial selection and on different ecological environment.

Genetic Analysis on Plant Height in Rice in Different Growing Seasons

[Objective] The aim was to carry out the genetic analysis on plant height of rice（Oryza sativa L.）cultivated in different seasons.[Method] Three rice parents with great difference in plant height including CB1（83.1 cm）,CB4（105.5 cm）and CB7（115.6 cm）were chosen to construct two parental combinations：CB1×CB4 and CB7×CB4,and the corresponding filial generations P1,F1,P2,B1,B2 and F2 were obtained.The 6 populations were planted in middle and late seasons respectively to measure their height traits.The Akaike＇s information criterion（AIC）of the mixed major gene and polygene model was used to indentify the existence of major genes affecting quantitative traits in B1,B2,F2 populations.When the major genes existed,the genetic effects of the major genes and polygenes and their genetic variance were estimated through segregation analysis.[Result] One additive major gene plus additive-dominance polygenes was the most fitted genetic model for the trait in all B1,B2,F2 populations in two planting seasons.The heritability values of the major genes varied from 38.63% to 78.53% and those of polygenes varied from 1.72% to 36.04%,and the total heritability values were 45.52-92.93%.The additive effect d value of the two genetic populations under two planting seasons was-4.56,-9.16,-7.19,and-9.38,respectively,as suggested that additive effect of the major genes would decrease the express of the plant height trait.[Conclusion] The heritability of plant height trait was affected by planting seasons and the combinations clearly as a whole.

Age-specific heterogeneity of genetic susceptibility to cardiovascular disease might have opposite outcomes depending on the presence of prediabetes

Examining age-specific heterogeneity of susceptibility to cardiovascular disease is also essential in individuals without prediabetes to determine its relative size and direction compared to those with prediabetes.Of particular interest,age-specific heterogeneity in genetic susceptibility may exhibit opposite directions depending on the presence or absence of prediabetes.

Morphological characteristics and genetic differentiation of Lutraria maxima in coast waters off southeast China

To explore genetic diversity and estimate the genetic differences among populations of Lutraria maxima in the coastal waters off south to southeast China,the morphology of the species of five different geographical populations(Beihai,Weizhou Island,Zhanjiang,Xiamen,and Fuzhou)in Guangxi,Guangdong,and Fujian provinces was studied statistically in combination with the microsatellite markers.As revealed by morphological principal component analysis(PCA),the cumulative contribution rate of the first three principal components was 72.596%.The discrimination accuracy ranged from 47.5%to 80.0%,and the scatter plots of principal component and discriminant analysis were consistent in overall,showing that the Xiamen and Fuzhou populations were overlapped obviously.For microsatellite markers,10 pairs of polymorphic primers were obtained by high-throughput transcriptome sequencing,and used for genetic diversity analysis.It was showed that the average number of alleles and eff ective alleles observed in each population ranged from 8.100 to 10.900,and from 3.497 to 4.228,respectively.The average observed heterozygosity(H_(o))and expected heterozygosity(H_(e))in the five populations ranged from 0.541 to 0.615,and from 0.642 to 0.733,respectively.The genetic distance(DA)ranged from 0.078 to 0.523,and the population genetic differentiation index(F_(ST))ranged from 0.027 to 0.139.The unweighted pair-population method with arithmetic means(UPGMA)and structure analysis showed that the five populations could be divided into two main clusters,the Beibu Gulf group(Beihai and Weizhou Island)and the Southeast China Sea group(Zhanjiang,Xiamen,and Fuzhou),suggesting that L.maxima has been separated geographically by the barrier of the Leizhou Peninsula into two groups in evolution,which provided us with a scientific clue to better protect the bioresource and establish an appropriate fishery management stocks for L.maxima populations in south China.

Analysis of genetic effects and correlations for nutrient quality traits of indica rice in different environments

Understanding the variation for the expressionof genes in different environments is one of themajor goals in qualitative genetics. In this pa-per, the genetic models for quantitative traitsof endosperm in cereal crops were used to eval-uate the seed, cytoplasm and maternal geneticeffects as well as the genotype × environment(GE) interaction effects, and to predict thebreeding value of parents and genotypic corre-lation for nutrient quality traits of indica rice (Oryza sativa L.).

Assessment of Different Traits to Evaluate Genetic Divergence in Some Wheat (<i>Triticum aestivum</i>L.) Genotypes under Late Sowing Condition

The research work was undertaken to identify the extent of genetic diversity in different parameters of wheat related to heat tolerance mechanism. Performances of currently available 25 spring wheat genotypes were studied at the Regional Wheat Research Institute, Shyampur, Rajshahi during the winter season of 2016/2017. All these genotypes (25) were grouped into five clusters on the basis of non-hierarchical clustering parameters viz. cluster I (G2, G5, G6, G16, G20), II (G4, G7, G9, G11, G12, G17), III (G10, G24), IV (G1, G13, G19, G21) and V (G3, G8, G14, G15, G18, G22, G23, G25). These groups were arranged into five (5) pairs of clusters viz. cluster I and III;II and III;II and V;III and IV;IV and V considering their similar potentiality of different traits. Results revealed that the maximum number of genotypes (8) was found in cluster V while cluster III comprised minimum genotypes (2). The inter-cluster distance was higher than intra-cluster distances. The highest and second highest eigenvalues belonged to spike/m2 (25.23%) and spikelets/spike (20.18%) respectively, along with positive canonical values in both the vectors 1 and 2 for these two traits identified them as major traits by exposing their highest potential toward genetic divergence. Cluster III produced the highest spike/m2 (388.8), grain/spike (48.1), plant height (89.5 cm), SPAD (54.2), yield (2799 kg/ha) and biomass (7758.1 Kg/ha) with lowest heading days (64.7 days), maturity days (98.7 days), canopy temperature at vegetative stage (21.7°C) and canopy temperature at grain filling stage (22.4°C). In contrast, cluster V produced the lowest 1000-grain weight (30.4 g) and grain yield (2172 kg/ha) belonging to the highest canopy temperature at both stages (23.8°C and 24.7°C). However, results suggested that the genotypes G10 and G24 under the cluster III, and genotypes G01, G13, G19 and G21 under the cluster IV could be considered as parents for future hybridization program, as well as the five pairs of clusters viz. cluster I and III;II and III;II and V;III and IV;IV and V might be matched as considered for getting more heterotic F1. The results of the study would help to identify the divergent genotypes associate with heat tolerance and this might be helpful in designing future breeding program.

Evaluation of Genetic Divergence in Various Potato Genotypes Grown in Bangladesh through Different Traits Assessment

The goal of the study was to quantify the genetic diversity of different potato varieties. Five groups were named to classify the 25 genres of potatoes as: Cluster I (Lalpakri, Diamond), Cluster II (Hagrai, Green Mountain, G.M.O., Elvera), Cluster III (Atlantic, Shepody, Raja, Fundy, Multa, Granulla, Shibilati, Japanese Red), Cluster IV (Atlas, Brondy, Yucon Gold, Monona, Petrones, Cheroki), and Cluster V (Calwhite, Prelude, Allblue, Russet, Burbank, TPS-67). The highest and lowest genotypes are found in Clusters III and I, respectively. The two groups’ maximum inter-cluster distance (the cluster’s distance between them) demonstrates the enormous diversity between Clusters II & III. Cluster III had the greatest intra-cluster distance (distance within a set), whereas Cluster V had the smallest. In most cases, the distance between gaps was more significant than the distance within the holes, showing greater genetic diversity between different groups’ genotypes. The highest, second highest, and third highest eigenvalues, accompanying the positive canonical values for Vectors I and II of three characteristics: average tuber weight in each plant, the tubers number in each plant, and the eyes number in each tuber, showed the most outstanding contribution to the complete difference between genotypes. Of the nine features, the smaller leaves number in each plant, the shorter plant height, the more minor genotypes, the fewer eyes per tube generated from Cluster I, the maximum height of the plants, the high-quality tubers in each plant, the tubers number in each plant, the fresh weight in each plant, and the leaf number in each plant from Cluster II could be chosen in the role of parents in this program for hybridization. Given the size of the genetic distance, the various characteristics that contribute to the overall difference, and the average population size, Hagrai, Green Mountain, O.M.G., Elvera Cluster II and Cluster I, Lalpakri, and Diamond genotypes can be regarded as parents of hybridization programs in the future. Thus, producers can get guidance to enhance genetic diversity by selecting materials from different relatives and reducing their vulnerability to diseases and climate change.

Analysis of genetic effects and heritabilities for amylose content of indica rice in different environments

An understanding of the genetic effects of em-bryo genes for rice quality traits is of impor-tance for rice quality improvement. Analysisof embryo, endosperm, cytoplasmic, and ma-ternal genetic effects and genotype×environ-

Research on Sex and Tissue Differences in Isozymic Phenotype of Varicorhinus macrolepis through Isozyme Electrophoresis

Polyacrylamide gel electrophoresis (PAGE) and biochemical staining method were used in this study for the analysis on malate dehydrogenase (MDH,E.C. 1.1.1.37) isozymes zymogram in 11 different types of tissues of male and female Varicorhinus macrolepis. It had been found for the first time that the phenotype of malate dehydrogenase (MDH),acid phosphatase (ACP) and superoxide dismutase (SOD) showed difference between male and female V. macrolepis,and there was no difference among different individuals in the same sex. Therefore,the electrophoresis band of malate dehydrogenase,acid phosphatase and superoxide dismutase could be used as an indicator for the identification of gender and tissues of V. macrolepis,which would provide basic data for the developmental genetics,variety improvement and directed breeding of V. macrolepis groups,thus facilitating the development and protection of this valuable fish species.

RAPD-PCR Analysis on Genetic Relationships Between Cultivars of Tree Peony

Random amplified polymorphic DNA (RAPD) was used to analyze genetic polymophism of 35 Tree Peony cultivars with 7 different color groups. Thirty four primers amplified 418 DNA fragments and 337 polymorphic bands (80.6%), including specific DNA markers for 18 cultivars that could be used to differentiate cultivars. The UPCMA method was used to analyze the genetic relationship among cultivars. The results showed that 35 Peony cultivars could be divided into 2 cluster groups when using similarity criteria of 1.5, and into 4 cluster groups when using similarity criteria of 1.0. The result confirmed that the flower color has no relation to the genetic clusters and the Tree Peony cultivars originated from the same area has close genetic relationship. Therefore, genetic background has no large effect on the genetic relationship. The sequence based on polymorphic rate from high to low was Blue groups > Yellow groups > Bark red groups > Blake groups > White groups>Green groups>Red groups.