Genetic Diversity in Main Cultivars of Safflower in Xinjiang Uighur Autonomous Region Based on RAPD Analysis

[Objective] Study on the genetic diversity in main cultivars of safflower distributing in Xinjiang Uighur Autonomous Region by means of RAPD makers.[Method] Genomic DNAs of 29 safflower accessions from Xinjiang Uighur Autonomous Region were extracted for PCR amplification using 20 RAPD primers.[Result] Totally 156 bands were amplified,among which 144 bands were polymorphic(accounting for 92.31%),indicating that safflower is endowed with plentiful genetic diversity.Based on the DNA fingerprint,the 29 safflower accessions were grouped into four populations,the classification results may be not related with ecological regionality.[Conclusion] RAPD technique is an available tool to analyze the genetic diversity of safflower germplasm at molecular level.

RAPD analysis of genetic diversity of nine strains of Auricularia auricular cultivated in Heilongjiang Province

Polymorphism of nine strains （CF05, CF09, 29, 916, AU9, Chang10, Chang7, 8808 and AU. Japanese） of A. auricular cultivated in Heilongjiang Province were analyzed by RAPD （Random Amplication polymorphic DNA）. Thirteen primers were selected from forty PCR primers with 10bp long random primer. The results showed that nine strains of A. auricular have a high level of genetic diversity and the percentage of DNA polymorphic was 96.05. The genotypes of 9 strains of Auricularia auricular were identified by the fingerprints from primer 27 and primer 46 by RAPD analysis. The results are helpful for quickly identifying strains of A. auricular in its early breeding time, and also provides a powerful theoretic basis to differentiate strains （Auricularia auricular） whose morphology is very similar in breeding programs of edible fungus.

Genetic Diversity and Clustering Analysis of 48Cultivars of Olea euyopaea L.

Inter-simple sequence repeat（ISSR） molecular markers were applied to analyze the genetic diversity and clustering of 48 introduced and bred cultivars of Olea euyopaea L. Totally 106 DNA bands were amplified by 11 screened primers, including 99 polymorphic bands; the percentage of polymorphic loci was 93.40%, indicating a rich genetic diversity in Olea euyopaea L. germplasm resources. Based on Nei＇s genetic distances between various cultivars, a dendrogram of 48 cultivars of Olea euyopaea L. was constructed using unweighted pair-group（UPMGA）method,which showed that 48 cultivars were clustered into four main categories; 84.6% of native cultivars were clustered into two categories; most of introduced cultivars were clustered based on their sources and main usages but not on their geographic origins. This study will provide references for the utilization and further genetic improvement of Olea euyopaea L. germplasm resources.

RAPD Analysis for Genetic Diversity of Varanus salvator

[Objective] The aim was to carry out RAPD analysis on genetic diversity of Varanus salvator. [Method] 20 random primers were used for PCR amplification of genomic DNA of 36 individuals of V. salvator. [Result] 10 primers could produce highly reproducible RAPD bands. A total of 2 952 DNA fragments were successfully amplified. Each individual got 82 amplified bands on average,47 of which showed polymorphism. The polymorphic locus percent was 57.32%. The genetic distance among 36 individuals ranged from 0.035 9 to 0.335 9 with an average of 0.135 9. The Nei＇s gene diversity index （H） and Shannon＇s information index （I） were 0.181 9 and 0.263 0,respectively,indicating that V. salvator had greater genetic diversity. [Conclusion] The phylogenetic tree was inferred by using UPGMA analysis,it was found that the 36 individuals could be classified as one group,and there was no obvious population differentiation.

Morphological Diversity Analysis of Red-seed Watermelon (Citrullus lanatus ssp. vulgaris var. megalaspermus Lin et Chao) Germplasm Resources

[Objective] This study aimed to analyze the morphological diversity of red- seed watermelon （Citrullus lanatus ssp. vulgaris var. megalaspermus Lin et Chao） germplasm resources. [Method] Multiple cluster analysis and principal components analysis on the morphological traits of 51 red-seed watermelon germplasm resources were carried out. [Result] The coefficient of variations （CVs） of 39 morphological traits in 51 red-seed watermelon idioplasm resources ranged from 5.37% to 66.95%, with an average of 22.87%. The average of Shannon diversity information indices was 1.55. Among them, the Shannon diversity information index of seed length was the highest （2.16） and that of seed shell figure pattern was the lowest （0.32）. In ad- dition, the morphological diversity information indices of quantity characters were higher than that of quality characters. The principal components analysis revealed that the variance contribution rates of the first, second and third principal compo- nents were 19.49%, 15.32% and 9.55%, respectively. Cluster analysis divided the 51 materials into three broad branches based on the morphological traits. There was only one material in the fist branch and two in the second branch, and all the three materials were wild. The other 48 materials were divided into the third branch and all of them were cultivars. [Conclusion] This study provided a theoretical basis for the protection and utilization of red-seed watermelon resources.

Genetic Diversity Analysis of the Main Commercial Varieties of Brassica napus in Guizhou Province

[Objective] The aim was to investigate the genetic diversity of the main commercial varieties of Brassica napus in Guizhou Province at the molecular level. [Method] Nine main commercial rapeseed cultivars in Guizhou were detected by 40 pairs of SSR primers used in the national regional trial of B. napus, and then clus-tering analysis was carried out. [Result] A total of 191 bands were amplified, and 143 （accounting for 75%） of them showed polymorphism among the nine rapeseed cultivars. By cluster analysis, the nine cultivars were divided into two groups. Group A included seven varieties, and group B consisted of two cultivars from Guizhou In-stitute of Oil Crops. The cultivars in group A were further divided into sub-groups A1 and A2 at the similarity coefficient of 0.643 4. Sub-group A1 included three culti-vars from Guizhou Rapeseed Institute, and sub-group A2 included the other four cultivars from Guizhou Institute of Oil Crops. [Conclusion] The cultivars bred by the same institute had similar genetic background. The cultivars from Guizhou Institute of Oil Crops showed wider genetic basis. However, the genetic similarity coefficient between Qianyou 17 and Qianyou 29 was up to 0.87, suggesting that they shared closer genetic basis.

Analysis of Genetic Diversity of Processing Apple Varieties

Genetic diversity of 18 processing apple varieties and two fresh varieties were evaluated using 12 simple sequence repeats （SSR） primer pairs previously identified in Malus domestica Borkh. A total of 87 alleles in 10 loci were detected using 10 polymorphic SSR markers selected within the range of 5-14 alleles per locus. All the 20 varieties could be distinguished using two primer pairs and they were divided into four groups using cluster analysis. The genetic similarity （GS） of groups analyzed using cluster analysis varied from 0.14 to 0.83. High acid variety Avrolles separated from other varieties with GS less than 0.42. The second group contained Longfeng and Dolgo from Northeast of China, the inherited genes of Chinese crab apple. The five cider varieties with high tannin contents, namely, Dabinette, Frequin rouge, Kermerrien, M.Menard, and D.Coetligne were clustered into the third group. The fourth group was mainly composed of 12 juice and fresh varieties. Principal coordinate analysis （PCO） also divided all the varieties into four groups. Juice and fresh apple varieties, Longfeng and Dolgo were clustered together, respectively, using both the analyses. Both the analyses showed there was much difference between cider and juice varieties, cider and fresh varieties, as well as Chinese crab apple and western European crab apple, whereas juice varieties and fresh varieties had a similar genetic background. The genetic diversity and differentiation could be sufficiently reflected by combining the two analytical methods.

Spatial and temporal analysis of beta diversity in the Barro Colorado Island forest dynamics plot, Panama

Background: Ecologists are interested in assessing the spatial and temporal variation in ecological surveys repeated over time. This paper compares the 1985 and 2015 surveys of the Barro Colorado Forest Dynamics plot(BCI), Panama,divided into 1250(20 m × 20 m) quadrats.Methods, spatial analysis: Total beta diversity was measured as the total variance of the Hellinger-transformed community data throughout the BCI plot. Total beta was partitioned into contributions of individual sites(LCBD indices), which were tested for significance and mapped.Results, spatial analysis: LCBD indices indicated the sites with exceptional community composition. In 1985,they were mostly found in the swamp habitat. In the 2015 survey, none of the swamp quadrats had significant LCBDs.What happened to the tree community in the interval?Methods, temporal analysis: The dissimilarity in community composition in each quadrat was measured between time 1(1985) and time 2(2015). Temporal Beta Indices(TBI) were computed from abundance and presence-absence data and tested for significance. TBI indices can be decomposed into B = species(or abundances-per-species) losses and C = species(or abundances-per-species) gains. B-C plots were produced; they display visually the relative importance of the loss and gain components, through time, across the sites.Results, temporal analysis: In BCI, quadrats with significant TBI indices were found in the swamp area, which is shrinking in importance due to changes to the local climate. A published habitat classification divided the BCI forest plot into six habitat zones. Graphs of the B and C components were produced for each habitat group. Group 4(the swamp) was dominated by species(and abundances-per-species) gains whereas the five other habitat groups were dominated by losses, some groups more than others.Conclusions: We identified the species that had changed the most in abundances in the swamp between T1 and T2.This analysis supported the hypothesis that the swamp is drying out and is invaded by species from the surrounding area. Analysis of the B and C components of temporal beta diversity bring us to the heart of the mechanisms of community change through time: losses(B) and gains(C) of species, losses and gains of individuals of various species. TBI analysis is especially interesting in species-rich communities where we cannot examine the changes in every species individually.

Comparative Analysis of Genetic Diversity and Structure in Rice Using ILP and SSR Markers

Genetic diversity of 36 rice entries from the United States Department of Agriculture （USDA） rice collection was assessed using 103 ILP （intron length polymorphism） and 54 SSR （simple sequence repeats） markers. A total of 236 and 332 alleles were detected by the ILP and SSR markers, respectively. On average, the SSR markers produced higher polymorphism information content value and number of alleles than the ILP markers. Whereas the Nei＇s genetic distance measured using the SSR markers was much higher than that measured using the ILP markers. Manters test indicated that there was a statistically significant correlation （r=0.827, P〈0.001 ） between the two marker systems. UPGMA clustering based on the ILP and SSR markers resulted in consensus dendrograms. The cophenetic correlation coefficient （r=0.918, 0.878 and 0.924, P〈0.001 for the ILP, SSR and combined markers, respectively） showed a highly accurate dendrogram represented the genetic distance among these entries. The 36 entries were divided into four groups. Four African Oryza glaberrima accessions were clustered within a distinct group （I）, and the remaining entries were separated into three groups （11, III and IV）. All the entries could be also clustered into two main groups： One was composed of III and IV, considered as indica group, and the other was composed of I （O. glaberrima） and II （japonica-like）. Model-based cluster analysis revealed that the japonica-like group maintained very pure ancestry while the indica group shared mixed ancestry, especially for group III, which had seven admixtures sharing from 19.5% to 30.0% of ancestry with group IV （based on SSR markers）. It is suggested that ILP and SSR markers could be very useful for the genetic study and breeding in rice.

Molecular Diversity and Association Analysis of Drought and Salt Tolerance in Gossypium hirsutum L. Germplasm

Association mapping is a useful tool for the detection of genes selected during plant domestication based on their linkage disequilibrium（LD）. This study was carried out to estimate genetic diversity, population structure and the extent of LD to develop an association framework in order to identify genetic variations associated with drought and salt tolerance traits. 106 microsatellite marker primer pairs were used in 323 Gossypium hirsutum germplasms which were grown in the drought shed and salt pond for evaluation. Polymorphism（PIC=0.53） was found, and three groups were detected（K=3） with the second likelihood ΔK using STRUCTURE software. LD decay rates were estimated to be 13-15 cM at r2 0.20. Significant associations between polymorphic markers and drought and salt tolerance traits were observed using the general linear model（GLM） and mixed linear model（MLM）（P 0.01）. The results also demonstrated that association mapping within the population structure as well as stratification existing in cotton germplasm resources could complement and enhance quantitative trait loci（QTLs） information for marker-assisted selection.

Genetic Diversity among Parents of Hybrid Rice Based on Cluster Analysis of Morphological Traits and Simple Sequence Repeat Markers

The genetic diversity of 41 parental lines popularized in commercial hybrid rice production in China was studied by using cluster analysis of morphological traits and simple sequence repeat （SSR） markers. Forty-one entries were assigned into two clusters （i.e. early or medium-maturing cluster; medium or late-maturing cluster） and further assigned into six sub-clusters based on morphological trait cluster analysis, The early or medium-maturing cluster was composed of 15 maintainer lines, four early-maturing restorer lines and two thermo-sensitive genic male sterile lines, and the medium or late-maturing cluster included 16 restorer lines and 4 medium or late-maturing maintainer lines. Moreover, the SSR cluster analysis classified 41 entries into two groups （i.e, maintainer line group and restorer line group） and seven sub-groups. The maintainer line group consisted of all 19 maintainer lines, two thermo-sensitive genic male sterile lines, while the restorer line group was composed of all 20 restorer lines. The SSR analysis fitted better with the pedigree information. From the views on hybrid rice breeding, the results suggested that SSR analysis might be a better method to study the diversity of parental lines in indica hybrid rice.

PCR-DGGE Analysis of Nematode Diversity in Cu-Contaminated Soil

A wheat pot experiment was conducted under greenhouse conditions to assess the effect of copper contamination on soil nematode diversity by polymerase chain reaction-denaturing gradient gel electrophoresis （PCR-DGGE） method and morphological analysis. The soil was treated with CuSO4.5H2O at the following concentrations： 0, 50, 100, 200, 400, and 800 mg kg^-1 dry soil, and the soil samples were collected at wheat jointing and ripening stages. Nematode diversity index （H′） from morphological analysis showed no difference between the control and the treated samples in either of the sampling dates. At the wheat ripening stage, nematode diversity obtained by the PCR-DGGE method decreased noticeably in the Cu800 treatment in comparison with the control. With optimization of the method of nematode DNA extraction, PCR-DGGE could give more information on nematode genera, and the intensity of the bands could reflect the abundance of nematode genera in the assemblage. The PCR-DGGE method proved promising in distinguishing nematode diversity in heavy metal coritaminated soil.

Variations of plant life form diversity along the Northeast China Transect and its direct gradient analysis

Plant life form diversity and its direct gradient analysis on a larger scale climate change gradient were tested, based on the data from Northeast China Transect platform. The results showed that the species numbers, life form richness and life form diversity were relative higher at the eastern forests and the ecotone between typical vegetation, while those on the meadow grasslands and typical steppes were lower. Although plant life forms can reflect the climate variations, life form diversity is not consistent with the major global gradient along the NECT.

Genetic diversity and population structure analysis of 161 broccoli cultivars based on SNP markers

To better understand the genetic diversity and population structure of broccoli cultivars planted in China,a total of 161 representative broccoli cultivars in the past 25 years were collected and analysed based on single nucleotide polymorphism(SNP)markers.Ten pairs of primers with good polymorphism and high resolution were screened from 315 pairs of SNP primers by 3 broccoli accessions(inbred lines)with different phenotypes and maturity.The 10 pairs of SNP primers were selected,producing 78 alleles.The diversity analysis indicated that the polymorphism information content(PIC)of SNP primer ranged from 0.64 to 0.90.The observed number of alleles(Na)was 2.00,the effective number of alleles(Ne)was 1.11–2.00,the Nei’s gene diversity(H)was 0.10–0.50,and Shannon information index(I)was 0.20–0.70 using PopGene32 software.The clustering results showed that the 161 broccoli cultivars could be divided into 4 major subgroups(A,B,C and D),foreign cultivars were all assigned to subgroup A,and domestic cultivars were assigned to 3 subgroups of B,C,and D.This study indicated that some domestic cultivars and foreign cultivars were similar in genetic background,but most domestic cultivars were still different from the Japanese cultivars.When K=2,the population structure result presented that 161 broccoli cultivars could be divided into 1 simple group(2 groups)and 1 mixed group.When Q≥0.6,143(88.82%)broccoli cultivars belonged to the simple groups.In simple groups 68(42.24%)broccoli cultivars of group 1 were derived from Japan,the United States,Switzerland,the Netherlands,China-Taiwan,and China-Mainland;75(46.58%)broccoli cultivars belonged to group 2;when Q<0.6,18(11.18%)broccoli cultivars belonged to the mixed groups.This study is helpful to understand the diversity and resolution of broccoli cultivars from worldwide,which is beneficial to plant breeding and materials innovation.And meanwhile,this result is also used for construction of broccoli fingerprint serving for cultivar identification.

Genetic Diversity Analysis of Coffee (<i>Coffee arabica</i>L.) Germplasm Accessions Growing in the Southwestern Saudi Arabia Using Quantitative Traits

Coffee (Coffea arabica) is an economically important crop cultivated on the terraced slopes and narrow valleys of the mountains in the south-western Saudi Arabia. The objective of the study was to evaluate genetic diversity among nineteen coffee accessions collected from different coffee growing areas based on quantitative morphological and pomological traits. Data of 17 quantitative traits were collected and subjected to various statistical analyses. The analysis of variance showed significant differences (P < 0.05) among the accessions for the majority of quantitative traits measured. A principal component analysis (PCA) and hierarchical cluster analysis (HCA) were used to determine the nature and degree of divergence among accessions. PCA showed that four principal components explained about 85.62% of the total variation. Differentiation of germplasm into different clusters was because of cumulative effects of a number of characters. Cluster and distance analysis of quantitative traits revealed the existence of five different groups. The maximum distance was seen between clusters IV and V (76.4) while the minimum was seen between I and II (16.13). Accessions like KSA6 and KSA8 from Tallen valley and KSA10 and KSA11 from Hada and Shada valleys collection are recommenced for the next breeding work as they are high yielder accessions compared to the others. However, it is suggested to complete the present results by additional assessment of the in situ collection and variety trials. These results are of great interest for future breeding programs for this species.

GENETIC DIVERSITY OF FIVE FRESHWATER MUSSELS IN GENUS ANODONTA (MOLLUSCA: BIVALVIA) REVEALED BY RAPD ANALYSIS

Unionidae are an important group of benthic freshwater species. Due to the convergence phenomenon within freshwater mussels, there is still much controversy in the classification of Chinese Unionidae. In China, most studies on freshwater mussels emphasized resource investigation, biology and morphology, while little has been done in genetics, and particularly not in population genetic structure as well as genetic diversity. In order to further understand the status of genetic diversity of different species, random amplified polymorphic DNA (RAPD) markers were used to detect genetic diversity of populations in five species of the genus Anodonta: Anodonta arcaeformis, A. arcaeformis flavotincta, A. fluminea, A. woodiana woodiana and A. w.pacifica. DNA extraction method was based on phenol-chloroform and extracted genomic DNA from the adductor muscle and mantle tissues. Sixteen random primers were used for RAPD amplification and the polymorphism of amplified loci were analyzed. The results demonstrated that the percentage of amplified polymorphic loci for various populations ranged from 34.5% to 62.8%, the mean Shannon’s genetic diversity indices ranged from 0.2021 to 0.3552, and the mean intra-population Nei’s genetic distance ranged from 0.1386 to 0.1713. In all populations of the five species, the genetic diversity for A. arcaeformis was the largest, and that of A. fluminea was the lowest. The inter-population genetic distance between A. w. woodiana and A. w. pacifica was 0.3186, so they can be considered as two sister species at the genetic angle.

Analysis on Nutritious Balance in Recipes Based on Diversity Indices and Cluster Analysis of Food Ingredients

This thesis research on nutritious balance of specific examples in Chinese recipes applying diversity indices and cluster analysis. Initially, based on data of the nutritional ingredients of food, such as proteins, fat and vitamins, we categorize 1200 kinds of specific food using cluster analysis;then, according to a recipe given by a local restaurant, we calculate and compare the diversity indices based on the components of 25 single dishes in the recipe and analyze the nutritious balance of each dish.

Genetic Diversity Analysis of Guangxi Donglan Black-bone Chicken

[Objective] This study aimed to understand the genetic diversity and breed conservation effect, and to provide reference for future germplasm resources protection and breeding researches of Guangxi Donglan black-bone chicken. [Method] The wing venous blood of Donglan Black-bone chicken（silky feather and contour feather） was collected, and the total DNA was extracted. The 18 microsatellite loci were amplified by PCR technology, and the obtained gene fragments were scanned. The number of alleles（Na）, number of effective alleles（Ne）, heterozygosity（H） and polymorphism information content（PIC） were determined using Pop Gen 32 biological software to do cluster analysis of Guangxi indigenous chicken breeds. [Result] The18 microsatellite loci of Donglan black-bone chicken were found to be highly polymorphic. A total of 98 alleles were detected out from 80 Donglan black-bone chicken samples. The averages of Na, Ne, PIC and H per locus were 5.44, 2.78, 0.5382 and 0.596 3, respectively. A total of 93 and 98 alleles were detected out from silky- and contour-feather Donglan black-bone chickens, respectively. The averages of Ne per locus were 2.62 and 2.76, of PIC per locus were 0.508 8 and 0.539 8,of H per locus were 0.624 7 and 0.599 1, respectively. The results of cluster analysis showed that there was greater genetic distance between Donglan black-bone chicken and any of other Guangxi indigenous chicken breeds, including three yellow chicken, Xiayan chicken and Nandan Yao chicken, which was consistent with the breed evolution, geographical distribution and breeding history of Donglan black-bone chicken. [Conclusion] There are greater genetic variation and abundant genetic diversity in the conserved population of Donglan black-bone chicken, suggesting abundant genetic diversity and great breeding potential of Donglan black-bone chicken.

Diversity Analysis in Selected Non-basmati Scented Rice Collection

Diversity analysis among 23 rice varieties including 16 non-basmati scented accessions, 5 basmati accessions and 2 non-scented accessions was performed by random amplified polymorphic DNA （RAPD） and inter-simple sequence repeat （ISSR） marker systems. The varieties analyzed by 11 RAPD and 8 ISSR primers yielded an average of 65% and 80% polymorphism, respectively. The average number of polymorphic bands generated per RAPD primer was 6 and per ISSR primer was 5.87. RAPD and ISSR data analysis individually could not segregate basmati and non-basmati scented rice accessions. However, the analysis using a combined data could group basmati and non-basmati scented rice accessions separately. The bands present specifically among three accessions of non-basmati scented rice were also identified. The study revealed a high genetic diversity among non-basmati scented rice accessions.

Exploratory analysis of structural diversity indicators at stand level in three Italian beech sites and implications for sustainable forest management

The present study introduces an exploratory data analysis based on structural indicators with the aim to assess the effect of silvicultural practices on tree stand structure. The study was carried out in three Italian beech forests of different ages with stand structures that originated from dissimilar regeneration and cultivation techniques(Cansiglio, northern Italy, Chiarano, central Italy,and Mongiana, southern Italy). Ten structural indicators were considered when investigating the latent multivariate relationship between stand structure attributes before and after thinning operations by using a multiway factor analysis(MFA). The MFA results identified the older stand at Cansiglio as more homogeneous for cultivation regimes,and more stable to practices when compared with the younger sites(Chiarano and Mongiana). Heterogeneous stands were sensitive to silvicultural practice thus suggesting their possible impact on forest attributes. The proposed approach proved to be an operational tool to evaluate comprehensively the response of forest structure to planned interventions.