Genetic diversity in cucumber (Cucumis sativus L.): I. A reevaluation of the U.S. germplasm collection

Genetic variation within the U.S. cucumber collection (Cucumis sativus var. sativus L. and var. hardwickii (Royle) Alef.) was assessed by examing the variation at 21 polymorphic isozyme loci and comparing the results of this investigation with a similar previous analysis of 14 loci. About 29% (15 of 51) of the enzyme systems examined in an initial survey were polymorphic. Seven loci (Ak-2, Ak-3, Fdp-1, Fdp-2, Mpi-1, Pep-gl and Skdh) which were not previously used to estimate genetic diversity, were assessed. On average, 1.4 loci were polymorphic per enzyme system and 2.2 alleles were present per polymorphic locus. The frequency of polymorphisms was relatively low for Fdp-1(2) (0.01), Mpi-1(1) (0.03), and Skdh(1) (0.02). Principal component and cluster analyses of allelic variation at polymorphic loci separated a diverse array of 757 cucumber accessions from the U.S. National Plant Germplasm Systesm's (NPGS) collection into distinct groups by country (45 nations examined). All accessions of C. s. var. sativus were isozymically distinct from C. s. var. hardwickii, which were themselves dissimilar from each other. Data suggest that C. s. var. hardwickii is not a feral derivative of extant C. s. var. sativus populations. The allelic profile of C. s. var. sativus accessions originating from Burma, Thailand, Indonesia, Hong Kong, Zimbabwe and Ethiopia were distinct from the other accessions examined. Allelic fixation has occurred at Pgd-2 in accessions from Burma, and at Ak-2 in accessions from Zimbabwe and Ethiopia. Some of the countries examined that were in close geographic proximity (e.g., Thailand, Indonesia and Hong Kong) contained accessions with similar isozyme profiles. Accessions are fixed for certain alleles [e.g., Gr(1) (100%), Fdp-1(1) (100%) and Mpi-2(2) (50%) for accessions from Thailand, Indonesia and Hong Kong]. Grouping countries by continent or sub-continent (i.e., North and South American, China, Eastern Europe, Western Europe) and by numbers of accessions examined (i.e., India/Burma, Iran, Japan, Turkey, and remaining accessions) was used to identify accessions with unique allozymic profiles [PIs 209064 (USA), 257486 (China), 188749 (Egypt), 285607 (Poland), 369717 (Yugoslavia), 357844 (Poland), 255936 (Netherlands), 183127 (India), 200818 (Burma), 200815 (Burma), 137836 (Iran), 227013 (Iran), 227235 (Iran), 451976 (Japan), 181752 (Syria), 181874 (Syria), 169383 (Turkey), 171613 (Turkey)].     

Genetic diversity in cucumber (cucumis sativus L.): Iii. An evaluation of Indian germplasm

Genetic variation in cucumber (Cucumis sativus L. var. sativus) accessions from India was assessed by examining variation at 21 polymorphic isozyme loci. Forty-six accessions acquired by the U.S. National Plant Germplasm System (NPGS) before 1972 were compared with 146 accessions collected during a 1992 U.S.–India expedition to the states of Rajasthan, Madhya Pradesh and Uttar Pradesh, India. Isozymic profiles of these Indian accessions were also compared with 707 previously examined U.S. NPGS cucumber accessions. Two distinct groups (Group 1 and Group 2) were identified within accessions collected in 1992 (0.025 > P > 0.01). Variation at Ak-2, Fdp-2, Gr, Mdh-2, Mpi-1, Per, Pgm and Skdh was important in the detection of this difference. A previously unreported Pgm allele [Pgm (3) – 105] was detected in accessions collected in a market in Pali, Rajasthan. Group 1 contained 37 (27 Madhya Pradesh + 10 Uttar Pradesh) accessions and Group 2 contains 102 (84 Rajasthan + 18 Madhya Pradesh) accessions. Seven accessions (5 Madhya Pradesh + 2 Rajasthan) were not associated with either group. The accessions 20664 (Tonk, Rahjasthan), 20666 (Jaipur, Rahjasthan), 20872 (Sehore, Madhya Pradesh), 20881 (Ashtok, Sehore, Madhya Pradesh) and 21026 (Bhatta, Dehra Dun, Uttar Pradesh) were heterozygous for at least nine loci and represent the genetic diversity within this collection. Isozymic variation in U.S. NPGS accessions acquired before 1972 differed significantly (P > 0.005) from those collected during 1992. All loci were important in the detection of this difference, except Ak-2, Pep-pap, and Pgd-2. When Indian accessions taken collectively (i.e., those acquired before 1972 and during 1992) were compared with an array of 707 C. sativus accessions examined previously, relationships between accessions grouped by country or subcontinent differed from those found in previous work.     

Genetic diversity in cucumber (Cucumis sativus L.): IV. An evaluation of Chinese germplasm1

Genetic variation in cucumber (Cucumis sativus L. var. sativus) accessions from China was assessed by examining variation at 21 polymorphic isozyme loci. One hundred and forty-six Chinese accessions acquired by the U.S. National Plant Germplasm System (NPGS) before 1994 were compared to 67 recently collected Chinese accessions. Of the 67, 39 were collected during a 1994 U.S.–China expedition and 28 were donated in 1996. Isozymic profiles of all of these Chinese accessions were also compared with 853 previously examined NPGS cucumber accessions. Principal component analysis of allele frequencies identified two distinct groups of Chinese accessions: one containing accessions collected in 1994 (Group 1) and the other containing accessions received by NPGS in 1996 (Group 2) (P<0.01). Variation at Gpi, Gr, Mdh-2, Mpi-2, Pep-gl and Pep-la was important in the detection of this difference. Isozymic variation in U.S. NPGS accessions of Chinese origin acquired before 1994 differed significantly (P<0.01) from those collected during 1994 and those received in 1996. Eleven loci (Fdp-1, Gpi, Gr, Idh, Mpi-2, Pep-gl, Pep-la, Pep-pap, Per, Pgm and Pgd-1), were important in the detection of this difference. When Chinese accessions taken collectively (i.e., those acquired before 1994, and those during 1994 and 1996) were compared with an array of 853 C. s. var. sativus accessions examined previously, relationships between accessions grouped by country or subcontinent differed from those found in the previous work. Accessions from China and India were distinct from each other and from all other groupings and the C. s. var. hardwickii (feral form of C. s. var. sativus) accessions examined. Thus, Chinese and Indian accessions represent the most diverse genetic variation present in the NPGS cucumber collection. Further collection in India and China would be strategically important for increasing genetic diversity of the U.S. NPGS cucumber collection.     

Multivariate approach to evaluate the penetrometer resistance in different tillage systems

At present, the penetrometer is the most widely used instrument for assessing in situ soil strength, one of the extrinsic factors affecting plant growth and crop productivity. In this paper we propose a method that discriminates penetrometer resistance due to different soil treatments, by means of Principal Component (PC) analysis. We hypothesized and demonstrated that penetrometer resistance values measured at different soil depths are correlated among themselves (multicollinearity). Considering measurements at each depth as different variables, PC analysis restructured data sets containing these correlated variables into a smaller number of components, whose scores were utilized in univariate analysis of variance (ANOVA) to test differences among imposed soil treatments. We applied the procedure to penetrometer resistance values measured by means of a hand-held cone penetrometer in two long-term experiments conducted in southern Italy, on durum wheat (Triticum durum Desf.) under continuous cropping. In the first trial, four different soil tillage treatments were compared; in the second, two different tillages and two residue management systems were examined. In both trials, PC analysis reduced the original 14 depths of measurements into only 4 PC's, based on correlations of their resistance values, explaining more than 80% of the total variation. Furthermore, ANOVA applied to the scores of each PC, clearly indicated treatment effects on soil strength.

The proposed method has thus allowed assemblage a posteriori of penetration resistance data into only a few significative intervals, using correlations among the measurements made at the different depths. This way, the possible resistance differences due to tillage and/or management treatments have been more easily and more unambiguously showed.     

A method for establishing a core collection of Saccharum officinarum L. germplasm based on quantitative-morphological data

A technique is proposed for establishing a representative core collection of S. officinarum accessions from the world collection of sugarcane germplasm maintained at the Sugarcane Breeding Institute-Research Centre, Cannanore, India. In the proposed method, the accessions were first sorted based on their relative contributions to the total variability by means of principal component scores based on a set of quantitative characters. Then, the cumulative proportion of their contributions to the total variance was computed. A logistic regression model was fitted to evaluate the functional relationship between the cumulative proportion of variance and the number of accessions. The size of the core set was decided as the inflection point on that fitted curve, i.e., the point beyond which the rate of increase in cumulative proportion of variability contributed by an accession began to decline. A method for eliminating entries with a high degree of similarity from the selected core set is also proposed.     

Multivariate analysis of genetic variation in Aegilops tauschii from the world germplasm collection

A study of Aegilops tauschii subspecies constitution was undertaken. The data on allozyme and morphologic variation among 308 plants from 154 accessions were used for multivariate analysis. ACPH1 and (glume width)/(rachis segment width) ratio were found to be reliable criteria to distinguish between sspp. tauschii and strangulata.     

The development of a new approach for establishing a core collection using multivariate analyses with tulip as case

A methodology is developed for the establishment of a core collection based on phenotypic data. A case is worked out for the tulip cultivar collection of the Hortus Bulborum, consisting of approximately 1000 cultivars. The methodology is based on cluster analysis of phenetic characters, selection of cultivars from the resulting clusters according to a combination of the proportional and genetic diversity dependent strategies, optimisation of the selection, and validation by means of principal component analysis and by the diversity indices of Nei and Shannon & Weaver. A core collection with 104 cultivars (approx. 10%: CORE-1) did not give a sufficient representation of the existing diversity. A set of 152 cultivars (approx. 15%: CORE-2) showed a far better representation. The variation in resistance levels for Fusarium is almost completely represented in CORE-2. Although a set of 200 cultivars (approx. 20%: CORE-3) reached a nearly complete representation of the total diversity, a better representation of the resistance levels was not achieved. The newly presented methodology for defining a core collection appears to be a useful approach. The included steps for optimising and validating the choice of accessions makes it a reliable and broadly applicable method.     

The Application of Multivariate Statistical Methods for the Evaluation of Soil Profiles (8 pp)

Background, Aim and Scope   Contamination of soils does not only occur on their surface over large areas, but also in depth. Therefore a characterization of soil state after pollution demands a three-dimensional soil sampling, by what a large number of samples has to be analyzed. Analytical results could be evaluated by multivariate statistical methods, which have already been used for the evaluation of data sets containing results from soil sampling of two dimensions like areas or single profiles. In this case study, multivariate statistical methods were applied to investigate structure and interactions between features in a data set containing results of three-dimensional soil sampling. The investigated soil profiles were contaminated by emissions of a former cement and phosphate fertilizer plant. The aim of this study was to determine the remaining extent of contamination and to analyze whether pollutants are mobilized and vertically transported within the profiles. Materials and Methods: Three soil profiles were sampled in the surroundings of the plant. Grain size, organic and carbonatic bonded carbon, pH value, and the total contents of Ca, Cd, Co, Cu, F, Fe, K, Mn, Mg, Na, Ni, P, Pb, and Zn were determined. The resulting data set was evaluated by cluster analysis, linear discriminant analysis, and principal components analysis. The sequential extraction procedure according to Zeien and Brümmer was applied to analyze the binding properties of Ca, Cd, Cu, Na, Pb, and Zn from selected samples. Results: Cd was identified as contaminant of the top soils. The pH values of the bottom soils were determined to be in alkaline range, which is unnaturally high. Variables were clustered according to enrichment of variables in top soils. The samples were classified regarding their pollution state and their substrate by cluster analysis, which was confirmed by linear discriminant analysis. Geogenic and anthropogenic sources of variables as well as relationships between variables like the binding of heavy metals at organic matter were detected by using principal components analysis. The binding of heavy metals at organic matter in the top soils was confirmed by the results of the applied sequential extraction. A vertically altered distribution of Na binding was determined. Discussion: According to the current soil conditions, the uptake of heavy metals had probably occurred by the over ground part of plants during the deposition. The distribution of Na should likely result from the vertical transport of Na, which would also explain the high pH values of the bottom soils by ion exchange. Altogether, the main amount of deposited Ca, F, Na, P, and heavy metals is likely nearly insoluble bound in the top soils. Conclusions: Ten years after the end of production, the pollution of top soils in the surroundings of the former plant is still high. However, regarding the ecotoxicological relevance the now explored interactions between several soil features and elements strongly indicate that there is no short-term to medium-term risk of a mobilization of the deposited elements with the exception of Na. Recommendations and Perspectives: The results of this case study prove that multivariate statistical methods are powerful tools to explore interactions of variables and relationships in a data set derived from three dimensional soil sampling. The methods applied in this work can be highly recommended for evaluations of large data sets resulting from two- or three-dimensional samplings. Multivariate statistical methods enable the characterization of soils and their pollution state in a simple and economic way.     

主成分聚类分析在土地利用生态安全评价中的应用

土地资源是人类赖以生存的资本，土地利用生态安全问题也日益被重视。该文采用主成分聚类分析的方法对土地利用生态安全进行评价并分类。先建立土地利用生态安全评价的指标体系，然后用主成分分析剔除存在相关性、信息重叠的指标，再利用主成分分析得到的具有代表性的主成分指标代替原来的评价指标，对土地利用生态安全进行聚类分析，所得结果客观，为土地利用生态安全评价提供参考依据。     

Multivariate analysis of morphological variation in sorghum (Sorghum bicolor (L.) Moench) germplasm from Ethiopia and Eritrea

Multivariate methods, including principal component, cluster and discriminant analyses, were used to assess the patterns of morphological variation and to group 415 sorghum accessions for 15 quantitative characters. The first five principal components explained 79% of the total variation with plant height and days to 50% flowering being the most important characters in the first principal component. Cluster analysis grouped the accessions into ten clusters. A greater proportion of accessions of similar adaptation zones and accessions from regions of origin with similar agro-climatic conditions were grouped together. Moreover, discrimination of accessions was more pronounced when discriminant analysis was based on zone of adaptation rather than regions of origin. Based on the observed patterns of variation, it is concluded that the morphological variation in the material studied is structured by environmental factors. The implications of the results for plant breeding and germplasm conservation programmes arediscussed.     

Univariate and multivariate analysis performed on bio-agronomical traits of Cucumis melo L. germplasm

A large collection of melon (Cucumis melo L.) germplasm has been established at the Section of Genetics and Plant Breeding, Bari University (Italy). In the present work, data regarding the variation of 20 bio-agronomical traits recorded on entries and landraces collected in Albania and Apulia region (Southern Italy) are reported. The main objective of the study was to assess and describe, by means of univariate and multivariate analyses, the genetic diversity in the collection composed by genotypes classified in the Inodorus and Cantalupensis groups. The results obtained showed a large variation for all the traits examined. Furthermore, it was possible to identify valuable genotypes for future breeding programmes aimed at improving melon traits, particularly for the Inodorus group, which is an important crop in many Southern Italian sites. Genotypes of interest were especially selected for earliness and lateness, fruit shape, soluble solids content, storage time and fruit firmness.     

基于主成分分析和判别分析的白酒品牌鉴别方法

白酒的香气物质决定了白酒产品的差异。为了实现不同白酒产品的区分鉴别,提出了基于气相色谱分析技术结合模式识别实现白酒区分的方法。采集了7种产品共70个白酒样本的气相色谱数据,定性定量分析了己酸乙酯、乳酸乙酯等10种基本香气物质的含量,并对测定的物质进行主成分分析,验证区分效果,最后利用线性判别法建立判别函数,对不同白酒进行区分。结果表明,2种分析方法均可用于区分不同白酒,主成分分析结果显示,前3个主成分累计贡献率为86.527%,能有效描述香气物质和产品之间的复杂关系;线性判别分析对所有样本均得到准确的判别,正确率为100%,对预测样本的正确判别率达93.9%,建立的判别函数能准确区分不同白酒。研究表明,利用气相色谱技术结合模式识别的方法可用于不同白酒的区分鉴别。     

寒地沙棘种质资源果实品质分析与综合评价

为寒地沙棘种质资源开发利用、新品种选育提供科学依据,开展寒地沙棘种质资源果实品质分析及综合评价,筛选果实品质优异的沙棘资源。以22份寒地沙棘种质资源果实为试材,测定果实10项品质指标,进行变异分析、相关性分析、主成分分析和系统聚类分析,构建综合评价模型,计算果实品质综合得分并排序。不同沙棘种质资源果实品质指标变异系数分布在9.339%～62.528%之间,其中糖酸比变异程度最大,果实横径变异程度最小。各个品质指标间存在不同程度的相关性。主成分分析提取了3个主成分,累积贡献率为86.053%。根据3个主成分得分和相应的权重进行线性加权,建立了沙棘种质资源果实品质综合评价模型,综合得分较高的是‘小柳树’、‘侍丛’、‘向阳’、HS-12。系统聚类分析将22份沙棘种质资源分为3类,分类结果与主成分综合评价结果基本一致。综合评价模型得出：‘小柳树’、‘侍丛’、‘向阳’、HS-12为寒地沙棘优异种质资源,研究结果为沙棘种质资源利用与新品种选育提供参考依据。     

基于近红外光谱技术的葡萄酒原产地辨识方法

该文以鉴别葡萄酒原产地为目的,利用快速无损的近红外光谱分析技术,对47份来自昌黎、沙城和法国波尔多（Bordeaux）的红葡萄酒样品进行逐步回归分析选取光谱区域,再进行主成分分析和聚类识别,建立了判别葡萄酒原产地的预测模型。试验结果表明：昌黎、沙城和波尔多产地的葡萄酒产地鉴别的光谱区域为1 400～1 550 nm 和2 000～ 2 300 nm;3个产地的葡萄酒在主成分特征空间中基本为独立分布,其中波尔多酒样和国内酒样间距离最远,国内昌黎和沙城酒样间有小部分交叉;利用9个独立预测集样本对由38个训练集样品所建立的预测模型进行验证,产地的正确识别率达到了88.9%。因此,应用近红外光谱分析技术可准确、快速地辨别葡萄酒的产地。     

Variation among maize (Zea mays L.) accessions of Bendel State,Nigeria

Summary Variability in maize zein protein band mobilities in sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) was characterized to classify 27 maize accessions (OTUs) collected from Bendel State, Nigeria. The classification of the OTUs was achieved using two numerical procedures: average linkage cluster analysis and principal component analysis (PCA). Five clusters were delineated by the cluster analysis whereas the PCA complemented the cluster analysis by separating the OTUs with yellow kernels into one group and OTUs with early maturity into another. OTUs from the same geographical contiguity commonly grouped together. However some regional overlappings of the OTUs occurred. Results of the PCA revealed that zein bands that stained less intensely more strongly separated the OTUs into various clusters than did those that stained more intensely.     

Evaluation of soil fertility under different Cupressus chengiana forests using multivariate approach

The distribution and growing conditions of Cupressus chengiana forests along with the physical and chemical properties of soils in Northwest Sichuan were studied in 2002 to investigate the conditions and characteristics of soil fertility of C. chengiana and to compare and investigate differences of soil fertility for six C. chengiana populations and their relationships with vegetation, climate and disturbance. The results of the study at 0-20 cm soil depth showed that 1） significant differences （P〈0.05） existed among populations for soil bulk density, soil total porosity, capillary porosity, maximum water-holding capacity, capillary water-holding capacity and topsoil natural water content; 2） chemical characteristics of soil organic matter, total N, total P, alkali-hydrolyzable N, available P, available K and cation exchange capacity were significantly different among the populations; and 3） based on the significant effect of soil fertility factors on forest growth, soil physical and chemical characteristics could be selected as an integrated fertility index （IFI） for evaluation of different C. chengiana populations. Principal component and cluster analyses showed significant differences probably due to the difference of vegetation conditions, management measurements, human-induced disturbances and environmental factors. In order to protect the soil ecological functions in fragile ecological regions, C. chengiana could be used in programs enclosing the hill for natural afforestation, natural forest protection programs, and programs replacing agriculture with afforestation measures.     

伊朗西部地区哈马丹市农业土壤钾地位的多元统计分析

Multivariate statistical technique was used to determine the potassium (K⁺) status and to assess soil fertility and K leaching potential in some calcareous soils. Water-soluble K⁺ (H₂O-K) and ammonium acetate-extractable K⁺ (NH₄OAc-K) ranged from 0.019 to 0.590 (mean value 0.095) and 0.390 to 3.320 (mean value 0.954) cmolc kg^-1, respectively. The nitric acid-extractable K⁺ (HNO₃-K) varied from 1.03 to 13.63 (mean value 5.37) cmol_c kg^-1. The proportion of H₂O-K ranged from 0.34% to 14.8% of HNO₃-K, and 2.2% to 53.2% of NH₄OAc-K. The proportion of NH₄OAc-K ranged from 5.8% to 80% of HNO₃-K (mean value 23% of HNO₃-K). The tendency of the soil to lose K⁺ by leaching was examined by determining K⁺-Ca²⁺ exchange isotherms. The soils mostly had moderate to high values of K⁺ sorption capacity, ranging from 10% to 58% (mean value 28%) of added K⁺. The Gapon coefficient varied widely from 1.1 to 12.0 (L mol^-1)^-1/2. Clay minerals were dominated by illite, smectites and vermiculite with small amounts of kaolinite. Principal component analysis (PCA) showed that the first four components accounted for 27.7%, 21.4%, 13.8%, and 8.9% of total variation, respectively. The non-hierarchical cluster analysis (k-means clustering) grouped 75 sampling sites into six clusters, based on the similarity of soil quality characteristics. The results suggested that such classes could form a basis for variable-rate application to maintain an adequate K⁺ status for crop production and to reduce potential K⁺ loss from soil by leaching.