Unweighted Pair Group Method Of Averages Research Articles

Construction of the Core Collection of Catalpa fargesii f. duclouxii (Huangxinzimu) Based on Molecular Markers and Phenotypic Traits

To promote the conservation and utilization of Catalpa fargesii f. duclouxii (Huangxinzimu) germplasm resources, a total of 252 accessions were used to construct a preliminary core collection according to phenotypic traits and single nucleotide polymorphism (SNP) markers. In this study, 24 phenotypic traits, namely, 9 quantitative traits and 15 qualitative traits, were investigated. The core collection of C. fargesii f. duclouxii (Huangxinzimu) was constructed to remove redundant samples from the collected materials. First, the phenotypic core collection, with a sample proportion of 30, consisting of 24 clones, was constructed according to two genetic distances (Euclidean distance and Mahalanobis), four system clustering methods (the unweighted pair-group average method, Ward’s method, the complete linkage method, and the single linkage method), and three sampling methods (random sampling, deviation sampling, and preferred sampling). The best construction strategies were selected for further comparison. Three core collections (D2C3S3-30, D2C3S3-50, and D2C3S3-70) were constructed according to the optimal construction strategy at three sampling proportions. The core collection D2C3S3-30 with the best parameters was evaluated by using six parameters: the mean difference percentage (MD), variance difference percentage (VD), periodic rate of range (CR), changeable rate of the coefficient of variation (VR), minimum rate of change (CRMIN), and maximum rate of change (CRMAX). Three core collections (M-30, M-50, and M-70) were constructed by molecular markers, and the optimal core collection M-30 was selected by using five parameters, namely, Ho, He, PIC, MAF, and loci. The combination of D2C3S3-30 and M-30 was used to construct the final core collection DM-45, 45 samples representing the complete range of phenotypic and genetic variability. In this study, phenotypic traits combined with molecular markers were used to construct core collections to effectively capture the entire range of trait variation, effectively representing the original germplasm and providing a basis for the conservation and utilization of C. fargesii f. duclouxii (Huangxinzimu).

Pola Pergerakan Perilaku Agonistik Lobster Air Tawar Cherax quadricarinatus (Von Martens, 1868)

This research on movement patterns of agonistic behavior in crayfish Cherax quadricarinatus was conducted at laboratory and used an aquarium size 25 cm x 10 cm x 15 cm. The patterns of agonistic behavior were recorded by using a CCD and digital camera. The recorded data were analyzed using The Adobe Premier computer program and using Jaccard similarity to solve the reciprocal movement patterns. Clustering based on the UPGMA (Unweighted Pair Group Method Average) indicated that the dissimilarity value was about 0,98 and the moving pattern of the agonistic behaviors were grouped into five groups, namely: 1) threatening; 2) arranging the strategy; 3) testing the enemies capability; 4) fighting; 5) avoiding and defending.

RAPD-evaluated Genetic Polymorphisms and Relations among three River Nile Catfish (Siluriformes) Species from Qena, Egypt

Genetic discrepancies among three River Nilecatfish; Schilbe mystus Linnaeus, 1758 (Schilbeidae), Bagrus bajad Forsskal, 1775 (Bagaridae) and Clarias gariepinus Burchell, 1822 (Claridae) was evaluated by RAPD-PCR technique using 8 deca oligonucleotides (A-03, A-04, A-05, A-06, A-09, A-10, A-11, and A-12). A total of 52 amplified bands were produced, from them 5 bands were common with level of monomorphism of % 9.62, and 47 bandswere polymorphicwith level of polymorphism of 90.38%. An instructive RAPD fingerprint profile was generated with various band size lengths ranging from 200 to 2900 base pair. According to Nei-72 distance matrix of genetic and the unweighted pair group method average (UPGMA), the three studied catfish species are related to each other and likely have the most sharing common ancestor. However, Schilbe mystus (Schilbeidae)and Bagrus bajad (bagaridae) are genetically more close to each other than to Clarias gariepinus. The subset of Clarias gariepinus as sister clade to Schilbe mystus and Bagrus bajad suggested monophyly of the family Clarridae. The study suggested occurrence of genetic variations among the investigated River Nile catfish, with high level of genetic convergence/relation between Schilbe mystus and Bagrus bajad. This probably be useful for enhancing their potential use in aquaculture breeding programs, as well as providing insights on their taxonomic status within the Siluriformes.

Establishment of DNA identity card and analysis of genetic similarity among 58 varieties in Lonicera japonica

A total of 58 varieties in Lonicera japonica from 20 producing areas were amplified by 22 pairs of SSR primers. Seven pairs of polymorphic primers were screened and their primers were used to establish DNA identity card and analyze genetic similarity.All the 58 varieties could be distinguished each other by the DNA identity card constituted by 7 pairs of core SSR primers.The genetic similarity coefficients of 58 varieties ranged from 0.366 7 to 0.916 7 by using PopGene32（vesion1.32）. Furthermore, all the varieties consistency were classified into 4 groups and constructed an evaluation table according to cluster analysis by an un-weighted pair-group average method with arithmetic mean. As expected, the results of cluster and evaluation table reflected 58 varieties relatives, which provide reference information for the selection of fine germplasm of L. japonica and the theoretical basis for the study of Dao-di herbs.

Genetic Diversity of Marrubium Species from Zagros Region (Iran), Using Inter Simple Sequence Repeat Molecular Marker

This study concerns the genetic diversity and taxonomic status of Marrubium species from central and south-west of Zagros region, Iran. It is investigated by Inter-Simple Sequence Repeat analysis. A total of 68 accessions from five Marrubium species were collected from their natural habitats. Molecular analysis was approved with 17 primers, of which 12 were carried out in the reaction mixture. Moreover, a data matrix was designed to estimate genetic parameters. To determine the genetic structure and taxonomic status, analysis of molecular variance, clustering analysis with UPGMA (Unweighted Pair Group Method Average) and the Jaccard similarity coefficient were estimated using NT-SYS-pc and Gene Alex software. Supplementary morphological evidences of calyx teeth features were also provided. The results of this study revealed that both sections Marrubium, Microdonta, and Ballota aucheri displayed a high percentage of polymorphism (PP=100%). In addition, their genetic diversity (Gst=0.99), number of effective alleles (Ne=1.53) and Shannon information index (I=0.51) showed a high percentage. Notably, all of the 12 primers produced reproducible bands. Analysis of molecular variance detected low quantities of gene variation among species (18%) from which high proportion of variation presented among populations within species (82%). Based on cluster analysis, M. cuneatum, M. vulgare and M. anisodon were definitely separated. Moreover, M. crassidens and M. vulgare were closely grouped. The calyx teeth features of M. cuneatum and M. crassidens revealed high variations which is consistent with molecular results. In conclusion, high genetic diversity in Marrubium species and accessions presents a valuable genetic resource in Zagros region, Iran.

Population Genetic Structure of the Blood Clam,Tegillarca granosa, Along the Pacific Coast of Asia: Isolation by Distance in the Sea

ABSTRACT The blood clam, Tegillarca granosa, is widely distributed along the coasts of the Indo-Pacific region, providing an excellent opportunity to study gene flow in sessile marine mollusks. In the present study, amplified fragment length polymorphism (AFLP) DNA markers were used to analyze the genetic structure of five blood clam populations. Genetic differentiation (Gst) and Nei's genetic distances between population pairs were found to range from 0.0245 to 0.0785 and 0.0398 to 0.1125, respectively. An AMOVA analysis showed that 89.09% of the genetic variation occurred within populations and only 10.92% occurred among populations, indicating a high degree of genetic homogeneity, probably due to considerable gene flow (average Nm = 7.1853) among populations. Cluster analysis using the unweighted pair group method average (UPGMA) showed that geographically closer populations were clustered, suggesting isolation by distance, which was further supported by a significant positive correlation between Gst a...

Assessing the Genetic Diversity and Genealogical Reconstruction of Cypress (Cupressus funebris Endl.) Breeding Parents Using SSR Markers

To identify genetic diversity, genetic structure and the relationship among accessions, and further establish a core collection for the long-term breeding of cypress (Cupressus funebris Endl.), the genealogy of breeding parents was reconstructed using simple sequence repeat (SSR) molecular markers. Seventeen SSR markers were used to detect molecular polymorphisms among 290 cypress accessions from five provinces and 53 accessions with unknown origin in China. A total of 92 alleles (Na) were detected with 5.412 alleles per locus and an average polymorphism information content (PIC) of 0.593. The haplotype diversity (H) ranged from 0.021 to 0.832, with an average of 0.406. The number of alleles (Na) and the effective number of alleles (Ne) ranged from 4.294 to 5.176 and from 2.488 to 2.817 among five populations, respectively. The pairwise population matrix of Nei’s genetic distance ranged from 0.008 to 0.023. Based on the results of unweighted pair group method average (UPGMA) cluster and population structure analyses, 343 breeding parents were divided into two major groups. Lower genetic differentiation coefficients and closer genetic relationships were observed among cypress breeding parents, suggesting that the genetic basis was narrow, and the genetic relationship was confused by frequent introduction and wide cultivation. Moreover, we reconstructed the genealogy between breeding parents and 30 accessions of breeding parents from an identified core collection. According to the present study, not only geographic origin but also the relationship of the individuals should be considered in future crossbreeding work.

Utilização de marcadores ISSR na avaliação da divergência genética entre acessos de biribazeiro

O biribazeiro é uma planta frutífera nativa das matas Atlântica e Amazônica. Seus frutos têm grande aceitação popular para consumo in natura. Objetivou-se com este estudo a avaliação da diversidade genética de acessos de biribazeiro (Rollinia mucosa [Jacq.] Baill) com a utilização de marcadores moleculares ISSR. Foram analisados 16 acessos com 20 primers ISSR, os quais produziram um total de 118 bandas, sendo 96 polimórficas e 22 monomórficas. Os valores de dissimilaridade genética, calculados de acordo com o complemento do índice de Jaccard, variaram de 0,0909 a 0,5147. O método UPGMA (Unweighted Pair Group Method Average) agrupou os acessos em seis grupos. Os acessos 1 e 5 foram mais dissimilares e 11 e 12 os menos dissimilares. Os marcadores ISSR utilizados neste estudo demonstraram eficiência na detecção de polimorfismos moleculares, revelando variabilidade genética entre os 16 acessos. Diante dos resultados obtidos neste trabalho, é possível inferir que existe considerável variabilidade genética entre os acessos de biribazeiro, demonstrando a importância dos marcadores na análise de variabilidade de espécies pouco estudadas, como Rollinia mucosa [Jacq.]Baill.

Variabilidade genética entre acessos de Umbu-Cajazeira mediante análise de marcadores ISSR

A umbu-cajazeira (Spondias sp.) é uma frutífera nativa do Semiárido brasileiro, ainda em fase de domesticação, cujos frutos apresentam excelentes perspectivas de aproveitamento comercial. O objetivo deste trabalho foi caracterizar a variabilidade genética entre acessos de umbu-cajazeira pertencentes ao Banco Ativo de Germoplasma de Fruteiras Tropicais da Embrapa Mandioca e Fruticultura, por meio de marcadores moleculares ISSR (Inter Simple Sequence Repeat). Foram analisados 17 acessos de umbu-cajazeira, com 25 marcadores ISSR, os quais produziram um total de 249 bandas, sendo 201 bandas polimórficas e 48 monomórficas. As dissimilaridades genéticas entre os acessos variaram de 0,247 a 0,665, com base no coeficiente de Jaccard. O método UPGMA (Unweighted Pair-Group Method Average) agrupou os acessos em cinco grupos, sendo que 'Preciosa' e 'Suprema' foram os acessos mais similares. A maior dissimilaridade foi observada entre os acessos 'Esperança' e 'Pomar'. O alto grau de polimorfismo encontrado demonstrou a eficiência dos marcadores ISSR, indicando que estes podem ser utilizados com sucesso na caracterização molecular de germoplasma e em futuros trabalhos de melhoramento genético dessa frutífera. Existe considerável variabilidade genética entre os acessos de umbu-cajazeira presentes no BAG Fruteiras Tropicais, que pode ser explorada para a conservação e o melhoramento da espécie.

Long-Term Use of Copper-Containing Fungicide Affects Microbial Properties of Citrus Grove Soils

Long-term use of Cu-containing fungicides in citrus groves has resulted in Cu buildup in the soil, but the eff ects of Cu contamination on microbial properties of citrus grove soils remain poorly understood. Th e objective of this study was to investigate the infl uence of long-term application of Cu-containing fungicides on microbial biomass, and bacterial community structure and diversity in fi ve representative commercial citrus groves (5, 21, 27, 36, and 43 yr of planting history, respectively) soils, with one adjacent pasture soil as a reference. With increasing planting time of citrus, Cu concentrations in the soils increased, while microbiological properties including microbial biomass carbon (Cmic), microbial quotient (MQ), and the diversity of operational taxonomic units based on denaturing gradient gel electrophoresis (DGGE) community fi ngerprinting decreased. Stepwise multiple regression analysis showed that Cmic, microbial quotient, and bacterial community diversity were aff ected by Cu concentration and other soil properties such as total N and available P, but the eff ect of Cu was dominant. Th ese results indicate that long-term application of Cu-containing fungicides has adverse eff ects on microbial biomass and bacterial community diversity in citrus grove soils. Sequencing of partial 16S rRNA gene fragments revealed that a shift of total bacterial community composition occurred as a result of Cu contamination, and the soils of more severely Cu-polluted citrus groves were dominated by bacteria g-Proteobacterium, Acidobacteria, Firmicutes, and b-Proteobacterium, whereas certain strains of s-Proteobacterium, g-Proteobacterium, Firmicutes, and Cyanobacteria were the dominant bacteria in the young citrus grove soils. Abbreviations: AP, available P; C mic , microbial biomass carbon; C org , total organic carbon; DGGE, denaturing gradient gel electrophoresis; LSD, least signifi cant diff erence; MQ, soil microbial quotient; PCR, polymer chain reaction; SI, Shannon index; TCu, total recoverable Cu; TN, total N; UPGMA, unweighted pair-group method average.

Prey selection in the trap-nesting wasp Trypoxylon (Trypargilum) opacum Brèthes (Hymenprtera; Crabronidae)

The purpose of our research was to document and discuss the temporal patterns of prey use shown by the trap-nesting wasp Trypoxylon opacum in two different habitats in Southern Brazil. It was carried out from December 2001 to December 2004. Twenty nine species belonging to five families of spiders were captured by T. opacum. Araneidae was the most captured family and has been strongly represented by the genus Eustala. Through Bray-Curtis s coefficient and the unweighted pair group method average (UPGMA), the spiders can be divided into three groups: the smaller group includes the most abundant species (Alpaida sp2, Bertrana rufostriata, Eustala sp1, Eustala sp2, Eustala sp3 and Eustala sp4), the second group includes species with intermediate abundance (Alpaida, Alpaida gracia and Mangora sp2), and the third and largest group includes the less abundant species, (Acacesia villalobosi, Alpaida argenata, Alpaida sp1, Araneus blumenau, Araneus sicki, Crysometa boraceia, Crysometa sp3, Eustala sp8, Eustala sp11, Larinia t-notata, Mangora sp1, Ocrepeira aff gnomo, Sanogasta sp., Sanogasta sp2, Sanogasta sp3, Salticidae sp2, Theridion sp1, Theridion sp2, Wagneriana eupalaestris, Wagneriana iguape). Of 1,053 identified spiders, 362 were captured in the grassland areas and 691 in the swamp, since T. opacum built nests only in these two habitats. The diversity, richness and evenness of spiders in T. opacum nests were higher in grassland than in the swamp.

Characterization of Agro-diversity by Seed Storage Protein Electrophoresis: Focus on Rice Germplasm from Uttarakhand Himalaya, India

The characteristics of 48 rice varieties from Uttarakhand Himalaya, India were detected by morphological and biochemical markers. The grains of the selected rice varieties varied in their morphological (grain length, grain width and grain weight) and biochemical characters (sodium dodecyl sulfate polyacrylamide gel electrophoresis, SDS-PAGE). Based on the presence of 70, 65, 60, 57, 37–39, 22–23, 13 and 10 kDa protein bands in the 48 rice varieties, seven types of profiles were identified. An unweighted pair group average method with arithmetic mean (UPGMA) dendrogram based on cluster analysis of genetic similarity of the protein bands showed two distinct groups with 1%–78% similarity coefficients. The presence of characteristic bands in selected varieties is a useful parameter for identification of rice germplasm.

Genetic diversity of different geographical populations of <I>Oxya chinensis</I> based on AFLP analysis

In order to study the genetic diversity and genetic structure of populations, 7 populations of Oxya chinensis from 7 provinces (or cities) of China were analyzed using AFLP technique. A total of 336 reproducible bands were amplified with 7 primer combinations from 128 individuals. Two hundred and ninety-two bands (86.90%) were polymorphic. High genetic diversity was found among O. chinensis populations and Wanning population had higher genetic diversity than other populations. Mantel test (r=0.27, P=0.89) suggested that there was no significant association between genetic distance and geographic distance. Remarkable genetic differentiation was found among populations. Unweighted pair group method average (UPGMA) tree showed that the 7 O. chinensis populations were divided into 3 groups: Changping of Beijing, Tai-yuan of Shanxi and Jining of Shandong populations in the north; Hanzhong of Shaanxi, Changsha of Hunan and Laibin of Guangxi populations in the south; and Wanning of Hainan population. Principal component analysis indicated significant genetic differentiation of the north and the south populations and island and continent populations existed in the 7 O. chinensis populations because of geographic isolation.

Genetic Diversity of Twelve Switchgrass Populations Using Molecular and Morphological Markers

Switchgrass (Panicum virgatum L.) is a warm season, C4 perennial grass native to most of North America with numerous applications, including use as a bioenergy feedstock species. To date, no studies on genetic diversity in switchgrass have been conducted that use both molecular and morphological markers. The objectives of this study were to assess genetic diversity and determine differences among and between 12 switchgrass populations grown in New Jersey by examining both morphological and molecular characteristics, and to determine whether morphological, molecular, and/or combined data sets can detect ecotype and/or geographical differences at the population level. Twelve plants from each population were characterized with 16 switchgrass expressed sequence tag-simple sequence repeat markers (EST-SSRs) and seven morphological characters. Data was analyzed using GenAlEx and Unweighted Pair-Group Method of Averages (UPGMA) cluster analysis. Most (64%) of the molecular variation in switchgrass populations exists among individuals within populations, with lesser amounts between populations (36%). Upland and lowland populations were distinguished in all three data sets. Some eastern US and midwestern US populations were distinct in all three data sets. Similarities were observed between all three data sets indicating molecular markers may be useful for identifying morphological differences or other adaptive traits. The combined data set was the most useful in differentiating populations based on geography and found separation between midwestern and eastern upland populations. The results indicate that the combination of morphological and molecular markers may be useful in future applications such as genetic diversity studies, plant variety protection, cultivar identification, and/or identifying geographic origin.

Molecular Characterization of Sclerospora graminicola, the Incitant of Pearl Millet Downy Mildew Using ISSR Markers

AbstractThe DNA polymorphism among 22 isolates of Sclerospora graminicola, the causal agent of downy mildew disease of pearl millet was assessed using 20 inter simple sequence repeats (ISSR) primers. The objective of the study was to examine the effectiveness of using ISSR markers for unravelling the extent and pattern of genetic diversity in 22 S. graminicola isolates collected from different host cultivars in different states of India. The 19 functional ISSR primers generated 410 polymorphic bands and revealed 89% polymorphism and were able to distinguish all the 22 isolates. Polymorphic bands used to construct an unweighted pair group method of averages (UPGMA) dendrogram based on Jaccard’s co‐efficient of similarity and principal coordinate analysis resulted in the formation of four major clusters of 22 isolates. The standardized Nei genetic distance among the 22 isolates ranged from 0.0050 to 0.0206. The UPGMA clustering using the standardized genetic distance matrix resulted in the identification of four clusters of the 22 isolates with bootstrap values ranging from 15 to 100. The 3D‐scale data supported the UPGMA results, which resulted into four clusters amounting to 70% variation among each other. However, comparing the two methods show that sub clustering by dendrogram and multi dimensional scaling plot is slightly different. All the S. graminicola isolates had distinct ISSR genotypes and cluster analysis origin. The results of ISSR fingerprints revealed significant level of genetic diversity among the isolates and that ISSR markers could be a powerful tool for fingerprinting and diversity analysis in fungal pathogens.

Method of Constructing Core Collection for Malus sieversii in Xinjiang, China Using Molecular Markers

The method for constructing core collection of Malus sieversii based on molecular marker data was proposed. According to 128 SSR allele of 109 M. sieversii, an allele preferred sampling strategy was used to construct M. sieversii core collection, using the UPGMA (unweighted pair-group average method) cluster method according to Nei & Li, SM, and Jaccard genetic distances, by stepwise clustering, and compared with the random sampling strategy. The number of lost allele and t-test of Nei's gene diversity and Shannon's information index were used to evaluate the representative core collections. The results showed that compared with the random sampling strategy, allele preferred sampling strategy could construct more representative core collections. SM, Jaccard, and Nei & Li genetic distances had no significant difference for construction of M. sieversii core collection. SRAP (sequence-related amplified polymorphism) data and morphological data showed that allele preferred sampling strategy was a good sampling strategy for constructing core collection of M. sieversii. Allele preferred sampling strategy combined with SM, Jaccard, and Nei & Li genetic distances using stepwise clustering was the suitable method for constructing M. sieversii core collection.

Patterns of prey selection of Trypoxylon (Trypargilum) lactitarse Saussure (Hymenoptera: Crabronidae) in southern Brazil

This study was carried out in the Parque Municipal das Araucárias, in the municipality of Guarapuava, southern Brazil. A total of 449 T. lactitarse nests were collected using trap-nests of different diameters. Fifty three species of spiders belonging to 7 families were captured by T. lactitarse. Araneidae was the most captured family and has been strongly represented by the genus Eustala. Through Bray-Curtis's coefficient and the unweighted pair group method average (UPGMA), the spiders species can be divided into 3 groups: the smaller group includes the most abundant species (Eustala sp1, Eustala sp2, Acacesia villalobosi, Alpaida sp1 and Araneus corporosus), the second group includes species with intermediate abundance (Wagneriana iguape, Araneus omnicolor, Eustala sp4, Alpaida grayi, Eustala sp3, Larinia t-notata, Mangora sp1 and Wagneriana iguape), and the third and largest group includes the least abundant species (Aysha gr. brevimana 1, Eustala sp5, Wagneriana eupalaestra, Alpaida scriba, Alpaida veniliae, Araneus aff. omnicolor, Araneus sicki, Eustala sp8, Mangora sp2, Mangora sp3, Wagneriana juquia, Alpaida sp2, Araneus blumenau, Eustala sp6, Eustala sp7 and Ocrepeira galianoae). Of 2,029 identified spiders, 1,171 were captured in the Araucaria forest, 612 in grassland areas and 246 in the swamp. Grassland and swamp areas evidenced greater similarity between them than to the Araucaria Forest, regarding presence-absence of spider species in T. lactitarse's diet, as well as regarding species abundance in these habitats. The juvenile number (56%) was significantly higher than the female (38%) and male (6%) percentages.

Chloroplast DNA Diversity in Prunus and Its Implication on Genetic Relationships

Chloroplast DNA (cpDNA) in 84 Prunus L. accessions (interspecific hybrids and Prunus species) were analyzed to confirm the maternal origin of the interspecific hybrids of Prunus and to establish genetic relationships among Prunus species. The polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) method, which included amplification of cpDNA regions with three universal primer pairs (K1K2, HK, DT) and subsequent digestion with three restriction enzymes (AluI, HinfI, TaqI), revealed 33 haplotypes for the 84 accessions studied. Fourteen from these cpDNA haplotypes were shared by two or more accessions, and 19 were unique. Accessions sharing the same haplotype have maternal relationships among them, which allowed identity confirmation of maternal progenitors of Prunus interspecific hybrids in these cases. Unweighted pair group method average (UPGMA) and minimum-length spanning tree (MST) analyses were performed based on shared common fragments and the number of mutational differences among the 33 haplotypes, respectively. The cpDNA polymorphisms detected made possible the analysis of genetic relationships among the studied Prunus accessions. Most of the recovered relationships are in agreement with current taxonomic hypotheses and artificial crosses.

A strategy on constructing core collections by least distance stepwise sampling

A strategy was proposed for constructing core collections by least distance stepwise sampling (LDSS) based on genotypic values. In each procedure of cluster, the sampling is performed in the subgroup with the least distance in the dendrogram during constructing a core collection. Mean difference percentage (MD), variance difference percentage (VD), coincidence rate of range (CR) and variable rate of coefficient of variation (VR) were used to evaluate the representativeness of core collections constructed by this strategy. A cotton germplasm collection of 1,547 accessions with 18 quantitative traits was used to construct core collections. Genotypic values of all quantitative traits of the cotton collection were unbiasedly predicted based on mixed linear model approach. By three sampling percentages (10, 20 and 30%), four genetic distances (city block distance, Euclidean distance, standardized Euclidean distance and Mahalanobis distance) combining four hierarchical cluster methods (nearest distance method, furthest distance method, unweighted pair-group average method and Ward's method) were adopted to evaluate the property of this strategy. Simulations were conducted in order to draw consistent, stable and reproducible results. The principal components analysis was performed to validate this strategy. The results showed that core collections constructed by LDSS strategy had a good representativeness of the initial collection. As compared to the control strategy (stepwise clusters with random sampling strategy), LDSS strategy could construct more representative core collections. For LDSS strategy, cluster methods did not need to be considered because all hierarchical cluster methods could give same results completely. The results also suggested that standardized Euclidean distance was an appropriate genetic distance for constructing core collections in this strategy.

Genetic Diversity and Ecogeographical Phylogenetic Relationships among Peach and Nectarine Cultivars Based on Simple Sequence Repeat (SSR) Markers

The genetic relationships among 96 peach and nectarine [Prunus persica (L.) Batsch.] genotypes and botanical varieties originating from different ecogeographical regions of China, Japan, North America, and South Korea were evaluated with 33 SSR markers screened from 108 published SSR markers developed for peach or sweet cherry (P. avium L.). The 33 SSRs detected polymorphisms among 96 genotypes and revealed a total of 283 alleles with an average of 8.6 alleles per locus. The polymorphism information content (PIC) value ranged from 0.40 (BPPCT041) to 0.98 (BPPCT009) with an average of 0.80. Unweighted pair group method average (UPGMA) cluster analysis based on Nei's genetic distances classified genotypes into six groups, corresponding to their ecogeographical origin. Group I consisted of northern Chinese and northwestern Chinese local cultivars, and was divided into two subgroups, white and yellow peaches. Group II contained mainly southern Chinese local, Japanese, and North American cultivars and can be divided into four subgroups: Japanese white, Chinese flat, North American yellow, and some Chinese local ornamental peach cultivars. Groups III, IV, and V were comprised of Chinese local ancient cultivars, and contained `Xinjiangdatianren' and `Renmiantao', Chinese dwarf cultivars, and `Fenshouxing', respectively. Group VI had only `Baishanbitao', a Chinese ornamental cultivar. Northern and northwestern Chinese local cultivars clustered together with a greater diversity than southern Chinese local cultivars, indicating that the northern and northwestern Chinese local cultivars are similar ecotypes, and southern Chinese local cultivars are a subset of the northern Chinese group. Moreover, the Japanese and North American genotypes had a close phylogenetic relationship with southern Chinese local cultivars. The taxonomic placement of P. ferganensis (Kost. et Kiab) Kov. et Kost. and the phylogenetic relationship of `Baishanbitao' with peaches are discussed.