Unweighted Pair Group Mean Average Research Articles

Autecology of the extant ostracod fauna of Lake Ohrid and adjacent waters - a key to paleoenvironmental reconstruction

Understanding the ecology of bioindicators such as ostracods is essential in order to reconstruct past environmental and climate change from analysis of fossil assemblages preserved in lake sediment cores. Knowledge of the ecology of ancient Lake Ohrid’s ostracod fauna is very limited and open to debate. In advance of the Ohrid ICDP-Drilling project, which has potential to generate high-resolution long-term paleoenvironmental data of global importance in paleoclimate research, we sampled Lake Ohrid and a wide range of habitat types in its surroundings to assess 1) the composition of ostracod assemblages in lakes, springs, streams, and short-lived seasonal water bodies, 2) the geographical distribution of ostracods, and 3) the ecological characteristics of individual ostracod species. In total, 40 species were collected alive, and seven species were preserved as valves and empty carapaces. Of the 40 ostracod species, twelve were endemic to Lake Ohrid. The most common genus in the lake was Candona, represented by 13 living species, followed by Paralimnocythere, represented by five living species. The most frequent species was Cypria obliqua. Species with distinct distributions included Heterocypris incongruens, Candonopsis kingsleii, and Cypria lacustris. The most common species in shallow, flooded areas was H. incongruens, and the most prominent species in ditches was C. kingsleii. C. lacustris was widely distributed in channels, springs, lakes, and rivers. Statistical analyses were performed on a “Lake Ohrid” dataset, comprising the subset of samples from Lake Ohrid alone, and an “entire” dataset comprising all samples collected. The unweighted pair group mean average (UPGMA) clustering was mainly controlled by species-specific depth preferences. Canonical Correspondence Analysis (CCA) with forward selection identified water depth, water temperature, and pH as variables that best explained the ostracod distribution in Lake Ohrid. The lack of significance of conductivity and dissolved oxygen in CCA of Ohrid data highlight the uniformity across the lake of the well-mixed waters. In the entire area, CCA revealed that ostracod distribution was best explained by water depth, salinity, conductivity, pH, and dissolved oxygen. Salinity was probably selected by CCA due to the presence of Eucypris virens and Bradleystrandesia reticulata in short-lived seasonal water bodies. Water depth is an important, although indirect, influence on ostracod species distribution, which is probably associated with other factors such as sediment texture and food supply. Some species appeared to be indicators for multiple environmental variables, such as lake level and water temperature.

Exploring genetic diversity and Population structure of five Aegilops species with inter-primer binding site (iPBS) markers.

Turkey is not only a center of origin for wheat, but also contains wild forms of various cereals. Turkey, located in the Fertile Crescent, has conserved its genetic richness to the present day. The aim of the study was to investigate the genetic diversity of 70 wild wheat species, to evaluate the structure of diversity in germplasm and to generate useful data for further breeding programs. Genetic diversity and population structure of 70 wild wheat species (Ae. cylindrica, Ae. geniculata, Ae. triuncialis, T. dicocoides, Ae. columnaris) collected from Eastern and Southeastern Anatolia regions of Turkey were investigated in this study with the use of inter-primer binding site (iPBS) markers. Of 35 iPBS primers used, 11 yielded a total of 61 alleles. Number of alleles per marker varied between 2 (iPBS-2085) and 9 (iPBS-2394) with an average value of 5.55. Polymorphic information content (PIC) values varied between 0.22 and 0.47, with an average value of 0.35. Average number of effective alleles (Ne) was identified as 1.9488, Nei's genetic diversity (H) as 0,4861 and Shannon's information index (I) as 0.6791. Cluster analysis through unweighted pair-group mean average (UPGMA) method revealed that 70 wild wheats were divided into three main clusters. Genetic similarity between the genotypes, calculated with the use of NTSYS-pc software, varied between 19% (YB2 and YB70) and 98% (YB66 and YB67). Principal coordinate analysis (PCoA) revealed that three principal coordinates explained 62.33% of total variation. Moreover, population structure analysis showed that all genotypes formed three sub-populations. Expected heterozygosity values varied between 0.2666 (the first sub-population) and 0.2330 (third sub-population), with an average value of 0.2500. Average population differentiation measurement (Fst) was identified as 0.3716 for the first sub-population, 0.3930 for the second subpopulation and 0.4804 for the third sub-population. Based on present findings population structure of 70 wild wheat genotypes collected from Eastern and Southeastern Anatolia regions of Turkey were successfully characterized with the use of iPBS markers. Present findings suggested that iPBS-retrotransposon markers could reliably be used to elucidate genetic diversity of Aegilops genotypes.

SSR-Based Molecular Identification and Population Structure Analysis for Forage Pea (Pisum sativum var. arvense L.) Landraces.

Plant genetic diversity has a significant role in providing traits that can help meet future challenges, such as the need to adapt crops to changing climatic conditions or outbreaks of disease. Our aim in this study was to evaluate the diversity of 61 forage pea specimens (P. sativum ssp. arvense L.) collected from the northeastern Anatolia region of Turkey using 28 simple sequence repeat (SSR) markers. These primers generated a total of 82 polymorphic bands. The number of observed alleles (Na) per primer varied from 2 to 4 with a mean of 2.89 alleles/locus. The mean value of expected heterozygosity (Exp-Het = 0.50) was higher than the mean value of observed heterozygosity (Obs-Het = 0.22). The mean of polymorphic information content (PIC) was 0.41 with a range of 0.03–0.70. The mean number of effective alleles (Ne) was found to be 2.15, Nei’s expected heterozygosity (H) 0.49, and Shannon’s information index (I) 0.81. Cluster analysis through the unweighted pair-group mean average (UPGMA) method revealed that 61 forage pea landraces were divided into three main clusters. Genetic dissimilarity between the genotypes, calculated with the use of NTSYS-pc software, varied between 0.10 (G30 and G34) and 0.66 (G1 and G32). Principal coordinate analysis (PCoA) revealed that three principal coordinates explained 51.54% of the total variation. Moreover, population structure analysis showed that all genotypes formed three sub-populations. Expected heterozygosity values varied between 0.2669 (the first sub-population) and 0.3223 (third sub-population), with an average value of 0.2924. Average population differentiation measurement (Fst) was identified as 0.2351 for the first sub-population, 0.3838 for the second sub-population, and 0.2506 for the third sub-population. In general, current results suggest that SSR markers could be constantly used to illuminate the genetic diversity of forage pea landraces and can potentially be incorporated into future studies that examine the diversity within a larger collection of forage pea genotypes from diverse regions.

Analysis of genetic variation and population structure among of oregano (Origanum acutidens L.) accessions revealed by agro-morphological traits, oil constituents and retrotransposon-based inter-primer binding sites (iPBS) markers

The genetic associations among 31 oregano (Origanum acutidens (Hand.-Mazz.) Ietswaart) genotypes collected from different provinces of Turkey were determined by comparing their agro-morphological traits, essential oil components and molecular traits. In order to assess the genetic diversity in 9 agro-morphological traits and 9 essential oil components, 10 polymorphic iPBS primers were used. Principle component analysis (PCA) for agro-morphological traits had two axes explaining 81.35% of total variation and PCA for essential oil components had 4 axes explaining 89.67% of total variation. Cluster analysis yielded two main clusters for agro-morphological traits and four main clusters for essential oil components. Present iPBS primers generated 289 alleles. Number of alleles per polymorphic locus varied between 25 and 36 with an average value of 28.40. The average polymorphism ratio was as 98.36%. Polymorphic information content values varied between 0.28 and 0.42. The average number of alleles (ne), Nei’s genetic diversity (h) and Shannon’s information index (I) were obtained 1.61, 0.37 and 0.55, respectively. The 31 accessions were assembled into three main clusters according to the unweighted pair-group mean average based on iPBS markers. Similarity index value varied between 0.51 and 0.81. Moreover, population structure analysis using Bayesian method showed that all genotypes formed eight sub-population (K = 8) with an average value of 0.3544 for expected heterozygosity and 0.0400 for population differentiation measurements (Fst value). In present study, population structure of 31 oregano genotypes collected from different provinces of Turkey were successfully characterized with the aid of iPBS markers and model-based clustering. It was concluded based on present findings that iPBS markers could reliably be used in genetic diversity and molecular analysis of oregano genotypes.

Analysis of genetic diversity of soybean germplasm from five different origins using RAPD markers

ABSTRACTThe pattern of genetic diversity among 92 genotypes of soybean from 5 different origins/sources (Pakistan, the USA, Asian Vegetable Research Development Centre (AVRDC), Japan and North Korea) was analyzed using randomly amplified polymorphic DNA markers. Out of 20 random primers 6 tested, 10 were polymorphic among genotypes and they yielded 107 markers, with an average of 10.7 markers per primer. The proportion of polymorphic bands within genotypes ranged from 0.47 to 0.71 with an average of 0.59. Pakistani and US genotypes exhibited the highest number of polymorphic bands (95%), while North Korean genotypes revealed the lowest (60%). The mean band frequency of the primers among genotypes was 0.57 with a range of 0.08–0.99. The Shannon’s index and Nei’s genetic diversity index revealed that primer OPF-06 showed maximum genetic diversity among the genotypes. Dendrogram constructed using Unweighted Pair Group Mean Average (UPGMA) method divided the genotypes into 5 main groups consisting of 13 clusters. The results of cluster analysis indicated that the genetic diversity between Pakistani and US or AVRDC genotypes is much larger than that between Pakistani and North Korean or Japanese genotypes. The Pakistani genotypes had distinct bands from plant introductions. Therefore, the Pakistani genotypes may be useful to soybean breeders.

Impacts of chloride de-icing salt on bulk soils, fungi, and bacterial populations surrounding the plant rhizosphere

This study was conducted to investigate the dynamic changes of bulk soil and microbial populations in the surrounding plant rhizosphere under the influence of chloride de-icing salt. Each experimental plant was given 0.25L de-icing salt solution with an irrigation concentration of 200g/L, once every 3 days for 27 days. Samples were taken weekly from each soil layers (0–15cm, 15–30cm and 30–45cm). The results revealed that de-icing salt led to different effects in different soil layers in one month. A trend of increasing electric conductivity (EC) values, Na+ concentrations, and Cl− concentrations in the upper soil layer, compared with the other two soil layers, was apparent, which proved a stronger effect of de-icing salt on the upper soil layer. Soil cation exchange capacity (CEC) decreased with the accumulation of the de-icing salt. Denaturing gradient gel electrophoresis (DGGE) analysis indicated that de-icing salt decreased the Shannon diversity (H) and Evenness (E) of fungal populations in three soil layers and led to a decrease of bacterial H in the upper soil layers. However, a contrary trend for H and E of bacterial populations was seen in the middle and lower soil layers. Both the unweighted pair group mean average (UPGMA) cluster and canonical correspondence analysis (CCA) analysis indicated that the bacterial populations were more stable than the fungal populations in response to salinity stress. CCA analysis showed the dynamic changes of microbial populations and the soil properties (EC, CEC, Na+ and Cl−) were strongly correlative. The microbial populations were obtaining a new dynamic equilibrium at the end of the study. The dominant microbial populations were originally Crepidotus, Metarhizium, Penicillium and Acidobacterium, but converted to Pythium, Boletaceae, Cystofilobasidiales, Phacidium, Acidobacterium, Pseudomonas and Chloroflexi with the addition of de-icing salt. The obtained results suggest that the uses of chemical agents leading to soil salinization, such as de-icing salt, can destroy the micro-ecosystem of bulk soil surrounding plant rhizosphere and influence soil health.

Genetic Diversity of 41 Apple Rootstocks Based on Simple Sequence Repeat Markers

Molecular markers are valuable tools in evaluating genetic diversity and fingerprinting plant germplasm. In this report, simple sequence repeat (SSR) markers were used for assessing genetic diversity in 41 dwarf and semidwarf and early flowering apple (Malus sp.) rootstocks. Sixty-two of 112 pairs of SSR primers generated multiple, scorable fragments. The total number of scored bands was 4138 with the polymorphic frequency ranging from 22.0% to 68.6% with a mean value of 58.5% in 737 alleles. The number of alleles per locus ranged from 6 to 19 with an average of 11.9 alleles. Polymorphic information content per locus was ranged from 0.176 to 0.885 with an average value of 0.606. These results suggested a complex genetic background and genetic diversity in these apple rootstocks. Based on three principal components and unweighted pair group mean average (UPGMA) of SSR data, the 41 apple rootstocks were divided into five groups. Group I contained M. xiaojinensis ‘Xiaojinhaitang'. Group II consisted of M. hupehensis var. pingyiensis ‘Pingyitiancha'. Group III contained M. baccata ‘Shandingzi' and its offspring. Group IV was composed of 16 apple rootstocks, including Malling and Malling Merton series from Great Britain; ‘Budagovski 9' from Russia; ‘Polish 22' from Poland; ‘Cornell-Geneva 24' from the United States; and ‘GM.256', ‘Nei Meng 11', ‘MD.001', ‘7734', and ‘7848' from China. Group V consisted of 16 Shao series rootstocks, which were offspring of M. honanensis × M. domestica ‘Ralls Genet'. This research suggests that the breeding can achieve best performance with more robust rootstock if crosses were performed among these five major groups of germplasms rather than within the major groups.

SOMACLONAL VARIATION AMONG SOMATIC-EMBRYO DERIVED PLANTS OF OLEA EUROPAEA L “CV. KRONEIKI”

Frequency of somaclonal variation in embryogenic calli and plants of Olea europaea L cv.Kroneiki derived from somatic embryogenesis were examined by randomly amplified polymorphic DNA (RAPD) analysis. Radicle and cotyledon (proximal part) of mature zygotic embryo were cultured in OMc medium supplemented with IBA (5 mgL-1) and 2-ip (0.5 mgL-1). Somatic embryogenesis was induced in calli of radicles (55%) and proximal part of cotyledons (8%) on OM medium without any hormones. After culturing the embryogenic calli on OM medium in the presence of BAP (2 mgL-1), regenerated plants were obtained. DNA sample from the leave of the mother plants, seedlings (germinated from zygotic embryo), plantlets (regenerated from somatic embryo), embryogenic calli, non-embryogenic calli and zygotic embryos were subjected to RAPD analysis. 20 arbitrary decamer primers produced polymorphic amplification products. These primers gave a total of 315 reproducible fragments from which 221 (71%) were useful as polymorphic bands with an average of twelve RAPD marks obtained for each primer. A dandogram, based on the unweighted pair group mean average (UPGMA) method of cluster analysis, were constructed using a similarity matrix derived from the RAPD amplification generated by all primers. The estimation of genetic similarity coefficient based on RAPD band sharing data indicated that regenerated plants were less than 75% similar to mother plants.

Genetic Relationships Within and Between Capsicum Species

Genetic relationships were estimated among 24 accessions belonging to 11 species of Capsicum, using 2,760 RAPD markers based on touch-down polymerase chain reactions (Td-RAPD-PCR). These markers were implemented in analyses of principal coordinates, unweighted pair group mean average, and 2,000 bootstrap replications. The accessions were divided into four groups, corresponding to previously described Capsicum complexes: C. annuum complex (CA), C. baccatum complex (CB), C. pubescens complex (CP), and C. chacoense accessions (CA/B). Their overall mean genetic similarity index was 0.487 +/- 0.082, ranging from 0.88 to 0.32, based on Jaccard's coefficient. The highest genetic variation was observed among the accessions in CP; the accessions in CB had a low level of variation as judged from the standard deviations of the genetic similarity indices. Based on the Td-RAPD-PCR markers, the 24 accessions were divided into four major groups, three of which corresponded to the three distinct Capsicum complexes. Accessions of C. chacoense were found to be equally related to complexes CA, CB, and CP.

Genetic variation among seven strains of Dunaliella salina (Chlorophyta) with industrial potential, based on RAPD banding patterns and on nuclear ITS rDNA sequences

Dunaliella salina (Chlorophyta) is a halophilic microalga cultivated as a natural source of β-carotene in several countries, including Chile. Previous studies of some Chilean strains of this microalga have shown a great variability in their physiological and genetic attributes. Random amplified polymorphic DNA (RAPD) band patterns and nuclear ribosomal DNA internal transcribed spacer (ITS-1 and ITS-2) sequences were used to genotypically characterize three Chilean and four foreign (from Mexico, China, Australia and Israel) strains of D. salina with industrial potential. Unweighted pair group mean average (UPGMA) cluster analysis of RAPD data distinguished, at 70% similarity, two clusters. One cluster included all of the foreign strains, except the one from Australia, and the other grouped two of the Chilean strains (CONC-001 and CONC-007). The other Chilean strain (CONC-006) and the Australian strain appeared as single entities. Neighbor-joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) analyses of the ITS sequence data yielded four clades, most of them well supported: there were two clades containing exclusively one strain, CONC-006 from Chile (86–94% support) and the one from Australia (98–100% support); the third clade grouped the strains from Mexico, China and Israel (99–100% support), and, the fourth clade, the strains CONC-001 and CONC-007 from Chile (100% support). Both RAPD banding pattern and ITS sequence data were consistent in resolving the same genetic relatedness among the strains analyzed. For both approaches, the strain CONC-006 from Chile and the strain from Australia were the most divergent entities within the group. Furthermore, the strain CONC-006 appeared genetically more related to the foreign strains than to the other Chilean ones. The physiological attributes exhibited by these strains of D. salina are mostly in agreement with the genetic relationships deduced from this study.

Phylogeny reconstruction and hybrid analysis in Allium subgenus Rhizirideum

Amplified fragment length polymorphisms (AFLPs) for assessing nuclear DNA diversity have been used for the reconstruction of the phylogeny and evolu- tion of several sections of Allium subgenus Rhizirideum. A dataset of 355 characters for 33 accessions belonging to 20 species has been compiled. The band-sharing of five interspecific hybrids and of an F 2 population be- tween Allium cepa and Allium roylei with their parents indicated a heterozygosity level between 6 and 14%, which allows the use of dominant markers such as AFLPs for phylogeny reconstruction. A majority rule consensus tree based on 56 most-parsimonius trees (CI = 0.528) revealed a separate clade for each of the sections, Cepa, Rhizirideum and Schoenoprasum, and one clade combining the sections Oreiprason and Petroprason. An unweighted pair group mean average (UPGMA)- based dendrogram showed the same subdivision. The trees and the 'Hybrid Distance' approach both supported the assumption of a hybrid origin for A. roylei with con- siderable subsequent secondary evolution. The establish- ment of three alliances in the section Cepa and the close relationship of sections Oreiprason and Petroprason are now confirmed. The predictions of the Soybean domesti- cation scenario, i.e. selection of a crop from one progeni- tor with subsequent narrowing of the genetic diversity of the crop, which applies to the cultigens A. cepa and Alli- um fistulosum, is supported by the Hybrid Distance ap- proach.

AFLP analysis of African cassava (Manihot esculenta Crantz) germplasm resistant to the cassava mosaic disease (CMD)

Amplified fragment length polymophism was assessed in 20 land races and nine elite lines of cassava from Africa, resistant and susceptible to the cassava mosaic disease (CMD). Eleven accessions from a representative core collection from Latin America, previously studied by AFLPs, were included as a reference. AFLP data from all accessions was analyzed by both the unweighted pair group mean average (UPGMA) and multiple cluster analysis (MCA) methods of analysis. Genetic differentiation between clusters and the coefficient of genetic differentiation was also calculated. Results reveal a genetic divergence between African and Latin American accessions, although some overlap was found between them. African land races resistant to CMD, were also found to be genetically differentiated from susceptible land races and from resistant elite lines. AFLP analysis identified a considerable number of duplicates in the African accessions, suggesting a sizeable percentage of redundancy. A unique AFLP fragment, found in a relatively high frequency in African accessions, but absent in the Latin American accessions, was found to be associated with branching pattern by QTL mapping in an F1 progeny derived from African and Latin American parents. The likely source and the utility of the unique AFLP fragment in understanding the processes of genetic divergence in Africa is discussed.

Genetic analysis of type O viruses responsible for epidemics of foot-and-mouth disease in North Africa.

The nucleotide sequences of the 3' end of the capsid-coding region were determined for 30 serotype O foot-and-mouth disease (FMD) viruses isolated between 1987 and 1994 from outbreaks in North Africa and the Middle East. These sequences were compared with the previously published sequences of 9 field virus isolates from the Middle East and 5 vaccine virus strains, 3 of which originated from the Middle East (O1/Turkey/Manisa/69, O1/Sharquia/Egypt/72 and O1/Israel/2/85) and 2 from Europe (O1/Lausanne/Switzerland/65 and O2/Brescia/Italy/47). Cluster analysis of these sequences using the unweighted pair group mean average (UPGMA) method showed: (i) that the FMD viruses isolated from North Africa and the Middle East were very different from the classical European vaccine strains; (ii) that all the viruses isolated during the 1989-92 North African epidemic formed a cluster differing by no more than 6% from each other; (iii) a virus isolated in Libya in 1988 was unrelated to the aforementioned epidemic; and (iv) viruses from a second, less extensive epidemic, occurring in 1994, fell into yet another cluster.

Differentiation of bermudagrass (Cynodon spp.) genotypes by AFLP analyses

Bermudagrasses (Cynodon spp.) are major turfgrasses for home lawns, public parks, golf courses and sport fields, and are widely adapted to tropical and warmer temperate climates. Morphological and physiological characteristics are not sufficient to differentiate some bermudagrass genotypes because the differences between them are often subtle and subject to environmental influence. In this study, a DNA-typing technique, amplified fragment length polymorphism (AFLP), was used to differentiate bermudagrass genotypes and to explore their genetic relationships. Twenty seven bermudagrass cultivars and introductions, mostly from the Coastal Plain Experiment Station in Tifton, Ga., were assayed by the radioactive (32P) and the fluorescence-labeled AFLP methods. The AFLP technique produced enough polymorphism to differentiate all 27 bermudagrass genotypes, even the closely related ones. An average of 48–74 bands in the 30–600-bp size range was detected by the 32P-labeled AFLP method. The results indicated that most of the 14 primer combinations tested in this study could be used to distinguish bermudagrass genotypes, and that some single primer-pairs could differentiate all 27 of them. To test the reliability and reproducibility of the AFLP procedure, three DNA isolations (replications) of the 27 bermudagrass genotypes were assayed using five primer pairs. Only 0.6% of the bands were evaluated differently among the three replications. One replication of one genotype (which was most likely a planting contaminant) was grouped in an unexpected cluster using the Unweighted Pair Group Mean Average (UPGMA) method. A one- or two-band difference in scoring did not change the clustering of genotypes or the replications within genotypes. The 27 genotypes were grouped into three major clusters, many of which were in agreement with known pedigrees. Trees constructed with different primer combinations using 32P- and fluorescence-labelling formed similar major groupings. The semi-automated fluorescence-based AFLP technique offered significant improvements on fragment sizing and data handling. It was also more accurate for detection and more efficient than the radioactive labelling method. This study shows that the AFLP technique is a reliable tool for differentiating bermudagrass genotypes and for determining genetic relationships among them.