Unweighted Pair-group Method Using Arithmetic Averages Research Articles

Diversidade genética entre três linhagens de codorna selecionadas para produção de ovos

A diversidade genética entre três linhagens de codorna (Coturnix japônica) foi avaliada utilizando-se a técnica de random amplified polymorphic DNA (RAPD). As linhagens selecionadas para produção de ovos foram identificadas como amarela, azul e vermelha por meio de anilhas no pé esquerdo. Seis primers de RAPD amplificaram 55 loci, os quais geraram padrão de bandas intensa e reproduzível em gel de agarose. Os resultados indicaram polimorfismos dentro e entre as linhagens. A similaridade de Jaccard média e o índice de diversidade Shannon revelaram alta diversidade dentro das linhagens de codornas. O teste de Mantel por meio do algoritmo unweighted pair-group method using arithmetic average (UPGMA) e a dispersão de coordenadas principais indicaram diferenciação genética significativa, embora em baixo nível. Os resultados sugerem que a diversidade genética dentro e entre as linhagens de codornas da Universidade Estadual de Maringá são promissoras para uso em programas de melhoramento.

Investigation on Intera-Specific Biodiversity of 51 Peanut Cocoon Strains of Iran Silkworm (Bombyx mori) Germplasm Based on Reproductive Traits

This study was conducted in ordered to analyze of phylogenetic relationships and determination of relationship amounts in all peanut cocoon strains of Islamic Republic of Iran germplasm based on reproductive characteristics. Hierarchical agglomerative clustering was done by using NTSYS-pc, version 2.02e based on complete, single, UPGMA, UPGMC, FLEXI approaches and SAS-pc based on WARD and average approaches. However, method of average linkage between groups under UPGMA (Unweighted Pair-Group Method using Arithmetic average) was considered as major and final protocol for data conclusion and the resulting clusters were expressed as dendrograms. Various methods generated similar dendograms. This study reveals the phylogenetic relationship of peanut cocoon strains of Iran germplasm. Based on data from studied characters, we constructed dendrograms that resolved the 51 silkworm strains into 2 major clusters. However, the strains of the same origin did not grouped together, demonstrating they can have different biological and development performance. First cluster divided into one sub-group included five strains. However, second cluster divided into two sub-groups. Other strains were grouped together and far from other silkworm strains, indicating they might be suitable for future crossings, maintenance of parental strains and hybridizations with oval cocoon strains so as to maximize heterosis and to avoid depression inbreeding.

Genetic diversity of wild populations of Rheum tanguticum endemic to China as revealed by ISSR analysis

Rheum tanguticum is an important but endangered traditional Chinese medicine endemic to China. The wild resources have been declining. Establishing the genetic diversity of the species would assist in its conservation and breeding program. Inter-simple sequence repeats (ISSR) markers were used to assess the genetic diversity and population genetic structure in 13 wild populations of R. tanguticum from Qinghai Province. Thirteen selected primers produced 329 discernible bands, with 326 (92.94%) being polymorphic, indicating high genetic diversity at the species level. The Nei's gene diversity ( He) was estimated to be 0.1724 within populations (range 0.1026–0.2104), and 0.2689 at the species level. Analysis of molecular variance (AMOVA) showed that the genetic variation was found mainly within populations (71.02%), but variance among populations was only 28.98%. In addition, Nei's differentiation coefficients ( G st ) was found to be high (0.3585), confirming the relatively high level of genetic differentiation among populations. Mantel test revealed a significant correlation between genetic and geographic distances ( r = 0.573, P = 0.002), and the unweighted pair-group method using arithmetic average (UPGMA) clustering and Principal coordinates analysis (PCoA) demonstrated similar results. Meanwhile, the genetic diversity of R. tanguticum positively correlated with altitude and annual mean precipitation, but negatively correlated with latitude and annual mean temperature. This result might be an explanation that the natural distribution of R. tanguticum is limited to alpine cold areas. We propose conservation strategy and breeding program for this plant.

Genetic diversity of breeding popcorn lines determined by SSR markers

P1-3 and P8-1 was lowest, while P3-3 and P8-2 were genetically more similar. The cophenetic correlation showed that the Unweighted Pair-Group Method Using Arithmetic Averages (UPGMA) was reliable to discriminate the genotypes in five groups. The clusters were consistent with the estimates of genetic identity. There was a moderate coincidence degree between the groups and genealogy of lines. Higher levels of heterozygosity are expected from crosses between the group containing lines P3-3 and P7-3 with that of P1-3 and P7-4. Crosses between lines P1-3 and P8-1 are also promising.

Barley germplasms developed for scald disease resistance exhibited a high level of genetic diversity based on SRAP markers

The objective of this study was to assess the genetic diversity and genetic relationships among 59 Turkish barley (Hordeum vulgare L.) germplasm lines (maintained for scald disease resistance breeding) using sequence-related amplified polymorphism (SRAP) markers. Seventeen SRAP primer combinations produced 83 polymorphic markers, with a mean polymorphism of 73.5%. The dendrogram created based on Nei's unweighted-pair group method using arithmetic average (UPGMA) indicated that there were 4 main clusters, which was supported by principle component analysis (PCA). Cluster I primarily included only scald-resistant germplasm lines, while clusters III and IV consisted of only scald-sensitive lines, but cluster II had both scald-resistant and scald-sensitive barley germplasm lines. The coefficients of genetic similarity among the genotypes ranged from 0.58 to 0.96, with a cophenetic correlation (r = 0.71) suggesting that the cluster analysis moderately represented the similarity matrix. The results indicate that a large amount of the genetic diversity present could be of great use in the development of future scald-resistant barley lines.

Molecular characterization and phylogenetic relationships among and within species of Phalaenopsis (Epidendroideae: Orchidaceae) based on RAPD analysis

Random amplified polymorphic DNA (RAPD) analysis for 20 species of Phalaenopsis was conducted to determine their genetic distances and relationships. Among 20 different primers used for RAPD analysis, 10 primers showed polymorphism, and according to the primer type, 26 to 54 DNA fragments were amplified. A total of 414 polymorphic fragments were generated by 10 primers and used for correlation group analysis. The highest value of Similarity index was 0.28 between Ph. violacea malaysia and Ph. violacea witte. The dendrogram resulting from UPGMA (Unweighted Pair Group Method using Arithmetic average) hierarchical cluster analysis separated the original species into three groups: The first group had five species of Ph. violacea blue, Ph. belina, Ph. violacea malaysia, Ph. violacea witte, and Ph. gigantea; the second group included Ph. lamelligera, Ph. amabilis, Ph. parishii, Ph. labbi nepal, Ph. speciosa, Ph. lobbi yellow, Ph. venosa, Ph. hieroglyphica, and Ph. maculata; the third group consisted of Ph. minho princess, Ph. leopard prince, Ph. mannii, Ph. modesta, Ph. cornucervi and Ph. pantherina. RAPD markers can thus be successfully applied in this economically important group of orchids for the study of molecular characterization and relationships. The data acquired from this study could be used for identification and classification of other orchid genera and oriental Phalaenopsis.

Comparative Analysis of Trypanosoma rangeli Histone H2A Gene Intergenic Region with Distinct Intraspecific Lineage Markers

This study shows the characterization of the histone H2A intergenic region sequences (H2A IR) from Trypanosoma rangeli KP1(+) and KP1(-) strains isolated from distinct hosts and geographic regions. Also, a comparative unweighted pair-group method using arithmetic averages (UPMGA) analysis with polymerase chain reaction profiles of the 24Salpha rDNA and the miniexon genes was performed. Detailed H2A IR sequence analysis revealed a discrete size polymorphism among T. rangeli strains and the presence of single-nucleotide polymorphisms and minisatellite repeats, exclusively allowing an interspecific differentiation from T. cruzi strains representing the main parasite lineages. Differently from the H2A IR, UPMGA analysis of the 24Salpha rDNA and the miniexon genes profiles clearly branched T. rangeli strains into KP1(-) and KP1(+) lineages, clustering separately the Brazilian and Colombian KP1(-) strains. The evolutionary implications of these findings are discussed.

Effects of fungicides triadimefon and propiconazole on soil bacterial communities

The impact of fungicides triadimefon and propiconazole on soil bacterial populations from a strawberry field was investigated. Two fungicides were applied to the soil at concentrations of 10 mg/kg or 100 mg/kg with soil water contents 20.2% (fresh soil water content) or 26.0% (field capacity). Changes in bacterial communities were assessed using DNA extraction, polymerase chain reaction (PCR) amplification of the 16S rDNA and denaturing gradient gel electrophoresis (DGGE). High performance liquid chromatography (HPLC) was utilized to detect the residue of fungicides in soils. The results showed that propiconazole was more persistent than triadimefon in soils, and the two soil water contents did not cause significant differences in dissipation rates between the two fungicides. A high concentration of propiconazole could inhibit the existence of soil microbes while one of triadimefon might induce the microbial population in the first stage. From unweighted pair-group method using arithmetic averages (UPGMA) dendrograms, the effect of triadimefon and propiconazole at the two applied concentrations on a soil bacterial community could be long term. After triadimefon was applied for 60 days and propiconazole for 75 days, the compositions of microbial communities were not recovered. From the viewpoint of environmental protection, it was of significant importance to pay more attention not only to the residues of pesticide but also to the change in soil microbial communities.

Impact of cadmium on the bacterial communities in the gut of Metaphire posthuma

The effects of cadmium (Cd) contamination in soil onto the bacterial communities of the guts pooled from ten Metaphire posthuma were addressed during 14 days’ incubation. We found that about 50% of Cd (5 mg/kg, dry weight soil) in the contaminated soil was bio-accumulated into the earthworms. DNA was extracted from the guts of M. posthuma and their dwelling soil irrespective of Cd treatment for the analysis of the bacterial communities of guts in M. posthuma and in soil by PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis). A distinctive cluster of bacterial communities of the guts in the earthworm with and without Cd treatment using the analysis of unweighted pair-group method using arithmetic averages (UPGMA) was observed, indicating that the bacterial community of guts could be changed by Cd. However, no differences in the bacterial communities in soil irrespective of Cd treatment were observed, which could be resulted from the bioremediation of Cd by earthworms leading to insignificant effect of Cd on bacterial communities in soil. For the sequencing of some of the dominant bands in the DGGE profile, Bradyrhizobium japonicum, Stenotrophomonas sp. D2, and Labrys, sp. CC-BB4, whose sequences display an identity of more than 97% using blast program against a known sequence in the GeneBank database and Ribosomal database, were identified. Collectively, our results showed that earthworm treatment can decrease the concentrations of Cd in soil, and Cd cause a shift in the bacterial communities in the guts of M. posthuma. The application of M. posthuma for Cd bioremediation would be desired.

Identification and structure analysis of three tilapia species using microsatellite markers

AbstractSeventeen special loci were selected from 77 microsatellite markers to distinguish three varieties of tilapias, including the six differential loci UNH636, UNH117, UNH172, UNH738, UNH878 and UNH896 in Oreochromis aureus; five differential loci UNH913, UNH907, UNH222, UNH980 and UNH880 in O. niloticus; and six differential loci of UNH876, UNH899, UNH853, UNH932, UNH933 and UNH773 in O. mossambicus. Any one of the 17 loci could amplify particular bands to distinguish one tilapia from the other two. The genetic structure of O. aureus, O. niloticus and O. mossambicus stocks and their phylogenetic relationships were also analysed using these 17 loci. In total 142 alleles were detected, and the average number of alleles per locus was 8.35. Additionally, a clustering analysis was performed based on the result of the Popgen32 software package and phylogenetic trees were constructed by MEGA4 using the unweighted pair group method using arithmetic average (UPGMA). The results showed that the mean value of observed heterozygosity was 0.0941, 0.5490 and 0.2588, the mean value of expected heterozygosity was 0.1089, 0.7230 and 0.1965, and the polymorphism information content was 0.0869, 0.7149 and 0.1643, in O. aureus, O. niloticus and O. mossambicus, respectively. The UPGMA tree demonstrated that O. aureus was more closely related to O. mossambicus than to O. niloticus.

Identification of descendants of an extinct bovine population from the Algarve region of Portugal using numerical taxonomy analysis of morphological traits

The morphology of a sample of four bulls and 43 cows, presumed to be descendants of the extinct cattle breed 'Algarvia' (AG), was used to assign their relationship with animals from other Portuguese autochthonous breeds - Arouquesa (AR), Barrosã (BA), Cachena (CA), Marinhoa (MA), Maronesa (MO), Minhota (MN), Mirandesa (MI), (only bulls), Alentejana (AL), Garvonesa (GA), Mertolenga (ME) and Preta (PR). Standard numerical taxonomic methods were applied to a set of 183 (cows) and 170 (bulls) traits, to derive average pairwise taxonomic distances among the sample of 257 cows and 76 bulls. Distance coefficients (morphological index of distance) ranged from 0.22 to 2.62 (cows) and from 0.49 to 2.13 (bulls). Unweighted pair group method using arithmetic averages (UPGMA)-based phenograms and a principal coordinate analysis showed that bulls were highly clustered and cows showed a tendency to cluster according to their geographical and breed origin. The AG population grouped together with GA, AL, ME and MN breeds in the Red Convex group. The average taxonomic distance among breeds was 1.02, the highest being 1.39 (ME versus BA) and the lowest being 0.64 (MA versus AR). The approach allowed for the identification of a phenotypically differentiated set of animals, comprising 19 cows and four bulls representative of the AG breed, and which can be targeted in further studies aiming at the recovery of this extinct breed.

Estimation of protein similarities between four closely related Phyllotreta species (Coleoptera: Chrysomelidae: Alticinae) by means of isoelectric focusing and silver staining

We used isoelectric focusing and silver staining to detect differences in general protein banding patterns between four closely related Phyllotreta (Coleoptera: Chrysomelidae) species. Three measures of similarity were used for both intra- and interspecific comparisons. Unweighted Pair-Group Method Using Arithmetic Averages (UPGMA) dendrograms were constructed, revealing a very high similarity between Phyllotreta flexuosa (Illiger, 1794) and Phyllotreta tetrastigma (Comolli, 1859). Phyllotreta dilatata Thomson, 1866 is more similar to both these species than Phyllotreta ochripes (Curtis, 1837).

Clones identification of Sequoia sempervirens (D. Don) Endl. in Chile by using PCR-RAPDs technique

A protocol of polymerase chain reaction-random amplified polymorphic DNAs (PCR-RAPDs) was established to analyse the gene diversity and genotype identification for clones of Sequoia sempervirens (D. Don) Endl. in Chile. Ten (out of 34) clones from introduction trial located in Voipir-Villarrica, Chile, were studied. The PCR-RAPDs technique and a modified hexadecyltrimethylammonium bromide (CTAB) protocol were used for genomic DNA extraction. The PCR tests were carried out employing 10-mer random primers. The amplification products were detected by electrophoresis in agarose gels. Forty nine polymorphic bands were obtained with the selected primers (BG04, BF07, BF12, BF13, and BF14) and were ordered according to their molecular size. The genetic similarity between samples was calculated by the Jaccard index and a dendrogram was constructed using a cluster analysis of unweighted pair group method using arithmetic averages (UPGMA). Of the primers tested, 5 (out of 60) RAPD primers were selected for their reproducibility and high polymorphism. A total of 49 polymorphic RAPD bands were detected out of 252 bands. The genetic similarity analysis demonstrates an extensive genetic variability between the tested clones and the dendrogram depicts the genetic relationships among the clones, suggesting a geographic relationship. The results indicate that the RAPD markers permitted the identification of the assayed clones, although they are derived from the same geographic origin.

Monitoring microbial community structure and succession of an A/O SBR during start-up period using PCR-DGGE

Polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) protocol was employed for revealing microbial community structure and succession in a sequential anaerobic and aerobic reactor performing enhanced biological phosphorus removal (EBPR) during start-up period. High phosphorus removal was achieved after 15 d. On day 30, phosphorus removal efficiency reached to 83.2% and the start-up was finished. DGGE profiles of periodical sludge samples showed that dominant microbial species were 19 OTUs (operational taxonomy units). Unweighted pair-group method using arithmetic averages (UPGMA) clustering analysis revealed that rapid community succession correlated to low phosphorus removal rate and high phosphorus removal efficiency reflected on steady community structure. Sequencing results indicated that determined sequences (12 OTUs) belonged to Proteobacterium, Actinobacteria, Gemmatimonadales and unaffiliate group. Proteobacterium, Tetrasphaera elongate and Gemmatimonas aurantiaca may act important roles in phosphorus removal. With little amount as known glycogen accumulating organisms, Candidatus Competibacter phosphatis still at accumulating-phase had limited effect on microbial community structure. When climax community was obtained, dominant microbes were 14 OTUs. Microbes in a large amount were uncultured bacterium Thauera sp., uncultured gamma-Proteobacterium and Tetrasphaera elongata.

Genetic diversity and spatial genetic structure within a population of an aromatic shrub,Lippia origanoides(Verbenaceae), in the Chicamocha Canyon, northeastern Colombia

The geographical scale of genetic structure in a continuous population is highly dependent on its breeding system and dispersion capabilities, and this knowledge is important for the study of population dynamics as well as for conservation purposes. In the present study, spatial autocorrelation statistics and intersimple sequence repeat (ISSR) markers were used to describe the genetic structure of a natural population of a prominent aromatic plant, Lippia origanoides, native to the Chicamocha Canyon in northeastern Colombia. For this purpose, individuals were sampled from two localities within the Chicamocha Canyon, where the species is abundant and continuously distributed. Cluster (principal coordinate analysis (PCO) and unweighted pair group method using arithmetic averages (UPGMA)), analysis of molecular variance (AMOVA) and Bayesian analyses revealed a low level of genetic differentiation among the two localities, suggesting that they belong to a single population. Genetic diversity levels in this population, described as the percentage of polymorphic loci (P=86.21%) and quantified using Shannon's diversity index (I=0.453) and the average panmictic heterozygosity (HB=0.484), were shown to be comparable to or higher than that in other plant species with allogamous breeding systems and to other related Verbenaceae species. Fine-scale autocorrelation analyses showed a pattern consistent with the classical model of isolation by distance with moderate but significant levels of local spatial structure. Our results suggest that sampling individuals at distances greater than approximately 1.2 km may result in the collection of different genotypes, which could help preserve the levels of genetic diversity in a propagation programme. The causes of this spatial pattern are currently unknown and could be influenced by many contemporary factors such as restricted seed dispersal and/or short-distance pollen movement, among others.

Quality and endosperm storage protein variation in Argentinean grown bread wheat. I. Allelic diversity and discrimination between cultivars

Genetic variability for endosperm storage proteins was analysed in 119 Argentinean grown bread wheat cultivars. For the HMW-GS, three, six and two alleles were observed at the Glu-A1, Glu-B1 and Glu-D1 loci, respectively, in 17 allelic combinations. The majority of these combinations were considered to be associated with good quality. For the LMW-GS, eight, seven and four alleles were provisionally observed at the Glu-A3, Glu-B3 and Glu-D3 loci, respectively, in 51 allelic combinations. Regarding quality, the alleles present at Glu-D3 were mainly those previously shown to be associated with good quality, whereas at Glu-A3 and Glu-B3, some alleles previously associated with poor quality were present at high frequency. Relatively few cultivars carried combinations for all the loci studied that would be expected to be associated with high quality. The mean genetic variation index ( H) observed for the glutenin loci (0.589) was similar to values observed in other collections. Unweighted pair-group method using arithmetic averages (UPGMA) of the six loci plus the Chinese Spring-Cheyenne CSS–CNN difference showed that the 119 cultivars fell into 93 distinct combinations. For complete discrimination between all cultivars they would have to be analysed for additional loci. There remains scope for varietal quality improvement within this germplasm pool.

Genetic Diversity and Structure of Walnut Populations in Central and Southwestern China Revealed by Microsatellite Markers

Molecular markers were used to study the genetic diversity, structure, and relationship of Juglans L. with nine populations (five from Juglans regia L. and four from Juglans sigillata Dode) in central and southwestern China. A moderate level of genetic diversity was observed at the population level with the number of effect alleles per locus (A E) ranging from 1.75 to 3.35 (average 2.39) and the proportion of polymorphic loci (P) equaling 100.0%. The expected heterozygosity (H E) within populations ranged from 0.389 to 0.687, and the average was 0.525. The proportion of genetic variation presented among populations accounted for 18.6% of the total genetic diversity. The overall gene flow (N m) among populations equaled 1.10. The unweighted pair-group method using arithmetic averages (UPGMA) clustering and the Mantel test showed that genetic distances among the nine populations are in a good agreement with their geographic distribution, supporting the viewpoint that J. regia and J. sigillata belong to one species. We suggest that the central area of the southwestern mountain regions of China could be considered as a priority for walnut genetic resource conservation.

Diversity in Encephalartos woodii collections based on Random Amplified DNA markers (RAPD's) and Inter-Specific Sequence Repeats (ISSR's)

Variations in morphological characters inspired us to subject various genotypes of Encephalartos woodii to DNA based marker analyses. Genomic DNA of five genotypes of E. woodii growing in the environs of Durban, South Africa was amplified using 15 RAPD and 5 ISSR primers. The amplification profiles of both marker systems resulted in differences in the detected banding patterns. The dendrogram generated using the Unweighted Pair Group Method using Arithmetic Averages (UPGMA) grouped all the E. woodii genotypes in one group. The two genotypes of E. natalensis analyzed for comparison were clustered in a different group. Due to different hierarchical positions in the dendrogram it is clear that the genome of all E. woodii accessions is not exactly the same. The reasons for such variations could well be that the Ngoye and Krantzkloof types originally found in two very distinct parts of Natal did not originate from the same parent(s).

Inter simple sequence repeats separate efficiently hemp from marijuana (Cannabis sativa L.)

Cannabis sativa L. is a multiple-use plant that provides raw material for the production of seed oil, natural fiber for textiles, automotive and pulp industries. It has also been used in insulating boards, ropes, varnishes, animal feed, and as medicinal agents. Cannabis has potential to be used for phytoremediation: however, its cultivation is strictly controlled due to its psychoactive nature and usage in producing drugs such as marijuana, and hashish. In this study, psychoactive type Cannabis samples, which were seized from 23 different locations of Turkey, and nine hemp type Cannabis accessions, as well as an unknown accession were used. Our interest was to identify the genetic relatedness of the seized samples and to separate drug and hemp type plants. Inter Simple Sequence Repeats (ISSRs) were employed for analysis based on single plant material (SET1) and bulked samples of them (SET2). Data was analysed via cluster analysis and principal coordinate analysis (PCoA). PCoA analyses, by using SET1 and SET2, were able to efficiently discriminate the seized samples from the fiber type accessions. However, separation of the plants was not clear via unweighted pair-group method using arithmetic average (UPGMA) dendogram in SET1, while they were clearly separated in SET2. Hemp type accessions showed high levels of variation compared to drug type Cannabis both in SET1 and SET2.

Study on polymorphisms of microsatellite DNA of six Chinese indigenous sheep and goat breeds

The genomes of six populations were screened using microsatellites as molecular markers, including Ujmuqin sheep, small-tailed Han sheep, Tan sheep, Hu sheep, Tong sheep and Yangtse River Delta (YRD) white goat. A total of seven microsatellite markers were used and genetic diversity and genetic distance were also determined. The results showed that there were 224 alleles in six populations, all seven loci showed polymorphism in all populations. The average heterozygosity of all populations was 0.949 9, and the mean polymorphism information content (PIC) of all six populations was 0.842 5–0.929 4. The six sheep (goat) popualtions were lowly differentiated with all loci, and the coefficient of phaenotype differentiation (Fst) was 2.6%, which was consistent with the coefficient of gene differentiation (Gst). The global heterozygote deficit across of all populations (Fit) amounted to 0.5%. The overall significant deficit of heterozygotes because of inbreeding within breeds (Fis) amounted to −2.2%. Two Unweighted Pair-group Method using Arithmetic Averages (UPGMA) dendrograms were constructed on the basis of Nei’s standard genetic distance (DS) and Nei’s genetic distance (DA) respectively. Hu sheep and Tong sheep were grouped at first, Ujmuqin sheep and small-tailed Han sheep clustered and then clustered with Tan sheep. Finally, Yangtse River Delta white goat joined in with all above. From this study, Ujmuqin sheep belongs to “Mongolia sheep” group, which corresponds with the historical records exactly. Ujmuqin sheep and small-tailed Han sheep, Tan sheep, Hu sheep and Tong sheep all vest in the “Mongolia sheep” group.