Unweighted Pair Group Method Of Arithmetic Averages Research Articles

Genetic diversity in green gram accessions as revealed by STMS markers

Molecular characterization of green gram (Vigna radiata (L.) Wilczek) germplasm is essential for scientific assessment of variability and diversity for its better utilization in breeding programs. In this study, 120 accessions of green gram were analysed for 27 Sequence Tagged Microsatellites (STMS) loci. For data analysis, accessions were grouped into Indian and exotic. DNA profiling of the 120 accessions yielded 42 STMS products. The proportion of polymorphic products was 55.56% in Indian accessions and 51.85% in exotic accessions. Average Jaccard's similarity coefficient among all pairs of comparisons was 0.695. In unweighted pair group method of arithmetic averages (UPGMA) dendrogram, 5 major clusters were identified. High similarities among the Indian and exotic accessions were found and this could be due to free movement of Indian germplasm to other countries through international institutes. Analysis of molecular variance (AMOVA) analysis indicated that sampling should be practiced more extensively within populations to capture maximum variation. The study highlighted the need to make more elaborate collections from India to capture the diversity existing in green gram and to go for genetic enhancement for widening of the genetic base of cultivated green gram using wild relatives.

ISSR Analysis of the Genetic Structure of Torreya jackii Population in Tonglu County,Zhejiang Province

Using inter-simple sequence repeat(ISSR) molecular technique,six subpopulations of Torreya jackii(Taxaceae) collected from Baiyunyuan Forest Park of Tonglu county of Zhejiang province were analyzed,the genetic structure of T.jackii was revealed in small scale.Using 12 primers,87 polymorphic loci from total 194 loci were detected in 120 individuals from 6 subpopulations and the overall percentage of polymorphic loci(P) was 44.85% with an average of 29.21%.Shannon's information index(I) and Nei's gene diversity(h) of T.jackii were 0.166 3 and 0.103 5 with an average of 0.119 9 and 0.075 5,respectively.P,I and h indicated that the genetic diversity at species level was relatively high,while at subpopulation level was relatively low.Analysis of molecular variation(AMOVA) suggested that the variation was 21.45% among subpopulations and 78.55% within subpopulation.The coefficient of gene differentiation(Gst) was 0.270 5 among subpopulations and the gene flow was 1.347 8.The mean genetic distance of six T.jackii subpopulations was 0.037 0.Based on the genetic distance,the clustered result for six T.jackii subpopulations by unweighted pair group method arithmetic average(UPGMA) suggested that the subpopulations in the similar habitat were clustered together.

Genetic diversity and relationship analysis among accessions of Aegilops ssp. in Turkey using amplified fragment length polymorphism (AFLP) markers

Amplified fragment length polymorphism (AFLP) DNA markers were used to assess the genetic diversity and relationships between 55 accessions of genus Aegilops , including the species Aegilops triuncialis L. (UUCC), Aegilops geniculata Roth (MMUU), Aegilops cylindrica Host (CCDD) and Aegilops umbellulata Zhuk (UU). The samples were collected from Aegean region and East Anatolia, Turkey. 16 AFLP selective primer combinations generated a total of 3200 polymorphic amplification products. 50 Aegilops accessions were analyzed using the data analysis software, unweighted pair-group method arithmetic average (UPGMA) method and numerical taxonomy and multivariate analysis system (NTSYSpc-2.02k). The similarity index coefficients were calculated according to simple matching coefficient. Using 16 AFLP primer combinations, species from Aegean region and east Anatolia were clustered as four major groups. Aegilops species having U genome clustered together and A. cylindrica host was out grouped. Keywords: Aegilops cylindrica, Aegilops triuncialis, Aegilops umbellulata, Aegilops geniculata, amplified fragment length polymorphism (AFLP), Li-COR, genetic relationship, unweighted pair-group method arithmetic average (UPGMA), principle coordinate analysis.

Genetic diversity and population structure of four Iranian alfalfa populations revealed by sequence-related amplified polymorphism (SRAP) markers

In the present study, genetic diversity of 48 individual plants from four Iranian cultivated populations of alfalfa (Medicago sativa L.) was evaluated using sequence-related amplified polymorphism (SRAP) markers. Fourteen SRAP primer combinations produced 193 fragments of which 95 were polymorphic. The number of polymorphic fragments detected per primer combination ranged from 3 to 10 bands with an average of 6.78 bands. Average polymorphic information content (PIC) was 0.343 for all primer combinations. Although the AMOVA (analysis of molecular variance) results showed a significant difference in the genetic diversity among the populations (P < 0.0001), the genetic variation mainly caused by the variation of intra population accounted for 93.17% of the total genetic variation. Unweighted pair-group method arithmetic average (UPGMA) analysis of the marker data clearly separated the populations of subtropical (Yazdi) and semi-cold (Hamadani and Nikshahri) as well as Kodi, an improved population. It can be concluded that SRAP markers are useful for studying diversity and relationships among and within alfalfa populations.

Genetic divergence of Octopus vulgaris species in the eastern Mediterranean

Abstract Nucleotide divergence in cytochrome c oxidase subunit I ( COI ) gene of mitochondrial DNA was analyzed to determine interpopulational variation of common octopus ( Octopus vulgaris ) species sampled along eastern Mediterranean. Nucleotide composition and nucleotide pair frequency analyses of 440 individuals representing 11 populations were investigated. Estimation of evolutionary divergence between sequences was conducted using Tamura-Nei model. Considering 440 individuals, 35 (5%) variable sites and an average variation of 1.9% were found between specimens. Highest divergence was found between Med11 and Med04-Med07 populations; with a genetic distance value of 0.039 (3.9%). Estimation of transition/transversion bias ( R ) was made under the Tamura-Nei model and resulted as 2.32. Phylogenetic tree was constructed using four methods: neighbor joining (NJ), minimum evolution (ME), maximum likelihood (ML) and unweighted pair-group method of arithmetic average (UPGMA). Results from clustering patterns of the consensus tree, with the sum of branch length = 0.05189, pointed out a correlation between genetic and geographic distance.

Genetic diversity of Iranian soft-seed pomegranate genotypes as revealed by fluorescent-AFLP markers

The amplified fragment length polymorphism (AFLP) technique was used to examine the genetic relationships among 21 Iranian soft-seeded pomegranate (Punica granatum L.) genotypes. Out of 72 fluorescent-AFLP primer combinations screened, 31 were selected to produce the 503 polymorphic markers used in this study. Genetic similarity estimates between genotypes, calculated by the Jaccard's similarity coefficient, ranged from 0.17 to 1.00, while the cophenetic correlation coefficient between the genetic similarities and the unweighted pair group method of arithmetic averages (UPGMA) dendrogram was 0.98. The AFLP-based UPGMA dendrogram revealed two groups within the genotypes at 0.33 similarity coefficient, which reflect fruit traits such as peel and aril color, and seed firmness, as well as region of origin. Our study shows that the use of molecular markers is essential during all steps of germplasm management to avoid genotype redundancy and mislabeling. The present study will be used as a reliable reference to discriminate among these genotypes, to aid management of germplasm collections used to breed new varieties for the Iranian pomegranate industry.

Genetic variation in 14 Porphyra lines using restriction site amplified polymorphism (RSAP)

Restriction site amplified polymorphism (RSAP) is a molecular marker technique which just requires a simple polymerase chain reaction to amplify fragments around restriction sites. The RSAP analytic system was set up and applied to Porphyra genetic variation analysis in this study for the first time. Fourteen Porphyra lines were screened by the RSAP analytic system with 30 primer combinations, 12 of which produced stable and reproducible amplification patterns in three repeated experiments. The 12 primer combinations produced 408 amplified fragments, 402 of which (98.53%) were polymorphic, with an average of 33.5 polymorphic fragments for each primer combination, ranging in size from 50 to 500 bp. The 408 fragments were scored one by one and then used to develop a dendrogram of the 14 Porphyra lines with unweighted pair-group method arithmetic average. The genetic distance among these Porphyra lines ranged from 0.10 to 0.50. These Porphyra lines were divided into two major groups at the 0.71 similarity level: one group contained only Porphyra haitanensis lines and the other group contained Porphyra yezoensis lines. In addition, some specific RSAP markers were acquired from each Porphyra line apart from P. yezoensis Yqd-2-1, and five of them were sequenced. One of the specific markers, R1/R3-8119 from P. yezoensis Y-9101, was successfully converted into sequence characterized amplification region marker. The result suggested that TRAP was a simple, stable, polymorphic, and reproducible molecular marker technique for the classification and resource protection of Porphyra lines.

Distinguishing grapefruit and pummelo accessions using ISSR markers

Grapefruit is the fourth economically most important citrus fruit in the world. In this research Inter-Simple Sequence Repeat (ISSR) markers were used to distinguish twenty-nine grapefruit (Citrus paradisi Macf.), five pummelo (Citrus maxima (Burm.) Merr.) and one Citrus hassaku Hort. Ex Tanaka accessions. Twelve ISSR primers produced a total of 100 fragments and 62 of them were polymorphic. The number of average polymorphic fragments per primer was 5.2. The mean polymorphism information content (PIC) was 0.37. The unweighted pair group method arithmetic average (UPGMA) analysis demonstrated that the accessions had a similarity range from 0.79 to 1.00. The accessions were separated into two main clusters; group A with five pummelos and group B with grapefruits. In the pummelo cluster, all pummelos were distinguished whereas in the grapefruit cluster some accessions were not clearly separated. There was a low level of variation in the grapefruits due to their mutation origin.

Variety identification and genetic relationships of mungbean and blackgram in Thailand based on morphological characters and ISSR analysis

Genetic diversity and relatedness were measured in 17 mungbean (Vigna radiata (L.) Wilczek) and 5 blackgram (Vigna mungo (L.) Hepper) genotypes by means of inter-simple sequence repeat (ISSR) analysis and morphological characters. Unweighted pair-group method arithmetic average (UPGMA) analysis of 19 morpho-agronomic characters showed clear separation of the genotypes into 3 major groups; cluster I containing 15 Thai cultivated mungbean varieties and breeding lines, cluster III containing 4 Thai cultivated blackgram varieties, and cluster II containing a mungbean wild relative (subspecies sublobata), a blackgram wild relative (subspecies silvestris) together with an Indian mungbean landrace. Pair wise coefficients of genetic similarity between all genotypes ranged from 0.17 to 0.84 with an average of 0.52. In total, 341 ISSR fragments were amplified for the two Vigna species by ISSR analysis using 18 ISSR primers. The polymorphism revealed with the ISSR primers was 90.6%. The number of amplified fragments varied from 9 to 32, with a size range of 200 - 1500 bp. The average numbers of fragments per primer and polymorphic fragments per primer were 18.94 and 17.17, respectively. Polymorphism information content (PIC) values ranged from 0.23 to 0.37 with an average of 0.31 across all the genotypes. Pair wise coefficients of ISSR-based genetic similarity between all genotypes ranged from 0.70 to 0.99 with an average of 0.86, suggesting quite narrow genetic base of mungbean and blackgram in Thailand that might limit continued breeding success. UPGMA analysis based on ISSR exhibited 2 major clusters; cluster I containing all mungbean genotypes and cluster II containing all blackgram genotypes. It appeared that ISSR was more effective for classification at the species level although no clear separation at the subspecies level was found. All 22 mungbean and blackgram genotypes can be effectively distinguished by only 6 ISSR primers with the highest PIC values, suggesting the applicability of ISSR analysis for variety identification.

Variety discrimination of Tigridia pavonia (L.f.) DC. assesed by different length RAPD primers

Tigridia pavonia (L.f.) DC. is one of the important phytogenetic resources of Mexico. This species is used as ornamental, food and medicinal purposes. Despite its ornamental and economic potential, there is little information about the genetic variability. In this study, randomly amplified polymorphic DNA (RAPD) primers of 10, 15 and 20 bases were used to assess the level of genetic variation among nine botanical varieties of Tigridia pavoniacollected in three localities within State of Mexico. The total number fragments, polymorphic fragments, percentage of polymorphism and resolving power were greater for 15 base (55, 52, 94.5 and 5, respectively) and 20 base (47, 45, 95.7 and 3.8, respectively), in comparison with those obtained from 10 base primers (44, 41, 93.1 and 3.6, respectively).Resultsshowed the major effectiveness of 15 and 20 bases RAPD primers in the genetic differentiation of varieties as compared to 10 bases RAPD primers. The dendrograms based on un-weighted pair group method arithmetic average (UPGMA) analysis of the 10, 15, 20 and the pooled (10, 15 and 20) bases RAPD data were consistent in the clustering varieties, grouping them in two main clusters.

Assessment of genetic diversity among Pakistani wheat (Triticum aestivum L.) advanced breeding lines using rapd and sds-page

Genetic diversity was assessed among 32 advanced wheat breeding lines included in the National Uniform Wheat Yield Trials (2006-07) of Pakistan using molecular (DNA) and biochemical (SDS-PAGE) markers. Of the 72 RAPD primers used for initial screening, 15 were found polymorphic. A total of 140 bands (61.4% polymorphic) were generated by the 15 random decamer primers. Genetic similarity coefficients ranged from 0.81 to 0.94 for rainfed and from 0.70 to 0.93 for the normal seeding date group. Cluster analysis using the unweighted pair group method of arithmetic averages (UPGMA) clustered the 32 advanced wheat breeding lines into one major and three small groups. Maximum level of polymorphism (90%) was observed for the primer OPA-05. Lines N9 and N11 showed the least genetic similarities (0.70-0.82 and 0.71-0.83, respectively) with rest of the lines studied. Line RF1 had the maximum similarity (0.81-0.94) with other lines. Wheat lines included in the normal seeding date were relatively distantly related than those in the rainfed group. Seed storage protein analysis produced 19 subunits ranging from 29-120KDa. Similarity coefficients ranged from 0.53 to 1.0 for the normal seeding date and from 0.47 to 1.0 for the rainfed group. High molecular weight subunits (particularly 120KDa) showed greater polymorphism than the lower molecular weight subunits. Narrow genetic base was observed in wheat lines included in the rainfed group. DNA fingerprinting of advanced breeding lines may help to avoid release of varieties with narrow genetic base in the future.

Genetic diversity, relationships and demographic history of the small yellow croaker, Larimichthys polyactis (Pisces: Sciaenidae) from Korea and China inferred from mitochondrial control region sequence data

Genetic variation was surveyed at the mitochondrial control region (766bp) to test for the presence of genetic stock structure in the small yellow croaker, Larimichthys polyactis from the Yellow and East China Seas. Individuals of the small yellow croaker could not be distinguished on the basis of its location, as demonstrated using the neighbor-joining (NJ) method, unweighted pair-group method, arithmetic average (UPGMA) and the minimum spanning network (MSN). Analysis of molecular variance revealed no significant differences among collections of the small yellow croaker taken from the four locations (two locations each in Korea and China). Neutrality tests and a mismatch distribution analysis indicated that this species has recently expanded. Our findings suggest either that the small yellow croaker has a high migration capability that enables it to overcome the effects of genetic drift, or that this species expanded relatively recently and has not yet had sufficient time to differentiate.

Morphological characterization of cashew (Anacardium occidentale L.) in four populations in Malawi

An assessment of the genetic diversity in cashew (Anacardium occidentale L.) would assist in planning for future selection of good high yield germplasm that will produce nuts of high quality and fetch high prices on the market. The genetic diversity and relationship among 40 accessions of cashew collected from 4 populations (Liwonde, Nkope, Kaputu and Chikwawa) was characterized using quantitative and qualitative traits. The study results have revealed similarity values between 35 to 66%. Analyses of genetic similarity based on unweighted pair group method of arithmetic averages (UPGMA) grouped the 40 accessions into 4 clusters with 14 sub-clusters and the principal component analysis revealed that apple length, apple nut ratio, nut weight, kernel weight, out turn percent and flower sex ratio accounted for most of the variation. The variation could be attributed to genetic history, ecogeographic origin and selection for desired agronomic traits by farmers. Accessions LW41, NE2, NE4, CH18 and PAL26 showed potential for selection in nut and kernel weight and out turn percent suggesting that this could be a valuable source of variation for tree improvement programme in cashew nuts. The findings suggest availability of broad genetic base that could be exploited for future cashew selection and breeding in Malawi.

Research of Genetic Diversity in Seven Kobresia by AFLP in Tibetan Plateau

This work analyzed the genetic diversity of Kobresia accessions at the molecular level, and further obtained the necessary information for breeding and germplasm evaluation. Genomic DNA of Kobresia was amplified with four E+3 and M+3 primer combinations with AFLP (amplified fragment length polymorphism). AFLP analysis produced 164 scorable bands, of which 154 (93.96%) were polymorphic. The mean Nei's gene diversity index (H) was 0.2430, and the Shannon's information index (I) was 0.4012, indicating the abundant genetic diversity of Kobresia. The 11 Kobresia accessions from Tibetan Plateau, China, can be classified into five groups after cluster analysis based on the UPGMA (unweighted pair group method arithmetic average) method. In general, there was abundant genetic diversity among Kobresia accessions resources, and the genetic coefficient was unrelated to their geographic latitude. Natural habitats influenced genetic differentiation of Kobresia.

Genetic Diversity and Population Structure of Celosia argentea and Related Species Revealed by SRAP

Genetic diversity of 16 populations of Celosia argentea L. and 6 populations of Celosia cristata L. in China was investigated using sequence-related amplified polymorphism (SRAP). Ten SRAP primer combinations generated 507 scorable amplification bands ranging from 50 to 2000 bp, among which 274 were polymorphic, with an average of 54 polymorphic bands per primer combination. The unweighted pair group method of arithmetic averages (UPGMA) cluster analysis enabled construction of a phylogenetic tree for estimating genetic distance among populations, which agreed well with the geographic origin information. Twenty-two populations were distinctly separated into two major genetic groups. One typical representative fragment, M1E6 in C. argentea, provided an alternative approach to distinguish C. argentea from C. cristata. Also, great genetic diversity found in C. argentea populations by significant geographic difference was confirmed by a high level of population genetics parameters. The information may be beneficial to future breeding selection and conservation management for populations of C. argentea.

Genetic relationships in Eriobotrya species as revealed by amplified fragment length polymorphism (AFLP) markers

Although most of the species in Eriobotrya originated in China there are few studies on the genetics and genetic relationship of this genus. The aim of the present study was to clarify genetic relationships among 18 Eriobotrya accessions from China using amplified fragment length polymorphism (AFLP). Two close relatives Raphiolepis indica (L.) Lindl. and Photinia serrulata Lindl. were used as outgroups. The results showed that 5 selected AFLP primer combinations amplified 297 scorable bands, of which 282 were polymorphic, yielding a polymorphism rate of 95%. Genetic similarity coefficient among Eriobotrya accessions ranged from 0.82 (between E. bengalensis Hook.f. and E. bengalensis forma angustifolia Vidal) to 0.41 (between E. serrate Vidal and E. deflexa Nakai) indicating substantial genetic variations in the Eriobotrya accessions evaluated. The unweighted pair-group method of arithmetic averages (UPGMA) cluster analysis, based on genetic similarity coefficient, produced a dendrogram which grouped 20 accessions into three main clusters. The result of cluster analysis was generally in agreement with the known taxonomic grouping. Furthermore, the clustering of the 18 accessions of Eriobotrya was consistent with systematic classification based on morphological characteristics.

Genetic diversity and relationships within Citrus and related genera based on sequence related amplified polymorphism markers (SRAPs)

Sequence related amplified polymorphism (SRAP) markers were used to detect molecular marker polmorphisms among 86 citrus and their relatives in Aurantioidea. Twenty-one SRAP primer combinations produced a total of 376 polymorphic fragments with an average of 17.9 per primer combination and an average polymorphism information content (PIC) of 0.86. The unweighted pair group method arithmetic average (UPGMA) analysis demonstrated that the accessions had a similarity range from 0.28 to 1.00 with a mean of 0.64. The subtribe Clauseninae (tribe Clauseneae) separated from the subtribes of the tribe Citreae. The subtribe Balsamocitrinae (tribe Citreae) was the most distant from the others. In the Citrinae, ‘primitive citrus fruit trees’ and ‘near citrus fruit trees’ groups did not clearly separate from each other but all genera in these groups were distinct. On the other hand, subgenus Papeda and subgenus Citrus were not separated clearly in the dendrogram. C. maxima, C. medica and C. reticulata separated into three distinct clusters in agreement with three ‘true basic species’ thesis. Similarity-based analyses supported the theory of few ancestral species in Aurantioidea.

Genetic Diversity for Pink Snow Mold Resistance in Greens‐Type Annual Bluegrass

Unseeded annual bluegrass (Poa annua L.) is an important component of golf greens in many regions of Canada and the United States. Although this turfgrass species has desirable playing attributes, it suffers from susceptibility to environmental and biological stresses including subfreezing temperatures and snow molds. In this study, we compared 29 genotypes collected from golf greens located in Québec and Ontario for their resistance to pink snow mold (SM). Plants were inoculated with Microdochium nivale [(Fries) Samuels &amp; Hallett], causal agent of SM, and incubated under controlled conditions. High levels of variation in SM resistance were detected within the collection and between genotypes. Analysis of the relationship between climatic parameters at the sites of origin and SM susceptibility revealed that level of resistance was positively correlated to the duration of snow cover. Genetic diversity within the Poa collection was estimated using the sequence related amplified polymorphism (SRAP) technique. The UPGMA (unweighted‐pair group method arithmetic average) dendrogram yielded two main clusters that differed markedly in their proportion of SM‐resistant genotypes. Our results show that SM disease is a major selection pressure for the generation of genetic diversity among annual bluegrass biotypes that evolved on golf greens in northern climates. SRAP polymorphisms between bulked genotypes with contrasting resistance to SM were identified and could be used as markers for SM resistance in annual bluegrass.

Sequence-related amplified polymorphism analysis of tree peony (Paeonia suffruticosa Andrews) cultivars with different flower colours

SummarySequence-related amplified polymorphism (SRAP) was used to examine genetic relatedness and genetic diversity in 16 tree peony (Paeonia suffruticosa Andrews) cultivars having different flower colours. Twenty pairs of primers generated a total of 245 scorable PCR fragments among the 16 cultivars of tree peony, of which 175 bands (71.4%) were polymorphic. Genetic relationships were obtained using Nei and Li similarity coefficients. Cluster analyses of SRAP markers using the unweighted pair-group method of arithmetic averages (UPGMA) analysis, as well as Dollo and polymorphism parsimony analyses, were largely consistent. All revealed similar genetic relationships among the 16 tree peony cultivars having different flower colours. Groupings indicated that the division of cultivars was based largely on flower colour. Three main Groups were found after cluster analyses of the 16 cultivars based on SRAP markers. Cultivars with specific flower colours always grouped together. Estimates of genetic relationships and relatedness reflected the genetic diversity in flower colour in tree peony as a whole. The results also indicated that SRAP markers are informative and can provide new insights for genetic research in tree peony.

Genetic variability and aflatoxigenic potential of Aspergillus flavus isolates from maize

Various isolates of Aspergillus flavus collected from infected maize seeds were tested for their ability to produce aflatoxin B1 (AFB1) in vitro. The amount of AFB1 produced by the toxigenic isolates of A. flavus was ranged from 0.57 to 82.91 ng/ml. Among the 51 isolates of A. flavus tested, the isolate AFM1 produced the highest amount of (82.91 ng/ml) AFB1. Nineteen isolates did not produce aflatoxin B1. The genetic variability among the A. flavus isolates was investigated by PCR amplification of internal transcribed spacer (ITS) including ITS1, ITS2 and the intervening 5.8S rRNA region of ribosomal DNA followed by sequencing. PCR amplification of the ITS regions of the A. flavus isolates (AFM1, AFM3 and AFM5) by using ITS1 and ITS4 primers gave products of approximately 580 base pairs in length. The nucleotide sequences were compared with ITS sequences of A. flavus from Genbank database. Analysis of the genetic coefficient matrix derived from the nucleotide sequences of the ITS regions of A. flavus isolates showed that minimum and maximum percent similarities among the tested A. flavus strains were in the range of 12 and 99%, respectively. Phylogenetic analysis of ITS sequences by the unweighted pair group method arithmetic average (UPGMA) identified three main clusters (A, B and C). Cluster A consisted of only one strain and cluster C consisted of three strains including AFM5. The sequence of AFM5 was clustered with the sequence of a clinical isolate of A. flavus (AY677676) and about 76% similarity index was observed between them at molecular level. All the remaining strains belonged to cluster B, which includes AFM1 and AFM3. The genetic variability among A. flavus isolates should be considered when A. flavus isolates are required for testing in resistance breeding programmes.