Showing papers on "Dendrogram published in 2023"
TL;DR: The dendrogram indicated that the two populations of V. foetida are connected, and assumed as one large population in the past and were separated from larger population by habitat fragmentation, and was not genetically in danger.
Abstract: Vanda foetida J.J.Sm., which is an endemic orchid species in Sumatra has taxonomically disappeared for over 100 years since it was described in 1906. The distribution of V. foetida was limited due to over-exploitation of this orchid and changes to land-use. The study of genetic variation of V. foetida in its natural habitat, Mount Dempo and Padiampe, South Sumatra was conducted based on Random Amplified Polymorphic DNA (RAPD) analysis for genetic variation using 8 primers (OPU 3, OPU 5, OPU 6, OPU 7, OPU 12, OPU 13, OPU 14 and OPU 16). Genetic variation in each population was detected by h value (Nei’s genetic diversity) which was 0.1999 and 0.1778 for Mount Dempo and Padiampe, respectively. This value was higher compared to those of other rare orchid species even though it only has a small population. V. foetida originated from two populations forming two main clusters in dendrogram with 67 % (0.67) degree of similarity. The dendrogram indicated that the two populations are connected, and assumed as one large population in the past and were separated from larger population by habitat fragmentation. This species was not genetically in danger and will be able to survive if its natural habitats are remained.
3 citations
TL;DR: In this paper , a total of 34 phenological, vegetative, and yield traits were measured and analyzed statistically with R software and the results showed that TVSU-455 gave the highest values for the total number of pods (42.67), final plant stands (7.7), fresh seed weights (45.83), number of seeds per plant (46.62), hundred seed weight with a value (124.56), dry seed weight (27.14), fresh pod weight (92.65), harvest index of 0.57, yield per plot (45,83), and unshelled yield per plots (550.26).
Abstract: Bambara groundnut has significant role to play in terms of food security, even though researchers in agriculture have paid very little attention to the crop in the past. This study aimed to investigate the high-yielding accessions in three environments. A total of 34 phenological, vegetative and yield traits were measured and analyzed statistically with R software. There were significant differences in all the traits except for plant height, initial plant stand, panicle length per stem, and petiole length. Across the three environments, TVSU-455 gave the highest values for the total number of pods (42.67), final plant stands (7.67), fresh seed weights (45.83), number of seeds per plant (46.62), hundred seed weight with a value (124.56), dry seed weight (27.14), fresh pod weight (92.65), harvest index of 0.57, yield per plot (45.83) and unshelled yield per plot (550.26). TVSU-455 was the only accession in cluster I of the dendrogram based on its superiority over other accessions. The clustering analysis produced a dendrogram categorizing the 15 accessions into 4 groups based on the vegetative, phenological, and yield traits. There were significant differences among the correlations of the 34 traits. The first two principle components explained 56.16% of the total variation with each dimension accounting for 39.85% and 16. 31% variation, respectively. TVSU-455 can be recommended for stability analysis.
2 citations
TL;DR: In this paper , the application of sequence-related amplified polymorphism (SRAP) technique in characterization of 8 species of Salix (spp) from Iran by screening 22 primer combinations (PCs).
Abstract: This study reports the application of sequence-related amplified polymorphism (SRAP) technique in characterization of 8 species of Salix (spp) from Iran by screening 22 primer combinations (PCs). Twenty two SRAP primer combinations could amplify 116 scorable loci, of which 107 bands were polymorphic. The amplified DNA fragments were used for calculation and statistical analysis. The Complete linkage cluster was performed and dendrogram drawn with the help of NTSYS pc 2.02 software which revealed two main clusters and several sub-clusters. This investigation showed that genetic distance was relatively significant among these species. The Jaccard similarity coefficient ranged from 0.18 to 0.55. The results also propose that the SRAP marker is a useful tool for evaluation of genetic diversity and relationships among different Salix species.
2 citations
TL;DR: In this paper , the authors evaluated the relationship between thermal dissatisfaction and productivity in university classrooms through a cluster analysis by hierarchical and non-hierarchical (k-means clustering) methods to verify how thermal dissatisfaction influences students' productivity.
2 citations
TL;DR: In this article , the authors investigated the genetic diversity of 32 Cyclamen genotypes comprising 16 C. persicum varieties and 16 Cyclamen species using multivariate analysis for 36 morphological traits (19 quantitative and 17 qualitative) and molecular characterization (SRAP and SCoT markers).
Abstract: Morphological and molecular characterization of germplasm is essential for the improvement of cultivated plants efforts. This study investigated the genetic diversity of 32 Cyclamen genotypes comprising 16 C. persicum varieties and 16 Cyclamen species using multivariate analysis for 36 morphological traits (19 quantitative and 17 qualitative) and molecular characterization (SRAP and SCoT markers). The color CIELab parameters were collected via PCE-CSM7 that separately measured the leaves dark and silvery patterns and the flower’s slip (region of the petal top), eye (the region of the petal base) and sepal. Genetic diversity was also evaluated using Shannon Wiener (H′) and Simpson’s (λ) Indices, and Pilou evenness (J) using the library vegan from R software. According to the principal component analysis, the variables that contributed the most were leaf pattern color, leaf abaxial surface color, pedicel coiling, leaf and stem number. The color indicators of Cyclamen leaves showed decreased L* values in darker colored genotypes, whereas increased a* values were noticed in flower eye and lower in slip. Molecular characterization was based on 26 SRAP and 12 SCoT markers that produced clearly repeatable DNA bands and exhibited significant levels of polymorphism. Based on the morphological traits and molecular markers data, the UPGMA method for hierarchical clustering technique was used to generate the dendrograms, and their entanglement was obtained using the Tanglegram algorithm from the dendextend package with the R software. Entanglement analysis (0.30) between dendrograms obtained from the morphological and genetic analysis using SRAP markers showed a high association. Comparison between color measurements of flowers (entanglement=0.45) and leaves (entanglement=0.47) with SCoT analysis revealed differences at species level, discriminating between similar genotypes. Combined phenotypic and molecular analysis improved the comprehensive estimation of real diversity in the investigated Cyclamen genotypes. The findings of the present study are useful for quantifying diversity and genetic variability in Cyclamen breeding and genetic investigations.
2 citations
TL;DR: In this article , the authors used data from two mid-sized harvesters working in north-eastern Poland were analyzed using classical regression (linear and logarithmic), cluster analysis (dendrograms and k-means) and Principal Component Analysis (PCA).
Abstract: Data recorded automatically by harvesters are a promising and potentially very useful source of information for scientific analyses. Most researchers have used StanForD files for this purpose, but these are troublesome to obtain and require some pre-processing. This study utilized a new source of similar data: JDLink, a cloud-based service, run by the machine manufacturer, that stores data from sensors in real time. The vast amount of such data makes it hard to comprehend and handle efficiently. Data mining techniques assist in finding trends and patterns in such databases. Records from two mid-sized harvesters working in north-eastern Poland were analyzed using classical regression (linear and logarithmic), cluster analysis (dendrograms and k-means) and Principal Component Analysis (PCA). Linear regression showed that average tree size was the variable having the greatest effect on fuel consumption per cubic meter and productivity, whereas fuel consumption per hour was also dependent, e.g., on distance driven in a low gear or share of time with high engine load. Results of clustering and PCA were harder to interpret. Dendrograms showed most dissimilar variables: total volume harvested per day, total fuel consumption per day and share of work time on high revolutions per minute (RPMs). K-means clustering allowed us to identify periods when specific clusters of variables were more prominent. PCA results, despite explaining almost 90% of variance, were inconclusive between machines, and, therefore, need to be scrutinized in follow-up studies. Productivity values (avg. around 10 m3/h) and fuel consumption rates (13.21 L/h, 1.335 L/m3 on average) were similar to the results reported by other authors under comparable conditions. Some new measures obtained in this study include, e.g., distance driven in a low gear (around 7 km per day) or proportion of time when the engine was running on low, medium or high load (34%, 39% and 7%, respectively). The assumption of this study was to use data without supplementing from external sources, and with as little processing as possible, which limited the analytic methods to unsupervised learning. Extending the database in follow-up studies will facilitate the application of supervised learning techniques for modeling and prediction.
1 citations
TL;DR: In this article , the association between sequencing-based diversity array technology (DArTseq) and phenotypic character as well as differing indices related to drought tolerance in one hundred accessions of Bambara groundnut was investigated.
Abstract: Bambara groundnut (BG) (Vigna subterranea [L.] Verdc) is an indigenous, resilient, but underutilized leguminous crop that occurs mostly as genetically heterogeneous landraces with limited information on the drought tolerant attributes. This study elucidates the associations between sequencing-based diversity array technology (DArTseq) and phenotypic character as well as differing indices related to drought tolerance in one hundred accessions of Bambara groundnut.The field experiments were conducted at IITA research stations in Kano and Ibadan between 2016 and 2018 planting seasons. The experiments were arranged in randomised complete block design with three replications, under the different water regimes. The phenotypic traits evaluated was further to construct the dendrogram. Genome-wide association mapping was conducted based on 5927 DArTs loci with < 20% missing data.The genome wide association study predicted drought tolerance in Bambara accessions for geometric mean productivity (GMP) and stress tolerance index (STI). TVSu-423 had the highest GMP and STI values (28.50, 2.40), while TVSu-2017 had the lowest at GMP (1.74) and STI (0.01) respectively. The relative water content (%) was significantly higher for accessions; TVSu-266 (60.35, 61.49), TVSu-2 (58.29, 53.94), and TVSu-411 (55.17, 58.92) in 2016/2017 and 2017/2018, respectively. The phenotypic characters studied delineated the accessions into two major clusters and five distinct sub-clusters, indicating variations across all the geographical locations. The 5,927 DArTseq genomic markers in association with STI further grouped the 100 accessions into two main clusters. TVSu-1897 from Botswana (Southern Africa) was in the first cluster, while the remaining 99 accessions from Western, Central, and Eastern Africa made up the second cluster. The eight significant Quantitative Trait Loci (QTLs) (24346377|F|0-22:A>G-22:A>G, 24384105|F|0-56:A>G33 :A> G, 24385643|F|0-53:G>C-53:G>C, 24385696|F|0-43:A>G-43:A>G, 4177257|F|0-44:A>T-44:A>T, 4182070|F|0-66:G>A-66:G>A, 4183483|F|0-24:G>A-24:G>A, 4183904|F|0-11:C>T-11:C>T) identified with Bonferroni threshold was in association with STI, indicative of variations under the drought-stressed condition. The observation of consistent SNPs in the 2016 and 2017 planting seasons, as well as in combination with the 2016 and 2017 planting seasons, led to the designation of these QTLs as significant. The drought selected accessions could form basis for hybridization breeding. The identified quantitative trait loci could be useful in marker-assisted selection in drought molecular breeding programs.
1 citations
TL;DR: In this article , 77 microsatellite markers were employed to assess the genetic diversity of 75 Indian mustard genotypes and the average polymorphic information content (PIC) value was 0.67 and ranged between 0.43 and 0.76 (gi258660710gbGT071338.1).
Abstract: Indian mustard (Brassica juncea var. rugosa) constitutes an authoritative group of mustard crops in India. Evaluation of genetic diversity is a vivacious component of mustard breeding programmes for efficient utilization of plant genetic resources. In present study, 77 microsatellite markers were employed to assess the genetic diversity of 75 Indian mustard genotypes. Results revealed positive amplification for all SSRs, with 21 SSRs exhibiting polymorphic amplicons. A total of 99 alleles, ranging from 3 to 5 with an average of 4.71 alleles per SSR marker were obtained. The major allele frequency varied between 0.26 (cnu/m616) and 0.56 (ENA28F) with an average value of 0.36. The average polymorphic information content (PIC) value was 0.67 and ranged between 0.43 (ENA28F) and 0.76 (gi258660710gbGT071338.1). Mean value of 0.72 was detected for each pair of SSR primers, with the gene diversity per locus ranging between 0.53 (ENA28F) and 0.79 (gi258660710gbGT071338.1). The dendrogram grouped the 75 genotypes into three main clusters or subpopulations based on Unweighted Neighbour-Joining technique. The study revealed better understanding of the genetic diversity among different Indian mustard genotypes using genomic-SSR markers that could be exploited for the genetic improvement of the crop.
1 citations
TL;DR: In this article , an unbiased, probabilistic framework for partition number selection that ensures partitions comprise isolates that are statistically likely to belong to the same strain is presented. But the method is not suitable for large groups of similar isolates, as they get progressively larger as relationships become increasingly distant.
Abstract: Comparing parasite genotypes to inform parasitic disease outbreak investigations involves computation of genetic distances that are typically analyzed by hierarchical clustering to identify related isolates, indicating a common source. A limitation of hierarchical clustering is that hierarchical clusters are not discrete, they are nested. Consequently, small groups of similar isolates exist within larger groups that get progressively larger as relationships become increasingly distant. Investigators must dissect hierarchical trees at a partition number ensuring grouped isolates belong to the same strain; a process typically performed subjectively, introducing bias into resultant groupings. We describe an unbiased, probabilistic framework for partition number selection that ensures partitions comprise isolates that are statistically likely to belong to the same strain. We compute distances and establish a normalized distribution of background distances that is used to demarcate a threshold below which the closeness of relationships is unlikely to be random. Distances are hierarchically clustered and the dendrogram dissected at a partition number where most within-partition distances fall below the threshold. We evaluated this framework by partitioning 1,137 clustered Cyclospora cayetanensis genotypes including 552 isolates epidemiologically linked to various outbreaks. The framework was 91% sensitive and 100% specific in assigning epidemiologically-linked isolates to the same partition.
1 citations
TL;DR: In this article , the potential for polymorphism within samples of A. alternata isolates obtained from eight different geographical locations in South Africa was investigated, and the authors reported the first documented rapid and reliable technique for routine screening identification of pathogens causing Alternaria black spot.
Abstract: Alternaria black spot disease on pecan is caused by the opportunistic pathogen Alternaria alternata and poses a serious threat to the local South African and global pecan industry. Several diagnostic molecular marker applications have been established and used in the screening of various fungal diseases worldwide. The present study investigated the potential for polymorphism within samples of A. alternata isolates obtained from eight different geographical locations in South Africa. Pecan (Carya illinoinensis) leaves, shoots, and nuts-in-shuck with Alternaria black spot disease were sampled, and 222 A. alternata isolates were retrieved. For rapid screening to identify Alternaria black spot pathogens, polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) analysis of the Alternaria major allergen (Alt a1) gene region was used, followed by the digestion of the amplicons with HaeIII and HinfI endonucleases. The assay resulted in five (HaeIII) and two (HinfI) band patterns. Unique banding patterns from the two endonucleases showed the best profile and isolates were grouped into six clusters using a UPGMA (unweighted pair group method with arithmetic averages) distance matrix (Euclidean) dendrogram method on R-Studio. The analysis confirmed that the genetic diversity of A. alternata does not depend on host tissues or the pecan cultivation region. The grouping of selected isolates was confirmed by DNA sequence analysis. The Alt a1 phylogeny corroborated no speciation within the dendrogram groups and showed 98–100% bootstrap similarity. This study reports the first documented rapid and reliable technique for routine screening identification of pathogens causing Alternaria black spot in South Africa.
1 citations
03 Apr 2023
TL;DR: In this article , the authors evaluated genetic diversity and association patterns among 63 cultivar/genotypes through 19 morphological traits, oil yield (18.033%), and fatty acid compositions.
Abstract: Abstract Flax ( Linum usitatissimum L.) is an important crop for source of with the different uses of oil and fiber. In addition, flax, which has an important place in the world and our country, has a multi-purpose use area. The objectives of the current research were to assess genetic diversity and patterns of relationships among the relative cultivar/genotypes through morphological traits and microsatellite (SSR) markers. The present study evaluated genetic diversity and association patterns among 63 cultivar/genotypes through 19 morphological traits, oil yield (18.033%) and fatty acid compositions. The relative agro-morphological traits as well as, assessed genetic diversity through 16 loci strong amplicons SSR markers. According to the findings agronomic parameters; quality analyzes were performed to for promising varieties. The quality characteristics of the related fiber varieties were determined with the help of Scanning Electron Microscopy (SEM) and strength devices. As a result; It has been observed that the Eckendorfi can be promising. Principal Component Analysis (PCA) (JAMOVI 2022) performed to relevant parameters. Additionally, UPGMA (Arithmetic Mean Unweighted Double Group Method) is an individual marker system used to create the dendrogram. The average Polymorphic Information Content (PIC) values were recorded as (0.689), while the least and largest loci with allele dimensions were Lu9 (2) and Lu19-Lua613(6) respectively. These findings of the present study were supported by the results of the principal coordinate analysis. Morphological markers made use of in the study were found to be complementary to microsatellite-based markers in decoding, the genetic diversity and population structure of the flax germplasm.
TL;DR: In this paper , a genetic diversity analysis of eight Teucrium polium L. populations distributed in Aydın province of Türkiye was conducted using ten RAPD markers.
Abstract: In this study, genetic diversity analysis of eight Teucrium polium L. populations distributed in Aydın province of Türkiye was conducted using ten RAPD markers. As a result of the study, a total of 45 bands were obtained, of which eight were monomorphic and 37 were polymorphic. The total polymorphism rate was determined as 82.22%. UPGMA dendrogram consists of two clades. The lowest similarity (-0.100) was observed between the Koçarlı and Hamitler village populations, while the highest coefficient (0.646) was observed with the Çakmar (road) and Hamitler village populations. As a result, RAPD marker technique can be a useful marker for revealing the genetic diversity of Teucrium polium populations. In addition, this results it will be a references for different marker and sequence-based studies in the future.
TL;DR: In this article , the agronomic performance of ten commercial common bean varieties (Karaman 2016, Adabeyazı, Akın, Göksun, Bulduk, Akman 98, Zirve, Göynük 98, Özmen and Topçu) under rainfed and irrigated conditions for two years in a split plot randomized block design with four replications.
Abstract: This study was conducted to determine agronomic performance of ten commercial common bean varieties (Karaman 2016, Adabeyazı, Akın, Göksun, Bulduk, Akman 98, Zirve, Göynük 98, Özmen and Topçu), and two advanced lines (KF-Arp and KF-Arj) under rainfed and irrigated conditions for two years in a split plot randomized block design with four replications. Özmen, Zirve and Adabeyazı cultivars had the highest grain yields (irrigated conditions; 4152, 4018 and 3691 kg ha–1, rainfed conditions; 1456, 1318 and 1322 kg ha–1, respectively) in terms of grain yield according to the average data of the two years under irrigated and rainfed conditions. Eight Inter Simple Sequence Repeat (ISSR) markers were used to reveal the genetic diversity of the genotypes. The ISSR markers used in the study produced 140 polymorphic alleles, while the allele number per primer was found as 17.5 and the average PIC value was 0.96. A dendrogram was created for common bean genotypes that consisted of two main groups, as Akın was the only cultivar in the first group, and the remaining eleven cultivars were grouped together in the second main group with 11% genetic similarity.
TL;DR: In this paper , genetic diversity analysis of six Tulsi genotypes (Krishna, Ram, Lavangi, Pandharpuri, Daisil, and Kapoori) was performed using RAPD and SSR markers.
Abstract: Aims: To Analysis of genetic variability in Tulsi (Ocimum sanctum) genotypes by using RAPD & SSR Markers.
Place and Duration of Study: Department of Plant Biotechnology at K.K.Wagh College of Agricultural Biotechnology, Nashik.
Methodology: Ocimum tenuiflorum Linn., commonly known as Tulsi, is an aromatic plant with significant traditional and medicinal value. To assess the genetic diversity and relatedness of six Tulsi genotypes (Krishna, Ram, Lavangi, Pandharpuri, Daisil, and Kapoori), molecular techniques were employed. The genotypes were collected from Nagarjuna Medicinal and Aromatic Plant Park at Dr. P.D.K.V. Akola. DNA isolation was performed using alcohol fixation without liquid nitrogen, and the genotypes were analyzed using RAPD and SSR primers for molecular characterization.
Results: Genetic diversity analysis of six Tulsi genotypes (Krishna, Ram, Lavangi, Pandharpuri, Daisil, and Kapoori) was performed using RAPD and SSR markers. Five RAPD primers produced 15 bands, with 11 bands showing polymorphism (73.3%) and 4 bands showing monomorphism (26.7%). The PIC value ranged from 0.28 to 0.49 (average: 0.40). Four SSR primers generated 9 bands, with 8 bands showing polymorphism and 1 band showing monomorphism. The PIC value ranged from 0.24 to 0.57 (average: 0.39). The Jaccard coefficient revealed moderate to high similarity in RAPD (0.40 to 0.73) and SSR (0.44 to 0.88) analyses. The UPGMA dendrogram separated the genotypes into two main clusters. Cluster 1 included Krishna, Lavangi, Ram, Pandharpuri, and Daisil Tulsi, while cluster 2 consisted of Kapoori Tulsi. The SSR dendrogram also formed two clusters, with Krishna, Lavangi, Ram, Daisil, and Kapoori genotypes in cluster 1, and Pandharpuri Tulsi showing dissimilarity and forming cluster 2.
20 Apr 2023
TL;DR: In this paper , a UPGMA-based dendogram was designed to reveal the genetic diversity of 29 genotypes of flax through morphological traits and 12 iPBS and 33 ISSR markers.
Abstract: Abstract Flax is one of the significant crops owing to oilseed and fibre attributes, exhibiting a wide distribution in many parts of the world. The present study was designed to reveal the genetic diversity of 29 genotypes of flax through morphological traits and 12 iPBS and 33 ISSR markers. According to the UPGMA-based dendogram, genotypes of the flax were classified into the two major groups (A and B) and group B was composed of two sub-groups (B1 and B2) according to the six phenotypic attributes considered for analysis. Concerning molecular relationships of the genotypes, individual and combined UPGMA-based dendograms were constructed with respect to the ISSR and iPBS markers. According to the Jaccard similarity coefficients for ISSR data, flax genotypes were divided into two main groups (A and B) and the “Van-1” genotype was in group A alone. Also, group B was divided into two separate subgroups. “Afyon-1” and “İzmir-Kemeraltı” genotypes were located in group B1, while all the remaining genotypes were located in group B2. In addition, the average genetic similarity was 0.755 regarding the findings of iPBS-retrotsposon markers, flax genotypes were classified into two main groups (A and B), and these main groups formed two subgroups among themselves. While “Konya-1” is located alone in A1 subgroup, “Iğdır”, “İzmir-Kemeraltı”, “Mardin”, “Bitlis” and “Afyon-1” genotypes are located in A2 subgroup. While “Van-1” genotype was located in the B2 subgroup alone, other genotypes were found in the B2 subgroup. The average genetic similarity was determined as 0.578 according to Jaccard binary similarity coefficient. According to the combined data of two markers, two separate groups (A and B) were revealed, similar to the dendrogram constructed with ISSR data. “Van-1” genotype was located in group A alone. Group B was divided into two subgroups (B1 and B2). The average genetic similarity was 0.722 according to the Jaccard similarity coefficient of matrix.
01 Apr 2023
TL;DR: In this article , a well-known statistical method, which has not been previously used for such problems, was used, which makes it possible to orthogonally decompose multidimensional variability into intra- and inter-taxon variability and analyze them separately.
Abstract: Currently, the search for manifestations of selection under the influence of the environment in molecular sequences is usually carried out within closely related species or at the intraspecific level. It is believed that at high taxonomic levels this is unpromising due to phylogenetic relationship. Cytochrome b amino acid sequences of 67 rodent and lagomorph species with known geographic coordinates were digitized using the AAindex database. Based on more than 200 thousand characters, the principal components were obtained. A well-known statistical method, which has not been previously used for such problems, was used, which makes it possible to orthogonally decompose multidimensional variability into intra- and intertaxon variability and analyze them separately. The subfamily level was selected. For the second principal component (17.05% of intertaxon variability), a correlation with latitude was found (r = 0.561; n = 67; p < E-5). The clear division into two groups, revealed by the first principal component (39.48% of intertaxon variability), which does not coincide with the taxonomic one, indicates a possible physicochemical underlying cause for the differences between them. This requires further research.
TL;DR: In this article , the authors analyzed the genetic diversity of twenty-two durum wheat landraces using sixteen morphological descriptors and sequence-related amplified polymorphism (SRAP) markers.
TL;DR: In this article , the authors describe the population genetic structure and gene flow of Ixodes ovatus and Haemaphysalis flava and their infection rates along an altitudinal gradient, which can be used in understanding the relationship between the tick vector, its pathogen, and environmental factors, such as altitude, and for the control of tick-borne diseases.
Abstract: Ixodid ticks, such as Ixodes ovatus and Haemaphysalis flava, are important vectors of tick-borne diseases in Japan, such as Japanese spotted fever caused by Rickettsia japonica. This study describes the population genetic structure and gene flow of I. ovatus and H. flava and their Rickettsia infection rates along an altitudinal gradient. A total of 346 adult I. ovatus and 243 H. flava were analyzed for the presence of Rickettsia by nested PCR targeting the 17kDA, gltA, rOmpA, and rOmpB genes. Population genetic structure was performed using the mitochondrial cytochrome oxidase 1 (cox1) marker. The Rickettsia infection rates were 13.26% in I. ovatus and 6.17% in H. flava. For I. ovatus, the global FST value revealed significant genetic differentiation among the different populations, whereas H. flava showed non-significant genetic differentiation. The cox1 I. ovatus cluster dendrogram showed two cluster groups, while the haplotype network and phylogenetic tree showed three genetic groups. The two cluster groups and the three genetic groups found in I. ovatus showed a significant difference in their Rickettsia infection rates and mean altitude per group. No significant differences were found in the mean altitude or Rickettsia infection rates of H. flava. Our results suggest that low gene flow in the I. ovatus populations has caused spatially heterogenous Rickettsia infection rates along the altitudinal gradient. This information can be used in understanding the relationship between the tick vector, its pathogen, and environmental factors, such as altitude, and for the control of tick-borne diseases in Japan.
TL;DR: ScBubbletree as mentioned in this paper is a scalable method for visualization of scRNA-seq data, which identifies clusters of cells of similar transcriptomes and visualizes such clusters as "bubbles" at the tips of dendrograms (bubble trees), corresponding to quantitative summaries of cluster properties and relationships.
Abstract: Motivation Visualization approaches transform high-dimensional data from single cell RNA sequencing (scRNA-seq) experiments into two-dimensional plots that are used for analysis of cell relationships, and as a means of reporting biological insights. Yet, many standard approaches generate visuals that suffer from overplotting, lack of quantitative information, and distort global and local properties of biological patterns relative to the original high-dimensional space. Results We present scBubbletree, a new, scalable method for visualization of scRNA-seq data. The method identifies clusters of cells of similar transcriptomes and visualizes such clusters as “bubbles” at the tips of dendrograms (bubble trees), corresponding to quantitative summaries of cluster properties and relationships. scBubbletree stacks bubble trees with further cluster-associated information in a visually easily accessible way, thus facilitating quantitative assessment and biological interpretation of scRNA-seq data. Availability and Implementation the R package scBubbletree is freely available at: https://bioconductor.org/packages/scBubbletree/ Contact simo.kitanovski@uni-due.de, daniel.hoffmann@uni-due.de
TL;DR: In this article , a new approach using a hierarchical clustering algorithm is suggested for dealing with small files in Hadoop Distributed File System (HDFS) by identifying the files by their structure and via a special Dendrogram analysis, and then recommending which files can be merged.
Abstract: The Small Files Problem in Hadoop Distributed File System (HDFS) is an ongoing challenge that has not yet been solved. However, various approaches have been developed to tackle the obstacles this problem creates. Properly managing the size of blocks in a file system is essential as it saves memory and computing time and may reduce bottlenecks. In this article, a new approach using a Hierarchical Clustering Algorithm is suggested for dealing with small files. The proposed method identifies the files by their structure and via a special Dendrogram analysis, and then recommends which files can be merged. As a simulation, the proposed algorithm was applied via 100 CSV files with different structures, containing 2-4 columns with different data types (integer, decimal and text). Also, 20 files that were not CSV files were created to demonstrate that the algorithm only works on CSV files. All data were analyzed via a machine learning hierarchical clustering method, and a Dendrogram was created. According to the merge process that was performed, seven files from the Dendrogram analysis were chosen as appropriate files to be merged. This reduced the memory space in the HDFS. Furthermore, the results showed that using the suggested algorithm led to efficient file management.
17 May 2023
TL;DR: In this article , the morphological and yield values of the forage kochia populations collected from 5 different locations in Konya were examined during 2018-2019, and according to morphological, yield and genetic diversity parameters of the populations were obtained using the GenAlEx program, and it was found that the mean He was 0.209 and the percentage of polymorphic loci was 81.20%.
Abstract: Abstract Forage kochia, a naturally growing and semi-shrub in Türkiye's flora, tolerates adverse soil and climatic conditions. In the research, the morphological and yield values of the forage kochia populations collected from 5 different locations in Konya were examined during 2018–2019. According to morphological and yield values, we determined 80 plants, 76 plants with excellent yield potential, and four outgroup plants for molecular studies. A total of 250 polymorphic fragments were obtained from these 80 plants. In our study, the average PIC value was 0.322, and the mean MI value was 8.99. Genetic diversity parameters of the populations were obtained using the GenAlEx program, and it was found that the mean He was 0.209, and the percentage of polymorphic loci was 81.20%. According to the results of AMOVA, among-population variation was 9%, while within-population variation was 91%. The dendrogram obtained as a result of the study determined that the genetic distance between plants varied between 0.63 and 0.90. According to the similarity index used in the study, it was stated that there was a high degree of similarity (90%) between 3212 and 5419 coded plants. Furthermore, it was noted that the markers related with plant height were associated with canopy diameter, number of main branches, and leaf color. The results show us that these populations are a treasured gene resource for plant breeding.
TL;DR: In this paper , the authors proposed to use optimally ordered orthogonal neighbor-joining (O $^{3}$ NJ trees as a new way to visually explore cluster structures and outliers in multi-dimensional data.
Abstract: We propose to use optimally ordered orthogonal neighbor-joining (O $^{3}$
TL;DR: In this paper , the authors evaluated the morphological, anatomy, genetic polymorphism, and relationships among 16 lime and lemon accessions based on six ISSR markers and found that 88.1% were polymorphic.
Abstract: Despite the fact that lime and lemon groups have been collected as germplasm in the Indonesian Citrus and Subtropical Research Institute, a limited amount of research has been conducted on the identification and evaluation of these species. This study aimed to evaluate the morphological, anatomy, genetic polymorphism, and relationships among 16 lime and lemon accessions based on six ISSR markers. The research was conducted at Punten Experimental Garden, Batu, East Java, Indonesia from January to December 2021 in order to describe the morphology and anatomy characteristics. The results showed that 109 DNA bands were considered for the ISSR analysis, of which 88.1% were polymorphic. The dendrogram showed that the accessions were separated into two main groups at a coefficient of 0.62. The first group was divided into three clusters, i.e. A, B, and C consist of introduced varieties, most of the local lemons, and limes, respectively. The second group has only a single member (Limo Kwit). The closest genetic distances were between Cai Kahuripan and Lemon Jumbo (88.1%) and Uereka with Lime Bearr (88.3%). In contrast, the lowest ones were Montaji with Lemo Kwit (52.9%) and Lemon Swanggi with Jari Buda (51.2%). In general, genetic traits reflected in existing clusters contributed to differences in their morphology and anatomy of plants. It is assumed that the local accession of Lemo Kwit is a hybrid of subgenus papeda, so it is separated from the lime and lemon groups that belong to Cluster II. This finding is very useful for breeding programs in Indonesia.
TL;DR: Genetic divergence for yield and yield attributes were evaluated in 33 bitter gourd genotypes for 17 characters such as, days to first female flower appearance, node of first male flower appearance and number of male flowers per vine as discussed by the authors .
Abstract: Genetic divergence for yield and yield attributes were evaluated in 33 bitter gourd genotypes for 17 characters. Characters such as, days to first male flower appearance, days to first female flower appearance, node of first male flower appearance, node of first female flower appearance, number of male flowers per vine, number of female flowers per vine, days to first harvest, number of harvests, fruit length (cm), fruit girth (cm), individual fruit weight (g), vine length (cm), number of primary branches per vine, number of fruits per vine, sex ratio, number of seeds per fruit and yield of fruits per vine (g) were used for analysing the divergence among the genotypes. Genotypes were grouped into five clusters using D2 statistics, and a dendrogram was created using Ward's approach. Out of the five clusters, cluster I was the largest comprising of 14 genotypes. Maximum inter cluster distance was observed between cluster III and cluster V, hence diverse parents for hybridization can be selected from these two clusters.
TL;DR: Araucaria araucana is an important seed and timber-yielding tree that grows naturally in the tropical and subtropical regions of the Andes in Argentina and Chile, and has also been introduced as an ornamental species in Europe as discussed by the authors .
Abstract: Araucaria araucana is an important seed and timber-yielding tree that grows naturally in the tropical and subtropical regions of the Andes in Argentina and Chile, and has also been introduced as an ornamental species in Europe. Genetic diversity has been observed in A. araucana native populations, but there have been no prior studies on the genetic diversity estimates of this species introduced in Europe. On the other hand, assessment of the genetic variation in Araucaria populations occurring in Europe might be an important tool in the selection of appropriate germplasms for ornamental nursery production and breeding strategies. In this study, morphological and genetic diversity was analysed using a previously defined descriptor list and SSR molecular markers in four putative populations of A. araucana, individuated in the Pistoia Nursery District (Tuscany, Italy). In total, 26 morphological descriptors and 28 SSR primer pairs were used for a diversity assessment of specimens. Results provide evidence for genetic and morphological correspondence among the four putative Araucaria populations. PCA and cluster analyses based on morphological traits clearly revealed three distinct clusters of specimens. SSR primers yielded 68% polymorphic loci among the considered populations, and 18 of them displayed informativeness for population genetics, according to a Polymorphic Information Content value larger than 0.25. This marker set revealed significant genetic differentiation, and UPGMA analysis enabled separation of these populations on the basis of their genetic distances into three main groups, which largely overlapped with clusters in the dendrogram obtained from the morphological data. In particular, in both cluster diagrams, all accessions belonging to a specific population were well separated from all the others due to matrix distances and differences in the canopy density that are more similar to conifers such as spruce, pine, or fir. ANOVA analysis and the FST value indicated a large between-population genetic variation. The Mantel test suggested that genetic differentiation between the four studied populations was positively correlated with morphological distance (r = 0.141, p < 0.05). Thus, both morphological and genetic markers showed applicability across populations of different seed origins and proved suitable for the identification and characterization of A. araucana accessions.
TL;DR: Wang et al. as discussed by the authors explored the genetic diversity and molecular characteristics at the population level of hollyhock and revealed extensive variation among 11 traits and strong correlations between several quantitative traits.
Abstract: Hollyhock (Alcea rosea (Linn). Cavan) is an herbaceous flowering plant with significant applications in urban greening, soil remediation, and traditional medicine. However, its genetic diversity and molecular characteristics at the population level have not been explored yet. Here, the phenotypic and genetic diversity of 162 hollyhock accessions from China revealed extensive variation among 11 traits and strong correlations between several quantitative traits. Whole-genome re-sequencing of 32 randomly chosen accessions identified 10,468,760 core single-nucleotide polymorphisms (SNPs) distributed evenly across the genome, except for on chromosome 21, and the average nucleotide diversity (π) was calculated to be 0.00397. Principal component analysis showed that these 32 accessions could be divided into four subpopulations, which was in agreement with the population structure analysis, and the subpopulations were strongly correlated with geographic location. A neighbor-joining dendrogram displayed similar clusters, except for accessions HuB25 and HLJ28, which formed two separate clusters. Our findings illuminate the genetic diversity in hollyhock and provide valuable information for hollyhock breeding.
TL;DR: In this paper , 28 genotypes of soybean were analyzed using 37 start codon targeted (SCoT) markers and 37 primers produced 260 DNA fragments with an average of 7.03 bands per primer.
Abstract: In the present investigation 28 genotypes of soybean were analysed using 37 start codon targeted (SCoT) markers and 37 primers produced 260 DNA fragments with an average of 7.03 bands per primer. From these 37 primers, primers SCoT 33 and SCoT 65 wos the most polymorphic, where 10 polymorphic amplification products were detected. The lowest number of amplified polymorphic fragments (2) was detected by primers SCoT 8, SCoT 14, SCoT 19, SCoT 31 and SCoT 59. Of the 260 amplified bands, 200 (77.27 %) were polymorphic, with an average of 5.41 polymorphic bands per primer. To determine the level of polymorphism in the analysed group of soybean genotypes, polymorphic information content (PIC) was calculated. The polymorphic information content (PIC) value ranged from 0.512 (ScoT 66) to 0.968 (SCoT 12) with an average of 0.777. The dendrogram of genetic relationships among 28 soybean genotypes based on 37 SCoT markers was constructed. The hierarchical cluster analysis showed that the soybean geno-types were divided into 4 main clusters. The markers used in this study created a number of polymorphic bands among the different cultivars that can be utilized as molecular markers for their differentiation. The obtained data indicated that SCoT technique could be used efficiently for identification and differentiation of the soybean genotypes.
TL;DR: In this paper , the genetic diversity of ten C. citratus accessions collected around Nigeria was investigated using Simple Sequence Repeat (SSR) and inter simple sequence repeat (ISSR) markers.
Abstract: Leaves and essential oils for therapeutic purposes are important traits in lemongrass (Cymbopogon citratus). In this study, the genetic diversity of ten C. citratus accessions collected around Nigeria was investigated using simple sequence repeat (SSR) and inter simple sequence repeat (ISSR) markers. Also, we determined the chemical content of C. citratus essential oil. In this study, the essential oil was extracted using hydro-distillation and the constituents of the oil were determined with gas chromatography-mass spectrophotometry (GC-MS). The markers produced a total of 47 alleles with a mean PIC value of 0.73 in the accessions. The cluster analysis grouped the accessions into two major groups showing genetic relatedness between the accessions: LG07, LG03 and LG01 are the closest members, while LG08 is very distant from the other accessions. In addition, the factorial analysis categorized the ten accessions into four quadrants, which have some similarities to the dendrogram grouping. GC-MS analysis resulted in the identification of 18 compounds. Essential oils of LG02 and LG03 had a citral content of 49.38 % and 66.47 %, respectively. These results revealed the genetic diversity among the accessions evaluated that can be used to maximize the use of genetic resources of C. citratus varieties.
01 Jan 2023
TL;DR: In this article , the authors examined the quality of surface water in the Mahanadi Basin, Odisha, for the 2019-2022 timeframe using multivariate approaches like Principal Component Analysis (PCA) and Cluster Analysis (CA).
Abstract: Water is a vital, finite resource whose quantity and quality are deteriorating as the world population increases. For agriculture, industry, and the needs of people and wildlife, rivers are essential. Weighted Arithmetic (WA) Water Quality Index (WQI), Canadian Council of Ministers of the Environment (CCME) WQI, and multivariate approaches are used in this work to examine the quality of the surface water in the Mahanadi Basin, Odisha, for the 2019–2022 timeframe. All physical-chemical parameter findings were compared to the ranges or values specified by WHO guidelines. The geographic distribution maps were created in ArcGIS 10.5 using the Inverted Distance Weighted (IDW) interpolation method to understand the changing behavior of parameters in surface water. For effective management of surface water quality, multivariate techniques like Principal Component Analysis (PCA) and Cluster Analysis (CA) were used to evaluate the water conditions. The findings show that 10.53 % (CCME WQI) and 15.8 % (WA WQI) of the samples depict extremely poor and poor water quality. Twenty surface water metrics and 19 sampling locations consist of three major clusters with related surface water properties, were investigated using dendrogram plots, for identification of elemental associations. The PCA creates the five primary components, which strongly influence the hydro-chemistry of river water by 93.915%. The results of the combined analysis of the two–water quality (WQ) indices with GIS, CA, and PCA indicate that the majority of the samples come from the areas ST–8 (Cuttack D/s), ST–9 (Paradeep), and ST–19 (Choudwar D/s) and are categorized as poor to extremely poor. Numerous human-made activities, organic waste, as well as the outflow of sewage wastewater, were shown to be the principal reasons for the deterioration in water quality. According to the current study, surface water in the region with poor water quality needs to be treated before being consumed. This study provides insight into fundamental processes that are significant for the sustainable management of surface water resources.
TL;DR: In this article , SRAP markers were used to determine the genetic diversity and relationships between four local and three registered safflower cultivars for use in cross-breeding programs, and twelve primer combinations yielded a total of 101 bands, including 33 polymorphic bands.
Abstract: Safflower (Carthamus tinctorius L.), a member of the Asteraceae family, is an important plant grown in the world as a source of vegetable oil. In addition, it is a versatile crop that is also used as biodiesel, animal feed, spice, dye, and medicinal plant. In this study, SRAP markers were used to determine the genetic diversity and relationships between four local and three registered safflower cultivars for use in cross-breeding programs. The twelve primer combinations yielded a total of 101 bands, including 33 polymorphic bands. The polymorphic band ratio is 34.5%. The level of polymorphism of SRAP markers which are represented by the average number of total bands (NTB) (8.4), the average number of polymorphic bands (NPB) (2.8), percentage of polymorphism (34.5 %), resolving power (RP) (1.48), effective multiplex ratio (EMR) (1.17), and marker index (MI) (0.43) was low. The polymorphism information content of the SRAP primer combinations used in the study ranged from 0.24 to 0.46, with an average of 0.35. Genetic similarity was calculated according to Dice similarity and varied from 0.12 to 0.92, with a mean genetic similarity (GS) of 0.58. The cophenetic correlation between the Dice similarity matrix and corresponding dendrogram obtained by SRAP (r = 0.95) revealed very good compliance. The genetically nearest varieties were Remzibey05 - TR64702 and TR49119 - TR42630 (GS=0.91). Also, Dinçer5-118 and Yenice5-38 registered varieties were the most genetically distant varieties (GS=0.12). Besides, Dinçer5-118 is genetically very different from other varieties (GS=0.29).