UPGMA Cluster Research Articles

Genetic diversity among early provitamin A quality protein maize inbred lines and the performance of derived hybrids under contrasting nitrogen environments

BackgroundInformation on population structure and genetic diversity of germplasm in a breeding programme is useful because it enhances judicious utilisation of genetic resources to achieve breeding objectives. Seventy early maturing provitamin A (PVA) quality protein maize (QPM) inbreds developed by the IITA- maize improvement programme were genotyped using 8171 DArTseq markers. Furthermore, 96 hybrids derived from 24 selected inbreds plus four checks were evaluated under low-N and optimal environments in Nigeria during 2016 and 2017. Genotypic and phenotypic data of inbreds and hybrids respectively, were analysed to (i) assess the level of genetic dissimilarities and population structure of the inbreds, and (ii) investigate the grain yield performance of derived hybrids under low-N, optimal and across environments.ResultsGenetic diversity among the seventy inbreds was high varying from 0.042 to 0.500 with an average of 0.357. Sixty-six inbred lines with probabilities ≥0.70 were assigned to a single group. The population structure analysis, the UPGMA phylogeny, and the principal Coordinate Analysis (PCoA) of the DArTseq markers revealed a clear separation of five groups and each followed pedigree records. Clustered inbreds displayed common characteristics including high PVA levels, and drought and low-N tolerance. The top performing hybrid, TZEIORQ 40 × TZEIORQ 26 out-yielded the best hybrid control, TZEIOR 127 × TZEIOR 57 by 8, 3, and 9% under low-N, optimal, and across environments, respectively. High repeatability estimates were detected for grain yield under each and across environments. Similarly, high breeding efficiency of 71, 70 and 72% were computed under low-N, optimal, and across environments, respectively.ConclusionsThe UPGMA clustering, the structure analysis, and the PCoA consistently revealed five groups which largely followed pedigree information indicating the existence of genetically distinct groups in the inbred lines. High repeatability and breeding efficiency values estimated for grain yield of hybrids under low-N, optimal and across environments demonstrated that high productive hybrids could be developed using inbreds from the opposing clusters identified by the DArTseq markers. The 15 top performing hybrids identified, particularly TZEIORQ 40 × TZEIORQ 26 and TZEIORQ 29 × TZEIORQ 43 should be further evaluated for release and commercialization in SSA.

Morphological and genetic diversity of Slovene lettuce landrace ‘Ljubljanska ledenka’ (Lactuca sativa L.)

A set of accessions of lettuce landrace ‘Ljubljanska ledenka’ (Lactuca sativa L.) was characterized by morphological and molecular markers and for resistance to Bremia lactucae, with the aim of assessing the variability of the collection, exploring the genetic structure and potentially identifying the characters responsible for differentiation of the accessions. Wide phenotypic variation was observed among 51 accessions screened for 26 morphological and phenological traits. UPGMA cluster analysis and principal component analysis based on phenotypic data enabled the studied accessions to be divided into four clusters. The most important character by which the largest two clusters were differentiated was anthocyanin coloration. The clustering pattern of the AFLP dendrogram where two major clusters were identified was similar but not identical to the pattern of the phenotypic dendrogram. The Mantel test showed a high correlation between the phenotypic and the molecular data obtained (r = 0.67). In spite of the weak genetic differentiation between the accessions, STRUCTURE analysis based on AFLP data provided a clear indication for the existence of sub-groups within the two clusters. Thirty-four accessions were screened for resistance to 12 races of B. lactucae. The results show that the accessions very frequently express various reaction patterns of race specificity. Expression of race-specificity was not uniform across the set of accessions and at least 11 different reaction patterns were recorded, indicating that different race-specific resistance factors (R-factors) or genes (Dm genes) could be expected. This conclusion is supported by the results obtained in morphological and molecular studies, showing that lettuce landrace ‘Ljubljanska ledenka’ is not genetically uniform and is represented by a variety of genotypes.

DNA barcoding Cinnamomum osmophloeum Kaneh. Based on the partial non-coding ITS2 region of ribosomal genes

This paper investigated the DNA barcoding of indigenous cinnamon. The essential oil composition of leaves and the partial non-coding internal transcribed spacer (ITS2) region of ribosomal genes from indigenous cinnamon plants (Cinnamomum osmophloeum Kaneh.) were investigated. Leaf essential oils from seven geographical strains of C. osmophloeum Kaneh. were obtained by hydrodistillation and characterized by gas chromatography-mass spectrometry. Six chemotypes, including cinnamaldehyde, cinnamaldehyde/cinnamyl acetate, cinnamyl acetate, linalool, camphor and mixed, were identified. Seven representative geographical strains were further used to study their genetic diversity based on the partial ITS2 region using PCR amplification and DNA sequencing to evaluate the region's use in the application of DNA barcoding C. osmophloeum Kaneh. A phylogenetic tree was constructed using UPGMA clustering method. Our results indicate that the partial ITS2 nucleotide sequences for all seven geographical strains are identical and not correlated with essential oil composition. The partial ITS2 sequences is sufficient for barcoding C. osmophloeum Kaneh., while that additional genes will need to be analyzed to identify samples of various chemotypes. We believe that this partial ITS2 locus serves as a good starting point for large-scale testing of DNA barcoding of other plant species across Taiwan.

Genetic structure, molecular and phytochemical analysis in Iranian populations of Ruscus hyrcanus (Asparagaceae)

Ruscus hyrcanus Woronow a commercially important ornamental and medicinal plant belonging to the Asparagaceae family, has various applications in Iranian traditional medicine due to its diuretic, appetizing, cathartic, vasoconstrictor, anti-hemorrhage, ant-nephritis, anti-infection, aperient and anti-varicose properties. In the present study, morphological, phytochemical and molecular markers were investigated in twelve R. hyrcanus (RH) populations collected from the Hyrcanian ecoregion in the north of Iran. Phytochemical characteristics were remarkably variable among the studied populations, but little morphological variation was observed. The highest contents of ruscogenin and neoruscogenin in the underground parts of the plant were recorded in populations RH9 (Abbasabad 3.41 mg/g DW) and RH6 (Darab Kola 1.44 mg/g DW), respectively. A total of 66 bands were obtained from 11 inter-simple sequence repeat (ISSR) markers, 62 (93.94 %) of which were polymorphic. Although the ISSR evaluation indicated an inter-population genetic differentiation (GST = 0.27), most of the genetic diversity was intra-populational (PPB = 32.26–75.81 %, He = 0.11−0.24, I = 0.17−0.36). A UPGMA cluster analysis of 120 samples of R. hyrcanus was carried out to categorize the studied populations, based on a molecular data matrix calculated with Jaccard’s similarity coefficient. A multiple regression analysis of the relationships between the ISSR bands and morphological and phytochemical traits demonstrated that eight ISSR fragments were related to ruscogenin in the plant materials. Several ISSR markers showed association with some morphological traits. This study provided the comprehensive preliminary data on morphological, phytochemical, and genetic characteristics of R. hyrcanus populations in order to exploit genetic reserves conservation programs.

Molecular diversity analysis using Simple sequence repeats (SSRs) in ‘A’ and ‘R’ lines of Ogura CMS system in Indian mustard

Fifty-eight SSR primers were used for molecular diversity analysis among 45 ‘A’ and ‘R’ lines (5 A lines and 40 restorers) of Indian mustard. Out of 58 primers 33 primers were found to be polymorphic. A total of 95 alleles were detected across all 45 genotypes. The PCR amplified products ranged from 70 bp to 350 bp in size. The number of alleles per locus varied from 2 to 5 with an average of 2.89. The PIC value varied from 0.206 to 0.749 with an average of 0.519. The highest PIC value was obtained for BG 132 (0.749) followed by BG 114 (0.744). The UPGMA cluster analysis suggested demarcation of 45 genotypes into six distinct groups in dendrogram wherein three groups had single genotype (restorer line) each. Cluster VI consisted of all five Ogura CMS lines only. In the remaining clusters, restorer lines were distributed. Based on similarity coefficient, cross combinations viz., RH 0749-OA & IOR-17, RH 0749-OA & IOR-20 and RH 119-OA & OR-17 were identified as diverse and might be suitable for using parent in heterosis exploitation in Indian mustard.

Genotyping of rice accessions using SSR markers

Molecular characterization of germplasm accessions of rice revealed genetic polymorphism and ensured unambiguous identification. A total of 24 SSR markers were used covering all the chromosomes of rice for their molecular characterization and discrimination. After analysis of the data generated, a total of 69 alleles were detected in 24 accessions of rice. The number of alleles per locus generated by each marker ranged from 1 to 6 alleles with an average number of 2.87 alleles per locus. The highest number of alleles (6) was detected in the locus RM 22565 while, lowest number of alleles (1) detected on each of locus OSR 13, RM 431, RM 454 and Xa5s. The PIC value ranged from 0.00 (OSR 13, RM 431, RM 454 and Xa5s) to 0.76 (RM 12146). Microsatellite markers (SSR) are also used to detect the genetic similarity of germplasm accessions of rice. The genetic similarity coefficient ranged from 0.24 to 1.00 as revealed by UPGMA cluster analysis using the 24 SSR markers. A total of five distinct groups resulted at a cut-off similarity coefficient of 0.46 among the 24 rice accessions, below which the similarity values narrowed conspicuously. Coefficient of similarity revealed that the rice accessions of cluster I were genetically distant from cluster IV. Thus, Peeleeluchai (135131) and Mahuwadeta Lal of cluster I; whereas, Kadamphool and Ram Karoni of cluster IV seems to be promising and should be utilized in hybridization programme. Molecular markers like RM 1, RM 12146, RM 215, RM 22710 RM 154 and RM 25 could potentially be used for molecular characterization of rice germplasm accessions from various sources on the basis of polymorphic reactions and high PIC values.

Molecular Distinguishness among rice (Oryza sativa L.) landrace of Central India using microsatellite markers

Molecular characterization of the genotypes gives precise information about the extent of genetic diversity which helps in the development of an appropriate breeding program. A total of 16 microsatellite (SSR) markers distributed across the rice genome were used for molecular characterization and discrimination of 100 local landraces of rice. The molecular data revealed a total of 24 alleles in 100 rice accessions, The number of alleles per locus generated by each marker ranged from 1 to 5 alleles with the mean of 1.5 alleles per locus and an average polymorphism information content (PIC) of 0.387. This suggests that these markers could be potentially used for molecular characterization of rice accession from various sources. Microsatellite markers (SSR) are also used to detect the genetic similarity of accessions of rice under study. The genetic similarity coefficient ranged from 0.76-1.00 as revealed by UPGMA cluster analysis using the 16 SSR markers. A total of four distinct groups resulted at a cut-off similarity coefficient of 0.83 among the 100 rice accessions. Allelic variability among the SSR markers was high enough to categorize landraces and to catalogue the genetic variability observed for future use. The information about the genetic diversity will be very useful for proper identification and selection of appropriate parents for breeding programs, including gene mapping, and ultimately for emphasizing the importance of marker-assisted selection (MAS) in rice improvement.

Hıyar (Cucumis sativus L.) Genotiplerinin Morfolojik Karakterler ve AFLP Analizi ile Genetik Çeşitliliğinin Değerlendirilmesi

For this purpose, 18 cucumber lines were evaluated for their genetic diversity using six morphological characterizations (plant morphology, plant length, length of leaf blade, fruit length, fruit diameter and fruit stem length) and eight AFLP markers. These AFLP primer combinations amplified well and also showed polymorphism. Thus, 1975 AFLP fragments were obtained and 1468 fragments were polymorphic (75.34%). Dendrograms were drawn using UPGMA (Unweighted Pair Group Method) arithmetical averages and according to the UPGMA dendrogram, the cucumber accessions clustered into two main groups. The genetic distances of the dendrogram varied between 0.92 and 0.96. Cluster analysis based on morphological data discriminated all lines into three major clusters in UPGMA dendrogram. The similarity coefficient ranged between 0.888 and 0.982 indicating that the cucumber lines used in the study have a low level of genetic variation. Results obtained from the phylogenetic dendrogram by 8 pairs of AFLP primers were consistent with those from the UPGMA clustering analysis, which were in according with the morphological taxonomy on cucumber.

Transcriptome profiling, simple sequence repeat markers development and genetic diversity analysis of potential industrial crops Capsicum chinense and C. frutescens of Northeast India

Capsaicinoids, a group of secondary metabolites (alkaloids) which imparts hot property, are unique to the Capsicum fruits and have high value in the pharmaceutical and food industries. In spite of having high capsaicinoids content with ethnopharmacological and economic importance, the C. chinense and C. frutescens of the Northeast India, are underexplored for the genetics and breeding programs. In this study, we developed transcriptome-based Simple sequence repeat (SSR) markers and analyzed the expression(s) of capsaicinoids and carotenoid biosynthesis pathway genes in flower and fruit tissues at three developmental stages (early, breaker and mature) of C. chinense, C. frutescens and C. annuum. A total of 4988 and 4781 genic SSRs were identified from 123,118 and 121,017 de novo assembled unigenes, in C. chinense and C. frutescens, respectively. Also, the reference-based transcriptome analysis identified 70.8–73.6 % commonly expressed transcripts in all tissues besides 2929, 1327, 1193 and 937 unique transcripts in flower, early, breaker and mature fruits, respectively. The gene expression profiling showed significantly high expression of the key capsaicinoids and carotenoid biosynthetic pathway genes at breaker and mature fruit stages. Furthermore, in silico analysis identified a total of 335 polymorphic SSRs between C. chinense and C. frutescens with allelic size difference of >4 bases. The trinucleotide repeats was found to be predominant in both C. chinense (50.6 %) and C. frutescens (52.2 %). High genetic-diversity of SSRs was observed with mean gene diversity of 0.51 and polymorphism information content (PIC) of 0.53. Based on twenty polymorphic SSRs, the UPGMA cluster analysis differentiated 96 genotypes belonging to C. chinense, C. frutescens and C. annuum into distinct groups. The identified SSRs and diverse Capsicum genotypes will serve as important genetic resources for future applications in genetics study and breeding of Capsicum varieties with improved metabolites (pungency, carotenoids etc.) and agronomic traits (fruit shape, size etc.) for agricultural, food and pharmaceutical industries.

Efficiency and reliability of random DNA markers (RDMs) for evaluation of genetic variability and relationship in Ocimum accessions

The genus Ocimum is characterized by a great variability in both morphological features and chemical composition because the cross-pollination appears leads to various species, subspecies, varieties and forms. In addition, the taxonomy of Ocimum is complicated by the existence of numerous botanical varieties, cultivar names, and chemotypes within the species that may not differ significantly in morphology. In the present study, genetic diversity and relationships within and among 24 Ocimum accessions from five different agro-climatic regions of West Bengal were developed using PCR-based Random Amplified polymorphic DNA (RAPD) and Inter Simple Sequence Repeats (ISSR) markers. The RAPD primers developed 191 robust loci, which revealed 69.42% polymorphism and 83 ISSR markers generated 67.46% polymorphism. Genetic diversity parameters [average and effective number of alleles, percent polymorphism, average heterozygosity, intralocus gene diversity, polymorphic information content (PIC)] for RAPD, ISSR, and RAPD+ISSR along with UPGMA clustering based on Jaccard's coefficient were estimated with a view to assess efficiency of the marker system in Ocimum. The UPGMA dendrogram generated using cumulative data revealed significant relationships among the genotypes. All 24 genotypes studied grouped into three clusters irrespective of their geographical affiliations with 100% bootstrap value except few genotypes, suggesting considerable diversity among the genotypes. Further the results demonstrate the efficiency and reliability of RAPD and ISSR markers in determining the genetic diversity and relationships among the Ocimum germplasm. RAPD and ISSR profiling have identified diverse Ocimum genotypes, which could be further utilized in various genetic improvement programmes including conventional as well as marker assisted breeding towards development of new and desirable Ocimum genotypes.

Development of genome wide transposable elements based repeat junction markers in Jatropha (Jatropha curcas L.).

Jatropha curcas is a potential biodiesel crop and a highly adaptable species to various agro-climatic conditions. In this study, we have utilized transposable elements' (TE) repeat junctions (RJs) which are an important constituent of the genome, used to form a genome-wide molecular marker platform owing to its use in genomic studies of plants. We screened our previously generated Jatropha hybrid genome assembly of size 265 Mbp using RJPrimerspipeline software and identified a total of 1274 TE junctions. For the predicted RJs, we designed 2868 polymerase chain reaction (PCR) based RJ markers (RJMs) flanking the junction regions. In addition to marker design, the identified RJs were utilized to detect 225,517 TEs across the genome. The different types of transposable repeat elements mainly were scattered into Retro, LTR, Copia and Gypsy categories. The efficacy of the designed markers was tested by utilizing a subset of RJMs selected randomly. We have validated 96 randomly selected RJ primers in a group of 32 J. curcas genotypes and more than 90% of the markers effectively intensified as amplicons. Of these, 10 primers were shown to be polymorphic in estimating genetic diversity among the 32 Jatropha lines. UPGMA cluster analysis revealed the formation of two clusters such as A and B exhibiting 85.5% and 87% similarity coefficient respectively. The various RJMs identified in this study could be utilized as a significant asset in Jatropha functional genomics including genome determination, mapping and marker-assisted selection.

Responses of freshwater biofilm formation processes (from colonization to maturity) to anatase and rutile TiO2 nanoparticles: Effects of nanoparticles aging and transformation

Most of the current studies on the toxicology of pristine nanoparticles (NPs) are environmentally irrelevant, because their ‘‘aging’’ process accompanied by the physicochemical transformation is inevitable in the environment. Considering aging phenomenon will gain a better understanding of the toxicity and fate of NPs in the environment. Here, we focused on the physicochemical transformation of anatase-NPs (TiO2-A) and rutile-NPs (TiO2-R) after 90 days of aging and investigated the responses of freshwater biofilm formation to the stress changes of naturally aged TiO2-NPs (aTiO2-NPs). We found that after aging, the TiO2-NPs underwent sophisticated physicochemical transformations in the original morphology and microstructure owing to organic and crystal salts inclusions, such as energy band changes and the formation of Ti3+ on the NPs surfaces. These comprehensive transformations increased the stability of NPs in the exposed suspension. However, the physicochemical transformations were crystal-forms-dependent, and aging did not change the crystal structure and crystallinity. Interestingly, compared to pristine NPs, aTiO2-NPs showed much lower cytotoxicity and had the weaker ability to promote or inhibit the biofilm formation (p < 0.05) owing to the passivation of photoactivity caused by the comprehensive effect of the inclusions, especially for aTiO2-A. Regardless of aging or not of crystal forms, responses of biofilm formation were exposure-concentration-dependent, namely low concentration promotion (0.1 mg/L) and high concentration inhibition (10 mg/L), e.g., role transition of the pioneers (algae or bacteria) in initial colonization, extracellular polymeric substances (EPS) secretion and compositions of development stages with polysaccharide (PS)-rich and protein (PRO)-rich stages, and biomass and cell activity at different depths of mature biofilms. The reactive oxygen species (ROS) induced by TiO2-NPs showed typical hormesis. The changing trends of the autoinducers (c-di-GMP and quorum sensing signals including AHL and AI-2) were highly consistent with the growth stages of biofilms and were stimulated or suppressed by TiO2-NPs. The NPs crystal-dependently changed the microorganism community structures, while the UPGMA clustering of bacteria was based on the growth stages of the biofilms. The toxic mechanisms revealed that photoactivity and nanoscale retention of particles are the main reasons for the differences in the ecological stress capacity of four kinds of TiO2-NPs. Aging reduced characteristic differences of two pristine NPs and even reversed their relative stresses levels (p > 0.05). However, the toxicity of high-concentration aTiO2-NPs (10 mg/L) remained serious in a water environment. This study provides a better understanding for the water environmental risks evaluation and policy control of nanoparticles, that is, the effect of time aging has to be considered.

Plant parasitic nematodes occurrence and genetic diversity of banana cultivars grown in Tanzania

The genetic diversity of bananas (Musa spp.), one of the most economically important crops in Tanzania, is underestimated with scarce reports available. In addition, cultivation of banana is severely constrained by plant parasitic nematodes (PPN). We assessed genetic diversity and population structure of 159 banana varieties from four agro-ecological zones (Northern, Southern highlands, Lake and Zanzibar islands) of Tanzania using 20 SSR markers analysed with UPGMA method. We also, assessed the PPN occurrence through isolation and counting of PPN from each banana genotype where leaf samples were collected. SSR primer pairs were polymorphic; and generated 63 distinct reproducible bands. The polymorphic information content values of each SSR marker ranged from 0.50 to 0.75 indicating high level of genetic diversity among banana varieties. The 159 banana varieties were grouped into two clusters: A and B, based on UPGMA cluster and population structure analysis. A total of 128 independent and 31 overlapping genotypes were identified. Higher kinship among genotypes was observed in cluster A compared with cluster B. Some of the clusters in A and B genotypes showed high genetic distance. The most prevalent and abundant nematode species was Pratylenchus goodeyi with a mean count of 63%, followed by Radopholus similis (31%) and P. coffeae (6%). The results from this study provides a foundation for understanding genetic variability of bananas existing in Tanzania and PPN occurrence that will be valuable information for breeding disease and pest-resistant bananas with high yield traits.

Biochemical, functional and molecular characterization of pigeon pea rhizobia isolated from semi-arid regions of India.

Pigeon pea (Cajanus cajan (L.) Millspaugh) is among the top ten legumes grown globally not only having high tolerance to environmental stresses along, but also has the high biomass and productivity with optimal nutritional profiles. In the present study, 55 isolates of rhizobia were identified from 22 nodule samples of pigeon pea collected from semi-arid regions of India on the basis of morphological, biochemical, plant growth promoting activities and their ability to tolerate the stress conditions viz. pH, salt, temperature and drought stress. Amongst all the 55 isolates, 37 isolates showed effective nodulation under in vitro conditions in pigeon pea. Further, five isolates having multiple PGP activities and high in vitro symbiotic efficiency were subjected to 16S rRNA sequencing and confirmed their identities as Rhizobium, Mesorhizobium, Sinorhizobium sp. Further these 37 isolates were characterized at molecular level using ARDRA and revealed significant molecular diversity. Based on UPGMA clustering analysis, these isolates showed significant molecular diversity. The high degree of molecular diversity is due to mixed cropping of legumes in the region. The assessment of genetic diversity and molecular characterization of novel strains is a very important tool for the replacement of ineffective rhizobial strains with the efficient strains for the improvement in the nodulation and pigeon pea quality. The pigeon pea isolates with multiple PGPR activities could be further used for commercial production.

Analysis of the Intestinal Flora in Male Versus Female Swamp Eels (Monopterus albus).

This study aimed to analyze the intestinal flora of male versus female swamp eels, which have the unique characteristic of sex reversal. Same-aged swamp eels from the same parents, kept under the same conditions in terms of environment, diet, etc., were used as the study materials. After breeding for 1 year, 18 healthy swamp eels (nine males and nine females), weighing 39.4 ± 2.3 g, were selected. The intestinal contents of three swamp eels of the same sex were combined and labeled as follows: FM1-FM3 (n = 3) for females and MM1-MM3 (n = 3) for males. High-throughput sequencing was used to research the v3-v4 region of 16S rDNA in the intestinal flora. The results suggested significant differences in the structure, composition, and diversity of the intestinal flora of male versus female swamp eels. The relative abundances of Actinobacteria and Spirochaetes in female swamp eels were significantly higher (p < 0.05) than in male swamp eels at the phylum level. The relative abundances of Mycobacterium, Bacillus, and Vagococcus in female swamp eels were considerably higher (p < 0.05) than in male swamp eels at the genus level. The Alpha diversity of females was higher than that of males, and the Shannon index of females was also significantly higher (p < 0.05, Tukey’s HSD) than that in males. Investigations of Beta diversity, including NMDS ordination, UPGMA cluster analysis, and PLS-DA analysis, showed that female and male swamp eels could be clearly distinguished based on significant differences in intestinal flora between the FM group and the MM group. LEfSe analysis showed that the dominant bacteria were Cetobacterium in male swamp eels and Clostridium_sp_ND2, Mycobacterium, Alphaproteobacteria, and Bacilli in female swamp eels. The results showed dramatic differences in the intestinal flora between the sexes, which indicates the need for a more in-depth study on sex reversal in the future.

Multivariate analysis of resistance components of the saccharin and biomass sorghum to Ramulispora sorghi

The objective of this work was to evaluate the reaction of biomass and saccharin sorghum genotypes to a isolate of the Ramulispora sorghi. The experiment was conducted in a completely randomized design with three replications in a greenhouse. The variables analyzed were: area below the disease curve progress; lesion length (LL), lesions width (LW); normalized area below the curve of the lesion area expansion; incubation period and latency period. Data were submitted to analysis of variance, Pearson correlation and multivariate analysis based on Mahalanobis distance, using the Tocher and UPGMA clustering method. Significant differences were observed in the level of (p&lt;0.01) and (p&lt;0.05), for almost all variables analyzed. Of the 45 correlations, only 22 (48.89%) were significant by t-test, regardless of significance (p&lt;0.01 or 0.05), where it was observed that in all significant correlations were positive, indicating that the reaction symptoms correlate between the variables evaluated. The groupings generated by the Tocher and UPGMA clustering method were in agreement to group genotypes with the same behavior in relation to reaction to Ramulispora sorghi. From the observed results, it was verified that all evaluated genotypes presented ramulispora spot symptoms, thus demonstrating their susceptibility to the pathogen.

Genetic Diversity Based on Morphological Traits of 19 Maize Genotypes Using Principal Component Analysis and GT Biplot

Among the phenotypic, biochemical, and molecular methods employed in assessment of genetic diversity, the phenotypic method has proven efficient for the assessment, description and classification of germplasm collections to enhance their use in maize breeding. The objectives of the present study were: (i) to assess the extent of genetic diversity in a collection of Egyptian commercial maize hybrids and populations, through field evaluation under water and N stressed and non-stressed conditions, using morphological data based on Principle Component Analysis (PCA), (ii) to measure the genetic distance among these genotypes using UPGMA cluster analysis and (iii) to assess the relationship between grain yield and yield-related traits of maize genotypes using GT-biplot analysis. A two-year field experiment was conducted in a split-split plot design with 3 replications, where 2 irrigation regimes, three N rates and 19 maize genotypes occupied the main plots, sub plots and sub-sub plots, respectively. The germplasm was assessed for 21 agronomic traits. Highly significant differences (P ≤ 0.01) were observed among the maize hybrids and populations for all measured traits. Results of the GT biplot in the present study indicated that high values of 100-Kernel weight, ears/plant, kernels/plant, kernels/row, plant height, nitrogen use efficiency, nitrogen utilization efficiency, and grain nitrogen content and short ASI could be considered reliable secondary traits for improving grain yield under stressed and non-stressed conditions. The highest genetic distance was found between G9 (SC-2055) and each of G15 (American Early Dent), G18 (Midland) or G19 (Ried Type). The Agglomerative Hierarchical Clustering based on phenotypic data assigned the maize genotypes into five groups. The different groups obtained can be useful for deriving the inbred lines with diverse features and diversifying the heterotic pools.

Study of metabolite variability in Plumbago zeylanica Linn. collected from different localities of the Gangetic plains of India

The metabolite contents of the plants may vary with season and geographic variations, and this induces the biological potential of the plant species. The present study aimed to identify the elite chemotype(s) of Plumbago zeylanica, collected from the natural habitat of Gangetic plains on the basis of plumbagin content. The effect of intra-specific variability in the plumbagin content among the population was estimated by using high-performance thin-layer chromatography (HPTLC) densitometric method. Roots of thirteen naturally occurring populations of P. zeylanica from the entire range were collected, covering the wide topography from foothills up to the highest peak. The method developed for quantification of plumbagin was validated and found to be linear, specific and accurate with precision and accuracy. LOD and LOQ were 1.04 and 3.16 ng/spot. Precision studies (both inter-day and intra-day) were within the standard limit of API, with RSD (%) less than 3%. Quantification of plumbagin within population reveals that it varies from 0.0048 ± 0.0005 μg (NBP-22) to 0.1696 ± 0.003 μg (NBC-25) percent on per dry weight basis. Analysis of variance (ANOVA) suggests that there is a significant difference in plumbagin content among the population. UPGMA cluster analyses based on plumbagin content bifurcate the populations into two major clusters, representing the variation in metabolite content. The first major cluster having NBP-25 and NBP-18 accessions, NBP-25 having maximum plumbagin content was collected from Bankura, West Bengal. The study suggests the presence of chemotaxonomic variation among the population which may be due to the change in environmental/phytogeographical factors.

Caracterização molecular de Prosopis juliflora (Sw.) DC. por meio de marcadores moleculares e índices de similaridade genética

Algaroba, Prosopis juliflora (Sx.) DC., é uma espécie arbórea adaptada no Brasil com valor alimentício animal e ambiental para reflorestamento. Porém pouco se sabe sobre sua diversidade genético-molecular. Portanto objetivou-se estudar diferentes índices de similaridade a partir de caracterizações genéticas da algaroba obtidas por meio dos marcadores ISSR e RGA em indivíduos naturalizados no sudoeste da Bahia. Folhas jovens de 36 indivíduos foram coletadas no município de Itapetinga, Bahia. O DNA foi extraído pelo método SDS 10% e quantificado pela razão de absorbância A260/A230 e A 260/A280 nm. Dez pares de RGA e 23 iniciadores ISSR foram utilizados para a reação de PCR, cujas reações foram submetidas à eletroforese em gel de agarose a 2% por 2 h. O resultado da genotipagem (matriz binária) foi utilizado para cálculo dos índices de similaridade de Jaccard, Simple Matching e Sorensen Dice. Por fim, foram realizados os agrupamentos UPGMA, otimização de Tocher e PCA. Foram observados 205 e 68 marcas polimórficas, com heterozigosidade esperada de 0,28 e 0,21; informação polimórfica de 91,71% e 0,17% e distância genética de 8,0 e 8,53 para ISSR e RGA, respectivamente. Essas informações contribuem para o entendimento da distribuição e adaptação da espécie em áreas reflorestadas.

Colonization-related functional traits of plants in a 50-hectare plot of secondary tropical forest

ABSTRACT The growth-survival trade-off hypothesis states that functional traits of stem, wood, leaves and fruits govern acquisitive and conservative strategies of plant species that grow/survive differently in forests. We aimed to determine whether heterogeneity during the colonization of a secondary Atlantic Forest fragment causes differences in colonization-related traits and determines taxonomic composition of subplots. A total of 5,078 subplots were censused with leaf and fruit traits and height measurements being determined for each tree of each species, and with averaged-abundance-weighted values calculated for each subplot. A dendrogram was generated from the taxonomic composition of subplots using Sorensen similarity and UPGMA clustering. A total of 74,335 trees of 178 species were recorded. Clustering revealed five main groups of subplots that were tested against each other and found to differ in terms of average leaf width, leaf-width/petiole-width, wood density, mean height, height mode, fruit width and fruit length. Greater leaf averages in subplots were associated with greater fruit averages, and with higher wood densities and greater heights among groups of subplots, revealing that heterogeneity during colonization directed the communities of the 50-ha plot. The averaged values of functional traits detected subplots associated with conditions favorable to colonization, thereby reinforcing the growth-survival trade-off hypothesis.