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Agro-morphological characterization of rice is vital for rice breeding programs, which help to document phenotypical differences. The research was conducted in Sundarbazar, Lamjung, during the spring season from February to August 2023, where the design was completely randomized with two replications. Twenty-five quantitative and thirty-nine qualitative traits were recorded according to the characterization descriptors of the International Rice Research Institute, Sixteen quantitative traits were observed for 16 landraces, and 11 showed high coefficient of variance (CV) values. In comparison, for the remaining nine traits, two traits showed a high CV value for all 20 landraces. Three principal components with an eigenvalue greater than one accounted for 88.2% variation. Furthermore, principal component analysis bolsters our results by clustering rice landraces into four clusters. The intra-cluster distance was most significant in cluster I (4.25) and the lowest in cluster IV (2.16), thereby indicating that genotype diversity was the greatest in cluster I and least diverse in cluster IV. Three of the four clusters did not follow geographic distribution, possibly indicating free exchange of landraces among the farmers and adaption of the landraces in both districts. Monomorphism was observed for leaf blade: lemma: anthocyanin in keel and lemma: anthocyanin of the area below apiculus, while high polymorphism was observed for lemma: the colour of apiculus (early observation) (1.542) according to Shannon-Weiner diversity index (H′). Even distribution was observed for traits ligule: colour (0.971), lemma: colour of apiculus: (late observation) (0.920), and sterile lemma: shape (0.908). The Simpson evenness index was maximum for lemma: colour of apiculus (0.783), indicating a higher probability of obtaining two characters for a trait under random selection. Thus, the present study is the preliminary depiction for characterization and diversity analysis in cultivated rice landraces with potential for further rice improvement programs. [ABSTRACT FROM AUTHOR]

Buckwheat is an important nutritional and nutraceutical crop; however, owing to its low yield and productivity, its potential has not been harnessed on account of its cultivation in low-input marginal farming systems, where its productivity is limited by various abiotic stresses, including water stress. Roots play a critical role in plant growth, development, and tolerance to drought stress. The present study was the first comprehensive attempt to understand the root system architecture (RSA) of buckwheat using root morphology and in-depth features of RSA through root scanning. A total of 117 diverse genotypes of buckwheat, comprising both common and Tartary buckwheat, were cultivated in polyvinyl chloride columns in the greenhouse. The study revealed substantial variability for all the root and shoot traits of buckwheat. Comparative analysis indicated that Tartary buckwheat has better root features compared to common buckwheat. The correlation analysis showed the surface area, medium root length, and medium root volume were positively correlated and branching frequency and root shoot ratio were negatively correlated. The study identified potential genotypes with robust RSA that can be used for the development of climate-resilient buckwheat varieties. [ABSTRACT FROM AUTHOR]

The study investigated early blight, a major fungal disease affecting tomatoes, across two distinct agroclimatic zones in India, resulting in a collection of 90 Alternaria isolates. Morpho-cultural characterization grouped these isolates into 11 putative clusters, which were subjected to further analysis. Pathogenicity tests revealed that all 11 isolates were pathogenic on the Pusa-Ruby tomato cultivar. Molecular analysis, specifically comparing nucleotide sequences of the ß-tubulin (ß-tub), cytochrome-B (cyt-B) and Alternaria major allergen gene (Alt a1) using the MycoCosm and NCBI databases, identified these isolates as Alternaria alternata. The phylogenetic tree, constructed via the Maximum-Likelihood method using the Alt a1 gene, demonstrated that all 11 isolates clustered with A. alternata, Sector—Alternaria, alongside reference strains from the NCBI database. Additionally, Alt a1 showed the capability to differentiate sub-groups within Sect.—Alternaria, indicating its intraspecific discriminatory potential. In conclusion, the study confirms the widespread presence of pathogenic A. alternata on tomatoes and highlights the importance of marker gene, Alt a1 in discerning the identity of Alternaria species. [ABSTRACT FROM AUTHOR]

This paper introduces a multi-objective variant of the Greylag Goose Optimizer (MOGGO) to tackle complex structural optimization problems. Inspired by the cooperative behavior of geese in flight, MOGGO employs dynamic grouping to enhance problem-solving efficiency. Six truss structures undergo simultaneous topology, shape, and size optimization using MOGGO, aiming to maximize reliability while minimizing structural mass. By incorporating non-dominance sorting and archiving techniques, MOGGO extends the single-objective Greylag Goose Optimizer to effectively address trade-offs between competing objectives. Evaluation metrics and statistical tests demonstrate MOGGO's superior performance in handling large structural optimization problems, preserving more Pareto-optimal sets, and achieving greater convergence and variance in objective and decision spaces. MOGGO’s ability to manage conflicting objectives is further validated through diversity analysis, with swarm plots illustrating its superior convergence behavior across iterations. Overall, MOGGO proves to be an efficient and effective approach for addressing challenging reliability-based multi-objective structural optimization problems. Query ID="Q1" Text="Please confirm if the author names are presented accurately and in the correct sequence (given name, middle name/initial, family name). Author 1 Given name: [specify authors given name] Last name [specify authors last name]. Also, kindly confirm the details in the metadata are correct." [ABSTRACT FROM AUTHOR]

A swarm intelligence-based optimization algorithm, named Duck Swarm Algorithm (DSA), is proposed in this study, which is inspired by the searching for food sources and foraging behaviors of the duck swarm. Two rules are modeled from the finding food and foraging of the duck, which corresponds to the exploration and exploitation phases of the proposed DSA, respectively. The performance of the DSA is verified by using multiple CEC benchmark functions, where its statistical (best, mean, standard deviation, and average running-time) results are compared with seven well-known algorithms like Particle swarm optimization (PSO), Firefly algorithm (FA), Chicken swarm optimization (CSO), Grey wolf optimizer (GWO), Sine cosine algorithm (SCA), and Marine-predators algorithm (MPA), and Archimedes optimization algorithm (AOA). Moreover, the Wilcoxon rank-sum test, Friedman test, and convergence curves of the comparison results are utilized to prove the superiority of the DSA against other algorithms. The results demonstrate that DSA is a high-performance optimization method in terms of convergence speed and exploration–exploitation balance for solving the numerical optimization problems. Also, DSA is applied for the optimal design of six engineering constrained optimization problems and the node optimization deployment task of the Wireless Sensor Network (WSN). Overall, the comparison results revealed that the DSA is a promising and very competitive algorithm for solving different optimization problems. [ABSTRACT FROM AUTHOR]

The spatial and temporal variations in the distribution, abundance, and assemblage structure of zooplankton were examined in the Chiffa Wadi River, north central Algeria. Samples were taken seasonally from autumn 2020 to summer 2022. Nine physical and chemical variables were recorded, and their relationship with the density of 39 zooplankton species was established using canonical correspondence analysis. In order to study the structure of the zooplankton, Shannon–Wiener diversity indices (H′), Margalef richness index (Dmg), Pielou evenness (E), and abundance were calculated. During the analysis, rotifera was the dominant group in the zooplankton community, represented by 27 taxa, followed by Cladocera (9 taxa) and Copepoda (3 taxa). The diversity index indicated the higher richness, abundance, and evenness of zooplankton at a eutrophic site (S2) compared with other sites. The canonical correspondence analysis (CCA) showed that the structure of zooplankton is influenced by local environmental factors. The present study demonstrates that anthropogenic activities including urban discharge and the construction of Algeria's Medea-Chiffa highway, which increased the nutrient load in the aquatic system, disrupted water quality. Consequently, the distribution and quantity of zooplankton were dramatically impacted by these changes in water quality. [ABSTRACT FROM AUTHOR]

Background: Fleas belonging to the Pulicidae are prevalent ectoparasites infesting mammals and birds in Iran. This study focused on genetically identifying and characterizing Ctenocephalides canis collected both off-host and infesting humans and various domestic animals in the country. Methods: A total of 918 adult flea samples were collected from 10 sites in western and northwestern Iran between April 2018 and May 2019. Out of these, 71 specimens were found off-host, while the remaining fleas were collected from humans (121), sheep (126), goats (184), and dogs (416). Morphological identification at the genus level was performed on all fleas, and ten selected specimens selected based on the sampling sites and hosts were subjected to molecular detection at the species level by using partial amplification and sequencing of the internal transcribed spacer 1 and 2, as well as the cytochrome oxidase I (COXI) markers. Results: The morphological identification confirmed all fleas as Ctenocephalides spp. Alignment and phylogenetic analysis of nuclear and mitochondrial partial sequences confirmed the presence of C. canis. However, molecular divergence was observed among the ten isolates based on the ITS1 and ITS2 with diversity rates estimated at 0.15% and 3.36%, respectively. Notably, the analysis of the COXI marker revealed no molecular divergence among the partial sequences representing the ten studied isolates from C. canis. Conclusions: This study explores the diversity of C. canis in the western and northwestern regions of Iran, providing insights into their molecular taxonomy and potential role as disease vectors in these areas. [ABSTRACT FROM AUTHOR]

The genus Bipolaris is found to be commonly associated with leaf spots, leaf blights, root rots, foot rots and other disease symptoms mainly in high value field crops in the family Poaceae. Spot blotch caused by Bipolaris sorokiniana (Sacc.) Shoemaker is one of the most important diseases of wheat and barley. The fungus causes germination failure, seed mortality and spot blotch development with small, dark brown lesions without chlorotic margin. Therefore, in the present study, attempts were made to investigate the morphological variations among different Bipolaris isolates collected from the different graminaceous hosts in north-western regions of India and to assess the genetic diversity of the fungus using SSR markers. The results revealed that all the 50 isolates exhibited various levels of morphological and cultural variations. Colony colour varied from dark ash to white with raised and irregular margins in most of the isolates. The size of the conidia varied from 31–75 µm × 15–27 µm, slightly curved, elliptical or oblong, mostly tapering towards ends, light to dark brown in colour, 3–12 distoseptate, having bipolar germination. The molecular identification of the pathogen associated with all the test isolates carried out using B. sorokiniana-specific primer pair, i.e. COSA_F/R, also cross-identified the pathogen to be B. sorokiniana by producing one sharp band (519 bp) in all the test isolates. All the ten SSR primers exhibited different levels of polymorphism among the different isolates. The PIC values revealing allelic diversity and frequency among all the isolates varied from 0.153 in the case of primer pair BS051 to 0.493 in primer pair BS065 and this variation in PIC values among the ten primer pairs indicated variability in amplified product and allelic frequency among the isolates. [ABSTRACT FROM AUTHOR]

The diversity, composition, and abundance of soil fungi from three sacred groves in Kerala, namely Iringole kavu of Ernakulam District, Kollakal Thapovanam of Alappuzha District, and Poyilkavu of Kozhikode District were analysed using Metagenomics analysis and Illumina sequencing. A total of 30,584, 78,323, and 55,640 reads were obtained from these groves, respectively. Ascomycota constitutes over 96% of the total fungi, making it the most abundant phylum, followed by Mortierellomycota, Basidiomycota, Chytridiomycota, and Rozellomycota. These phyla were subdivided into 20 classes, 40 orders, 83 families, 119 genera, and 135 species, while 1269 OTUs remained unidentified at the species level. Eurotiomycetes predominates the class, while the genus Talaromyces from the family Trichomaceae dominates the genera. Neocarmospora falciformis, Trichoderma lixii, and Candida ethanolic are the most abundant fungal species. Diversity analysis shows that Kollakal Thapovanam is rich in fungal species, while Poyilkavu is rich in biodiversity, with a high degree of dominance. Several species were found only in a particular grove and were absent in others and vice-versa, indicating high fungal specificity. Therefore, fungi have to be preserved in their original habitat. The Principal Coordinate Analysis revealed that each grove is distinct highlighting the importance of preserving the unique diversity of each sacred grove. In conclusion, this research provides valuable information about the soil fungal genera in their natural habitat. It emphasizes the need for more systematic research to understand the actual diversity and ecological role of fungi in sacred groves. This study is the first of its kind to analyse and compare soil fungal diversity in sacred groves using the metagenomics approach. [ABSTRACT FROM AUTHOR]

The present investigation assesses the bacterial microbiome and antibiotic resistance genes (ARGs) of the river Ganga from Uttarakhand (upstream region; US group) and Uttar Pradesh (downstream region; DS group) regions using a 16S rRNA amplicon-based metagenomic approach. Gram-negative, aerobic, and chemo-organotrophic bacteria made up the majority of the bacterial genera during the overall analysis. Physicochemical analysis revealed a higher concentration of nitrate and phosphate in the downstream sites of the Ganga River. The prevalence of Gemmatimonas, Flavobacterium, Arenimonas, and Verrucomicrobia in the water of the DS region indicates a high organic load. Pseudomonas and Flavobacterium emerged as the most prevalent genera among the 35 significantly different shared genera (p-value < 0.05) in the US and DS regions, respectively. Overall antibiotic resistance analysis of the samples showed the dominance of β-lactam resistance (33.92%) followed by CAMP (cationic antimicrobial peptide) resistance (27.75%), and multidrug resistance (19.17%), vancomycin resistance (17.84%), and tetracycline resistance (0.77%). While comparing, the DS group exhibited a higher abundance of ARGs over the US group, where the CAMP resistance and β-lactam ARGs were dominant in the respective regions. The correlation (p-value < 0.05) analysis showed that most bacteria exhibit a significant correlation with tetracycline resistance followed by the phenicol antibiotic. The present findings draw attention to the need for regulated disposal of multiform human-derived wastes into the Ganga River to reduce the irrepressible ARGs dissemination. [ABSTRACT FROM AUTHOR]

Chickpea (Cicer arietinum L.) is one of the major sources of dietary protein for the majority of populations in developing countries like India. It also increases soil fertility through its symbiotic nitrogen fixation in association with Mesorhizobium ciceri. In the present study, 40 M. ciceri isolates were recovered from root nodules and the rhizospheric soil of chickpea collected from different chickpea-producing areas of the mid-Gangetic Plains, Uttar Pradesh, India. The isolates were characterized on the basis of biochemical characteristics as well as 16S rDNA sequences. All the isolates were investigated for stress tolerance and plant growth-promoting (PGP) characteristics. M. ciceri isolates have shown wide diversity in their tolerance to high temperatures, salinity and extreme pH. Large numbers of these isolates showed an ability of mineral mobilization, i.e. phosphate (55%) and zinc (42%). Also M. ciceri isolates exhibited PGP characteristics such as production of siderophores (27.5%), ammonia (20%), hydrogen cyanide (10%) and indole acetic acid (5%). Furthermore, a high genetic diversity among the isolates was observed based on the enterobacterial repetitive intergenic consensus-PCR amplified band patterns. In conclusion, these stress-tolerant PGP isolates of M. ciceri may be very crucial for the chickpea production in sustainable agriculture. [ABSTRACT FROM AUTHOR]

Background: The narrow genetic diversity of chickpea is a serious impediment to modern cultivar creation. Seed storage proteins (SSPs) are stable and have minimal or no degradation when subjected to isolation and SDS-PAGE. Methods and results: We have characterized SSPs of 436 chickpea genotypes, belonging to nine annual Cicer species, originated from 47 countries by SDS-PAGE and determined the extent of genetic diversity in chickpea through clustering. Based on scoring, a total of 44 bands (10 to 170 kDa) were identified, which were all polymorphic. The least appeared protein bands were 11, 160 and 170 kDa where band of 11 and 160 kDa was present exclusively in wild type. Five bands were present in < 10% of genotypes. Bands appeared in 200–300 genotypes were suggested less polymorphic, on contrary bands present in 10–150 genotypes were suggested more polymorphic. Polymorphism of protein bands in context to their potential functions reported in literature were explored and suggested that the glubulins were most and glutelins were least abundant, whereas albumins with their known role in stress tolerance can be used as marker in chickpea breeding. Cluster analysis produced 14 clusters, interestingly three clusters contained only Pakistani genotypes and thus Pakistani genotypes appeared as a separate entity from the rest of the genotypes. Conclusion: Our results indicate that SDS-PAGE of SSPs is a powerful technique in determining the genetic diversity plus it is easily adaptable, due to its cost effectiveness in comparison to other genomics tools. [ABSTRACT FROM AUTHOR]

Purpose: The present study aimed to evaluate the effect of chia flour associated with a high fat diet on intestinal health in female ovariectomized Wistar rats. Methods: The study was conducted with 32 adult female ovariectomized Wistar rats, which were separated into four groups: standard diet (ST), standard diet with chia (STC), high fat diet (HF) and high fat diet with chia (HFC) for 18 weeks. Cecum content pH, short chain fatty acid content, brush border membrane functionality and morphology and the gut microbiota were evaluated. Results: This study demonstrated that the consumption of chia flour increased the production of acetic and butyric acids, the longitudinal and circular muscle layers and crypt thickness. It also improved the expression of aminopeptidase (AP) and sucrose-isomaltase (SI) and decreased the cecum content pH. Further, the consumption of chia improved richness and decreased diversity of the microbiota. Operational Taxonomic Units (OTUs) clustering indicated difference between the ST and STC groups. In the linear discriminant analysis effect size (LEfSe) analysis, the Bacteroides genus and members of the Muribaculaceae and Lachnospiraceae families were enriched in the STC treatment group. The STC group demonstrated the enrichment of Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways related to peptidoglycan and coenzyme A biosynthesis. Conclusion: Our results suggest that chia flour, which is rich in dietary fiber and phenolic compounds, presented potential properties to improve intestinal health. [ABSTRACT FROM AUTHOR]

Aim: The present study aimed to investigate the effect of dry heated whole sorghum BRS 305 hybrid flour on the gut microbiota modulation and gut health of rats fed with a high-fat high-fructose diet (HFHF). Methods: In phase I (8 weeks), 45–50 days, male Wistar rats, were separated into the AIN93-M group (n = 10; fed with normal diet) and HFHF group (n = 20; fed with diet rich in saturated and simple carbohydrate). In phase II (10 weeks), we maintained the AIN-93-M group, and the HFHF group was divided into the HFHF group (n = 10) and HFHF plus sorghum flour group (n = 10). Results: The consumption of sorghum flour increased the circular muscle layer and propionic acid when compared to the HFHF group. The sequencing of the 16S rRNA gene of the cecal microbiota presented no changes in the α-diversity and β-diversity between. However, the sorghum group exhibited higher relative abundance of Firmicutes and higher Firmicutes/Bacteroidetes ratio compared to the other experimental groups, and lower abundance of Bacteroidetes, compared to the HFHF group. Despite, sorghum increased the abundance of the genera Roseburia and Lachnospiraceae_NK4A136_group compared to the HFHF group. No differences were observed in total goblet cell number, crypt thickness and height, circular muscle layer, secretory IgA, and butyric acid between all groups. Conclusions: The consumption of sorghum flour can modulate the gut microbiota composition, abundance of SCFA-producing bacteria, and intestinal morphology even with consumption of an HFHF diet. [ABSTRACT FROM AUTHOR]

Crop wild relatives are genetically related wild taxa of crops with unique resources for crop improvement through the transfer of novel and profitable genes. The in situ and ex situ conservation gap analyses for priority crop wild relatives from West Africa were evaluated using species distribution modelling, ecogeographic diversity, and complementary analyses. A total of 20, 125 unique occurrence records were used for the conservation gap analysis, however, 26 taxa had no occurrence data. 64 taxa (62.7%) occurred in protected areas, 56 taxa (55%) were conserved ex situ, while 76.7% (43) of the accessions are underrepresented with less than 50 accessions conserved ex situ. Areas of highest potential diversity were found in the Woroba and Montangnes districts in Cote d'Ivoire, Nzerekore, Faranah, Kindia, and Boke regions of Guinea, South-South, and North-East zones of Nigeria, and Kono and Koinadugu districts in Sierra Leone. Hotspots were found in Atlantique, Littoral, Mono, Kouffo, Atakora, Donga, and Colline provinces of Benin, Accra, and Volta regions of Ghana, North–Central Nigeria, and Lacs district of Cote d'Ivoire and Nzerekore region of Guinea. 29 reserve sites for active in situ conservation were identified, 11 occur in protected areas, while 18 are located outside protected areas. The establishment of the reserve sites will complement existing PAs and ensure long-term active in situ and ex situ conservation and sustainable utilization of priority crop wild relative to underpin food security and mitigate climate change in the region. [ABSTRACT FROM AUTHOR]

Phylogenetic and evolutionary analyses were performed on the P1 and CP genes of global isolates to clarify the phylogrouping of leek yellow stripe virus (LYSV, genus Potyvirus), a pathogen affecting Allium spp. worldwide, into different types based on genetic variation and host species. The constructed phylogenetic trees divided the isolates into three major groups: S, L, and N. Low nucleotide (nt) and amino acid (aa) percent identities among the three groups were observed on full ORF (75.4–99.0 and 79.1–99.0), P1 (59.1–98.3 and 36.8–98.3), and CP (76.6–100 and 75.7–100) coding regions. The dN/dS values of P1 and CP confirmed that both genes are under strong negative (purifying) selection pressure. Neutrality tests on Eastern Asian isolates suggested that the ancestors of current LYSV isolates evolved with garlic while they were in Asia before spreading to other world regions through garlic propagative materials. Genetic differentiation and gene flow analysis showed extremely frequent gene flow from S group to L and N groups, and these phylogroups differentiated from each other over time. Host differences, inconsistent serological test results, substantial nt and aa variation, and phylogenetic and diversity analyses in this study supported previous reports that LYSV can be separated into three major evolutionary lineages: S, L, and N types. [ABSTRACT FROM AUTHOR]

Cluster bean [Cyamopsis tetragonoloba (L.) Taub.] is an important vegetable crop of industrial importance known as gaur, it is a self-pollinating and deep rooting crop, thus it is well adapted to semi-arid and arid rainfall areas. This legume crop is being grown for wider uses like human food, animal feed as well as fodder, and also for industrial uses for galactomannan gum extraction from a commercial perspective. In the crop genetic improvement is being limited, which could be due to insufficient diversity, or lack of exploitation of genetic resources. Therefore, we collected 70 gaur genotypes and were employed to estimate the genetic diversity along with four varieties using simple sequence repeat (SSR) markers. The PIC value ranged from 0.05 to 0.62, with an average of 0.38, while SSR marker amplification with 23 polymorphic primers detected 99 alleles with a mean of 4.30 alleles per SSR marker. Three separate groups emerged from the clustering analysis. Furthermore, twenty-four morphological traits were studied for the analysis of morphological diversity, and the genotypes and varieties were divided into eight subgroups based on standardized morphological data based on Mahalanobis D2 statistics. Cluster IV had the greatest intracluster distance (D2 = 7698.63), and clusters IV and VIII had the greatest intercluster distance (D2 = 195,694.80). Thus, the study revealed that collected genotypes contain a wide range of diversity, and the molecular markers can be utilized in conjunction with morphological characterization for a better description of the level and pattern of genetic diversity, as well as for the cluster bean breeding and improvement programs. [ABSTRACT FROM AUTHOR]

The passion fruit genus (Passiflora) is comprised of more than 600 species with several species admired for their tropical fruit and ornate flowers. Passiflora edulis Sims is the most important species and includes yellow or purple fruit types. Major threats to commercial production include both abiotic and biotic stresses, and recent advances in passion fruit genomics are facilitating systematic plant improvement. Marker-assisted breeding of passionfruit enables parental selection, confirmation of hybrid parentage, correction of mis-identified accessions, and resolution of species assignments. Therefore, the purpose of this study was to develop single nucleotide polymorphism (SNP) markers to characterize 59 accessions from 21 species that included native and naturalized Passiflora species found in Florida, USA. Over 2 million SNPs were identified and 26,191 were used for downstream analyses. Phylogenetic, STRUCTURE, and Principal Component Analyses separated species and identified mislabeled accessions. Passiflora edulis accessions including yellow and purple-fruited types were grouped by fruit type. Eight species found in Florida including P. biflora Lam., P. foetida L., P. incarnata L., P. lutea L., P. mulitiflora L., P. pallens Poepp. ex Mast., P. sexflora Juss., and P. pallida L. were well-separated from other species. Sequencing four naturally-pollinated P. laurifolia L. seedlings demonstrated that this accession is self-compatible. The results from this study could aid the genetic improvement of passion fruit in the future. [ABSTRACT FROM AUTHOR]

Limited and fragmented information is available about the effects of conservation agriculture, increasingly adopted by grain producers in sub-Saharan African countries, on nematode assemblages in maize-based cropping systems. Rhizosphere samples were obtained from three treatments, viz. conservation (CA) and conventional maize (CTA) fields, as well as from natural veld (NV) areas (serving as the reference) adjacent to maize fields in South African production areas. Forty-nine nematode genera (12 plant-parasitic and 37 non-parasitic/beneficial) were identified. Prominence values (PV) showed that Rotylenchulus and Meloidogyne (in descending order) dominated in 50 g roots of all three treatments, Pratylenchus in 5 g roots, and Rotylenchulus and Scutellonema in 200 g soils from CA and CTA maize, as opposed to Helicotylenchus and Rotylenchulus in soils from NV. Pratylenchus abundance in 5 g roots was significantly higher in CA and CTA maize compared to NV, with the Shannon diversity index values (H') also being the highest for species of this genus in CA, followed by CTA and NV. Rotylenchulus abundance/50 g roots was significantly higher in CA compared to both CTA and NV, while Meloidogyne abundance/50 g roots did not differ significantly among the three treatments. For soil nematodes, the H' was highest for NV, but not significantly compared to CA and CTA. Ninety-one percent of beneficial nematode genera and families were associated with NV soils, generally with higher PV and significant higher abundance (for bacterivores and predators) and diversity (for bacterivores, omnivores and predators) compared to CA and CTA. Nonetheless, most soils from the three treatments represented resource-depleted soil nematode communities indicating that soil health should be improved by using strategies such as cover cropping, incorporation of organic materials and inclusion of crop rotation sequences using cultivars with poor-host status or resistance to the dominating, target plant-parasitic nematode species to enable sustainable crop production. Associations of nematode assemblages, plant-parasitic and beneficial, with selected soil properties are also illustrated. [ABSTRACT FROM AUTHOR]

Genetic diversity analysis of 46 commercially prominent mandarins grown in different countries was carried out based on molecular and fruit traits. Out of 110 SSR markers, 64 polymorphic markers amplified a total of 155 alleles. Twenty SSR primers revealed 20 unique alleles which generated DNA fingerprints in 17 genotypes. The Polymorphism information content values ranged from 0.13 (CIBE 5156) to 0.73 (CCSM 40), with an average value of 0.45 across all genotypes. The diversity analysis illustrating the genetic relationships classified the genotypes into four major clusters. The 'Nagpur' and 'Mudkhed' mandarins in cluster I were closely related as these showed the highest genetic similarity having a similarity coefficient of 0.99. In fruit traits, higher heritability (h2) was observed in fruit weight while the higher genotypic coefficient of variation (GCV) was estimated for a number of seeds demonstrating the magnitude of genetic variability in a population. [ABSTRACT FROM AUTHOR]

Background: Biocontrol is an effective strategy in the integrated management of plant diseases, now more as a necessity than choice, in the present era of environmental and health awareness. Microbial diversity is a wonder by nature that inspires to explore and accordingly, the diversity analysis of the isolated microbes revealed their morphological and molecular differences. The DNA provides a common platform to store the microbial information in the form of databases in public domain that can be used by anyone from anywhere. Results: Exploration for native microbes in the present study resulted in isolation of different isolates of Trichoderma and Bacillus. The microbes were identified using morphological traits and molecular markers and the key conserved 18S and 16S gene sequences submitted with the appropriate repositories. Nucleotide analysis indicated a close phylogenetic relationship between BIK 2 and BIK 3 (Bacillus isolates) and within all the 5 Trichoderma isolates. The percent disease reduction of Rhizoctonia solani and Xanthomonas oryzae pv. oryzae (Xoo) was more in plants treated with consortia of the Trichoderma (61.13%) and Bacillus (53.59%) isolates, respectively. Screening of plant growth promotion activities, percentage increase in root (41.00%) and shoot length (44.77%) were found to be maximum in Trichoderma consortia treated plants. Conclusions: Three Bacillus and one Trichoderma strains, viz., B. velezensis, B. subtilis and B. paralicheniformis and Trichoderma asperellum, were identified and found to be effective against R. solani and Xoo pathogens of rice. In vitro and in vivo studies indicated that TAIK1 and BIK3 were found to be the most potential isolates among others isolated. Ability to improve plant growth was more pronounced by consortia of microbes. [ABSTRACT FROM AUTHOR]

Pests and diseases present major obstacles to poplar growth, which have been overcome via transgenic engineering applications. However, given the long growth cycle of transgenic poplars, long-term environmental safety assessments are needed for transgenic poplars planted in the field. Therefore, we investigated the effects of exogenous genes in transgenic poplar on the diversity of endophytic and rhizosphere soil bacterial communities in poplars. The composition and diversity of bacterial communities in trunk tissue, root tissue, and rhizosphere soil samples of transgenic Populus × euramericana cv. ‘74/76’ containing the high-resistance gene HPb1 (hereafter, HPb1) and non-transgenic Populus × euramericana cv. ‘74/76’ (hereafter, 107) in a 4-year-old experimental forest were analyzed using high-throughput sequencing. In terms of bacterial abundance at the phylum level, in trunk tissue, Bacteroidetes was the dominant phylum in both poplar lines (HPb1: 32.17%; 107: 47.42%). In root tissue, Proteobacteria was the dominant phylum in both lines (HPb1: 67.52%; 107: 65.96%). In rhizosphere soil, Proteobacteria was the dominant phylum in both lines (HPb1: 39.75%; 107: 37.98%). There were no significant differences in the richness and diversity of bacterial communities between HPb1 and 107. Finally, the bacterial community compositions in root tissue and rhizosphere soil were highly similar, both of which differed somewhat from that in trunk samples. This study provides a reference for ecological safety assessments of transgenic poplars and allows for a more systematic understanding of the potential ecosystem risk posed by environmental release of transgenic poplars. [ABSTRACT FROM AUTHOR]

Genotyping by sequencing (GBS) is a flexible and cost-effective strategy for genome-wide SNP discovery and high-throughput genotyping. Here, we employed the GBS approach to explore population structure, genetic variability, and patterns of linkage disequilibrium (LD) among 220 peach genotypes (Prunus persica), representative of the Brazilian breeding germplasm. This selected panel is mainly composed by locally adapted peaches developed in mild winter and high relative humidity conditions, and represents a worldwide reference of peach germplasm for low-chilling areas. A total of 93,353 SNP markers were discovered, and after filtering, 18,373 high-quality SNPs were used in analyses. Thirty-four percent of selected SNPs were located in genic regions and about 70% of these in the coding sequence. Principal coordinate analysis (PCoA) and Bayesian clustering (fastSTRUCTURE) successfully detected population genetic structure in our germplasm panel, supporting the identification of three main distinct subpopulations. The distribution of the genotypes within subpopulations reflected their fruit-related traits: melting and non-melting flesh cultivars. LD patterns revealed a medium LD level in peach, with the extent of LD highly dependent on the subpopulation and genome regions. The use of GBS-SNPs to perform genome-wide association studies (GWAS) was also exploited by using phenotypic information from five fruit quality traits. The observed significant SNP-trait associations were always in the regions previously predicted by linkage and association mapping analysis, providing valuable insights to incorporate the use of marker-assisted selection in the breeding program. [ABSTRACT FROM AUTHOR]

Purpose: The "Hoya del Rincón de Parangueo (HRP)" is a maar that contained a perennial alkaline lake that drained in the 1980s so that a sediment with high pH and extreme salinity remained. The aim of this work was to determine how the bacterial and archaeal community was controlled by these extreme conditions. Materials and methods: Sediment samples were collected from the 0–20-cm layer along a crater-wide transect. Physicochemical characteristics and the archaeal and bacterial community were determined by analysis of the 16S rRNA through Illumina sequencing. Results and discussion: The sediment samples had a pH 10 and an electrolytic conductivity (EC) that ranged from 29.8 to 74.4 dS m−1. Three archaeal and 37 bacterial phyla were detected with Euryarchaeota (relative abundance 62.7 ± 17.6%) dominating the Archaea, and Proteobacteria (28.2 ± 10.7%) and Actinobacteria (21.1 ± 6.4%) the Bacteria. The most abundant archaeal genus was Candidatus Nitrososphaera while Euzebya, Halomonas, KSA1 and Planctomycetes dominated the bacterial gene. Thaumarchaeota were enriched in sediment samples with a higher Pb content and Euryarchaeota in sediment with a higher Mg content, while Crenarchaeota and Candidatus Nitrososphaera were enriched in sediment with a higher sand, total N and organic C content. Proteobacteria were enriched in sediment with a higher organic C and total N, Si and sand content, while Bacteroidetes and Planctomycetes in sediment with a higher water holding capacity and clay and Mg content. Members of KSA1 and Euzebya were enriched in sediment with a lower EC, organic C and total N content. Although a large number of bacterial and archaeal groups were correlated significantly with a range of sediment characteristics, the sediment characteristics explained the variation of only two bacterial groups > 50% (TM6 and Desulfonatronospira) using the machine learning tool randomForest and none of the archaeal groups. Archaeal and bacterial functional guilds were dominated by ammonium oxidation and nitrite reduction. Conclusions: Although the different sediment samples were dominated often by similar bacterial and archaeal groups, the measured sediment characteristics explained little of the variation found between the sampling points. The high bacterial and archaeal diversity indicated that the site might be a source of unclassified species and phylotypes with specific metabolic capacities involved in the N and S cycles. [ABSTRACT FROM AUTHOR]

Alternaria black leaf spot disease of oilseed mustard is a primary cause of yield penalty not only in India but also throughout the world. To assess the degree of tolerance, 47 Indian mustard (Brassica juncea) genotypes were evaluated based on the performance against the causal pathogen Alternaria brassicicola. Genotypes were divided into six tolerance groups including resistant, highly tolerant, moderately tolerant, moderately susceptible, susceptible, and highly susceptible, keeping the nonhost resistant Sinapis alba as resistant control. Genotypes EC399312 and PAB-9511 were found to be the most tolerant. Fourteen morphological traits were evaluated which revealed considerable morphological variability among the genotypes. A number of seeds/siliqua and 1000 seed weight were positively correlated with yield per plant. Insignificant negative correlations had been found among plant height, days to maturity, and disease resistance with yield per plant. Correlation data indicate that seeds/siliqua and siliqua on the main shoot can be highly effective for higher grain yield. Genetic diversity of all genotypes was evaluated using simple sequence repeats (SSR) markers. The genotypes were evaluated for polymorphisms after amplification with 41 SSR primer pairs. Nineteen SSR markers in total were found to be highly informative with a polymorphic information content value > 0.50. The evaluation of genetic similarity and cluster analysis together with disease resistance provides some useful guides for assisting plant breeders in selecting suitable genetically diverse parents for the crossing program as well as for the development of mapping population. [ABSTRACT FROM AUTHOR]

Basing to the controversy on the function of the effective microorganisms (EM) microbial agent in manure aerobic composting, the differences of physical and biomass indexes of the experimental group (EP) (manure with EM inoculant) and the control group (CK) (manure without the EM inoculant) were studied and compared during composting. The results showed that the differences of physical indexes variation between the EP and the CK were similar during the process of composting. The number of operational taxonomic units (OTU) in the EP was lower than that in the CK at the beginning, while it was on the contrary in the end. The current study suggested that the presence of the EM microbial agent did not improve the number of OTU at the initial stage and early warming stage of aerobic composting. And, it intensified the competition with indigenous microorganisms in the piles. Furthermore, no obvious difference effects were observed between the EP and the CK. Considering the composting cost, the addition of the EM bacteria was unnecessary. [ABSTRACT FROM AUTHOR]

Breast cancer is a global health problem which mainly affects the female population. It is known that early detection increases the chances of effective treatment, improving the disease prognosis. It remains a challenge to detect the lesion with high detection rate and ensure, at the same time, low rates of false positives. Aiming this objective, this work proposes an efficient method for detection of mass regions on digitized mammograms though diversity analysis, geostatistical and concave geometry (Alpha Shapes). We evaluate the detection rate for each feature extraction using Support Vector Machine in MIAS and DDSM database, with 74 and 621 mammograms, respectively, all containing at least one mass region. The obtained results are promising, reaching 97.30% of detection rate and 0.89 false positive per image for MIAS database and also 91.63% of detection rate and 0.86 false positive per image for DDSM database. Specifically, in DDSM obtaining high detection rate and low rate of false positives when using concave geometry to extract features in a large database. [ABSTRACT FROM AUTHOR]

Common bean (Phaseolus vulgaris L.) is an important staple crop for smallholder farmers, particularly in Eastern and Southern Africa. To support common bean breeding and seed dissemination, a high throughput SNP genotyping platform with 1500 established SNP assays has been developed at a genotyping service provider which allows breeders without their own genotyping infrastructure to outsource such service. A set of 708 genotypes mainly composed of germplasm from African breeders and CIAT breeding program were assembled and genotyped with over 800 SNPs. Diversity analysis revealed that both Mesoamerican and Andean gene pools are in use, with an emphasis on large seeded Andean genotypes, which represents the known regional preferences. The analysis of genetic similarities among germplasm entries revealed duplicated lines with different names as well as distinct SNP patterns in identically named samples. Overall, a worrying number of inconsistencies was identified in this data set of very diverse origins. This exemplifies the necessity to develop and use a cost-effective fingerprinting platform to ensure germplasm purity for research, sharing and seed dissemination. The genetic data also allows to visualize introgressions, to identify heterozygous regions to evaluate hybridization success and to employ marker-assisted selection. This study presents a new resource for the common bean community, a SNP genotyping platform, a large SNP data set and a number of applications on how to utilize this information to improve the efficiency and quality of seed handling activities, breeding, and seed dissemination through molecular tools. [ABSTRACT FROM AUTHOR]

Identifying the best performing hybrid without a field test was essential to save resources and time. In this study, the genetic divergence was estimated using morphological and expressed sequence tag (EST)-derived simple sequence repeats (SSR) markers. Cluster analysis showed that APMS6A and RPHR 1005 belong to groups I and II, respectively, and the hybrid combination recorded the highest mean grain yield of 32.25 g among generated 40 F1s with standard heterosis of 8.4% over hybrid check, KRH2. The coefficient of marker polymorphism (CMP) value was calculated based on EST-SSR markers; it ranged from 0.40 to 0.80, and a higher CMP value of 0.80 was obtained for the parental combination APMS6A × RPHR1005. We predicted heterosis for 40 F1s based on correlation between CMP and standard heterosis in different traits with standard varietal and hybrid checks indicating positive correlation and significant value for grain yield per plant (r=0.58**), productivity per day (r=0.54**), productive tillers (r=0.34*) and panicle weight (r=0.42**). This study revealed that the relationship of molecular marker heterozygosity, along with the combining ability, high mean value of different traits, grouping of parental lines based on morphological and molecular characterization is helpful to identify heterotic patterns in rice. [ABSTRACT FROM AUTHOR]

The present commentary deals with the diversity of rotifers from three different habitats that include a river, lake and an irrigation canal from Manipur, India. Using the samples (n = 288) spanning over a 2-year period the species richness and the abundance of rotifers were assessed. A total of 34 species of rotifers from 11 families were observed with varying relative abundance, with the diversity indices (Shannon-Wiener, H’) ranging between 2.98 and 3.23. The species composition of the three habitats differed considerably, as evident from the multivariate analysis. In the lake habitat, the dominant species was Brachionus calyciflorus (7.9%), while in the irrigation canal the dominant species was Brachionus ruben (10.4%), and for the river habitat the dominant species was B. calyciflorus (11.5%). Using relative abundance of the rotifer species as explanatory variables, the ordination of the 34 species yielded significant differences based on the similarity in the abundance over the sampling period. On the basis of the overall differences in the species composition of rotifers, the three habitats could be segregated significantly (P < 0.05) based on the discriminant function analysis. Although the species composition of rotifers remained similar to other freshwater bodies of the this geographical region, the diversity and community analysis suggested considerable differences with reference to the three habitats, implying significance for limnological management. [ABSTRACT FROM AUTHOR]

A survey was undertaken to determine the mycoflora associated with stored wheat in four states across Australia including Western Australia, South Australia, Victoria and New South Wales. A total of 482 fungal isolates from 15 genera were isolated. The most common genera isolated were Alternaria spp., Aspergillus sp., Aureobasidium sp., Cladosporium spp., Drechslera sp., Fusarium spp., Mucor sp., Nigrospora sp., Penicillium sp., Rhizopus sp., Stemphylium sp., Eutiarosporella spp., Ulocladium sp., Epicoccum sp., and an undescribed genus from the Hypocreales. Diversity profiling also identified fungi that were not isolated using traditional methods including Paecilomyces spp., Dendryphiella and Cryptococcus. The results indicate that the mycoflora of stored wheat varies between Australian grain growing regions, and that diversity profiling analysis identifies different fungal contaminants compared to traditional methods. This study also revealed that some pathogens of high risk to humans (e.g. Cryptococcus) may occur with a high frequency in wheat. [ABSTRACT FROM AUTHOR]

This article uses a bundle of bibliometric and text-mining techniques to provide a systematic assessment of the intellectual core of the Social Media-based innovation research field. The goal of this study is to identify main research areas, understand the current state of development and suggest potential future directions by analysing co-citations from 155 papers published between 2003 and 2013 in the most influential academic journals. The main clusters have been identified, mapped, and labelled. Their most active areas on this topic and the most influential and co-cited papers have been identified and described. Also, intra- and inter-cluster knowledge base diversity has been assessed by using indicators stemming from the domains of Information Theory and Biology. A t test has been performed to assess the significance of the inter-cluster diversity. Five co-existing research streams shaping the research field under investigation have been identified and characterized. [ABSTRACT FROM AUTHOR]

Microbial systems are widely used to treat different types of wastewater from domestic, agricultural, and industrial sources. Community composition is an important factor in determining the successful performance of microbial treatment systems; however, a variety of uncultured and unknown lineages exist in sludge that requires identification and characterization. The present study examined the archaeal community composition in methanogenic, denitrifying, and nitrogen-/phosphate-removing wastewater treatment sludge by Archaea-specific 16S rRNA gene sequencing analysis using Illumina sequencing technology. Phylotypes belonging to Euryarchaeota, including methanogens, were most abundant in all samples except for nitrogen-/phosphate-removing wastewater treatment sludge. High levels of Deep Sea Hydrothermal Vent Group 6 (DHVEG-6), WSA2, Terrestrial Miscellaneous Euryarchaeotal Group, and Miscellaneous Crenarchaeotic Group were also detected. Interestingly, DHVEG-6 was dominant in nitrogen-/phosphate-removing wastewater treatment sludge, indicating that unclear lineages of Archaea still exist in the anaerobic wastewater treatment sludges. These results reveal a previously unknown diversity of Archaea in sludge that can potentially be exploited for the development of more efficient wastewater treatment strategies. [ABSTRACT FROM AUTHOR]

This article uses document co-citation analysis to objectively explore the underlying structure of the intellectual property research domain, taken from a managerial and strategic standpoint. The goal of this study is identifying its main research areas, understanding its current state of development and suggesting potential future directions, by analyzing the co-citations from 181 papers published between 1992 and 2011 in the most influential academic journals. Five main clusters have been identified, mapped, and labeled as follows: Economics of patent system, technological and institutional capabilities, university patenting, intellectual property exploitation, and division of labor. Their most active areas on this topic, and the most influential and co-cited papers have been identified and described. Also, intra- and inter-cluster knowledge base diversity has been assessed by using indicators stemming from the domains of information theory and biology. A t test has been performed to assess the significance of the inter-cluster diversity. The knowledge bases of these five clusters are significantly diverse, this meaning that they are five co-existing paradigms. [ABSTRACT FROM AUTHOR]

Tomato ( Solanum lycopersicum L.) is the second most highly consumed vegetable in the world after potato. Traits including physicochemical (lycopene, total titratable acid (TTA), total soluble solids (TSS) and vitamin C), morphological (fruit shape and size) and colors contribute to the overall fruit quality of tomato. The primary objective of the present study was to evaluate vintage tomato varieties representing a wide genetic background for fruit quality including physicochemical, morphological and color traits in multiple environments and to analyze consistency of their performances across locations. In order to achieve this objective, we acquired 44 vintage tomato varieties and evaluated them in five environments (NC, NY, OH in 2009, and NC and OH in 2010). Analysis of the data revealed that there was a significant ( p < 0.01) difference among genotypes and environments for all quality traits, Genotype × Environment interaction was significant ( p < 0.01) for all quality traits except for TSS. Broad-sense heritability of physicochemical traits ranged from 5.8 % (lycopene) to 35.7 % (TTA) whereas that for morphological traits ranged from 8.1 % (proximal eccentricity) to 97.3 % (fruit shape index external 1), and color from 69.0 % (a*-value) to 99.3 % (b*-value). Pearson's correlation analysis indicated that estimated lycopene content was negatively correlated with the other physicochemical traits whereas vitamin C, TSS and TTA were positively correlated with each other. Principal component analysis (PCA) based on phenotypic data identified five components explaining at least 82 % of the total variation. Cluster analysis based on phenotypic data revealed the clusters of vintage tomato varieties were not distinct whereas single nucleotide polymorphism data revealed three distinct populations. This information including heritability and correlation coefficients from the present study may be useful to tomato breeding programs to choose germplasm, improve the response to selection and simultaneously improve multiple traits for tomato fruit quality. [ABSTRACT FROM AUTHOR]

Genetic diversity and identification of simple sequence repeat markers correlated with Fusarium wilt resistance was performed in a set of 36 elite cultivated pigeonpea genotypes differing in levels of resistance to Fusarium wilt. Twenty-four polymorphic sequence repeat markers were screened across these genotypes, and amplified a total of 59 alleles with an average high polymorphic information content value of 0.52. Cluster analysis, done by UPGMA and PCA, grouped the 36 pigeonpea genotypes into two main clusters according to their Fusarium wilt reaction. Based on the Kruskal-Wallis ANOVA and simple regression analysis, six simple sequence repeat markers were found to be significantly associated with Fusarium wilt resistance. The phenotypic variation explained by these markers ranged from 23.7 to 56.4%. The present study helps in finding out feasibility of prescreened SSR markers to be used in genetic diversity analysis and their potential association with disease resistance. [ABSTRACT FROM AUTHOR]

In 4G broadband wireless communications, multiple transmit and receive antennas are used to form multiple input multiple output (MIMO) channels to increase the capacity (by a factor of the minimum number of transmit and receive antennas) and data rate. In this paper, the combination of MIMO technology and orthogonal frequency division multiplexing (OFDM) systems is analyzed for wideband transmission which mitigates the intersymbol interference and hence enhances system capacity. In MIMO-OFDM systems, the coding is done over space, time, and frequency domains to provide reliable and robust transmission in harsh wireless environment. Also, the performance of space time frequency (STF) coded MIMO-OFDM is analyzed with space time and space frequency coding as special cases. The maximum achievable diversity of STF coded MIMO-OFDM is analyzed and bit error rate performance improvement is verified by simulation results. Simulations are carried out in harsh wireless environment, whose effect is mitigated by using higher tap order channels. The complexity is resolved by employing sphere decoder at the receiver. [ABSTRACT FROM AUTHOR]

To find out the genetic diversity of Indian Foc isolates of banana, a total of 107 isolates of Fusarium which includes 98 Foc isolates obtained from different banana growing regions of India and seven Foc isolates belong to all known VCGs obtained from Australia and two non-pathogenic Fusarium oxysporum (np Fo) isolates were subjected to ISSR analysis. In the initial screening of ISSR primers, out of 34, 10 primers which generated more polymorphic bands were selected for further analysis. The Phylogenetic analysis carried out based on the fingerprints obtained through ISSR analysis indicated the presence of wide genetic diversity among the Foc isolates of India and also its polyphyletic nature. Totally, seven different clusters were obtained and these clusters differentiated the Foc isolates of India based on the races/VCGs. Besides, the cluster analysis clearly distinguished the freshly emerged Foc strain obtained from cv. Grand Naine (Cavendish-AAA) and Poovan (Mysore-AAB) from the other Foc isolates. The non-pathogenic F. oxysporum isolates which have been included for comparison purpose also clustered separately. All these above said findings indicates for the first time the discriminatory power of ISSR to clearly distinguish and separate the Foc isolates according to its race/VCGs and also its virulence. This study would be useful not only to design and develop effective management strategies but also useful for quarantine purposes. [ABSTRACT FROM AUTHOR]

Jatropha curcas L. (Euphorbiaceae) has acquired a great importance as a renewable source of energy with a number of environmental benefits. Very few attempts were made to understand the extent of genetic diversity of J. curcas germplasm. In the present study, efforts were made to analyze the genetic diversity among the elite germplasms of J. curcas, selected on the basis of their performance in field using random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP) and simple sequence repeats (SSR). The plants were selected on the basis of height, canopy circumference, number of seeds per fruit, weight of 100 seeds, seed yield in grams per plant and oil content. Out of 250 RAPD (with 26 primers), 822 AFLP (with 17 primers) and 19 SSR band classes, 141, 346 and 7 were found to be polymorphic, respectively. The percentage polymorphism among the selected germplasms using RAPD, AFLP and SSR was found to be 56.43, 57.9, and 36.84, respectively. The Jaccard's similarity coefficient was found 0.91, 0.90 and 0.91 through RAPD, AFLP and SSR marker systems, respectively. Principle component analysis (PCA) and dendrogarm analysis of genetic relationship among the germplasm using RAPD, AFLP and SSR data showed a good correlation for individual markers. The germplasm JCC-11, 12, 13, 14 and 15 whose yield found to be high were clustered together in dendrogram and PCA analysis though JCC11 is geographically distinct from others. In overall analysis JCC6 (in RAPD), JCC8 (in AFLP) and JCC 6 and JCC10 (in SSR) were found genetically diverse. Characterization of geographically distinct and genetically diverse germplasms with varied yield characters is an important step in marker assisted selection (MAS) and it can be useful for breeding programs and QTL mapping. [ABSTRACT FROM AUTHOR]

Current methods for molecular fingerprinting of cassava ( Manihot esculenta Crantz) have limited throughput or are costly, thus preventing the characterization of large germplasm collections such as those held by the International Agricultural Research Centers or National Research Institutions, which comprise hundreds to thousands of accessions. Here, we report the development of a fluorescence-based multiplex simple sequence repeat (SSR) marker kit that enables accurate and cost-effective cassava fingerprinting. The kit comprises 16 SSR markers assembled into five multiplex panels and was tested on 21 cassava cultivars alongside one accession of Manihot epruinosa, a wild relative. A total of 68 alleles were detected with, on average, 4.25 alleles per locus and a polymorphism information content of 0.53. The marker kit reported here is comparable to previously published amplified fragment length polymorphism and SSR marker systems in terms of discriminating power and informativeness while offering significant advantages in speed and cost of marker analysis. Previous molecular genetic diversity studies have suggested that cassava germplasm collections contain duplicate entries based on the occurrence of identical genetic profiles. Using the newly developed microsatellite kit, three out of six putative duplicate accessions could be readily differentiated, showing that these are distinct genotypes. The relevance of these findings with respect to the characterization and management of large cassava germplasm collections is discussed. [ABSTRACT FROM AUTHOR]

total of 24 candidate plus trees (CPTs) of Pongamia pinnata (L.) Pierre. were selected to elucidate their variation and diversity based on thirteen quantitative traits (4 pod traits, 6 seed traits of parent trees and 3 progeny traits) at Forest Research Centre, Institute of Forest Productivity - Mandar, Ranchi district during 2005-2007. The results show that, CPT-19 had maximum for seven traits viz, pod length (65.6 mm), 100-pod weight (542.4 g), seed 2D (two dimension) area (351.2 mm), seed length (27.9 mm), seed breadth (17.4 mm), 100-seed weight (217.9 g) and plant height (164.3 cm). The traits, 100-pod weight and 100-seed weight had a high heritability (98.4%, 96.9%) accompanied with high genetic advance (46.0%, 34.9%). There is a positive significant correlation between 100-pod weight and 100-seed weight traits at both genotypic and phenotypic levels with plant height, collar diameter and volume index at 30 MAS (months after sowing). Volume index expressed a moderate heritability (47.4%) accompanied with high genetic advance (48.4%), indicating that the character is governed by additive gene effects. In divergence study, 24 accessions were grouped into 6 clusters on the basis of non-hierarchical euclidian cluster analysis. The genotypes in cluster IV (CPT-5, CPT-6, CPT-7, CPT-12, CPT-16, CPT-18, CPT-22) and cluster III (CPT-4, CPT-8, CPT-9, CPT-20, CPT-21) were most heterogeneous and can be best used within group hybridization. The wide diversity exists between the cluster V and II, followed by cluster II and I and crosses between CPTs of these clusters may result in substantial segregates. It is revealed that the existence of substantial variation and diversity can be utilized for genetic resource conservation and further tree improvement programmers of the species. [ABSTRACT FROM AUTHOR]

Cultivated groundnut ( Arachis hypogaea L.) is an agronomically and economically important oilseed crop grown extensively throughout the semi-arid tropics of Asia, Africa and Latin America. Rust ( Puccinia arachidis) and late leaf spot (LLS, Phaseoisariopsis personata) are among the major diseases causing significant yield loss in groundnut. The development of varieties with high levels of resistance has been constrained by adaptation of disease isolates to resistance sources and incomplete resistance in resistant sources. Despite the wide range of morphological diversity observed in the cultivated groundnut gene pool, molecular marker analyses have thus far been unable to detect a parallel level of genetic diversity. However, the recent development of simple sequence repeat (SSR) markers presents new opportunities for molecular diversity analysis of cultivate groundnut. The current study was conducted to identify diverse disease resistant germplasm for the development of mapping populations and for their introduction into breeding programs. Twenty-three SSRs were screened across 22 groundnut genotypes with differing levels of resistance to rust and LLS. Overall, 135 alleles across 23 loci were observed in the 22 genotypes screened. Twelve of the 23 SSRs (52%) showed a high level of polymorphism, with PIC values ≥0.5. This is the first report detecting such high levels of genetic polymorphism in cultivated groundnut. Multi-dimensional scaling and cluster analyses revealed three well-separated groups of genotypes. Locus by locus AMOVA and Kruskal–Wallis one-way ANOVA identified candidate SSR loci that may be valuable for mapping rust and LLS resistance. The molecular diversity analysis presented here provides valuable information for groundnut breeders designing strategies for incorporating and pyramiding rust and late leaf spot resistances and for molecular biologists wishing to create recombinant inbred line populations to map these traits. [ABSTRACT FROM AUTHOR]

A software tool was developed for the identification of simple sequence repeats (SSRs) in a barley (Hordeum vulgare L.) EST (expressed sequence tag) database comprising 24,595 sequences. In total, 1,856 SSR-containing sequences were identified. Trimeric SSR repeat motifs appeared to be the most abundant type. A subset of 311 primer pairs flanking SSR loci have been used for screening polymorphisms among six barley cultivars, being parents of three mapping populations. As a result, 76 EST-derived SSR-markers were integrated into a barley genetic consensus map. A correlation between polymorphism and the number of repeats was observed for SSRs built of dimeric up to tetrameric units. 3′-ESTs yielded a higher portion of polymorphic SSRs (64%) than 5′-ESTs did. The estimated PIC (polymorphic information content) value was 0.45 ± 0.03. Approximately 80% of the SSR-markers amplified DNA fragments in Hordeum bulbosum, followed by rye, wheat (both about 60%) and rice (40%). A subset of 38 EST-derived SSR-markers comprising 114 alleles were used to investigate genetic diversity among 54 barley cultivars. In accordance with a previous, RFLP-based, study, spring and winter cultivars, as well as two- and six-rowed barleys, formed separate clades upon PCoA analysis. The results show that: (1) with the software tool developed, EST databases can be efficiently exploited for the development of cDNA-SSRs, (2) EST-derived SSRs are significantly less polymorphic than those derived from genomic regions, (3) a considerable portion of the developed SSRs can be transferred to related species, and (4) compared to RFLP-markers, cDNA-SSRs yield similar patterns of genetic diversity. [ABSTRACT FROM AUTHOR]

Plants were regenerated by shoot multiplication from four clones of Melia azedarach L. during 12 mo. of subculturing. One hundred and one of these plants were examined by randomly amplified polymorphic DNA analysis. All regenerated plants showed at least one polymorphism. However, no chromosome number alterations were observed. The pattern of variation obtained by principal coordinated analysis showed a random distribution of variation among regenerated plants and their controls, indicating that genetic alterations were not cumulative during in vitro culture. Similar results were found using Shannon's index, which revealed that 50% of the observed diversity resided among plants coming from the same subculture generation. This high intraclonal variation does not provide a clear scenario for predicting the amount of culture time required to preserve genetic fidelity in commercially micropropagated M. azedarach plants. Our work suggests that other mechanisms, such as chimerism, contribute to intraclonal heterogeneity in vitro. [ABSTRACT FROM AUTHOR]

Greengram [ Vigna radiata (L.) Wilczek], also known as mung bean, widely cultivated in a large number of countries, is an important pulse crop of Asia and is considered one of the ancestral species of the genus Vigna. Since yields of greengram have remained low across subtropical and tropical Asia, it is important to estimate genetic diversity in existing cultivars in order to see if the lack of genetic variability might be a constraining factor. In this study, 32 Indian cultivars of greengram were subjected to random amplified polymorphic DNA (RAPD) analysis using 21 decamer primers. A total of 267 amplification products were formed at an average of 12.71 per primer with an overall polymorphism of 64%. The extent of polymorphism was moderate to low. Jaccard similarity coefficient values ranged from 0.65 to 0.92. The cluster analysis resulted in mainly three clusters revealing greater homology between cultivars released from the same source. The results of principal components analysis also substantiated this conclusion. The close genetic similarity between the cultivars could be explained due to the high degree of commonness in their pedigrees. The narrow genetic base of the greengram cultivars revealed in the present analysis emphasises the need to exploit the large germplasm collections having diverse morphoagronomic traits in cultivar improvement programs. [ABSTRACT FROM AUTHOR]

A combinatorial approach towards identifying inhibitors of VALA-4 was investigated. A library of piperazine-peptoid-bisarylureas was assembled in solid phase and screening in the novel v-well assay enabled the identificationof active compounds [ABSTRACT FROM AUTHOR]

A collection (5,072 lines) of wheat germplasm was screened at the seedling stage for tolerance to salinity concentrations having electrical conductivities of 0.8 (control), 12.5, 18.75 and 25.0 dS/m. Surviving seedlings were expressed for each line as a percentage of the control value. The 442 lines with greater than 70% surviving seedlings were tested for whole-life cycle survival under each salinity condition. The data of the reactions to salinity at both the seedling stage and maturity were used to classify the collection according to: (1) country of origin (2) species and ploidy level. The data were then subjected to a diversity analysis using the Shannon-Weaver information index. Seedling stage tolerance to 12.5 dS/cm salinity was widely distributed in the collection (79% of lines), whereas only 9% were tolerant at 25.0 dS/m salinity. The seedling stage tolerance was indicative of maturity tolerance. At the seedling stage, entries from USA and Egypt showed the largest proportions of tolerant lines. In addition, USA, Mexico and Egypt entries exhibited the widest variability. Diversity among regions was greater than among countries within regions, while the diversity among species was greater than among ploidy levels. Tetraploids exceeded hexaploids and diploids in the proportion of tolerant lines and diversity. Wheat-rye derivatives showed a good potential for salt tolerance at early stages. Screening more germplasm from the arid and semi-arid regions especially from countries with salt affected soils was recommended. [ABSTRACT FROM AUTHOR]

A Lead Discovery Library ofpiperazine-2-carboxamide derivatives was produced forgeneral screening. This paper discloses two novelsolid phase synthetic routes used to produce 15 000single compounds via the Irori directed sortingtechnique. Computational methods such as reagentclustering and library profiling were used to maximizereagent diversity and optimize pharmacokineticparameters. The results of a four center pharmacophoreanalysis revealed the added diversity gained by usingtwo independent synthetic routes. [ABSTRACT FROM AUTHOR]