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The study characterized 34 Job's tears accessions from the northeastern Himalayan region using yield-related traits and simple sequence repeats (SSR) markers. Genotyping with 17 SSR markers revealed an average of 3.18 alleles per locus, varying from 2 to 4. Polymorphism information content values ranged from 0.27 to 0.52, averaging 0.41. Clustering and principal coordinate analysis (PCoA) based on SSR markers grouped the accessions into three major groups. The first three principal coordinates in the PCoA cumulatively explained 41.96% of the variability in the accessions, with the first and second principal coordinates explaining 22.51% and 10.39% of the molecular variability, respectively. The model-based genetic structure analysis detected the maximal ΔK (80.87) at K = 2, grouping the entire accessions into two subgroups. The analysis of molecular variance (AMOVA) indicated higher genetic variation within individuals (52.86%) than among individuals (47.14%). The FST value (0.2), STRUCTURE analysis, and PCoA analysis indicated moderate population differentiation. Yield-trait-based analysis resulted in four clusters. Cluster I included six accessions with short height, cluster II comprised 12 accessions with high test weight, cluster III comprised six accessions with high yield, and cluster IV had nine accessions with early flowering, respectively. Principal component analysis (PCA) extracted three components explaining 67.4% of the total variation, with PC1 emphasizing yield and growth-related traits and PC2 highlighting days to flowering and panicle length. Most traits showed positive correlations with yield per plant, especially test weight (0.65, P ≤ 0.01). Path coefficient analysis revealed a strong positive direct effect of test weight and the number of internodes per plant on yield per plant. Cluster analysis and genotype-by-trait biplot analysis showed similar patterns among accessions. However, the Mantel test indicated no significant correlation between genetic and morphological distances (r2 = 0.010, P = 0.41). Additive main-effects and multiplicative interaction (AMMI) analysis and multi-trait stability index (MTSI) identified three promising accessions (IC600638, IC540181, and IC540256) suitable for selection in future breeding programs with 10% intensity. [ABSTRACT FROM AUTHOR]

The 1:100,000-scale Porang sheet in South Khorasan province is prone to skarn, massive sulfide, and sedimentary mineralization due to the presence of intermediate to ultrabasic volcanic and plutonic rocks and the variety of sedimentary rocks. This paper introduces the Principal Coordinate Analysis (PCoA) method. The PCoA method, along with the Principal Component Analysis (PCA) and Correspondence Analysis (CA) methods, has been used to identify the possible type of mineralization in the study area. Geological and mineralogical data and the analysis results of 25 elements from 314 stream sediment samples, taken from the study area, have been used for this purpose. The results of the data analysis show that the D1 coordinate, PC1 score, and location in the first cluster maps of the samples are most likely related to the mineralization in ultrabasic, basic, and listivinite rocks. After that, the D2 and D3 dimension maps, the PC2 and PC5 score maps, and the sample location map in the fifth cluster related to sedimentary rocks attribute the most probability to sedimentary mineralization, especially of Mn and Fe mineralization types, in the study area. Finally, there is the possibility of skarn and massive sulfide mineralization, whose locations can be predicted by the D4 dimension maps, the PC3 score map, and the sample location maps in second, third, and fourth clusters. Also, the comparison of data analysis results with two multivariate statistical methods shows that by choosing the number of dimensionality reductions, the principal components method can cover more variability than the principal dimensions method. While connecting the principal coordinate maps to the mineralization is easier and more reliable than the principal component score maps. Therefore, the proposal of this paper is the simultaneous use of PCoA and PCA methods to analyze geochemical data in an exploration region. [ABSTRACT FROM AUTHOR]

Introduction: Iran, a country in the Middle East, has several ethnic and ethno‐religious groups and needs its own ethnic‐specific databases for the forensic statistical parameters and allele frequency of STR markers. Methods: We have investigated 600 unrelated Turk individuals from four northwestern provinces of Iran using the Identifiler™ system (TPOX, FGA, vWA, TH01, CSF1PO, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, and D21S11). Furthermore, STR allelic frequencies were compared to previously population‐based data. Results and conclusion: After Bonferroni correction, deviation from Hardy‐Weinberg equilibrium (HWE) was observed in the FGA, TPOX, VWA, and D19S433 loci (P value < 0.05). The combined power of discrimination (CPD) and exclusion (CPE) values for all 15 STR loci were 0.9999999999999999999984 and 0.9999999, respectively. In comparison with Azerbaijani and Turkish populations, there were no significant differences on all STR markers. However, in the Chinese Han population, differences at 13 STR loci were detected. Additionally, comparisons of Fischer genetic distance indices (FST) P‐values did not reveal any statistically significant difference between Northwestern Iran, Azerbaijan and Iran (Fars) populations. PCA and PCoA analyses showed that our population was grouped with different populations in different quarters, showing a positive and negative correlation, respectively. In the NJ and UPGMA phylogenetic trees, Iranian populations were grouped together. These results demonstrated that the given set of STR markers can be confidently used for all identification tests in Northwestern Iran. [ABSTRACT FROM AUTHOR]

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An in-depth understanding of the extent and pattern of genetic diversity and population structure in crop populations is of paramount importance for any crop improvement program to efficiently promote the translation of genetic diversity into genetic gain. A reference collection of 150 common bean genotypes selected from the International Center for Tropical Agriculture's global core collection was evaluated using single-nucleotide polymorphism (SNP) markers to quantify the amount of genetic diversity, linkage disequilibrium, and population structure. The cultivars and landraces of the collection were diverse and originated from 14 countries, and wild accessions were used as controls for each gene pool. The collection was genotyped using an SNP array, generating a total of 5398 locus calls distributed across the entire bean genome. The SNP data quality was checked, and two datasets were generated. The first dataset (Dataset_1) comprised a set of 5108 SNPs and 150 genotypes after filtering for 10% missing alleles and an MAF < 0.05. The second dataset (Dataset_2) comprised a set of 2300 SNPs that remained after removing any null-allele SNPs and LD pruning for a criterion of r2 < 0.2. Dataset_1 was used for a principal coordinate analysis (PCoA), phylogenetic relationship determination, an analysis of molecular variance (AMOVA), and a discriminant analysis of principal components. Dataset_2 was used for a population structure analysis using STRUCTURE software and is proposed for a genome-wide association study (GWAS). The population structure analysis split the reference collection into two subpopulations according to an Andean or Mesoamerican gene pool. The Mesoamerican populations displayed higher genetic differentiation and tended to split into more groups that were somewhat aligned with common bean races. Andean beans were characterized by a larger average LD but lower LD percentage, a small average genetic distance between members of the population, and a higher major allele frequency, which suggested narrower genetic diversity compared to the Mesoamerican gene pool. In conclusion, the results indicated the presence of high genetic diversity, which is useful for a GWAS. However, the presence of significant linkage disequilibrium requires that genetic distance be considered as a co-factor for any further genetic studies. Overall, the molecular variation observed in the genotypes shows that this reference collection is valuable as a genebank-derived diversity panel which is useful for marker trait association studies. [ABSTRACT FROM AUTHOR]

The nutritional and medicinal significance of jujube (Ziziphus jujuba) has led to persistent efforts in genomics to accelerate the utilization of its germplasm resources. However, the absence of accurate genetic identity of existing germplasm limits these studies. In the United States, different names were frequently given to the same jujube cultivars because the pedigrees of the imported germplasm are unclear. The present study selected a panel of 147 single nucleotide polymorphism (SNP) markers distributed across the jujube genome to examine genetic identity, genetic diversity, and population structure in 177 jujube cultivars sampled from different locations in the United States. SNP profile multilocus matching reported a total of 23 synonymous groups including 116 samples that were identical to at least one other sample. This led to the detection of 74 unique genotypes for subsequent diversity analysis. Model-based genetic structure analysis divided the distinctive genotypes into three major groups, with some admixtures among the groups. The genetic differentiation among these groups was further validated by analysis of molecular variance (Fst = 0.199, P value < 0.001), principal coordinate analysis, and clustering analysis. Morphological traits were studied in some of the genetically identical commercial cultivar groups, (i.e., Li, Lang, and Jinsi). Results demonstrated significant morphological differences within genetically identical cultivars in the Jinsi group, indicating phenotypic variation resulting from mutations in these clones.

Simple Summary: Whole-genome sequencing (WGS)-based mungbean SSR markers have a high rate of cross-species transferability and are very useful in mungbean improvement programs. The genus Vigna is pan-tropical, having more than 200 species with many desirable economically important traits. This study aimed to validate the in silico polymorphism of whole-genome-sequence-developed mungbean-specific SSR markers and their transferability among different Vigna species. The present study utilized a set of 200 SSR markers developed from the whole-genome sequence of mungbean and validated them using a diversity panel of 25 accessions that belong to 13 Vigna species. Out of 200 SSR markers, 130 markers (65%) were polymorphic across the various Vigna species, and the number of alleles amplified varied from 7 to 24. The SSR markers showed more than 90 percent transferability across the different Vigna species accessions. Utilizing allelic data, the 25 Vigna accessions were clustered into three groups using the unweighted pair group method with arithmetic mean (UPGMA). The two integral coalitions explained 50.79 and 15.42% of the total variance. The principal coordinate analysis (PCA) biplot graph and UPGMA-based neighbor-joining clustering diagram showed a similar pattern of Vigna accession distribution. A population structure assessment grouped the cultivated and wild species accessions into two sub-populations based upon a maximum delta K value of 144.79, which drew a sharp peak at K = 2. The estimated marker parameters, such as the polymorphic information content (0.09–0.84), marker index (0.091–3.342), and effective multiplex ratio (1.0–4.0), suggested their adequacy for several genetic studies, such as parental selection, hybrid testing, genetic mapping, and marker-aided breeding programs, for the genetic enhancement of species belonging to the Vigna genus. [ABSTRACT FROM AUTHOR]

The notion of style has been the subject of much research and theoretical development in prehistoric archaeology. This vast concept touches several fields, including the morphology of artefacts, technical gestures and their function. The lithic typology of arrowhead armatures was widely developed in the twentieth century for the study of the French Mesolithic and includes some of these aspects. The functional, technical, or aesthetic nature of the morphological characteristics of these artefacts has received little attention, while the mapping of types has been overvalued This article presents a new approach combining statistical analysis with the use-wear analysis of arrowhead from several Breton sites, dated to the Late Mesolithic.

Flying pigeons (Columbia livia) are extensively studied for their physical endurance and superior sense of orientation. The extreme physical endurance of which these birds are capable creates a unique opportunity to investigate the possible impact of long-distance flying on the taxonomy and metabolic function of the gut microbiota. This project was enabled by access to two groups of pigeons raised by the same breeder in the same conditions, except that one group was trained in long-distance flying and participated in multiple races covering a total distance of over 2600 km over a 9-week period. In contrast, the second group did not fly. The fecal microbiota was analyzed using 16S amplicon sequencing, and the taxonomy and metabolic function were inferred from this sequence data. Based on phylogenetic distance and metabolic function, flying and non-flying pigeons were found to harbor distinct bacterial microbiota. The microbiota taxonomy varied extensively between the birds, whereas the inferred metabolic potential was relatively stable. Age was not a significant determinant of the fecal microbiota profile. In flying birds, the metabolic pathways annotated with biosynthesis were enriched, representing 60% of the 20 metabolic pathways that were most closely associated with flying. [ABSTRACT FROM AUTHOR]

IntroductionThe aim of this study was to investigate the effects of adding whole-plant ensiled corn stalks (WECS) to the diet of Holdorbagy geese on their growth performance, serum parameters, and cecal microbiota. Geese farming is an important agricultural practice, and optimizing their diet can contribute to better growth and health outcomes. However, there is limited research on the utilization of WECS as a feed source for geese. Understanding the potential effects of WECS on growth, blood parameters, and cecal microbiota can provide valuable insights into its feasibility and impact on geese farming practices.MethodsA total of 144 six-week-old Holdorbagy geese were randomly assigned to one of three groups: a control group (0% WECS), a group fed 15% WECS and 85% concentrated feed (15% WECS), and a group fed 30% WECS and 70% concentrated feed (30% WECS). The trial period lasted for three weeks, during which the growth performance, serum parameters, and cecal microbiota were assessed.ResultsThe results revealed significant findings in different aspects. Firstly, the feed-to-gain ratio (F/G ratio) of the 15% WECS group was significantly higher than that of the control group (p

Twenty-six selected genotypes of Phalaris aquatica L. from Iranian germplasm were evaluated to evaluate the genetic diversity of some agromorphological characteristics. Each selected genotype was cloned and planted as spaced single plants according to a randomized complete block design (RCBD) with four replications in 2016 and 2017. Large and significant (p < 0.01) differences among genotypes were found for all traits. The estimates of broad sense heritability were low to high (hb 2 = 0.16 - 0.75) for studied traits. High heritability estimates for dry matter yield (DMY) indicate a sufficient genetic variability for further improvement. There was the highest heritability rate and genetic advance for plant height and DMY. Selection for traits with high heritability and genetic advance can be successful. The dry matter yield cut 1 (DMY1) correlation with the number of days to flowering, number of days to pollination, plant height, and crown diameter cut 2 was positive and significant. In stepwise multiple linear regression, the plant height, number of stems per plant, and spike length explained more than 84% of the total variation of DMY1. The plant height was the most crucial component of DMY1. The path analysis showed that plant height positively affected DMY1 (0.83). The highest negative indirect effects on DMY1 were observed for plant height via the number of stems per plant (-0.238). Axes 1 and 2 of the principal coordinate analysis explained 40.94% and 18.48% of the variation, respectively, and, although not entirely separated, general groupings can be determined. In factor analysis, component 1 was positively associated with the traits dry matter yield cut 2 (DMY2) (0.855), dry matter yield (0.821), and plant height (0.755). Therefore, the first component can be called the biomass component. Finally, selection would be more effective in improving forage yield based on yield components. In conclusion, the results indicated appropriate genetic variability in the studied genotypes. However, the studied genotypes will deliver a valuable germplasm to employ in breeding programs for forage cultivar production. This progress is crucial in introducing these selected genotypes to develop a core collection of Phalaris aquatica germplasm in Iran. [ABSTRACT FROM AUTHOR]

Abstract Background Global food supply is highly dependent on field crop production that is currently severely threatened by changing climate, poor soil quality, abiotic, and biotic stresses. For instance, one of the major challenges to sustainable crop production in most developing countries is limited nitrogen in the soil. Symbiotic nitrogen fixation of legumes such as soybean (Glycine max (L.) Merril) with rhizobia plays a crucial role in supplying nitrogen sufficient to maintain good crop productivity. Characterization of indigenous bradyrhizobia is a prerequisite in the selection and development of effective bioinoculants. In view of this, bradyrhizobia were isolated from soybean nodules in four agro-climatic zones of eastern Kenya (Embu Upper Midland Zone, Embu Lower Midland Zone, Tharaka Upper Midland Zone, and Tharaka Lower Midland Zone) using two soybean varieties (SB8 and SB126). The isolates were characterized using biochemical, morphological, and genotypic approaches. DNA fingerprinting was carried out using 16S rRNA gene and restricted by enzymes HaeIII, Msp1, and EcoRI. Results Thirty-eight (38) bradyrhizobia isolates obtained from the trapping experiments were placed into nine groups based on their morphological and biochemical characteristics. Most (77%) of the isolates had characteristics of fast-grower bradyrhizobia while 23% were slow-growers. Restriction digest revealed significant (p

Introduction: Assessment of the genetic diversity of crops is vital to plant breeding and heritage conservation programs. Genetic diversity in plant species is important for selecting the right parents for hybridization and producing suitable offspring. The genetic diversity of durum wheat compared to other crops has decreased significantly during the time, initially due to the domestication of the plant and gradually due to the use of uniform and modified germplasm, which has shown this to be a threat.Materials and methods: Genetic diversity and population structure of a set of durum wheat germplasm, including 36 durum wheat landraces and five new cultivars, were evaluated using 15 Dof markers.Results: The total number of amplified bands was 117, of which 79 were polymorphic with an average polymorphism of 62.32%. The mean polymorphism information content, marker index, and resolving power in the population were 0.34, 1.61 and 1.9, respectively. According to the indices calculated in this study, Dof16, Dof20, Dof31 and Dof35 markers are more suitable for studying the genetic diversity of durum wheat. Population structure analysis divided germplasm into three subgroups (K=3). The molecular analysis of variance based on three subgroups obtained from STRUCTURE for Dof markers showed that the variance within and between subgroups was 85% and 15% of the total variance, respectively. Principal coordinate analysis partly corresponded to the result of population structure and divided the germplasm into three groups.Conclusion: The results of the present study showed a high level of polymorphism and diversity in Dof markers, indicating the efficiency of these markers in differentiating durum wheat genotypes in this study. Due to the very high conservation of Dof sequences, this specific marker is significant in plants, so this marker can be used to study genetic diversity in different plant species.

Homalomena aromatica Schott, is an industrially significant plant with extensive applications in pharmaceuticals and cosmetics, making deciphering its population structure and genetic diversity crucial for identifying elite and unique germplasm. The current study was therefore carried out to analyze the genetic diversity of H. aromatica using simple sequence repeat (SSR) marker for the first time. For this study, 119 H. aromatica accessions were collected from five states of northeast India and employed for molecular divergence analysis. Conservation of H. aromatica is essential due to overharvesting for its medicinal and cosmetic uses. Research on genetic diversity and community involvement can play a crucial role in preserving this valuable species, which in the future can support its sustainable use in various industries. In the present study, 44 SSR markers were chosen out of 50 on the basis of markers reproducibility and polymorphic nature. A total 208 numbers of polymorphic bands were produced by 44 numbers of primers, where the highest polymorphic information content (PIC) was exhibited by JHA27 (primer) with a value of 0.98. The JHA03 marker showed the highest number of polymorphic bands with a marker index (MI) value of 7.04, whereas primer JHA21 showed a highest resolving power (Rp) of 2.74. Population-based genetic diversity analysis across five grouped populations revealed average values of 1.50572 for an effective number of alleles (Ne), 0.44986 for Shannon's index (I), 1.88366 for the observed number of alleles (Na), and 0.2986 for Nei's diversity index (h). A dendrogram clustering was performed using an unweighted pair group method with arithmetic mean (UPGMA), where three clusters were formed and confirmed by the principal coordinate analysis (PCoA). Structure analysis revealed three genetically diverse populations, which further confirmed the UPGMA and PCoA results. From the Analysis of Molecular Variance (AMOVA), the genetic diversity among the populations was found to be 6 %, with genetic variation accounting for 82 % as well as 12 % was observed for within and among the individuals respectively. Based on current knowledge, this is the first report on H. aromatica molecular diversity and population structure analysis which highlights the novelty of the study. The present study will aid in the identification of unique genetic lines, conservation of the gene pool and use in varietal development program. [Display omitted] • Homalomena aromatica is a valuable medicinal plant having industrial demand. • First report on genetic diversity analysis using microsatellite marker. • A total of 119 accessions were subjected for genetic diversity analysis. • Forty four microsatellite marker showed 100 % polymorphism. • This research will help to identify elite lines and conservation of germplasm. [ABSTRACT FROM AUTHOR]

The genus Vigna is pan-tropical, having more than 200 species with many desirable economically important traits. This study aimed to validate the in silico polymorphism of whole-genome-sequence-developed mungbean-specific SSR markers and their transferability among different Vigna species. The present study utilized a set of 200 SSR markers developed from the whole-genome sequence of mungbean and validated them using a diversity panel of 25 accessions that belong to 13 Vigna species. Out of 200 SSR markers, 130 markers (65%) were polymorphic across the various Vigna species, and the number of alleles amplified varied from 7 to 24. The SSR markers showed more than 90 percent transferability across the different Vigna species accessions. Utilizing allelic data, the 25 Vigna accessions were clustered into three groups using the unweighted pair group method with arithmetic mean (UPGMA). The two integral coalitions explained 50.79 and 15.42% of the total variance. The principal coordinate analysis (PCA) biplot graph and UPGMA-based neighbor-joining clustering diagram showed a similar pattern of Vigna accession distribution. A population structure assessment grouped the cultivated and wild species accessions into two sub-populations based upon a maximum delta K value of 144.79, which drew a sharp peak at K = 2. The estimated marker parameters, such as the polymorphic information content (0.09–0.84), marker index (0.091–3.342), and effective multiplex ratio (1.0–4.0), suggested their adequacy for several genetic studies, such as parental selection, hybrid testing, genetic mapping, and marker-aided breeding programs, for the genetic enhancement of species belonging to the Vigna genus.

Mutation induction is an important method for generating genetic diversity. Purslane (Portulaca oleracea L.) has unique medicinal uses due to its high content of beneficial antioxidants and omega-3 fatty acids. In this study, the genetic diversity of 24 mutant lines of fourth-generation (M4) purslane obtained from dimethyl sulfate treatment together with the control was investigated in a randomized complete block design with 3 replicates. The differences among the lines were significant in traits including plant height, leaf length, leaf width, stem dry weight, and leaf chlorophyll in the 30-day-old plant. The principal coordinates and cluster analyses divided the lines into two separate clusters. The lines in cluster 1 had a significant advantage over the lines in cluster 2 for most traits such as stem fresh weight, leaf fresh weight, and number of capsules per plant. The number of leaves was significantly correlated with stem fresh weight, leaf fresh weight, plant fresh weight, number of capsules per plant and the ratio of plant dry weight to plant fresh weight. In sequential path analysis, stem fresh weight in the first order was the only trait affecting number of capsules per plant, and in the second-order, leaf fresh weight and plant height were the most important traits that had an effect on number of capsules per plant through the direct effect of stem fresh weight. L18 mutant line had a significant advantage over the control in some agronomic traits such as plant height, leaf length and number of capsules per plant, that can be used for future research, especially for cultivation, commercialization and extensive planting for uses as vegetables, oil extraction, and medicinal applications. [ABSTRACT FROM AUTHOR]

Objective This study was conducted to investigate the application of the start codon targeted (SCoT) markers in the genetic diversity of tomato. In addition, the genetic diversity in important cultivars of tomato, which have been previously cultivated, are being cultivated, or are hoped to be cultivated in Iran were assessed. Materials and Methods Ninety nine 99 tomato cultivars were investigated for SCoT polymorphism. DNA isolation and SCoT analysis were carried out using the fresh leaf samples. Thirty-six SCoT primers were initially screened for analysis and fifteen primers were considered for the further analysis. Results The cultivars produced 207 amplicons while the 206 were polymorphic. Amplicon size varied from 250 to 3200 base pair (bp). The average of polymorphism and the mean of polymorphic information content were 99.52 and 0.30, respectively. Also, Jaccard's similarity coefficient was applied and the mean Jaccard genetic similarity coefficient was 0.52. According to Jaccard's coefficient, the lowest similarity (0.17) has been observed for cultivars 34 and 97 while the highest similarity (0.84) were detected between cultivars 86 and 87. In addition, the cluster analysis was conducted based on Jaccard similarity coefficient and centroid method which classified cultivars into three clusters. Besides, the principal coordinate analysis was considered. Accordingly, the cultivars divided into four groups and the first three components explained 58.82% of the molecular variation. The results of the principal coordinate analysis were largely consistent with the results of the cluster analysis. Having high polymorphic information content, marker index, effective multiplex ratio, and resolution power, SCoT12 and SCoT23 primers were properly effective in differentiating the cultivars. Conclusions This study showed that SCoT molecular markers are appropriate for investigating the genetic diversity amongst tomato genotypes and generate a high level of polymorphism. Thus, these markers have considerable efficiency in differentiating tomato genotypes. In addition, this investigation indicated that SCoT12 and SCoT23 primers were suitably effective in differentiating the cultivars. Furthermore, our resech claimed that tomato cultivars that are used in Iran do not have high genetic diversity while for more precise conclusion; it is suggested to practice more SCoT primers along with other markers.

Flying pigeons (Columbia livia) are extensively studied for their physical endurance and superior sense of orientation. The extreme physical endurance of which these birds are capable creates a unique opportunity to investigate the possible impact of long-distance flying on the taxonomy and metabolic function of the gut microbiota. This project was enabled by access to two groups of pigeons raised by the same breeder in the same conditions, except that one group was trained in long-distance flying and participated in multiple races covering a total distance of over 2600 km over a 9-week period. In contrast, the second group did not fly. The fecal microbiota was analyzed using 16S amplicon sequencing, and the taxonomy and metabolic function were inferred from this sequence data. Based on phylogenetic distance and metabolic function, flying and non-flying pigeons were found to harbor distinct bacterial microbiota. The microbiota taxonomy varied extensively between the birds, whereas the inferred metabolic potential was relatively stable. Age was not a significant determinant of the fecal microbiota profile. In flying birds, the metabolic pathways annotated with biosynthesis were enriched, representing 60% of the 20 metabolic pathways that were most closely associated with flying.

Most of the main oilfields in China have entered the middle and late stage of exploitation, and its exploitation difficulty has further increased. Microbial oil recovery technology has the advantages of low cost, high efficiency, green and environmental protection, and has a wide application prospect in further enhancing oil recovery of remaining oil. Due to the lack of understanding of reservoir microbial community structure and the long selection cycle of activator formula, the field popularization and application of microbial oil displacement technology is limited. By analyzing the difference of community structure in the reservoir and the interaction between environmental factors and dominant bacteria, basic data and theoretical guidance were provided for directional activation of reservoir microorganisms. The reservoir high-throughput sequencing data were analyzed by species composition analysis, species diversity analysis, principal coordinate analysis (PCoA) analysis and redundancy analysis. The results show that the species composition difference between water injection wells and production wells in Oilfield A is large, and the species composition difference between water injection wells and production wells in Oilfield L is not obvious; In terms of species abundance, species average and species diversity, there is no obvious difference between a oilfield and l oilfield; However, in terms of species similarity between water injection wells and production wells based on genus level, oilfield a shows low similarity, while oilfield L shows high similarity. In the analysis of environmental factors, the microbial community in L oilfield is significantly correlated with salt content, while the microbial community composition in a oilfield is significantly correlated with temperature, pH and SO2- 4 concentration [ABSTRACT FROM AUTHOR]

Background: Global food supply is highly dependent on field crop production that is currently severely threatened by changing climate, poor soil quality, abiotic, and biotic stresses. For instance, one of the major challenges to sustainable crop production in most developing countries is limited nitrogen in the soil. Symbiotic nitrogen fixation of legumes such as soybean (Glycine max (L.) Merril) with rhizobia plays a crucial role in supplying nitrogen sufficient to maintain good crop productivity. Characterization of indigenous bradyrhizobia is a prerequisite in the selection and development of effective bioinoculants. In view of this, bradyrhizobia were isolated from soybean nodules in four agro-climatic zones of eastern Kenya (Embu Upper Midland Zone, Embu Lower Midland Zone, Tharaka Upper Midland Zone, and Tharaka Lower Midland Zone) using two soybean varieties (SB8 and SB126). The isolates were characterized using biochemical, morphological, and genotypic approaches. DNA fingerprinting was carried out using 16S rRNA gene and restricted by enzymes HaeIII, Msp1, and EcoRI. Results: Thirty-eight (38) bradyrhizobia isolates obtained from the trapping experiments were placed into nine groups based on their morphological and biochemical characteristics. Most (77%) of the isolates had characteristics of fast-grower bradyrhizobia while 23% were slow-growers. Restriction digest revealed significant (p < 0.015) variation within populations and not among the agro-climatic zones based on analysis of molecular variance. Principal coordinate analysis demonstrated sympatric speciation of indigenous bradyrhizobia isolates. Embu Upper Midland Zone bradyrhizobia isolates had the highest polymorphic loci (80%) and highest genetic diversity estimates (H' = 0.419) compared to other agro-climatic zones. Conclusion: The high diversity of bradyrhizobia isolates depicts a valuable genetic resource for selecting more effective and competitive strains to improve promiscuous soybean production at a low cost through biological nitrogen fixation. [ABSTRACT FROM AUTHOR]

Agaricus bisporus, commonly known as the button mushroom, is widely cultivated throughout the world. To breed new strains with more desirable traits and improved adaptability, diverse germplasm, including wild accessions, is a valuable genetic resource. To better understand the genetic diversity available in A. bisporus and identify previously unknown diversity within accessions, a phylogenetic analysis of 360 Agaricus spp. accessions using single-nucleotide polymorphism genotyping was performed. Genetic relationships were compared using principal coordinate analysis (PCoA) among accessions with known origins and accessions with limited collection data. The accessions clustered into four groups based on the PCoA with regard to genetic relationships. A subset of 67 strains, which comprised a core collection where repetitive and uninformative accessions were not included, clustered into 7 groups following analysis. Two of the 170 accessions with limited collection data were identified as wild germplasm. The core collection allowed for the accurate analysis of A. bisporus genetic relationships, and accessions with an unknown pedigree were effectively grouped, allowing for origin identification, by PCoA analysis in this study.

It is essential that the genetic variability of preserved accessions germplasm banks be evaluated and quantified, which allows, for example, the detection of duplicates, generating more reliable data, especially for groups of plants that have a wide genetic variability, as in the case of the Capsicum genus.. We examined the DNA from the leaves of nine accessions of Capsicum spp. from the Federal University of Maranhão Germplasm Bank. Amplification was performed using 78 microsatellite primers previously described as potential molecular markers for Capsicum accessions. Thirty-three microsatellite primers produced amplification products, seven of which were polymorphic and used to investigate genetic variability among nine accessions. The proportion of polymorphic loci in pepper accessions was estimated at 21%. A mean of 2.28 alleles was detected per polymorphic locus and the number of alleles ranged from 1 to 3. The highest effective number of alleles was 1.62, and the highest values of mean observed heterozygosity (Ho) and Shannon's diversity index (I) were 0.533 and 0.421, respectively. Private alleles were detected in two accessions: UFMA17 and UFMA35. The highest Ho value was found in the UFMA10 accession, whereas the lowest value was recorded in the UFMA35 accession. Fixation indices (FST) indicated that 65% of the total allele frequency variation occurred within the analyzed loci. The polymorphism information content ranged from 0.011 to 0.354. Clustering of samples based on Nei's genetic distance matrix revealed the formation of three genetically distinct groups that allowed identifying genetically distinct groups based on SSR markers and discriminating the most closely related accessions of Capsicum spp. Neighbor-joining cluster analysis and PCoA allowed identifying genetically distinct groups based on SSR markers and discriminating the most closely related accessions of Capsicum spp. [ABSTRACT FROM AUTHOR]

Macauba palm [Acrocomia aculeata (Jacq.) Lodd. ex Mart.] is a perennial oil, it stands out for having several characteristics of commercial interest, mainly for producing oil for biodiesel, it has high oil productivity, about 2.5 to 4.5 L·year-1. Despite its great potential, o its cultivation is carried out mainly in an extractive way, so the domestication and breeding programs has been incipient. The study hypothesis is that macauba populations collected in different locations have sufficient genetic variability to initiate a breeding program. Thus, the aim of this study was to estimate the genetic diversity and population structure of macauba palm genotypes by using single nucleotide polymorphism (SNP) markers in order to reveal genetic diversity and distribution of genetic variation within and between populations and use the genetic information obtained to assist breeding strategies. Leaf tissues were collected from 566 macauba plants belonging to the Embrapa Cerrados Active Germplasm Bank, composed of genotypes from five states in Brazil: Minas Gerais, Goiás, Pará, São Paulo, and Distrito Federal. Molecular variance analysis estimated, the genetic diversity parameters, the population structure and principal coordinate analysis. The genetic diversity is higher within than between populations. The results provided by PCoA and STRUCTURE were in agreement and indicated that the evaluated genotypes can be grouped into two groups. Genetic diversity parameters reveal the presence of inbreeding and a low number of heterozygotes, evidencing that the reproduction system of the species is mixed. The information revealed of the genotypes using SNP markers will be important for future studies using genome-wide selection and genomic association to develop cultivars of macauba with desirable traits, such as high yield of fruits and oil production. [ABSTRACT FROM AUTHOR]

Replacing herbicide fallow with alternative floor management can conserve soil and reduce agrochemical use in an orchard. Increased perennial weed resistance to foliar preparations has recently become an additional motivation to abandon herbicides. This study explores apple tree understory weed flora alteration after introducing Festuca ovina living mulch to the rows. Delayed cover crop sowing was tested as a possible approach to address the problem of high perennial weed dominance when a living mulch is introduced in the year of orchard establishment, in addition to reducing competition. The effect of replacing the M.9 dwarfing rootstock with the M.26 and P 60 semi‐dwarfing rootstocks to foster tree competitiveness was also investigated, and the influence of the mulch dominance on apple yield was analysed. Abundant perennial weed flora developed in the living mulch regardless of the mitigation strategy, and one of the cover crop cohorts exhibited unsatisfactory persistence when maintained under trees on P 60. This pattern was attributed to an interactive effect of shadowing by the more vigorous trees and by Glechoma hederacea and Artemisia vulgaris weeds, which abounded due to insufficient mowing frequency. More intensive tree understory management is recommended, especially in semi‐dwarf orchards, and G. hederacea should be studied more as a candidate mulch species, potentially superior to F. ovina. [ABSTRACT FROM AUTHOR]

Two anaerobic membrane bioreactors (AnMBRs) equipped with different membrane pore size (0.4 or 0.05 µm) were operated at 25˚C and fed with domestic wastewater. The hydraulic retention time (HRT) of the reactors was shortened. The microbial communities of the two AnMBRs were investigated by 16S rRNA gene amplicon sequencing to see the effects of HRT. The predominant Archaea was an aceticlastic methanogen Methanosaeta. The composition of hydrogenotrophic methanogens changed with the HRTs: the population of Methanobacterium was higher for longer HRTs, whereas the population of unclassified Methanoregulaceae was higher for shorter HRTs. The Anaerolineae, Bacteroidia and Clostridia bacteria were dominant in both of the reactors, with a combined relative abundance of over 55%. The relative abundance of Anaerolineae was proportional to the biogas production performance. The change in the population of hydrogenotrophic methanogens or Anaerolineae can be used as an indicator for process monitoring. The sum of the relative abundance of Anaerolineae and Clostridia fluctuated slightly with changes in the HRT in both AnMBRs when the reactor was stably operated. The co-occurrence analysis revealed the relative abundance of the operational taxonomic units belonging to Anaerolineae and Clostridia was functionally equivalent during the treatment of real domestic sewage. A principal coordination analysis revealed that the changes in the microbial community in each reactor were consistent with the change of HRT. In addition, both the HRT and the stability of the process are important factors for maintaining microbial community structures. [Display omitted] [ABSTRACT FROM AUTHOR]

Objective This study was conducted to investigate the application of the start codon targeted (SCoT) markers in the genetic diversity of tomato. In addition, the genetic diversity in important cultivars of tomato, which have been previously cultivated, are being cultivated, or are hoped to be cultivated in Iran were assessed. Materials and Methods Ninety nine 99 tomato cultivars were investigated for SCoT polymorphism. DNA isolation and SCoT analysis were carried out using the fresh leaf samples. Thirty-six SCoT primers were initially screened for analysis and fifteen primers were considered for the further analysis. Results The cultivars produced 207 amplicons while the 206 were polymorphic. Amplicon size varied from 250 to 3200 base pair (bp). The average of polymorphism and the mean of polymorphic information content were 99.52 and 0.30, respectively. Also, Jaccard's similarity coefficient was applied and the mean Jaccard genetic similarity coefficient was 0.52. According to Jaccard's coefficient, the lowest similarity (0.17) has been observed for cultivars 34 and 97 while the highest similarity (0.84) were detected between cultivars 86 and 87. In addition, the cluster analysis was conducted based on Jaccard similarity coefficient and centroid method which classified cultivars into three clusters. Besides, the principal coordinate analysis was considered. Accordingly, the cultivars divided into four groups and the first three components explained 58.82% of the molecular variation. The results of the principal coordinate analysis were largely consistent with the results of the cluster analysis. Having high polymorphic information content, marker index, effective multiplex ratio, and resolution power, SCoT12 and SCoT23 primers were properly effective in differentiating the cultivars. Conclusions This study showed that SCoT molecular markers are appropriate for investigating the genetic diversity amongst tomato genotypes and generate a high level of polymorphism. Thus, these markers have considerable efficiency in differentiating tomato genotypes. In addition, this investigation indicated that SCoT12 and SCoT23 primers were suitably effective in differentiating the cultivars. Furthermore, our resech claimed that tomato cultivars that are used in Iran do not have high genetic diversity while for more precise conclusion; it is suggested to practice more SCoT primers along with other markers. [ABSTRACT FROM AUTHOR]

Genome sequences of eleven avian influenza virus (AIV) subtypes have been reported in swine populations from seven countries until August 2020. To unravel the transmission dynamics and spillover events of AIVs from avian reservoirs to swine, full-length hemagglutinin (HA) sequences of AIV subtypes (n = 11) reported from various avian species and swine were retrieved from the 'Influenza Research Database'. Phylogenetic analysis identified closely related avian and swine AIV sequences suggesting potential spillover events from multiple domestic and wild avian species, including chicken, duck, pigeon, goose, quail, and aquatic birds to swine. Furthermore, N-linked glycosylation analysis of these closely related AIV sequences supported the possibility of multiple spillover events of highly pathogenic H5N1 and low pathogenic H9N2 viruses from various avian species to swine. The principal coordinate analysis further validated these findings for H5N1 and H9N2 viruses; however, spillover events of the other nine AIV subtypes were limited. Interestingly, the presence of potential mammalian adaptation markers, particularly in some of the swine H5N1, H7N9, and H9N2 viruses, suggested that these viruses may have already adapted in swine. The occurrence and circulation of these AIVs in swine, especially the H5N1 and H9N2 viruses with numerous spillover events from the avian reservoirs to swine, pose a significant threat in terms of their reassortment with endemic swine viruses or circulating human influenza viruses within the swine which may facilitate the emergence of a novel influenza virus strain with pandemic potential. [ABSTRACT FROM AUTHOR]

Copyright of China Brewing is the property of China Brewing Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The coevolution between human and bacteria colonizing the human body has profound implications for heath and development, with a growing body of evidence linking the altered microbiome composition with a wide array of disease states. Yet dimension reduction and visualization analysis of microbiome data are still in their infancy and many challenges exist. In this article, we introduce a general framework, zero-inflated probabilistic principal component analysis (ZIPPCA), for dimension reduction and data ordination of multivariate abundance data, and propose an efficient variational approximation method for estimation, inference, and prediction. Extensive simulations show that the proposed method outperforms algorithm-based methods and compares favorably with existing model-based methods. We further apply our method to a gut microbiome dataset for visualization analysis of community composition across age and geography. The method is implemented in R and available at . [ABSTRACT FROM AUTHOR]

History and background of blackberry cultivars and wild species is unclear in the south coast of the Caspian Sea as an origin of diversity center in Iran. In the present study, genetic diversity of 45 genotypes of blackberries (thorny and thornless) from the collection of Sari Agricultural Sciences and Natural Resources University (SANRU) located in south of the Caspian Sea were studied by using Inter Simple Sequence Repeats (ISSR) markers. Jaccard's similarity coefficient was used to plot the cluster diagram according to the Unweighted Pair-Group Method with Arithmetic averages (UPGMA) algorithm. Results showed that 10 ISSR primers amplified 345 fragments, of which 344 were polymorphic. The average numbers of bands were 34.5 per primers. Based on the Principal Coordinate Analysis (PCA) results, blackberry genotypes were classified in three groups. Some wild genotypes were located closed to commercial thorny cultivars. Cluster analysis divided the genotypes to six groups. Introduced genotypes that were in the same group were separated in sub-groups according to maturity time (early, mid, and late ripening cultivars). These genetic traits separated them and confirmed the morphological results, identifying them as thorny cultivars Silvan, Marion, and Tupi. The results indicated that gene pool of thornless blackberry is not limited to chimera type (as first generation of thornlessness) and it probably includes the two further steps in evolution, and even include some new and evolved types of native thornlessness. [ABSTRACT FROM AUTHOR]

Copyright of Agriscientia is the property of Revista AgriScientia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

ObjectiveTo determine the impact of 2 probiotic bifidobacteria on the fecal microbiota of premature infants fed either human milk or formula.Study designIn the first of two phase 1 clinical trials, 12 premature infants receiving formula feedings were assigned randomly to receive either Bifidobacterium longum ssp infantis or Bifidobacterium animalis ssp lactis in increasing doses during a 5-week period. In the second, 9 premature infants receiving their mother's milk received each of the two bifidobacteria for 2 weeks separated by a 1-week washout period. Serial stool specimens from each infant were analyzed by terminal restriction fragment-length polymorphism and quantitative polymerase chain reaction for bacterial composition.ResultsAmong the formula-fed infants, there was a greater increase in fecal bifidobacteria among infants receiving B infantis (Binf) than those receiving B lactis (Blac). This difference was most marked at a dose of 1.4 × 10(9) colony-forming units twice daily (P < .05). Bacterial diversity improved over dose/time in those infants receiving Binf. Among the human milk-fed infants, greater increases in fecal bifidobacteria and decreases in γ-Proteobacteria followed the administration of Binf than Blac. The B longum group (which includes Binf but not Blac) was the dominant bifidobacteria among the human milk-fed infants, regardless of the probiotic administered.ConclusionsBinf was more effective at colonizing the fecal microbiota than Blac in both formula-fed and human milk-fed premature infants. The combination of human milk plus Binf resulted in the greatest fecal levels of bifidobacteria.

Dyrosauridae is a clade of neosuchian crocodyliforms that diversified in terrestrial and aquatic environments across the Cretaceous-Paleogene transition. The postcranial anatomy of dyrosaurids has long been overlooked, obscuring both their disparity and their locomotive adaptations. Here we thoroughly describe of the postcranial remains of an unusually small dyrosaurid, Cerrejonisuchus improcerus, from the middle-late Paleocene Cerrejón Formation of Colombia, and we provide a wealth of new data concerning the postcranial anatomy of the key dyrosaurids: Congosaurus bequaerti and Hyposaurus rogersii. We identify a series of postcranial autapomorphies in Cerrejonisuchus improcerus (an elliptic-shaped odontoid laterally wide, a ulna possessing a double concavity, a fibula bearing a widely flattened proximal end, a pubis showing a large non-triangular distal surface) as well as functionally-important traits such as a relatively long ulna (85% of the humerus' length), short forelimb (83% of hindlimb's length), or thoracic vertebra bearing comparatively large lateral process (with widened parapophysis and diapophysis) along with strongly arched thoracic ribs allowing a more sturdy and cylindrical rib cage. These indicate a more terrestrial lifestyle for Cerrejonisuchus compared to the derived members of the clade. We also built a dataset of 187 traits on 27 taxa, that extensively samples the cranial and postcranial architectures of exemplar crocodyliforms. We analyze these data in via Principal Coordinate Analysis (PCoA) to visualize the postcranial morphospace occupation of Dyrosauridae, Thalattosuchia, and Crocodylia. Our data reveal the existence of a distinctive postcranial anatomy for Dyrosauridae that is markedly distinct from that of crocodylians. As a result, modern crocodylians are probably not good functional analog for extinct crocodyliformes. Postcranial data should also be more widely used in phylogenetic and disparity analyses of Crocodyliformes. [ABSTRACT FROM AUTHOR]

Rhizobia are soilborne bacteria that form symbiotic relations with legumes and fix atmospheric nitrogen. The nitrogen fixation potential depends on several factors such as the type of host and symbionts and on environmental factors that affect the distribution of rhizobia. We isolated bacteria nodulating common bean in Southern Ethiopia to evaluate their genetic diversity and phylogeography at nucleotide, locus (gene/haplotype) and species levels of genetic hierarchy. Phylogenetically, eight rhizobial genospecies (including previous collections) were determined that had less genetic diversity than found among reference strains. The limited genetic diversity of the Ethiopian collections was due to absence of many of the Rhizobium lineages known to nodulate beans. Rhizobium etli and Rhizobium phaseoli were predominant strains of bean-nodulating rhizobia in Ethiopia. We found no evidence for a phylogeographic pattern in strain distribution. However, joint analysis of the current and previous collections revealed differences between the two collections at nucleotide level of genetic hierarchy. The differences were due to genospecies Rhizobium aethiopicum that was only isolated in the earlier collection. [ABSTRACT FROM AUTHOR]

Background. Population genetic structure is one of the most important population genetic parameters revealing its demographic features. The aim of this study was to evaluate the homogeneity of the Lithuanian population on the basis of the genome-wide genotyping data. The comparative analysis of three methods – multidimensional scaling, principal components, and principal coordinates analysis – to visualize multidimensional genetics data was performed. The results of visualization (mapping images) are also presented. Materials and methods. The data set consisted of 425 samples from six ethnolinguistic groups of the Lithuanian population. Genomic DNA was extracted from whole venous blood using either the phenol-chloroform extraction method or the automated DNA extraction platform TECAN Freedom EVO. Genotyping was performed at the Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Lithuania, with the Illumina HumanOmniExpress-12 v1.1 and the Infinium OmniExpress-24. For the estimation of homogeneity of the Lithuanian population, PLINK data file was obtained using PLINK v1.07 program. The Past3 software was used to visualize the genotype data with multidimensional scaling and principal coordinates methods. The SmartPCA from EIGENSOFT 7.2.1 program was used in the principal component analysis to determine the population structure. Conclusions. Methods of multidimensional scaling, principal coordinate, and principal component for the genetic structure of the Lithuanian population were investigated and compared. The principal coordinate and principal component methods can be used for genotyping data visualization, since any essential differences in the results obtained were not observed and compared to multidimensional scaling. The Lithuanian population is homogenous whereas the points are strongly close when we use the principal coordinates or principal component methods.

Traditional hop (Humulus lupulus L.) cultivars have been used in the brewing industry for a long time. Globally, about ten new breeding lines were released to the market in each decade from ~1970 to 1999. Since 2006, the rate of release of new cultivars has increased tenfold. It is, therefore, important to identify their genotype and origin. Molecular genetic methods based on DNA are the most appropriate technology for this purpose. Recently, we developed an efficient marker system for the authenticity control of hop genotypes based on expressed sequence tag-simple sequence repeats (EST-SSR). In the present study, we enlarged the previously established EST-SSR set with 27 new polymorphic markers and evaluated molecular genetic variability within 135 traditional and new world hop cultivars. Two sets of 10 markers effectively differentiated all used cultivars, with the exception of cultivars derived from the same original genotype such as Saaz, Spalt, Tettnang and Nadwislawsky. Results of molecular genetic variability analyses corresponded with the genealogical and geographical origin of the key cultivars.

Agaricus bisporus, commonly known as the button mushroom, is widely cultivated throughout the world. To breed new strains with more desirable traits and improved adaptability, diverse germplasm, including wild accessions, is a valuable genetic resource. To better understand the genetic diversity available in A. bisporus and identify previously unknown diversity within accessions, a phylogenetic analysis of 360 Agaricus spp. accessions using single-nucleotide polymorphism genotyping was performed. Genetic relationships were compared using principal coordinate analysis (PCoA) among accessions with known origins and accessions with limited collection data. The accessions clustered into four groups based on the PCoA with regard to genetic relationships. A subset of 67 strains, which comprised a core collection where repetitive and uninformative accessions were not included, clustered into 7 groups following analysis. Two of the 170 accessions with limited collection data were identified as wild germplasm. The core collection allowed for the accurate analysis of A. bisporus genetic relationships, and accessions with an unknown pedigree were effectively grouped, allowing for origin identification, by PCoA analysis in this study. [ABSTRACT FROM AUTHOR]

Social robot capabilities, such as talking gestures, are best produced using data driven approaches to avoid being repetitive and to show trustworthiness. However, there is a lack of robust quantitative methods that allow to compare such methods beyond visual evaluation. In this paper a quantitative analysis is performed that compares two Generative Adversarial Networks based gesture generation approaches. The aim is to measure characteristics such as fidelity to the original training data, but at the same time keep track of the degree of originality of the produced gestures. Principal Coordinate Analysis and procrustes statistics are performed and a new Fréchet Gesture Distance is proposed by adapting the Fréchet Inception Distance to gestures. These three techniques are taken together to asses the fidelity/originality of the generated gestures. [ABSTRACT FROM AUTHOR]

In the present work, a novel analytical procedure by integrating principal coordinate analysis (PcoA) with excitation-emission matrix fluorescence (EEMF) spectroscopy was introduced for discriminating the commercial gasoline fuels. The PcoA technique involved analysis of the distance matrices containing the dissimilarity information and it can serve as an efficient tool for capturing the major as well as subtle compositional differences among the analyzed commercial gasoline samples. The utility of the proposed PcoA assisted EEMF analytical procedure was successfully tested by discriminating gasoline fuel samples belonging to five different industrial brands. The obtained results clearly showed that combination of PcoA and EEMF could provide a simple, sensitive and economical analytical procedure to carry out the rapid analyses of the gasoline samples belonging to different brands. [ABSTRACT FROM AUTHOR]

Indonesian durian (Durio zibethinus Murr.) germplasms cultivated on Nias Island were assessed for their genetic diversity and relationships using Random Amplified Polymorphic DNA (RAPD) markers. Fifty accessions were collected from five populations or zones in Nias Island, Indonesia. All RAPD fragments were polymorphic as revealed by the use of OPA-01, OPA-03, OPA-07, OPA-13, OPN-06, and RAPD-05 primers within and among the durian germplasms. Primer OPA-03 was evaluated as a highly informative marker. Similarity values (Jaccard) ranged from 0.216 to 0.423 between different populations and 0.00 to 0.89 within the populations. The genetic structure between populations ranged from 1.71 to 1.92 for mean number of alleles (na), and from 1.35 to 1.59 for effective number of alleles (ne). Shannon's diversity index (I) ranged from 0.34 to 0.51, and the Nei's gene diversity index (h) ranged from 0.21 to 0.34. Result of cluster analysis based on Unweighted Pair Group Method with Arithmetic Mean (UPGMA) grouped all germplasms into thirteen clusters, some were admixtures between different populations. Result of Principal Coordinate Analysis (PCoA) confirmed the UPGMA dendrogram with the results of five main clusters among durian accessions from Nias Island, Indonesia. [ABSTRACT FROM AUTHOR]

Genetic diversity is the foundation for any breeding program. The present study analyzed the genetic base of 163 soybean genotypes from three continents viz. Africa, America and Asia using 68 trait-linked simple sequence repeats (SSR) markers. The average number of alleles among the germplasm from the three continents followed the trend as Asia (9) > America (8) > Africa (7). Similar trends were observed for gene diversity (0.76 > 0.74 > 0.71) and polymorphism information content (PIC) (0.73 > 0.71 > 0.68). These findings revealed that soybean germplasm from Asia has wider genetic base followed by America, and least in Africa. The 163 genotypes were grouped into 4 clusters by phylogenetic analysis, whereas model-based population structure analysis also divided them into 4 subpopulations comprising 80.61% pure lines and 19.39% admixtures. The genotypes from Africa were easily distinguished from those of other two continents using phylogenetic analysis, indicating important role of geographyical differentiation for this genetic variability. Our results indicated that soybean germplasm has moved from Asia to America, and from America to Africa. Analysis of molecular variance (AMOVA) showed 8.41% variation among the four subpopulations, whereas 63.12% and 28.47% variation existed among and within individuals in the four subpopulations, respectively. Based on the association mapping, a total of 21 SSR markers showed significant association with days to flowering (DoF) and 100-seed weight (HSW). Two markers Satt365 and Satt581 on chromosome 6 and 10, respectively, showed pleiotropic effect or linkage on both traits. Genotype A50 (Gakuran Daizu/PI 506679) from Japan has 8 out of the 13 beneficial alleles for increased HSW. The diverse genotypes, polymorphic SSR markers and desirable alleles identified for DoF and HSW will be used in future breeding programs to improve reproductive, yield and quality traits. [ABSTRACT FROM AUTHOR]

Using agro-morphological characters and microsatellite markers, advance breeding lines of rice were discriminated for their ability to tolerate drought stress at reproductive stage. Experimental materials consisting of 17 advance breeding lines and a check were evaluated in randomized block design with three replications under irrigated condition and drought condition created under rainout shelter during three consecutive years. An analysis of variance revealed significant differences among the genotypes for all the ten agro-morphological characters evaluated under both the conditions across the years. Principal component analysis showed the relative importance of root length, number of tillers per plant, number of grains per panicle, harvest index and grain yield per plant among agro-morphological characters and stress tolerance level, stress susceptibility index, stress tolerance index and drought tolerance efficiency among drought tolerance indices as the important classification variables. Relative mean performance in respect of grain yield as well as drought tolerance indices reflected remarkably greater degree of drought tolerance in 11 advance breeding lines and the check, discriminating them from remaining entries under evaluation. Utilizing a panel of 32 microsatellite primers, selective amplification of targeted genomic regions revealed that the primers RM 72, RM 163, RM 212, RM 225, RM 231, RM 302, RM 327, RM 518, RM 521, RM 555, RM 1349, RM 3549 and RM 5443 were highly informative with greater gene diversity and discrimination ability. Hierarchical cluster analysis based on molecular profiles discriminated the entries into five genotypic groups and drought tolerant entries were accommodated into three distinct groups with remarkably greater efficiency (85.7%). Principal coordinate analysis based two dimensional plots of microsatellites dependent genetic profiles displayed a very close correspondence with the genotypic clustering pattern revealed from a perusal of dendrogram. Sequential exclusion of primers in cluster analysis led to identification of RM 212, RM 231, RM 324, RM 431, RM 521, RM 3549 and RM 6374 as the most useful primers for discrimination of drought tolerant and susceptible lines of rice. Molecular profiling based on these markers can be utilized as efficient tools for discrimination and identification of drought tolerant lines. [ABSTRACT FROM AUTHOR]

Genetic diversity among 40 chickpea (Cicer arietinum L.) genotypes was investigated using 125 microsatellite (SSR, simple sequence repeat) markers. Twenty five polymorphic markers with average genetic diversity and PIC (Polymorphic Information Content) value of 0.489 and 0.437, respectively, generated a total of 90 alleles. High PIC and gene diversity (HE) values indicated good variability amongst the chickpea genotypes. Sequential Agglomerative Hierarchical Non-overlapping (SAHN) grouping revealed two main clusters with 29 genotypes in cluster I and 11 genotypes in cluster II. The Cluster analysis did not follow geographical diversity rather it was in agreement for genetic diversity with respect to seed type and parentage/pedigree. Grouping clearly delineated the diverse kabuli and desi genotypes. Molecular variance analysis also indicated 97% variation within the populations and 3% variation among the populations. Principal coordinate analysis (PCoA) divided all the 40 genotypes into three populations based on their seed type and pedigree. The 2D plot largely supported the dendrogram with similar pattern of clustering. It also indicated that the material used was diverse. Thus, the study proved that SSR markers are informative tools for assessing genetic diversity and can be recommended for characterization studies in chickpea.

Sulfur dioxide (SO2) is an antioxidant and antimicrobial agent used in winemaking. Its effects on spoilage microorganisms has been studied extensively, but its effects on commercial Saccharomyces cerevisiae strains, the dominant yeast in winemaking, require further investigation. To our knowledge, no previous studies have investigated both the potential SO2 resistance mechanisms of commercial yeasts as well as their production of aroma-active volatile compounds in response to SO2. To study this, fermentations of two commercial yeast strains were conducted in the presence (50 mg/L) and absence (0 mg/L) of SO2. Strain QA23 was more sensitive to SO2 than Strain BRL97, resulting in delayed cell growth and slower fermentation. BRL97 exhibited a more rapid decrease in free SO2, a higher initial production of hydrogen sulfide, and a higher production of acetaldehyde, suggesting that each strain may utilize different mechanisms of sulfite resistance. SO2 addition did not affect the production of aroma-active volatile compounds in QA23, but significantly altered the volatile profiles of the wines fermented by BRL97. [ABSTRACT FROM AUTHOR]

Thiamine diphosphate‐dependent decarboxylases catalyze both cleavage and formation of CC bonds in various reactions, which have been assigned to different homologous sequence families. This work compares 53 ThDP‐dependent decarboxylases with known crystal structures. Both sequence and structural information were analyzed synergistically and data were analyzed for global and local properties by means of statistical approaches (principle component analysis and principal coordinate analysis) enabling complexity reduction. The different results obtained both locally and globally, that is, individual positions compared with the overall protein sequence or structure, revealed challenges in the assignment of separated homologous families. The methods applied herein support the comparison of enzyme families and the identification of functionally relevant positions. The findings for the family of ThDP‐dependent decarboxylases underline that global sequence identity alone is not sufficient to distinguish enzyme function. Instead, local sequence similarity, defined by comparisons of structurally equivalent positions, allows for a better navigation within several groups of homologous enzymes. The differentiation between homologous sequences is further enhanced by taking structural information into account, such as BioGPS analysis of the active site properties or pairwise structural superimpositions. The methods applied herein are expected to be transferrable to other enzyme families, to facilitate family assignments for homologous protein sequences. [ABSTRACT FROM AUTHOR]