scholarly journals Transferability of apple and pear SSRs to other temperate pome fruit crops of family Rosaceae

Genetika ◽  
2021 ◽  
Vol 53 (1) ◽  
pp. 195-208
Author(s):  
Himani Sharma ◽  
Parul Sharma ◽  
Rajnish Sharma
Keyword(s):  
Comparative Genomic ◽  
Fruit Crops ◽  
Pome Fruit ◽  
Pcr Product ◽  
Homologous Locus ◽  
Ssr Loci ◽  
Genomic Studies ◽  
Successful Amplification ◽  
High Level ◽  
Relationship Of

Extensive use of simple sequence repeat (SSR) is facilitated if loci would be transferable across species even in closely related genera to overcome high cost and efforts involved in their development as major constraints. In the present study, apple and pear genomic microsatellite primer pairs were used to amplify SSR loci in apple, pear, quince and loquat genotypes, respectively. Already reported SSRs were selected based on their polymorphic survey for successful amplification with at least one polymerase chain reaction (PCR) product of the approximate size expected for a homologous locus screened among apple and pear genotypes for further transferability exploration across other temperate pome fruit crops, respectively. Highest transferability of apple and pear SSR, 61.53 % and 73.33 % was observed in closely related quince and apple genotypes, respectively. This indicated that primer binding sites between these two closely related genera, Malus and Pyrus, are fairly well conserved. Maximum transferability rate was found to be 93.33 % and 80.00 % across all the subjected genotypes for primer CH05D11 and TSUenh016 in apple and pear, respectively. The transferability of markers is based on genomic similarity, and can reflect the relationship of genome collinearity and even evolution between species. This high level of transferability of apple and pear SSRs to other temperate pome fruit crops indicated their promise for application to future molecular screening, map construction, and comparative genomic studies, etc.

scholarly journals Broccoli: combining phylogenetic and network analyses for orthology assignment

2019 ◽  
Author(s):  
Romain Derelle ◽  
Hervé Philippe ◽  
John K. Colbourne
Keyword(s):  
Learning Algorithm ◽  
Phylogenetic Analyses ◽  
Gene Clustering ◽  
Comparative Genomic ◽  
Orthology Assignment ◽  
Bioinformatic Tools ◽  
Network Analyses ◽  
Benchmark Datasets ◽  
Genomic Studies ◽  
High Level

AbstractOrthology assignment is a key step of comparative genomic studies, for which many bioinformatic tools have been developed. However, all gene clustering pipelines are based on the analysis of protein distances, which are subject to many artefacts. In this paper we introduce Broccoli, a user-friendly pipeline designed to infer, with high precision, orthologous groups and pairs of proteins using a phylogeny-based approach. Briefly, Broccoli performs ultra-fast phylogenetic analyses on most proteins and builds a network of orthologous relationships. Orthologous groups are then identified from the network using a parameter-free machine learning algorithm. Broccoli is also able to detect chimeric proteins resulting from gene-fusion events and to assign these proteins to the corresponding orthologous groups. Tested on two benchmark datasets, Broccoli outperforms current orthology pipelines. In addition, Broccoli is scalable, with runtimes similar to those of recent distance-based pipelines. Given its high level of performance and efficiency, this new pipeline represents a suitable choice for comparative genomic studies.Broccoli is freely available at https://github.com/rderelle/Broccoli.

scholarly journals Broccoli: Combining Phylogenetic and Network Analyses for Orthology Assignment

2020 ◽  
Vol 37 (11) ◽  
pp. 3389-3396 ◽  
Author(s):  
Romain Derelle ◽  
Hervé Philippe ◽  
John K Colbourne
Keyword(s):  
Learning Algorithm ◽  
Phylogenetic Analyses ◽  
Gene Clustering ◽  
Comparative Genomic ◽  
Orthology Assignment ◽  
Bioinformatic Tools ◽  
Network Analyses ◽  
Genomic Studies ◽  
High Level ◽  
Free Machine

Abstract Orthology assignment is a key step of comparative genomic studies, for which many bioinformatic tools have been developed. However, all gene clustering pipelines are based on the analysis of protein distances, which are subject to many artifacts. In this article, we introduce Broccoli, a user-friendly pipeline designed to infer, with high precision, orthologous groups, and pairs of proteins using a phylogeny-based approach. Briefly, Broccoli performs ultrafast phylogenetic analyses on most proteins and builds a network of orthologous relationships. Orthologous groups are then identified from the network using a parameter-free machine learning algorithm. Broccoli is also able to detect chimeric proteins resulting from gene-fusion events and to assign these proteins to the corresponding orthologous groups. Tested on two benchmark data sets, Broccoli outperforms current orthology pipelines. In addition, Broccoli is scalable, with runtimes similar to those of recent distance-based pipelines. Given its high level of performance and efficiency, this new pipeline represents a suitable choice for comparative genomic studies. Broccoli is freely available at https://github.com/rderelle/Broccoli.

scholarly journals High-Density Genetic Map Construction and Identification of QTLs Controlling Leaf Abscission Trait in Poncirus trifoliata

2021 ◽  
Vol 22 (11) ◽  
pp. 5723
Author(s):  
Yuan-Yuan Xu ◽  
Sheng-Rui Liu ◽  
Zhi-Meng Gan ◽  
Ren-Fang Zeng ◽  
Jin-Zhi Zhang ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Linkage Map ◽  
Genetic Map ◽  
Expression Patterns ◽  
High Density ◽  
Poncirus Trifoliata ◽  
Leaf Abscission ◽  
Comparative Genomic ◽  
Map Comparison ◽  
Genomic Studies

A high-density genetic linkage map is essential for genetic and genomic studies including QTL mapping, genome assembly, and comparative genomic analysis. Here, we constructed a citrus high-density linkage map using SSR and SNP markers, which are evenly distributed across the citrus genome. The integrated linkage map contains 4163 markers with an average distance of 1.12 cM. The female and male linkage maps contain 1478 and 2976 markers with genetic lengths of 1093.90 cM and 1227.03 cM, respectively. Meanwhile, a genetic map comparison demonstrates that the linear order of common markers is highly conserved between the clementine mandarin and Poncirus trifoliata. Based on this high-density integrated citrus genetic map and two years of deciduous phenotypic data, two loci conferring leaf abscission phenotypic variation were detected on scaffold 1 (including 36 genes) and scaffold 8 (including 107 genes) using association analysis. Moreover, the expression patterns of 30 candidate genes were investigated under cold stress conditions because cold temperature is closely linked with the deciduous trait. The developed high-density genetic map will facilitate QTL mapping and genomic studies, and the localization of the leaf abscission deciduous trait will be valuable for understanding the mechanism of this deciduous trait and citrus breeding.

scholarly journals The Diversity and Evolution of Sex Chromosomes in Frogs

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 483
Author(s):  
Wen-Juan Ma ◽  
Paris Veltsos
Keyword(s):  
Sex Determination ◽  
Sex Chromosomes ◽  
Chromosome Evolution ◽  
Sex Chromosome ◽  
Comparative Genomic ◽  
Ancestral State ◽  
Heteromorphic Sex Chromosomes ◽  
Genomic Studies ◽  
Evolutionary Trajectories ◽  
Heterogametic Sex

Frogs are ideal organisms for studying sex chromosome evolution because of their diversity in sex chromosome differentiation and sex-determination systems. We review 222 anuran frogs, spanning ~220 Myr of divergence, with characterized sex chromosomes, and discuss their evolution, phylogenetic distribution and transitions between homomorphic and heteromorphic states, as well as between sex-determination systems. Most (~75%) anurans have homomorphic sex chromosomes, with XY systems being three times more common than ZW systems. Most remaining anurans (~25%) have heteromorphic sex chromosomes, with XY and ZW systems almost equally represented. There are Y-autosome fusions in 11 species, and no W-/Z-/X-autosome fusions are known. The phylogeny represents at least 19 transitions between sex-determination systems and at least 16 cases of independent evolution of heteromorphic sex chromosomes from homomorphy, the likely ancestral state. Five lineages mostly have heteromorphic sex chromosomes, which might have evolved due to demographic and sexual selection attributes of those lineages. Males do not recombine over most of their genome, regardless of which is the heterogametic sex. Nevertheless, telomere-restricted recombination between ZW chromosomes has evolved at least once. More comparative genomic studies are needed to understand the evolutionary trajectories of sex chromosomes among frog lineages, especially in the ZW systems.

scholarly journals Simple Sequence Repeat and S-Locus Genotyping to Assist the Genetic Characterization and Breeding of Polyploid Prunus Species, P. spinosa and P. domestica subsp. insititia

2021 ◽  
Author(s):  
Júlia Halász ◽  
Noémi Makovics-Zsohár ◽  
Ferenc Szőke ◽  
Sezai Ercisli ◽  
Attila Hegedűs
Keyword(s):  
Simple Sequence Repeat ◽  
Principal Component ◽  
Sequence Repeat ◽  
Breeding Programs ◽  
Allele Number ◽  
Genetic Potential ◽  
Ssr Loci ◽  
High Level ◽  
Diversity Studies ◽  
Simple Sequence

AbstractPolyploid Prunus spinosa (2n = 4 ×) and P. domestica subsp. insititia (2n = 6 ×) represent enormous genetic potential in Central Europe, which can be exploited in breeding programs. In Hungary, 16 cultivar candidates and a recognized cultivar ‘Zempléni’ were selected from wild-growing populations including ten P. spinosa, four P. domestica subsp. insititia and three P. spinosa × P. domestica hybrids (2n = 5 ×) were also created. Genotyping in eleven simple sequence repeat (SSR) loci and the multiallelic S-locus was used to characterize genetic variability and achieve a reliable identification of tested accessions. Nine SSR loci proved to be polymorphic and eight of those were highly informative (PIC values ˃ 0.7). A total of 129 SSR alleles were identified, which means 14.3 average allele number per locus and all accessions but two clones could be discriminated based on unique SSR fingerprints. A total of 23 S-RNase alleles were identified and the complete and partial S-genotype was determined for 10 and 7 accessions, respectively. The DNA sequence was determined for a total of 17 fragments representing 11 S-RNase alleles. ‘Zempléni’ was confirmed to be self-compatible carrying at least one non-functional S-RNase allele (SJ). Our results indicate that the S-allele pools of wild-growing P. spinosa and P. domestica subsp. insititia are overlapping in Hungary. Phylogenetic and principal component analyses confirmed the high level of diversity and genetic differentiation present within the analysed accessions and indicated putative ancestor–descendant relationships. Our data confirm that S-locus genotyping is suitable for diversity studies in polyploid Prunus species but non-related accessions sharing common S-alleles may distort phylogenetic inferences.

Relationship of Spiritual well-being and emotional intelligence among Iranian' nursing students

2021 ◽  
Vol 15 (6) ◽  
pp. 1634-1640
Author(s):  
Javad Jafari ◽  
Asra Nassehi ◽  
Mohammadali Zareez ◽  
Seydamalek Dadkhah ◽  
Najmeh Saberi ◽  
...  
Keyword(s):  
Emotional Intelligence ◽  
Nursing Students ◽  
Pearson Correlation ◽  
Well Being ◽  
Self Awareness ◽  
Spiritual Well Being ◽  
The Mean ◽  
High Level ◽  
Relationship Of ◽  
Religious Wellbeing

Background: Among all aspects of nursing care, the spiritual one is the issue that has received little attention. Having spiritual wellbeing (SWB) is a necessity to provide appropriate spiritual care. In addition to, the Emotional intelligence (EI) is one of the most important factors in social and professional success and is essential for effective nursing practice. Therefore, aim of study was evaluating the Relationship between SWB and EI among nursing students. Methods: The sample of this descriptive-analytic study consisted of 136 nursing students studying at Bam University of Medical Sciences selected by convenience sampling method. The Bradberry and Greaves 28-item EI scale, Palutzian and Ellison SWB Scale were used to assess the total score of EI and SWB. Collected data were analyzed using descriptive statistics (mean and standard deviation), Pearson correlation coefficient, independent t-test and one-way ANOVA with SPSS v18. Results: The mean score of SWB and EI were 97.1±11.56 and 123.4 + 123.6, respectively. The mean score dimensions of SWB include (religious wellbeing 47.9±6.6, existential wellbeing 49.1±5.7) and dimensions EI: self-awareness, self-management, social awareness, and relationship management were 27.2 3 3.2, 36.2 2 5.4, 25.1 + 3.5 and 35.1 + 4.5, respectively. The majority of students have reported moderate level SWB and high level of emotional intelligence. The factors influencing their level of SWB were academic semester and age (p<0.05). Conclusion: Although the level of students' EI and SWB were at a desirable level in this study, due to the nature of nursing and the interaction between nurses and patients, providing a suitable learning environment for the development of EI is essential. Therefore, it is suggested that nursing policymakers should develop appropriate educational programs for nurses and provide curriculum for students to promote their knowledge and skills. Keywords: spiritual, religious, wellbeing, existential, nursing, emotional intelligence

Relationship between Visitors’ Sense of Place, Recreation Behavior, and Acceptability of Resource Allocation Strategies at a Reservoir Facing a Water Crisis

2022 ◽  
Author(s):  
Zack Darby ◽  
Neelam Chandra Poudyal ◽  
Adam Frakes ◽  
Omkar Joshi
Keyword(s):  
Sense Of Place ◽  
Water Conservation ◽  
Water Allocation ◽  
Water Conditions ◽  
Alternative Water ◽  
High Level ◽  
Recreation Behavior ◽  
Relationship Of ◽  
Visitor Survey ◽  
Allocation Strategies

Municipal drawdowns at public reservoirs can negatively impact recreational uses on site. Therefore, sustaining recreation requires understanding how users relate themselves with the reservoir and the resource therein, and how they will respond to circumstances and policies impacting the resource. Researchers use placedbased theory, particularly sense of place (SOP), to assess the user community’s perspective on the natural resource or recreation site of interest. This study utilized visitor survey data (n=282) from Canton Reservoir in Oklahoma to assess visitors’ sense of place (SOP), and to evaluate the relationship of SOP with their acceptability of alternative water allocation strategies and future intention of visiting the reservoir under depleted water conditions. Visitors had a high level of SOP with the reservoir and supported protective water allocation strategies that either favor the retention of water on-site or ensure a fair distribution between recreation and municipal use. Results suggest a positive relationship between visitors' SOP and their intended trips to the reservoir even under depleted water conditions. The findings highlight the psychological, functional, and emotional benefits associated with the recreational use of the Canton Reservoir, which will in turn help managers make more informed and balanced decisions about water conservation and allocation. Insights from this study will also contribute in literature on the sense of place and protective norms and offers several implications for the management of public reservoirs.

Association of Hemoglobin A1C With TDP-43 Pathology in Community-Based Elders

Neurology ◽  
2021 ◽  
pp. 10.1212/WNL.0000000000012025
Author(s):  
Shahram Oveisgharan ◽  
Ana W. Capuano ◽  
Sukriti Nag ◽  
Sonal Agrawal ◽  
Lisa L. Barnes ◽  
...  
Keyword(s):  
Severity Score ◽  
Hemoglobin A1c ◽  
Oldest Old ◽  
Brain Regions ◽  
Inverse Association ◽  
Community Based ◽  
Cytoplasmic Inclusions ◽  
The Mean ◽  
High Level ◽  
Relationship Of

Objective.We tested the hypothesis that an inverse association exists between diabetes mellitus (DM) and hemoglobin A1C (A1C) with Transactive response DNA binding protein 43 (TDP-43) levels in older adults.Methods.We leveraged antemortem and postmortem data of decedents from three community-based clinical-pathological studies. DM status, A1C levels, and medications for DM were documented annually. TDP-43 cytoplasmic inclusions, evaluated in 6 brain regions using immunohistochemistry, were used to obtain a semiquantitative TDP-43 score (0-5) in each region, and scores were averaged across regions to obtain a TDP-43 severity score. We used linear regressions to test the association of DM and A1C with the TDP-43 severity score.Results.On average, participants (n=817) were 90 years old at the time of death, three fourth were women, and one fourth had DM. The mean A1C was 6.0% (SD=0.6). TDP-43 was observed in 54% of participants, and the mean TDP-43 score was 0.7 (range 0-4.5). A higher level of A1C was associated with a lower TDP-43 score (estimate=-0.156, S.E.=0.060, p=0.009) while DM had a borderline inverse association with the TDP-43 score (estimate=-0.163, S.E.=0.087, p=0.060). The association of higher levels of A1C with lower TDP-43 scores persisted after further adjustment by Apolipoprotein ε4, vascular risk factors, stroke, and hypoglycemic medications. Exclusion of the oldest old participants did not change the results.Conclusion.Overall, the results suggest that a high level of A1C is associated with less TDP-43 proteinopathy in older persons while the relationship of DM with TDP-43 needs further study.

scholarly journals Identification of RD5-EncodedMycobacterium tuberculosisProteins As B-Cell Antigens Used for Serodiagnosis of Tuberculosis

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Miao-Miao Zhang ◽  
Jun-Wei Zhao ◽  
Zhan-Qiang Sun ◽  
Jun Liu ◽  
Xiao-Kui Guo ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Detection Sensitivity ◽  
Comparative Genomic ◽  
Healthy Controls ◽  
Specific Diagnosis ◽  
Pulmonary Tb ◽  
Genomic Studies ◽  
Immunodominant Antigens ◽  
Genomic Regions ◽  
Hiv Negative

Comparative genomic studies have identified severalMycobacterium tuberculosis-specific genomic regions of difference (RDs) which are absent in the vaccine strains ofMycobacterium bovisBCG and which may be useful in the specific diagnosis of tuberculosis (TB). In this study, all encoded proteins from DNA segment RD5 ofMycobacterium tuberculosis, that is, Rv3117–Rv3121, were recombined and evaluated by enzyme-linked immunosorbent assays for antibody reactivity with sera from HIV-negative pulmonary TB patients (n=60) and healthy controls (n=32). The results identified two immunodominant antigens, that is, Rv3117 and Rv3120, both of which revealed a statistically significant antigenic distinction between healthy controls and TB patients (P<0.05). In comparison with the well-known early-secreted antigen target 6 kDa (ESAT-6) (sensitivity 21.7%, specificity 90.6%), the higher detection sensitivity and higher specificity were achieved (Rv3117: sensitivity 25%, specificity 96.9%; Rv3120: sensitivity 31.7%, specificity 96.9%). Thus, the results highlight the immunosensitive and immunospecific nature of Rv3117 and Rv3120 and indicate promise for their use in the serodiagnosis of TB.

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