Analysis Of Genetic Relationships Research Articles

Genetic divergence and rela tionship analysis among the okra genotypes by morphological traits

Genetic divergence and rela tionship analysis among the okra genotypes by morphological traits

Discovery of novel potent nuclear factor kappa-B inhibitors (IKK-β) via extensive ligand-based modeling and virtual screening.

Inhibitor kappa-B kinase-beta (IKK-β) controls the activation of nuclear transcription factor kappa-B and has been linked to inflammation and cancer. Therefore, inhibitors of this kinase should have potent anti-inflammatory and anticancer properties. Accordingly, we explored the pharmacophoric space of 218 IKK-β inhibitors to identify high-quality binding models. Subsequently, genetic algorithm-based quantitative structure activity relationship (QSAR) analysis was employed to select the best possible combination of pharmacophoric models and physicochemical descriptors that explain bioactivity variation among training compounds. Three successful pharmacophores emerged in 2 optimal QSAR equations (r12175 =0.733, r12LOO =0.52, F1=65.62, r12PRESS against 43 test inhibitors=0.63 and r22175 =0.683, r22LOO =0.52, F2=72.66, r22PRESS against 43 test inhibitors=0.65). Two pharmacophores were merged in a single binding model. Receiver operating characteristic curve validation proved the excellent qualities of this model. The merged pharmacophore and the associated QSAR equations were applied to screen the National Cancer Institute list of compounds. Ten hits were found to exhibit potent anti-IKK-β bioactivity, out of which, one illustrates IC50 of 11.0nM.

Ultrasensitive single-genome sequencing: accurate, targeted, next generation sequencing of HIV-1 RNA.

BackgroundAlthough next generation sequencing (NGS) offers the potential for studying virus populations in unprecedented depth, PCR error, amplification bias and recombination during library construction have limited its use to population sequencing and measurements of unlinked allele frequencies. Here we report a method, termed ultrasensitive Single-Genome Sequencing (uSGS), for NGS library construction and analysis that eliminates PCR errors and recombinants, and generates single-genome sequences of the same quality as the “gold-standard” of HIV-1 single-genome sequencing assay but with more than 100-fold greater depth.ResultsPrimer ID tagged cDNA was synthesized from mixtures of cloned BH10 wild-type and mutant HIV-1 transcripts containing ten drug resistance mutations. First, the resultant cDNA was divided and NGS libraries were generated in parallel using two methods: uSGS and a method applying long PCR primers to attach the NGS adaptors (LP-PCR-1). Second, cDNA was divided and NGS libraries were generated in parallel comparing 3 methods: uSGS and 2 methods adapted from more recent reports using variations of the long PCR primers to attach the adaptors (LP-PCR-2 and LP-PCR-3). Consistently, the uSGS method amplified a greater proportion of cDNAs, averaging 30% compared to 13% for LP-PCR-1, 21% for LP-PCR-2 and 14% for LP-PCR-3. Most importantly, when the uSGS sequences were binned according to their primer IDs, 94% of the bins did not contain PCR recombinant sequences versus only 55, 75 and 65% for LP-PCR-1, 2 and 3, respectively. Finally, when uSGS was applied to plasma samples from HIV-1 infected donors, both frequent and rare variants were detected in each sample and neighbor-joining trees revealed clusters of genomes driven by the linkage of these mutations, showing the lack of PCR recombinants in the datasets.ConclusionsThe uSGS assay can be used for accurate detection of rare variants and for identifying linkage of rare alleles associated with HIV-1 drug resistance. In addition, the method allows accurate in-depth analyses of the complex genetic relationships of viral populations in vivo.

Genetic Diversity and Population Structure of Rice Varieties Cultivated in Temperate Regions.

BackgroundAfter its domestication, rice cultivation expanded from tropical regions towards northern latitudes with temperate climate in a progressive process to overcome limiting photoperiod and temperature conditions. This process has originated a wide range of diversity that can be regarded as a valuable resource for crop improvement. In general, current rice breeding programs have to deal with a lack of both germplasm accessions specifically adapted to local agro-environmental conditions and adapted donors carrying desired agronomical traits. Comprehensive maps of genome variability and population structure would facilitate genome-wide association studies of complex traits, functional gene investigations and the selection of appropriate donors for breeding purposes.ResultsA collection of 217 rice varieties mainly cultivated in temperate regions was generated. The collection encompasses modern elite and old cultivars, as well as traditional landraces covering a wide genetic diversity available for rice breeders. Whole Genome Sequencing was performed on 14 cultivars representative of the collection and the genomic profiles of all cultivars were constructed using a panel of 2697 SNPs with wide coverage throughout the rice genome, obtained from the sequencing data. The population structure and genetic relationship analyses showed a strong substructure in the temperate rice population, predominantly based on grain type and the origin of the cultivars. Dendrogram also agrees population structure results.ConclusionsBased on SNP markers, we have elucidated the genetic relationship and the degree of genetic diversity among a collection of 217 temperate rice varieties possessing an enormous variety of agromorphological and physiological characters. Taken together, the data indicated the occurrence of relatively high gene flow and elevated rates of admixture between cultivars grown in remote regions, probably favoured by local breeding activities. The results of this study significantly expand the current genetic resources available for temperate varieties of rice, providing a valuable tool for future association mapping studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-016-0130-5) contains supplementary material, which is available to authorized users.

Deciphering Genetic Diversity in the Origins of Pepper (Capsicum spp.) and Comparison with Worldwide Variability

Several attempts in recent decades have been devoted to investigating the genetic and phenotypic diversity harbored by the genus Capsicum. Particular efforts have been directed to old varieties or landraces. However, the genus is still under‐researched, and further investigations that accurately define the relationships among species and identify those geographic regions with greater variability are required. In the present work, 107 Capsicum landraces from Ecuador, Peru, and Bolivia were evaluated with a set of 16 microsatellite markers. In total, 187 alleles were detected in the Andean collection, and 49.7% of those were recorded as unique alleles. Indices of genetic diversity were high and very similar in the three evaluated countries, although the domesticated Capsicum species carrying the highest diversity varied among them: C. frutescens (L.) in Ecuador, C. chinense (Jacq.) in Peru, and C. annuum (L.) in Bolivia. Comparison of Andean accessions with others coming from diverse origins revealed intraspecific genetic differentiation in C. annuum, C. chinense, C. frutescens, C. baccatum (L.), and C. pubescens (Ruiz et Pav.), following a geographic pattern. Similarly, assessment of the genetic diversity currently maintained in Ecuadorian Capsicum species brought to light a dramatic decrease in the genetic variability of cultivated peppers when compared with those harbored by old landraces. Analysis of genetic relationships among Capsicum species was in agreement with previous taxonomic classifications: C. annuum, C. chinense, and C. frutescens were clustered as independent and highly related species; C. cardenasii (Heiser et Smith) and C. eximium (Hunz.) were indistinguishable as a single species; and C. chacoense (Hunz.) was placed between C. pubescens and C. annuum complexes.

Relatedness and dispersal distance of eusocial bee males on mating swarms

AbstractStingless bee males (Hymenoptera: Apidae) aggregate themselves for reproductive purposes. The knowledge of relatedness among the males attending the aggregations and the distance that they disperse from their natal nests to aggregations may provide important data to effectively conserve these bees. Here, we estimated these properties for Tetragonisca angustula (Latreille, 1811) males. Microsatellite molecular markers were used to genotype bees sampled from local nests and in mating swarms in order to identify the nests of origin of males and maternal genotypes of concerning queens. The distances from assigned nests to the mating swarms allowed us to estimate the distances travelled by males. A genetic relationship analysis was conducted to verify whether T. angustula males were closely related to nests where they aggregated. A pairwise relatedness analysis was also performed among all T. angustula males in each mating swarm. Our results demonstrated that T. angustula mating swarms received dozens to hundreds of males from several colonies (up to 70). Only two of the five mating swarms contained any males that were closely related to the bees from the new nests in construction. The relatedness among males was also extremely low. Yet, dispersal distance of T. angustula males ranged hundreds of meters up to 1.6 km, with evidence of reaching 2.25 km according to their flight radius obtained from their foraging area for locality. These data indicate a highly efficient mating system with minimal inbreeding in this bee species, with a great dispersal capability not previously found for stingless bee males.

Development of a SCAR marker associated with salt tolerance in durum wheat (Triticum turgidum ssp. durum) from a semi-arid region

Durum wheat (Triticum turgidum ssp. durum) is one of the main species of cultivated wheat. In arid and semi-arid areas, salinity stress reduces durum wheat productivity. This study used 26 durum wheat accessions from semi-arid regions in Tunisia to analyze plant tolerance to salt stress. Salt stress was experimentally applied by regularly submerging pots in NaCl solution. The salt tolerance trait index (STTI) and salt tolerance index (STI) of various growth parameters were used as criteria to select for salt tolerance. Analysis of genetic relationships was carried out to determine the genetic distance between durum wheat accessions. Based on simple sequence repeats analysis, a molecular marker for salt stress resistance in durum wheat was developed. Salt-treated plants had reduced morphological traits compared to control plants. Most STTIs in all genotypes were below 100 %. Based on STI, 8 accessions were found to be salt-resistant, 16 were salt-moderate, two were salt-susceptible. Analysis of the genetic relationships among 28 Tunisian durum wheat accessions revealed that landraces of the same nominal type are closely related. Of the 94 SSR primers investigated, three were selected and used to design sequence characterized amplified region (SCAR) primers. One SCAR primer pair, KUCMB_Xgwm403_2, produced a 207 bp band that was present in salt-resistant durum wheat lines but absent in salt-susceptible lines. The results suggest that KUCMB_Xgwm403_2 could be a potential genetic tag for salt-tolerant durum wheats.

Genetic characterization of Moroccan and the exotic bread wheat cultivars using functional and random DNA markers linked to the agronomic traits for genomics-assisted improvement.

Genetic characterization, diversity analysis and estimate of the genetic relationship among varieties using functional and random DNA markers linked to agronomic traits can provide relevant guidelines in selecting parents and designing new breeding strategies for marker-assisted wheat cultivar improvement. Here, we characterize 20 Moroccan and 19 exotic bread wheat (Triticum aestivum L.) cultivars using 47 functional and 7 linked random DNA markers associated with 21 loci of the most important traits for wheat breeding. The functional marker analysis revealed that 35, 45, and 10 % of the Moroccan cultivars, respectively have the rust resistance genes (Lr34/Yr18/Pm38), dwarfing genes (Rht1b or Rht2b alleles) and the leaf rust resistance gene (Lr68). The marker alleles for genes Lr37/Yr17/Sr38, Sr24 and Yr36 were present only in the exotic cultivars and absent in Moroccan cultivars. 25 % of cultivars had 1BL.1RS translocation. 70 % of the wheat cultivars had Ppo-D1a and Ppo-A1b associated with low polyphenol oxidase activity. 10 % of cultivars showed presence of a random DNA marker allele (175 bp) linked to Hessian fly resistance gene H22. The majority of the Moroccan cultivars were carrying alleles that impart good bread making quality. Neighbor joining (NJ) and principal coordinate analysis based on the marker data revealed a clear differentiation between elite Moroccan and exotic wheat cultivars. The results of this study are useful for selecting suitable parents for making targeted crosses in marker-assisted wheat breeding and enhancing genetic diversity in the wheat cultivars.Electronic supplementary materialThe online version of this article (doi:10.1007/s13205-016-0413-y) contains supplementary material, which is available to authorized users.

Molecular Analysis and Study of Genetic Relationships among Species of Desmodium Desv. Using RAPD Markers

Molecular Analysis and Study of Genetic Relationships among Species of Desmodium Desv. Using RAPD Markers

Microsatellite-Based Analysis of Genetic Diversity and Relationship of Artificial Hybrid Jiyan-1 Puffer and their Parents, Takifugu flavidus and Takifugu rubripes

In this study, the genetic diversity and relationship of artificial hybrid Jiyan-1 puffer and their parents (T. flavidus ♀ and T. rubripes ♂) were evaluated using 15 microsatellite markers. The average number of alleles (Na), observed heterozygosity (Ho), and expected heterozygosity (He) of T. flavidus were higher than the average values of T. rubripes. Jiyan-1 puffer showed a relatively high level of genetic diversity, with an average allele number of 6.467 and mean observed and expected heterozygosity of 0.560 and 0.592, respectively. UPGMA cluster analysis indicated that Jiyan-1 puffer inherited more genetic information from female parents. This study indicates that the microsatellite markers will be useful for investigation of genetic background of puffer fish, as well as better conservation and sustainable utilization of puffer fish in aquaculture.

Analysis of Powdery Mildew Resistant Characteristic and Genetic Relationship of Cultivated Soybean, Glycine max, in Vietnam for Parental Selection

Analysis of Powdery Mildew Resistant Characteristic and Genetic Relationship of Cultivated Soybean, Glycine max, in Vietnam for Parental Selection

Molecular Characterization of New Zealand White and APAU Black Rabbits using Microsatellite Markers

Genetic diversity among two genetic groups (New Zealand White and APAU Black) was investigated with a set of 20 microsatellite markers in the present study. The results showed that out of 20 microsatellites, 12 rabbit specific markers were successfully amplified by PCR which were highly polymorphic. A total of 257 alleles were observed across the 12 loci amplified. Number of alleles ranged from 5 to 14 and 5 to 16 in New Zealand White and APAU Black populations, respectively. The overall mean values of observed heterozygosity (0.554 in New Zealand White and 0.556 in APAU Black), expected heterozygosity (0.870 in New Zealand White and 0.875 in APAU Black), Polymorphic Information Content (0.856 in New Zealand White and 0.862 in APAU Black) and the mean effective number of alleles (8.629 in New Zealand White and 8.876 in APAU Black) of these two genetic groups were high. Out of the 12 amplified loci 7 loci deviated significantly from Hardy-Weinberg equilibrium in New Zealand White and 5 loci deviated in case of APAU Black which may be due to selection followed. The mean FIS, FIT and FST values over all the population were found to be 0.377, 0.402 and 0.040, respectively. The results suggested that the 12 amplified rabbit specific microsatellite loci were effective markers for analysis of genetic relationships among rabbit populations.

Evaluation of horticultural traits and genetic relationship in melon germplasm

Horticultural traits and genetic relationship were evaluated for 83 melon (Cucumis melo L.) cultivars. Survey of a total of 36 characteristics for seedling, leaf, stem, flower, fruit, and seed and subsequent multiple analysis of variance (MANOVA) were conducted. Principal component analysis (PCA) showed that 8 principle components including fruit weight, fruit length, fruit diameter, cotyledon length, seed diameter, and seed length accounted for 76.3% of the total variance. Cluster analysis of the 83 melon cultivars using average linkage method resulted in 5 clusters at coefficient of 0.7. Cluster I consisted of cultivars with high values for fruit-related traits, Cluster II for soluble solid content, and Cluster V for high ripening rate. Genotyping of the 83 cultivars was conducted using 15 expressed-sequence tagged-simple sequence repeat (EST-SSR) from the Cucurbit Genomics Initiative (ICuGI) database. Analysis of genetic relatedness by UPGMA resulted in 6 clusters. Mantel test indicated that correlation between morphological and genetic distance was very low (r = -0.11).

Prevalence, enumeration, and pheno- and genotypic characteristics of Listeria monocytogenes isolated from raw foods in South China.

Listeria monocytogenes is an important foodborne pathogen that can cause serious illness in immunocompromised individuals, pregnant women, the elderly, and newborns. The aim of this study was to: (i) evaluate the prevalence and contamination level [most probable number (MPN)] of L. monocytogenes in 567 retail raw foods (fishery products, n = 154; raw/fresh meat, n = 123; frozen foods, n = 110; edible fungi, n = 108; vegetables, n = 72) collected from South China and (ii) to gain further knowledge on the phenotype and genotype distributions of this important foodborne pathogen. Approximately 22% of the samples were positive for L. monocytogenes. The contamination levels were between 0.3 and 10 MPN/g in 75.0%, between 10 and 100 MPN/g in 11.0% and less than 100 MPN/g in 14.0% of the countable samples. Five serogroups were identified among the 177 foodborne L. monocytogenes isolates, with 1/2a-3a (42.4%) and 1/2b-3b (26.0%) serogroups being the most dominant. Serogroups I.1 and II.2 were only found in the edible mushrooms, while serogroup III was dominant in the fishery products, suggesting that specific serogroups of L. monocytogenes may have distinct ecological niches. Ten (5.6%) L. monocytogenes isolates exhibited multidrug resistance. Genetic relatedness analysis revealed the absence of distinct associations between specific food types, antibiotic resistance, serogroups, and genetic diversity. The present study provided the first baseline data on the prevalence, contamination level, and characteristics of L. monocytogenes isolated from raw foods in South China. Some multidrug resistant strains belonged to the epidemiologically important serogroups (I.1 and II.1), implying a potential public health risk. In addition, these findings also provide basic information for the Chinese food safety associated authorities to draft appropriate standards to control L. monocytogenes contamination and improve microbiological safety of raw foods.

Genetic relatedness and recombination analysis of Allorhizobium vitis strains associated with grapevine crown gall outbreaks in Europe.

To analyse genetic diversity and epidemiological relationships among 54 strains of Allorhizobium vitis isolated in Europe during an 8-year period and to assess the relative contribution of mutation and recombination in shaping their diversity. By using random amplified polymorphic DNA (RAPD) PCR, strains studied were distributed into 12 genetic groups. Sequence analysis of dnaK, gyrB and recA housekeeping genes was employed to characterize a representative subcollection of 28 strains. A total of 15 different haplotypes were found. Nucleotide sequence analysis suggested the presence of recombination events in A. vitis, particularly affecting dnaK locus. Although prevalence of mutation over recombination was found, impact of recombination was about two times greater than mutation in the evolution of the housekeeping genes analysed. The RAPD analysis indicated high degree of genetic diversity among the strains. However, the most abundant RAPD group was composed of 35 strains, which could lead to the conclusion that they share a common origin and were distributed by the movement of infected grapevine planting material as a most common way of crossing long distances. Furthermore, it seems that recombination is acting as an important driving force in the evolution of A. vitis. As no substantial evidence of recombination was detected within recA gene fragment, this phylogenetic marker could be reliable to characterize phylogenetic relationships among A. vitis strains. We demonstrated clear epidemiological relationship between majority of strains studied, suggesting a need for more stringent phytosanitary measures in international trade. Moreover, this is the first study to report recombination in A. vitis.

Genetic variability and structure of SNP haplotypes in the DMPK gene in Yakuts and other ethnic groups of northern Eurasia in relation to myotonic dystrophy

The genetic variability of the DMPK locus has been studied in relation to six SNP markers (rs2070736, rs572634, rs1799894, rs527221, rs915915, and rs10415988) in Yakuts with myotonic dystrophy (MD) in the Yakut population and in populations of northern Eurasia. Significant differences were observed in the allele frequencies between patients and a population sample of Yakuts for three SNP loci (rs915915, rs1799894, and rs10415988) associated with a high chance of disease manifestation. The odds ratios (OR) of MD development in representatives of the Yakut population for these three loci were 2.59 (95% CI, p = 0,004), 4.99 (95% CI, p = 0.000), and 3.15 (95% CI, p = 0.01), respectively. Haplotype TTTCTC, which is associated with MD, and haplotype GTCCTT, which was observed only in Yakut MD patients (never in MD patients of non-Yakut origin), were revealed. A low level of variability in the locus of DMRK gene in Yakuts (H(e) = 0.283) compared with other examined populations was noted. An analysis of pairwise genetic relationships between populations revealed their significant differentiation for all the examined loci. In addition, a low level of differentiation in territorial groups of Yakut populations (F(ST) = 0.79%), which was related to the high subdivision of the northern Eurasian population (F(ST) = 11.83%), was observed.

Ploidy polymorphism and morphological variation among reciprocal hybrids ofPseudosciaena crocea(♀) × Miichthys miiuy(♂)

Diploid and triploid hybrids of large yellow croaker (Pseudosciaena crocea, Pc) and Miiuy croaker (Miichthys miiuy, Mm) were produced by interspecific hybridization. The result showed that Pc (♀) and Mm (♂) can be successfully crossed and hybrid offspring of normal hatch rate were produced. In contrast, a lower fertilize and hatch rate were produced for hybrids of Pc (♂) and Mm (♀), and the offspring died day 19 after hatching. To confirm the ploidy of hybrid offspring, we examined the karyotypes of offspring. The result of DNA relative content investigation and genetic relationship analysis demonstrated that the major hybrid offspring were hybrid diploid. In addition, a small number of hybrid were triploid and gynogenesis diploid. Morphological analysis based on the measurable traits data indicated the success of the interspecific crosses. The natural gynogenetic diploid large yellow croaker (PP), diploid hybrids (PM) and triploid hybrids (PPM) were closer to maternal parent (Pc) than paternal parent (Mm). This study provided genetic evidences of the chromosome, DNA content and morphological levels to support the successful establishment of the polyploidy hybrids of Pc (♀) and Mm (♂).

Start codon targeted (SCoT) and target region amplification polymorphism (TRAP) for evaluating the genetic relationship of Dendrobium species

Two molecular marker systems, start codon targeted (SCoT) and target region amplification polymorphism (TRAP), were used for genetic relationship analysis of 36 Dendrobium species collected from China. Twenty-two selected SCoT primers produced 337 loci, of which 324 (96%) were polymorphic, whereas 13 TRAP primer combinations produced a total of 510 loci, with 500 (97.8%) of them being polymorphic. An average polymorphism information content of 0.953 and 0.983 was detected using the SCoT and TRAP primers, respectively, showing that a high degree of genetic diversity exists among Chinese Dendrobium species. The partition of clusters in the unweighted pair group method with arithmetic mean dendrogram and principal coordinate analysis plot based on the SCoT and TRAP markers was similar and clustered the 36 Dendrobium species into four main groups. Our results will provide useful information for resource protection and will also be useful to improve the current Dendrobium breeding programs. Our results also demonstrate that SCoT and TRAP markers are informative and can be used to evaluate genetic relationships between Dendrobium species.

Variations in electrical impedance and phase angle among seedlings of Pinus densata and parental species in Pinus tabuliformis habitat environment

Electrical impedance (EI) and phase angle (PHI) parameters in AC impedance spectroscopy are important electrical parameters in the study of medical pathology. However, little is known about their application in variation and genetic relationship studies of forest trees. In order to test whether impedance parameters could be used in genetic relationship analysis among conifer species, EI and PHI were measured in a seedling experiment test composed of Pinus tabuliformis, Pinus yunnanensis, and Pinus densata in a habitat of Pinus tabuliformis. The results showed that variations in both EI and PHI among species were significant in different electric frequencies, and the EI and PHI values measured in the two populations of P. densata were between the two parental species, P. yunnanensis and P. tabuliformis. These results show that these two impedance parameters could reflect the genetic relationship among pine species. This was the first time using the two AC impedance spectroscopy parameters to test the genetic relationship analysis between tree species, and would be a hopeful novel reference methodology for future studies in evolution and genetic variation of tree species.

Genetic characterization and relationships of traditional grape cultivars from Serbia

Reference genetic profiles were generated for 12 traditional grapevine cultivars of Serbia through a genotyping approach that included the core set of 9 SSR markers for genetic identification and further 13 common microsatellites for strengthening genetic relationship analysis. Consistent matching with SSR markers of grapevines cultivated in neighbouring countries or maintained in European germplasm collections was found for most of the genotypes, suggesting possible synonyms and revealing that 'Muskat Krokan' corresponds to 'Muscat fleur d’Oranger' and two 'Tamjanika' cultivars are identical to 'Moscato Giallo' and 'Moscato Rosa'. When compared with germplasm representing the classical eco-geographic grouping of grapevine cultivars, Serbian non-Muscat genotypes clustered within the Convar pontica subconvar balcanica taxon thus supporting their indigenous origin.