Linkage Relationships Research Articles

Erratum to: Genetic structure of a QTL hotspot on chromosome 2 in sweet cherry indicates positive selection for favorable haplotypes

A genomic region of particular interest for sweet cherry (Prunus avium L.) breeding is a quantitative trait locus (QTL) “hotspot” on chromosome 2. QTLs for fruit size, firmness, sweetness, and flowering time are reported to map to this region. An understanding of genetic diversity, allele sources, linkage relationships, and historical recombinations is critical to enable the combining of favorable alleles at multiple loci. The objectives of this study were to characterize, visualize, and interpret the genetic structure of this previously identified QTL hotspot within North American sweet cherry breeding germplasm, using a pedigree-based haploblocking approach. Across the 29.4 cM (6.3 Mbp) region defined by single nucleotide polymorphism (SNP) information from the RosBREED cherry 6K SNP array v1, a total of 12 recombination events falling into six inter-marker regions were traced within the pedigree of elite and wild germplasm (n = 55). These recombinations defined five haploblocks containing 5–15 markers and exhibiting 7–11 haplotypes each. Over the entire QTL hotspot, 30 extended haplotypes were identified for which parental gametes could be determined. When the haploblocks and their haplotypes were used to explore genetic diversity, ancestry, and recombination patterns, and then integrated with previous QTL results for fruit size, the results indicated that favorable alleles at this QTL hotspot are under positive selection in breeding. The genetic framework provided by a haploblock approach and knowledge of haplotype-level diversity sets the stage for assigning breeding utility to these haplotypes.

Development of a molecular marker tightly linked to the C locus conferring a white bulb color in onion (Allium cepa L.) using bulked segregant analysis and RNA-Seq

To develop molecular markers linked to the C locus determining a white bulb color in onion (Allium cepa L.), a combination of bulked segregant analysis (BSA) and RNA-Seq was performed using bulked RNAs extracted from 12 plants each of yellow and white F2 bulbs. Ninety-seven genes showed at least five-fold increased expression in the yellow bulk. Eleven previously isolated structural genes were identified from these genes. Two homologous genes coding for phenylalanine ammonia lyase (PAL) and chalcone isomerase (CHI) were also identified. In addition, three glycosyltransferase genes and two acyltransferase genes showed increased transcription in the yellow bulk. Increased expression of 18 structural genes in the yellow F2 individuals were further confirmed by reverse transcription polymerase chain reaction (RT-PCR). Regarding regulatory genes, a gene encoding a WRKY transcription factor was most significantly down-regulated in the white bulk. In the MBW complex, known to control a flavonoid biosynthetic pathway, 47, four, and eight genes encoding putative MYB, bHLH, and WD40 proteins, respectively, were identified from transcriptome. Among them, two MYB-, one bHLH-, and one WD40-coding gene(s) showed up-regulation in the yellow bulk and high similarity with other known regulators of flavonoid biosynthesis. Among 1829 contigs containing single nucleotide polymorphisms (SNPs) or InDels, five contigs were shown to be linked to the C locus. In addition, SNPs in the gene encoding glutathione S-transferase (GST) also showed a linkage relationship. Six molecular markers were developed and a linkage map was constructed using 586 F2:3 individuals. The GST1 marker based on the GST-coding gene showed perfect linkage to the C locus.

A Targeted Capture Linkage Map Anchors the Genome of the Schistosomiasis Vector Snail, Biomphalaria glabrata.

The aquatic planorbid snail Biomphalaria glabrata is one of the most intensively-studied mollusks due to its role in the transmission of schistosomiasis. Its 916 Mb genome has recently been sequenced and annotated, but it remains poorly assembled. Here, we used targeted capture markers to map over 10,000 B. glabrata scaffolds in a linkage cross of 94 F1 offspring, generating 24 linkage groups (LGs). We added additional scaffolds to these LGs based on linkage disequilibrium (LD) analysis of targeted capture and whole-genome sequences of 96 unrelated snails. Our final linkage map consists of 18,613 scaffolds comprising 515 Mb, representing 56% of the genome and 75% of genic and nonrepetitive regions. There are 18 large (> 10 Mb) LGs, likely representing the expected 18 haploid chromosomes, and > 50% of the genome has been assigned to LGs of at least 17 Mb. Comparisons with other gastropod genomes reveal patterns of synteny and chromosomal rearrangements. Linkage relationships of key immune-relevant genes may help clarify snail–schistosome interactions. By focusing on linkage among genic and nonrepetitive regions, we have generated a useful resource for associating snail phenotypes with causal genes, even in the absence of a complete genome assembly. A similar approach could potentially improve numerous poorly-assembled genomes in other taxa. This map will facilitate future work on this host of a serious human parasite.

Fungal Sex: The Basidiomycota.

Fungi of the Basidiomycota, representing major pathogen lineages and mushroom-forming species, exhibit diverse means to achieve sexual reproduction, with particularly varied mechanisms to determine compatibilities of haploid mating partners. For species that require mating between distinct genotypes, discrimination is usually based on both the reciprocal exchange of diffusible mating pheromones, rather than sexes, and the interactions of homeodomain protein signals after cell fusion. Both compatibility factors must be heterozygous in the product of mating, and genetic linkage relationships of the mating pheromone/receptor and homeodomain genes largely determine the complex patterns of mating-type variation. Independent segregation of the two compatibility factors can create four haploid mating genotypes from meiosis, referred to as tetrapolarity. This condition is thought to be ancestral to the basidiomycetes. Alternatively, cosegregation by linkage of the two mating factors, or in some cases the absence of the pheromone-based discrimination, yields only two mating types from meiosis, referred to as bipolarity. Several species are now known to have large and highly rearranged chromosomal regions linked to mating-type genes. At the population level, polymorphism of the mating-type genes is an exceptional aspect of some basidiomycete fungi, where selection under outcrossing for rare, intercompatible allelic variants is thought to be responsible for numbers of mating types that may reach several thousand. Advances in genome sequencing and assembly are yielding new insights by comparative approaches among and within basidiomycete species, with the promise to resolve the evolutionary origins and dynamics of mating compatibility genetics in this major eukaryotic lineage.

Discussion on the Linkage Relationship between National Fitness Public Service and Competitive Sports Public Service

Using literature, logic analysis and other methods, discussed the relationship between the national fitness of public service and competitive sports public service , that the (1) national fitness public service provide the mass base for competitive sports public service . (2) Competitive sports public service provides the choice guidance for the national fitness public service. (3) The public service of competitive sports is the economy of national fitness public service. Both of the linkage development, mutual promotion, complements each other.

Bronx Teens Connection's Clinic Linkage Model: Connecting Youth to Quality Sexual and Reproductive Health Care

PurposeTeen pregnancy and birth rates in the Bronx have been higher than in New York City, representing a longstanding health disparity. The New York City Department of Health and Mental Hygiene implemented a community-wide, multicomponent intervention to reduce unintended teen pregnancy, the Bronx Teens Connection. The Bronx Teens Connection Clinic Linkage Model sought to increase teens' access to and use of sexual and reproductive health care by increasing community partner capacity to link neighborhood clinics to youth-serving organizations, including schools. MethodsThe Bronx Teens Connection Clinic Linkage Model used needs assessments, delineated the criteria for linkages, clarified roles and responsibilities of partners and staff, established trainings to support the staff engaged in linkage activities, and developed and used process evaluation methods. ResultsEarly results demonstrated the strength and feasibility of the model over a 4-year period, with 31 linkages developed and maintained, over 11,300 contacts between clinic health educators and teens completed, and increasing adherence to the Centers for Disease Control and Prevention–defined clinical best practices for adolescent reproductive health. For those eight clinics that were able to provide data, there was a 25% increase in the number of teen clients seen over 4 years. There are many factors that relate to an increase in clinic utilization; some of this increase may have been a result of the linkages between schools and clinics. ConclusionsThe Bronx Teens Connection Clinic Linkage Model is an explicit framework for clinical and youth-serving organizations seeking to establish formal linkage relationships that may be useful for other municipalities or organizations.

Genome-Wide Single Nucleotide Polymorphism Discovery and the Construction of a High-Density Genetic Map for Melon (Cucumis melo L.) Using Genotyping-by-Sequencing.

Although genotyping-by-sequencing (GBS) enables the efficient and low-cost generation of large numbers of markers, the utility of resultant genotypes are limited, because they are enormously error-prone and contain high proportions of missing data. In this study, we generated single nucleotide polymorphism (SNP) markers for 109 recombinant inbred lines of melon (Cucumis melo L.) using the GBS approach and ordered them according to their physical position on the draft double haploid line DHL92 genome. Next, by investigating associations between these SNPs, we discovered that some segments on the physical map conflict with linkage relationships. Therefore, to filter out error-prone loci, 4,110 SNPs in which we have a high degree of confidence were selected as anchors to test independence with respect to unselected markers, and the resultant dataset was then analyzed using the Full-Sib Family Haplotype (FSFHap) algorithm in the software TASSEL 5.2. On the basis of this analysis, 22,933 loci that have an average rate of missing data of 0.281% were used to construct a genetic map, which spans 1,088.3 cM across 12 chromosomes and has a maximum spacing of 6.0 cM. Use of this high-quality linkage map enabled the identification of several quantitative trait loci (QTL) known to control traits in fruit and validated our approach. This study highlights the utility of GBS markers for the identification of trait-associated QTLs in melon and facilitates further investigation of genome structure.

Direct and indirect effects of relationship status through satisfaction with relationship status and fear of being single on Polish young adults' well-being

The current research tested a model with satisfaction with relationship status and fear of being single as mediators in serial of the linkage relationship status – well-being measured in terms of life satisfaction, emotional and psychological well-being, and depression. Results from a sample of 556 Polish participants aged 20 to 35 (M=22.64, SD=3.34) demonstrated that the link between relationship status and well-being was fully mediated by satisfaction with relationship status and fear of being single operating as separate mediators, as well as by satisfaction with relationship status and fear of being single as mediators in serial. In addition, the indirect effect of relationship status on well-being through satisfaction with relationship status was larger than the indirect effect of relationship status on well-being through satisfaction with relationship status and fear of being single operating in serial.

A new model for measuring the impact of patent value growth trajectory

Patents play a crucial role in determining the economy, industrial development, and R&D of a country. Extant patent literature has focussed on the decision model of the econometric method, which enables researchers to understand the short-term explanatory power of various factors for patent value. However, this method cannot be used to observe the degradation rate and growth trajectory of the patent value. In this study, we proposed a dynamic time-series design to further explore the growth trajectory of patent value by using the latent growth curve model. The results show that backward citation, non-patent reference, and number of claims positively affect the patent value growth rate. Patent disclosure information and characteristics are crucial for exploring the value of patents. Patent value is typically established on the basis of knowledge stock, patent breadth and international linkage. Therefore, this study applied an experimental map to validate the linkage relationship of the studied dimensions to provide governments, industries and patent assignees with some practical suggestions.

Rapid Changes in the Sex Linkage of Male Coloration in Introduced Guppy Populations.

Theory predicts that the sex linkage of sexually selected traits can influence the direction and rate of evolution and should itself evolve in response to sex-specific selection. Some studies have found intraspecific differences in sex linkage associated with differences in selection pressures, but we know nothing about how fast these differences can evolve. Here we show that introduced guppy populations showing rapid evolution of male coloration also show rapid changes in sex-linkage patterns. A comparison, using hormonal manipulations in females, of introduced populations of different ages suggests a consistent increase of autosomal or X-linked coloration 2 years after introduction from high- to low-predation environments. Twenty years after introduction, populations already show the same pattern of coloration inheritance typical of natural low-predation populations in similar habitats. These results highlight that the contemporary evolution of sexually selected traits ought to be studied in concert with contemporary changes in linkage relationships.

Independent origins of diploidy in Metarhizium

In fungi, stable diploid genome arrangements are rare. Here we present evidence from nuclear intergenic DNA sequencing, microsatellite genotyping, and configuration of the mating-type locus to demonstrate two independent origins of persistent diploid genome organization in the Metarhizium majus species complex. Most taxa in the complex are genotypically haploid, with individual isolates consistently displaying a single allele across all nuclear loci, as well as having a single mating-type locus. In contrast, individuals of M. majus and the clade designated here MGT1 are shown to be diploid, based on a consistent finding of heterozygosity and the presence of both MAT1 and MAT2 mating-type loci. In single locus phylogenies, nuclear intergenic alleles of M. majus and MGT1 each form monophyletic groups, indicating that diploidy in both taxa likely originated by the union of conspecific individuals. Sequence divergence in the APN2/MAT1-1-3 and APN2/MAT2-1 intergenic spacers indicate the two MAT loci are physically separated in the genomes of both diploid taxa, although the linkage relationship of the MAT loci to one another is unknown. The presence of both mating genes in a single nucleus suggests these diploid genomes may represent a mating event that failed to complete meiosis. Whether or not these isolates are able to complete the sexual cycle under any conditions and form ascospores remains an open question.

Stability Analysis of a Five-phase Induction Motor Drive Using Variable Frequency Technique

This paper presents stability analysis of a five phase induction motor drive using different control techniques such as Root locus, Bode plot and Nyquist plot. A dynamic model based on voltage- current and voltage-flux linkage relationship is developed. To evaluate the control performance of the five phase induction motor drive, a linearized model is used. The voltage -flux linkage model is derived from the dynamic model in d-q axes. To evaluate the control performance of the motor small perturbations are applied with the model. Five- phase induction motor drive may become unstable at low values of frequency. Transfer function of the drive is determined at different rotor frequencies and the effect on the stability of the drive is assessed using different control techniques. The value of the rotor frequency at which the drive becomes unstable is reported. The effect of variation of rotor frequency on the performance of the motor drive is analyzed. The analysis is carried out using Matlab codes.

Ties to the Rest: Autocratic Linkages and Regime Survival

The relationship between international linkages and the nature and survival of political regimes has gained increasing attention in recent years, but remains one that is poorly understood. In this article, we make three central contributions to our understanding of international linkage politics and autocratic regime survival. First, we introduce and develop the concept of “autocratic linkage,” and highlight its importance for understanding the international politics of autocratic survival. Second, we use event history analysis to demonstrate that autocratic linkage has a systematic effect on the duration of authoritarian regimes. Finally, we complement our quantitative analysis with a focused comparison of autocratic linkage politics in the Middle East. We show that variation in Saudi Arabian support for autocratic incumbents in the wake of the Arab Spring protests can be explained in significant part by variation in linkage relationships.

Retracted: Flavonoid-Deficient Mutants in Grass Pea (Lathyrus sativus L.): Genetic Control, Linkage Relationships, and Mapping with Aconitase and S-Nitrosoglutathione Reductase Isozyme Loci.

[This retracts the article DOI: 10.1100/2012/345983.].

Nonlinear Lumped-Circuit Model for Switched Reluctance Motors Exhibiting Core Losses

A new nonlinear lumped parameter model is proposed for a switched reluctance motor (SRM) with core losses. The components of the model and their origin are justified by finite-element simulations and experimental tests. The winding resistance and the leakage inductance are analyzed by different methods taken from the literature, and a new algorithm is proposed to overcome their shortcomings such as the nonbiunivocal flux linkage versus current relationship. In contrast to previous works, the nonlinear elements for modeling the magnetic core, such as the incremental magnetizing inductance and the core-loss resistance, are determined together and simultaneously for each value of the phase current and the rotor position. The performance of the new model and the methodology proposed for estimating its components are analyzed for different excitation types and rotor positions. The core losses are evaluated by the proposed model and by two well-known predictive models, and the results are compared to illustrate the suitability of the former. Finally, the dynamic behavior of the model, acting as an ac self-excited generator, is considered.

A streamlined tethered chromosome conformation capture protocol.

BackgroundIdentification of locus-locus contacts at the chromatin level provides a valuable foundation for understanding of nuclear architecture and function and a valuable tool for inferring long-range linkage relationships. As one approach to this, chromatin conformation capture-based techniques allow creation of genome spatial organization maps. While such approaches have been available for some time, methodological advances will be of considerable use in minimizing both time and input material required for successful application.ResultsHere we report a modified tethered conformation capture protocol that utilizes a series of rapid and efficient molecular manipulations. We applied the method to Caenorhabditis elegans, obtaining chromatin interaction maps that provide a sequence-anchored delineation of salient aspects of Caenorhabditis elegans chromosome structure, demonstrating a high level of consistency in overall chromosome organization between biological samples collected under different conditions. In addition to the application of the method to defining nuclear architecture, we found the resulting chromatin interaction maps to be of sufficient resolution and sensitivity to enable detection of large-scale structural variants such as inversions or translocations.ConclusionOur streamlined protocol provides an accelerated, robust, and broadly applicable means of generating chromatin spatial organization maps and detecting genome rearrangements without a need for cellular or chromatin fractionation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2596-3) contains supplementary material, which is available to authorized users.

Further evidence for the genetic basis of qualitative traits and their linkage relationships in Dolichos bean (Lablab purpureus L.).

An investigation on inheritance of qualitative traits in dolichos bean revealed biallelic monogenic control of photoperiodinduced sensitivity to flowering time and flower colour in F₂ and F₂ generations. While, growth habit and pod curvature are each controlled by two genes that exhibit classical complementary epistasis, raceme emergence was controlled by two genes that displayed classical inhibitory epistasis. The dominant alleles, at two different unlinked pairs of genes are necessary for plants to exhibit indeterminate growth habit and bear straight pods. Any other combination of alleles at the two pairs of genes result in plants displaying determinate growth habit and bearing curved pods.While, the genes controlling growth habit, PSFT and raceme emergence are linked. Those controlling flower colour and pod curvature are segregated independent of each other. These results are discussed in relation to strategies for breeding dolichos bean.

Genetic and Linkage Studies of New Autosomal Sex-Limited Mutant Hairless Antenna in Anopheles stephensi Liston

A new morphological mutant hairless antenna (hla) was induced in the mosquito Anopheles stephensi by γ-irradiation. The expression of the mutant in the male adult revealed the antennae without the hairs. The inheritance pattern from our data demonstrates that hairless antenna is essentially sex-limited to males and is autosomal and recessive. The linkage relationships studies between the hairless antenna and greyish brown larva (grb) mutant indicated independent assortment and are present on different chromosomes, while the linkage relationship studies between the hairless antenna and ruby eye (ru) mutant revealed the suppression of hla by the ru gene in heterozygous condition. These mutants can be useful in conducting basic and applied research such as construction of linkage maps and understanding biochemical pathways and in genetic control programmes.

The Countermeasure Study of Finance to Promote the Construction of Shanghai (China) Science and Technology Innovation Center

In August 2015, Shanghai municipal government issued the《The Views Of Promoting The Innovation In Financial Services To Support The Implementation Of The Construction Of Shanghai Science And Technology Innovation Center》. Under the background, the paper studies how the finance to promote the construction of the science and technology innovation center in Shanghai. First of all, the paper discusses the current situation of the development of the finance and technical innovation of Shanghai to find the linkage relationship between the finance and technical innovation and analysis the existing problems about the process of the current financial innovation to the science and technology in the construction. Finally, it puts forward policy recommendations how the finance should promote the building of innovation and Technology Center in Shanghai and promote the release of the potential technological innovation. The aim is to speed up a global influence of science and technology innovation center construction of Shanghai, and to improve comprehensive national strength in China.

Relationship between glucokinase gene 6 tag single nucleotide polymorphism sites and type 2 diabetes mellitus

Objective To investigate the relationships between Glucokinase(GCK) gene 6 (tag single-nucleotide polymorphisms, tagSNPs)sites which named rs12702070, rs2971672, rs2268569, rs2268573, rs2300587 and rs1476891 polymorphisms and type 2 diabetes in Chinese Southern Han Population. Methods This study was designed as a case-control. 499 type 2 diabetes patients and 499 healthy controls were chosen. All subjects were from August 2013 to December 2014 in Zhongshan Affiliated Hospital of Sun Yat-sen University. 6 GCK tagSNPs sites were analyzed by improved multiple ligase detection reaction ( iMLDR), and genotype and allele frequency between T2D group and healthy controls could be determined by chi-square test, logistic regression analysis, and tagSNPs were further analyzed under three genetic modes(dominant, recessive and additive). What′s more, Haploview software was used to construct the haplotype of 6 GCK tagSNPs and the linkage disequilibrium(LD) and relationship between various GCK haplotype and T2D susceptibility could be analyzed. Results Genotype distribution of rs2268573, rs2300587, rs2268569 and rs1476891(χ2 were 3.361, 2.076, 0.582 and 0.918 respectively, all P>0.05) and allele frequency (χ2 were 0.222, 1.980, 0.590 and 0.851 respectively, all P>0.05) in T2D group were no significant differences with health controls. Significant differences in genotype distribution of rs2971672 and rs12702070 (χ2 were 6.896 and 7.990 respectively, all P 0.05), haplotype TA and CA reduce the individual risk of T2D with OR 0.81(95% CI: 0.66-1.00, P<0.05) and 0.78 (95% CI: 0.62-0.98, P<0.01)respectively. Conclusions The results indicated that GCK gene 2 tagSNPs sites included rs2971672 and rs12702070 imparts susceptibility to T2D in Han Chinese, but not rs2268573, rs2300587, rs2268569 and rs1476891.Haplotype TA and CA in rs2971672 and rs2300587 reduce the individual risk of T2D and four main haplotypes (TAG, TGG, TAT, CGG) in rs2268569, rs12702070 and rs1476891 have no relevance to T2D.(Chin J Lab Med, 2015, 38: 827-832) Key words: Diabetes mellitus, type 2; Glucokinase; Polymorphism, single nucleotide