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  • Frontiers Media SA  (35)
  • Wu, Rongling  (35)
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  • Frontiers Media SA  (35)
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  • 1
    Online Resource
    Online Resource
    Table_6.xlsx
    Frontiers Media SA ; 2022
    In:  Frontiers in Plant Science Vol. 13 ( 2022-12-12)
    Details
    In: Frontiers in Plant Science, Frontiers Media SA, Vol. 13 ( 2022-12-12)
    Abstract: Wheat sharp eyespot caused by Rhizoctonia cerealis is a serious pathogenic disease affecting plants. The effective strategy for controlling this disease is breeding resistant cultivar. However, to date, no wheat varieties are fully resistant to sharp eyespot, and only a few quantitative trait loci (QTLs) have been shown to be associated with sharp eyespot resistance. Methods To understand the genetic basis of this disease, a genome-wide association study (GWAS) of sharp eyespot resistance in 262 varieties from all China wheat regions was conducted. Results After cultivation for three years, only 6.5% of the varieties were resistant to sharp eyespot. Notably, the varieties from the middle and lower Yangtze River displayed higher sharp eyespot resistance than those from Huanghuai wheat zone. Only two varieties had the same resistance level to the control Shanhongmai. The results of GWAS showed that 5 single nucleotide polymorphism (SNP) loci were markedly related to sharp eyespot resistance in the three years repeatedly, and two QTLs, qSE-6A and qSE-7B, on chromosome 6A and 7B were identified. Based on the ‘CG’ haplotypes of significant SNPs, we found that the two QTLs exhibited additive effects on attenuating sharp eyespot resistance. Discussion These results provide novel insights into the genetic basis of sharp eyespot resistance in China wheat varieties. The SNPs related to sharp eyespot resistance can be applied for marker-assisted selection in plant breeding.
    Type of Medium: Online Resource
    ISSN: 1664-462X
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fpls.2022.1056935
    DOI: 10.3389/fpls.2022.1056935.s001
    DOI: 10.3389/fpls.2022.1056935.s002
    DOI: 10.3389/fpls.2022.1056935.s003
    DOI: 10.3389/fpls.2022.1056935.s004
    DOI: 10.3389/fpls.2022.1056935.s005
    DOI: 10.3389/fpls.2022.1056935.s006
    DOI: 10.3389/fpls.2022.1056935.s007
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2687947-5
    detail.hit.zdb_id: 2613694-6
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  • 2
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    Specialty Grand Challenge: Systems Genetics
    Frontiers Media SA ; 2021
    In:  Frontiers in Systems Biology Vol. 1 ( 2021-9-1)
    Details
    In: Frontiers in Systems Biology, Frontiers Media SA, Vol. 1 ( 2021-9-1)
    Type of Medium: Online Resource
    ISSN: 2674-0702
    URL: Article
    DOI: 10.3389/fsysb.2021.738155
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2021
    detail.hit.zdb_id: 3106041-9
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  • 3
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    Single Nucleotide Polymorphisms Interactions of the Surfactant Protein Genes Associated With Respiratory Distress Syndrome Susceptibility in Preterm Infants
    Frontiers Media SA ; 2021
    In:  Frontiers in Pediatrics Vol. 9 ( 2021-10-4)
    Details
    In: Frontiers in Pediatrics, Frontiers Media SA, Vol. 9 ( 2021-10-4)
    Abstract: Background: Neonatal respiratory distress syndrome (RDS), due to surfactant deficiency in preterm infants, is the most common cause of respiratory morbidity. The surfactant proteins ( SFTP ) genetic variants have been well-studied in association with RDS; however, the impact of SNP-SNP (single nucleotide polymorphism) interactions on RDS has not been addressed. Therefore, this study utilizes a newer statistical model to determine the association of SFTP single SNP model and SNP-SNP interactions in a two and a three SNP interaction model with RDS susceptibility. Methods: This study used available genotype and clinical data in the Floros biobank at Penn State University. The patients consisted of 848 preterm infants, born & lt;36 weeks of gestation, with 477 infants with RDS and 458 infants without RDS. Seventeen well-studied SFTPA1, SFTPA2, SFTPB, SFTPC , and SFTPD SNPs were investigated. Wang's statistical model was employed to test and identify significant associations in a case-control study. Results: Only the rs17886395 (C allele) of the SFTPA2 was associated with protection for RDS in a single-SNP model (Odd's Ratio 0.16, 95% CI 0.06–0.43, adjusted p = 0.03). The highest number of interactions ( n = 27) in the three SNP interactions were among SFTPA1 and SFTPA2 . The three SNP models showed intergenic and intragenic interactions among all SFTP SNPs except SFTPC . Conclusion: The single SNP model and SNP interactions using the two and three SNP interactions models identified SFTP -SNP associations with RDS. However, the large number of significant associations containing SFTPA1 and/or SFTPA2 SNPs point to the importance of SFTPA1 and SFTPA2 in RDS susceptibility.
    Type of Medium: Online Resource
    ISSN: 2296-2360
    URL: Article
    DOI: 10.3389/fped.2021.682160
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2021
    detail.hit.zdb_id: 2711999-3
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  • 4
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    Corrigendum: Single nucleotide polymorphisms interactions of the surfactant protein genes associated with respiratory distress syndrome susceptibility in preterm infants
    Frontiers Media SA ; 2022
    In:  Frontiers in Pediatrics Vol. 10 ( 2022-11-30)
    Details
    In: Frontiers in Pediatrics, Frontiers Media SA, Vol. 10 ( 2022-11-30)
    Type of Medium: Online Resource
    ISSN: 2296-2360
    URL: Article
    DOI: 10.3389/fped.2022.1069526
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2711999-3
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  • 5
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    DataSheet2.PDF
    Frontiers Media SA ; 2021
    In:  Frontiers in Genetics Vol. 12 ( 2021-11-12)
    Details
    In: Frontiers in Genetics, Frontiers Media SA, Vol. 12 ( 2021-11-12)
    Abstract: The effects of genes on physiological and biochemical processes are interrelated and interdependent; it is common for genes to express pleiotropic control of complex traits. However, the study of gene expression and participating pathways in vivo at the whole-genome level is challenging. Here, we develop a coupled regulatory interaction differential equation to assess overall and independent genetic effects on trait growth. Based on evolutionary game theory and developmental modularity theory, we constructed multilayer, omnigenic networks of bidirectional, weighted, and positive or negative epistatic interactions using a forest poplar tree mapping population, which were organized into metagalactic, intergalactic, and local interstellar networks that describe layers of structure between modules, submodules, and individual single nucleotide polymorphisms, respectively. These multilayer interactomes enable the exploration of complex interactions between genes, and the analysis of not only differential expression of quantitative trait loci but also previously uncharacterized determinant SNPs, which are negatively regulated by other SNPs, based on the deconstruction of genetic effects to their component parts. Our research framework provides a tool to comprehend the pleiotropic control of complex traits and explores the inherent directional connections between genes in the structure of omnigenic networks.
    Type of Medium: Online Resource
    ISSN: 1664-8021
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fgene.2021.769688
    DOI: 10.3389/fgene.2021.769688.s001
    DOI: 10.3389/fgene.2021.769688.s002
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2021
    detail.hit.zdb_id: 2606823-0
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  • 6
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    DataSheet1.docx
    Frontiers Media SA ; 2022
    In:  Frontiers in Genetics Vol. 13 ( 2022-3-24)
    Details
    In: Frontiers in Genetics, Frontiers Media SA, Vol. 13 ( 2022-3-24)
    Abstract: We studied associations of persistent respiratory morbidity (PRM) at 6 and 12 months after acute respiratory failure (ARF) in previously healthy children with single-nucleotide polymorphisms (SNPs) of surfactant protein (SP) genes. Of the 250 enrolled subjects, 155 and 127 were followed at 6 and 12 months after an ARF episode, respectively. Logistic regression analysis and SNP–SNP interaction models were used. We found that 1) in the multivariate analysis, an increased risk at 6 and 12 months was associated with rs1124_A and rs4715_A of SFTPC , respectively; 2) in a single SNP model, increased and decreased risks of PRM at both timepoints were associated with rs1124 of SFTPC and rs721917 of SFTPD , respectively; an increased risk at 6 months was associated with rs1130866 of SFTPB and rs4715 of SFTPC , and increased and decreased risks at 12 months were associated with rs17886395 of SFTPA2 and rs2243639 of SFTPD , respectively; 3) in a two-SNP model, PRM susceptibility at both timepoints was associated with a number of intergenic interactions between SNPs of the studied SP genes. An increased risk at 12 months was associated with one intragenic (rs1965708 and rs113645 of SFTPA2 ) interaction; 4) in a three-SNP model, decreased and increased risks at 6 and 12 months, respectively, were associated with an interaction among rs1130866 of SFTPB , rs721917 of SFTPD , and rs1059046 of SFTPA2 . A decreased risk at 6 months was associated with an interaction among the same SNPs of SFTPB and SFTPD and the rs1136450 of SFTPA1 . The findings revealed that SNPs of all SFTP s appear to play a role in long-term outcomes of ARF survivors and may serve as markers for disease susceptibility.
    Type of Medium: Online Resource
    ISSN: 1664-8021
    URL: Article
    URL: Article
    DOI: 10.3389/fgene.2022.815727
    DOI: 10.3389/fgene.2022.815727.s001
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2606823-0
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  • 7
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    Online Resource
    Modeling Haplotype-Haplotype Interactions in Case-Control Genetic Association Studies
    Frontiers Media SA ; 2012
    In:  Frontiers in Genetics Vol. 3 ( 2012)
    Details
    In: Frontiers in Genetics, Frontiers Media SA, Vol. 3 ( 2012)
    Type of Medium: Online Resource
    ISSN: 1664-8021
    URL: Article
    DOI: 10.3389/fgene.2012.00002
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2012
    detail.hit.zdb_id: 2606823-0
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  • 8
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    Data_Sheet_1.PDF
    Frontiers Media SA ; 2021
    In:  Frontiers in Microbiology Vol. 12 ( 2021-9-9)
    Details
    In: Frontiers in Microbiology, Frontiers Media SA, Vol. 12 ( 2021-9-9)
    Abstract: Phenotypic plasticity is the exhibition of various phenotypic traits produced by a single genotype in response to environmental changes, enabling organisms to adapt to environmental changes by maintaining growth and reproduction. Despite its significance in evolutionary studies, we still know little about the genetic control of phenotypic plasticity. In this study, we designed and conducted a genome-wide association study (GWAS) to reveal genetic architecture of how Staphylococcus aureus strains respond to increasing concentrations of vancomycin (0, 2, 4, and 6 μg/mL) in a time course. We implemented functional mapping, a dynamic model for genetic mapping using longitudinal data, to map specific loci that mediate the growth trajectories of abundance of vancomycin-exposed S. aureus strains. 78 significant single nucleotide polymorphisms were identified following analysis of the whole growth and development process, and seven genes might play a pivotal role in governing phenotypic plasticity to the pressure of vancomycin. These seven genes, SAOUHSC_00020 ( walR ), SAOUHSC_00176, SAOUHSC_00544 ( sdrC ), SAOUHSC_02998, SAOUHSC_00025, SAOUHSC_00169, and SAOUHSC_02023, were found to help S. aureus regulate antibiotic pressure. Our dynamic gene mapping technique provides a tool for dissecting the phenotypic plasticity mechanisms of S. aureus under vancomycin pressure, emphasizing the feasibility and potential of functional mapping in the study of bacterial phenotypic plasticity.
    Type of Medium: Online Resource
    ISSN: 1664-302X
    URL: Article
    URL: Article
    DOI: 10.3389/fmicb.2021.696730
    DOI: 10.3389/fmicb.2021.696730.s001
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2021
    detail.hit.zdb_id: 2587354-4
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  • 9
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    Online Resource
    DataSheet1.PDF
    Frontiers Media SA ; 2021
    In:  Frontiers in Genetics Vol. 12 ( 2021-10-15)
    Details
    In: Frontiers in Genetics, Frontiers Media SA, Vol. 12 ( 2021-10-15)
    Abstract: Genes play an important role in community ecology and evolution, but how to identify the genes that affect community dynamics at the whole genome level is very challenging. Here, we develop a Holling type II functional response model for mapping quantitative trait loci (QTLs) that govern interspecific interactions. The model, integrated with generalized Lotka-Volterra differential dynamic equations, shows a better capacity to reveal the dynamic complexity of inter-species interactions than classic competition models. By applying the new model to a published mapping data from a competition experiment of two microbial species, we identify a set of previously uncharacterized QTLs that are specifically responsible for microbial cooperation and competition. The model can not only characterize how these QTLs affect microbial interactions, but also address how change in ecological interactions activates the genetic effects of the QTLs. This model provides a quantitative means of predicting the genetic architecture that shapes the dynamic behavior of ecological communities.
    Type of Medium: Online Resource
    ISSN: 1664-8021
    URL: Article
    URL: Article
    DOI: 10.3389/fgene.2021.766372
    DOI: 10.3389/fgene.2021.766372.s001
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2021
    detail.hit.zdb_id: 2606823-0
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  • 10
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    Table_1.docx
    Frontiers Media SA ; 2022
    In:  Frontiers in Plant Science Vol. 13 ( 2022-6-15)
    Details
    In: Frontiers in Plant Science, Frontiers Media SA, Vol. 13 ( 2022-6-15)
    Abstract: Heterophylly is an adaptive strategy used by some plants in response to environmental changes. Due to the lack of representative plants with typical heteromorphic leaves, little is known about the genetic architecture of heterophylly in plants and the genes underlying its control. Here, we investigated the genetic characteristics underlying changes in leaf shape based on the model species, Populus euphratica , which exhibits typical heterophylly. A set of 401,571 single-nucleotide polymorphisms (SNPs) derived from whole-genome sequencing of 860 genotypes were associated with nine leaf traits, which were related to descriptive and shape data using single- and multi-leaf genome-wide association studies (GWAS). Multi-leaf GWAS allows for a more comprehensive understanding of the genetic architecture of heterophylly by considering multiple leaves simultaneously. The single-leaf GWAS detected 140 significant SNPs, whereas the multi-leaf GWAS detected 200 SNP-trait associations. Markers were found across 19 chromosomes, and 21 unique genes were implicated in traits and serve as potential targets for selection. Our results provide novel insights into the genomic architecture of heterophylly, and provide candidate genes for breeding or engineering P. euphratica . Our observations also improve understanding of the intrinsic mechanisms of plant growth, evolution, and adaptation in response to climate change.
    Type of Medium: Online Resource
    ISSN: 1664-462X
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fpls.2022.870876
    DOI: 10.3389/fpls.2022.870876.s001
    DOI: 10.3389/fpls.2022.870876.s002
    DOI: 10.3389/fpls.2022.870876.s003
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2687947-5
    detail.hit.zdb_id: 2613694-6
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