scholarly journals Phosphate/Zinc Interaction Analysis in Two Lettuce Varieties Reveals Contrasting Effects on Biomass, Photosynthesis, and Dynamics of Pi Transport

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Nadia Bouain ◽  
Mushtak Kisko ◽  
Aida Rouached ◽  
Myriam Dauzat ◽  
Benoit Lacombe ◽  
...  
Keyword(s):  
Correlation Analysis ◽  
Inorganic Phosphate ◽  
Genetic Basis ◽  
Interaction Analysis ◽  
Biological Significance ◽  
Normal Plant ◽  
Strong Negative Correlation ◽  
Pi Transport ◽  
Zn Concentration ◽  
Zn Homeostasis

Inorganic phosphate (Pi) and Zinc (Zn) are essential nutrients for normal plant growth. Interaction between these elements has been observed in many crop plants. Despite its agronomic importance, the biological significance and genetic basis of this interaction remain largely unknown. Here we examined the Pi/Zn interaction in two lettuce (Lactuca sativa) varieties, namely, “Paris Island Cos” and “Kordaat.” The effects of variation in Pi and Zn supply were assessed on biomass and photosynthesis for each variety. Paris Island Cos displayed better growth and photosynthesis compared to Kordaat under all the conditions tested. Correlation analysis was performed to determine the interconnectivity between Pi and Zn intracellular contents in both varieties. Paris Island Cos showed a strong negative correlation between the accumulation levels of Pi and Zn in shoots and roots. However, no relation was observed for Kordaat. The increase of Zn concentration in the medium causes a decrease in dynamics of Pi transport in Paris Island Cos, but not in Kordaat plants. Taken together, results revealed a contrasting behavior between the two lettuce varieties in terms of the coregulation of Pi and Zn homeostasis and provided evidence in favor of a genetic basis for the interconnection of these two elements.

scholarly journals Genomic Prediction with Genotype by Environment Interaction Analysis for Kernel Zinc Concentration in Tropical Maize Germplasm

2020 ◽  
Vol 10 (8) ◽  
pp. 2629-2639
Author(s):  
Edna K. Mageto ◽  
Jose Crossa ◽  
Paulino Pérez-Rodríguez ◽  
Thanda Dhliwayo ◽  
Natalia Palacios-Rojas ◽  
...  
Keyword(s):  
Genomic Prediction ◽  
Prediction Models ◽  
Interaction Analysis ◽  
Genotype By Environment Interaction ◽  
Zn Deficiency ◽  
Environment Interaction ◽  
Prediction Ability ◽  
Association Panel ◽  
Maize Germplasm ◽  
Zn Concentration

Zinc (Zn) deficiency is a major risk factor for human health, affecting about 30% of the world’s population. To study the potential of genomic selection (GS) for maize with increased Zn concentration, an association panel and two doubled haploid (DH) populations were evaluated in three environments. Three genomic prediction models, M (M1: Environment + Line, M2: Environment + Line + Genomic, and M3: Environment + Line + Genomic + Genomic x Environment) incorporating main effects (lines and genomic) and the interaction between genomic and environment (G x E) were assessed to estimate the prediction ability (rMP) for each model. Two distinct cross-validation (CV) schemes simulating two genomic prediction breeding scenarios were used. CV1 predicts the performance of newly developed lines, whereas CV2 predicts the performance of lines tested in sparse multi-location trials. Predictions for Zn in CV1 ranged from -0.01 to 0.56 for DH1, 0.04 to 0.50 for DH2 and -0.001 to 0.47 for the association panel. For CV2, rMP values ranged from 0.67 to 0.71 for DH1, 0.40 to 0.56 for DH2 and 0.64 to 0.72 for the association panel. The genomic prediction model which included G x E had the highest average rMP for both CV1 (0.39 and 0.44) and CV2 (0.71 and 0.51) for the association panel and DH2 population, respectively. These results suggest that GS has potential to accelerate breeding for enhanced kernel Zn concentration by facilitating selection of superior genotypes.

scholarly journals HBP: an integrative and flexible pipeline for the interaction analysis of Hi-C dataset

2016 ◽  
Author(s):  
Chao He ◽  
Ping Li ◽  
Minglei Shi ◽  
Yan Zhang ◽  
Bingyu Ye ◽  
...  
Keyword(s):  
Spatial Organization ◽  
Molecular Mechanisms ◽  
Gene Expression Regulation ◽  
Interaction Analysis ◽  
Rapid Development ◽  
3D Structure ◽  
Biological Significance ◽  
Sequencing Data ◽  
Chromatin Interactions ◽  
Wide Range

AbstractBackgroundThe spatial organization of interphase chromatin in the nucleus play an important role in gene expression regulation and function. With the rapid development of revolutionized chromosome conformation capture technology and its genome-wide derivatives such as Hi-C, investigation of the genome folding becomes more efficient and convenient. How to robustly deal with these massive datasets and infer accurate 3D model and within-nucleus compartmentalization of chromosomes becomes a new challenge.ResultThe implemented pipeline HBP (Hi-C BED file analysis Pipeline) integrates existing pipelines focusing on individual steps of Hi-C data processing into an all-in-one package with adjustable parameters to infer the consensus 3D structure of genome from raw Hi-C sequencing data. What’s more, HBP could assign statistical confidence estimation for chromatin interactions, and clustering interaction loci according to enrichment tracks or topological structure automatically.ConclusionThe freely available HBP is an optimized and flexible pipeline for analyzing the folding of whole chromosome and interactions between some specific sites from the Hi-C raw sequencing reads to the partially processed datasets. The other complex genetic and epigenetic datasets from public sources such as GWAS, ENCODE consortiums etc. will also easily be integrated into HBP, hence the final output results of HBP could provide a comprehensive in-depth understanding for the specific chromatin interactions, potential molecular mechanisms and biological significance. We believe that HBP is a reliable tool for the rapidly analysis of Hi-C data and will be very useful for a wide range of researchers, particularly those who lack of background in computational biology. HBP is freely accessible at https://github.com/hechao0407/HBP/blob/master/HBP_1.0.tar.gz.

scholarly journals QTL Mapping and integration as well as candidate gene prediction for branch number in soybean

2019 ◽  
Author(s):  
Yuhua Yang ◽  
Yang Lei ◽  
Zhiyuan Bai ◽  
Yichao Wei ◽  
Ruijun Zhang
Keyword(s):  
Genetic Architecture ◽  
Genetic Basis ◽  
Interaction Analysis ◽  
Gene Prediction ◽  
Phenotypic Variance ◽  
Environment Interaction ◽  
Orthologous Genes ◽  
Branch Number ◽  
Lateral Organs ◽  
Major Qtl

AbstractBranch number is an important factor that affects crop plant architecture and yield in soybean. With the aim of elucidating the genetic basis of branch number, we identified 10 consensus quantitative trait loci (QTLs) through preliminary mapping, which were on chromosome A1, B2, C1, C2, D1a, D1b, F, L and N, explained 0.3-33.3% of the phenotypic variance. Of these, three QTLs were identical to previously identified ones, whereas the other seven were novel. In addition, one major QTL-qBN.C2 (R2=33.3%) was detected in all three environments and another new major QTL-qBN.N (R2=19.6%) was detected in two environments (Taiyuan 2017 and Taiyuan 2018), but only in Taiyuan. Thus, the QTL × environment interaction analysis confirmed that QTL-qBN.N was strongly affected by the environment. We compared the physical positions of the QTL intervals of the candidate genes potentially involved in branching development, and five orthologous genes were ultimately selected and related to the establishment of axillae meristem organization and lateral organs, qBN.A1 (SoyZH13_05G177000.m1), qBN.C2 (SoyZH13_06G176500.m1, SoyZH13_06G185600.m1), and qBN.D1b-1 (SoyZH13_02G035400.m1, SoyZH13_02G070000.m3). The results of our study reveal a complex and relatively complete genetic architecture and can serve as a basis for the positional gene cloning of branch number in soybean.

scholarly journals Integration of Genetic and Immune Infiltration Insights into Data Mining of Multiple Sclerosis Pathogenesis

2021 ◽  
Author(s):  
Xiaoyun Zhang ◽  
Ying Song ◽  
Xiao Chen ◽  
Xiaojia Zhuang ◽  
Zhiqiang Wei ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Correlation Analysis ◽  
Immune Cells ◽  
Genetic Basis ◽  
Demyelinating Disease ◽  
Functional Enrichment ◽  
Hub Genes ◽  
Immune Infiltration ◽  
Ms Pathogenesis ◽  
Brain Tissues

Abstract Background: Multiple sclerosis (MS) is an immune-mediated demyelinating disease of the central nervous system. MS pathogenesis is closely related to the environment, genetic, and immune system, but the underlying interactions have not been clearly elucidated. This study aims to unveil the genetic basis and immune landscape of MS pathogenesis with bioinformatics.Methods:Gene matrix wasretrieved from the gene expression database NCBI GEO. Then, bioinformatics was used to standardize the samples and obtain differentially expressed genes (DEGs). The protein-protein interaction network was constructed with DEGs on the STRING website. Cytohubbaplug-in and MCODE plug-in were used to mine hub genes. Meanwhile, the CIBERSORTX algorithm was used to explore the characteristics of immune cellinfiltration in MS brain tissues. Spearman correlation analysis was performed between genes and immune cells, and the correlation between genes and different types of brain tissues was also analyzed using the WGCNA method.Results:A total of 90 samples from 2 datasetswere included, and 882 DEGs and 10 hub genes closely related to MS were extracted. Functional enrichment analysis suggested the roleof immune response in MS. Besides,CIBERSORTX algorithm results showed that MS brain tissuescontained a variety of infiltrating immune cells. Correlation analysis suggested that the hub genes were highly relevant to chronic active white matter lesions.Certain hub genes played a role in the activation of immune cells such as macrophages and natural killer cells.Conclusions: Our study shall provideguidance for the further study of the genetic basis and immune infiltration mechanism of MS.

scholarly journals Phosphorus Starvation- and Zinc Excess-Induced Astragalus sinicus AsZIP2 Zinc Transporter Is Suppressed by Arbuscular Mycorrhizal Symbiosis

2021 ◽  
Vol 7 (11) ◽  
pp. 892
Author(s):  
Xianan Xie ◽  
Xiaoning Fan ◽  
Hui Chen ◽  
Ming Tang
Keyword(s):  
Arbuscular Mycorrhizal ◽  
Am Fungi ◽  
Mycorrhizal Symbiosis ◽  
Dependent Manner ◽  
Astragalus Sinicus ◽  
Physiological Level ◽  
Zn Concentration ◽  
Pi Starvation ◽  
Zn Homeostasis ◽  
Nutrient Homeostasis

Zinc (Zn) is one of the most essential micronutrients for plant growth and metabolism, but Zn excess can impair many basic metabolic processes in plant cells. In agriculture, crops often experience low phosphate (Pi) and high Zn double nutrient stresses because of inordinate agro-industrial activities, while the dual benefit of arbuscular mycorrhizal (AM) fungi protects plants from experiencing both deficient and toxic nutrient stresses. Although crosstalk between Pi and Zn nutrients in plants have been extensively studied at the physiological level, the molecular basis of how Pi starvation triggers Zn over-accumulation in plants and how AM plants coordinately modulate the Pi and Zn nutrient homeostasis remains to be elucidated. Here, we report that a novel AsZIP2 gene, a Chinese milk vetch (Astragalus sinicus) member of the ZIP gene family, participates in the interaction between Pi and Zn nutrient homeostasis in plants. Phylogenetic analysis revealed that this AsZIP2 protein was closely related to the orthologous Medicago MtZIP2 and Arabidopsis AtZIP2 transporters. Gene expression analysis indicated that AsZIP2 was highly induced in roots by Pi starvation or Zn excess yet attenuated by arbuscular mycorrhization in a Pi-dependent manner. Subcellular localization and heterologous expression experiments further showed that AsZIP2 encoded a functional plasma membrane-localized transporter that mediated Zn uptake in yeast. Moreover, overexpression of AsZIP2 in A. sinicus resulted in the over-accumulation of Zn concentration in roots at low Pi or excessive Zn concentrations, whereas AsZIP2 silencing lines displayed an even more reduced Zn concentration than control lines under such conditions. Our results reveal that the AsZIP2 transporter functioned in Zn over-accumulation in roots during Pi starvation or high Zn supply but was repressed by AM symbiosis in a Pi-dependent manner. These findings also provide new insights into the AsZIP2 gene acting in the regulation of Zn homeostasis in mycorrhizal plants through Pi signal.

Geography of leg-colour dimorphism in the carabid beetle Nebria gyllenhali in Iceland and on the Faroe islands

1983 ◽  
Vol 14 (1) ◽  
pp. 57-66
Author(s):  
T. Solhöy ◽  
S.-A. Bengtson ◽  
P.H. Enckell ◽  
K.E. Erikstad
Keyword(s):  
Negative Correlation ◽  
Genetic Basis ◽  
Distribution Patterns ◽  
General Information ◽  
Stepwise Multiple Regression ◽  
Faroe Islands ◽  
Strong Negative Correlation ◽  
Definite Answer ◽  
Colour Form ◽  
Colour Dimorphism

AbstractIn Iceland and on the Faroes the carabid Nebria gyllenhali Schn. is dimorphic for legcolour; effectively all samples contained both red- and black-legged individuals. In Iceland (18 sites: 1-100 % red) the frequency of red-legged was lowest in the southern and highest in the northern and western parts. The frequencies at adjoining sites were positively autocorrelated (p ≅ 0.01) and a stepwise multiple regression analysis yielded a strong, negative correlation between the frequency of red-legged and temperature/precipitation variables (R2 = 0.994). On the Faroes (50 sites: 20-100 % red) the highest frequencies of red-legged occurred in the south but the geographic pattern was less distinct than in Iceland and the positive autocorrelation was weaker (p 0.05). Due to lack of detailed meteorological records the negative correlation between the frequency of red-legged and temperature/precipitation could only be inferred from general information and topography. The correlations between frequency of leg-colour form and climatic variables may be casual but different other possible reasons for the observed geographic distribution patterns are discussed. Naturally no definite answer can be given on the basis of the entirely observational data. A genetic basis for the leg-colour dimorphism is assumed, but cross-breeding experiments are required.

scholarly journals Inorganic Phosphate Modulates the Expression of the NaPi-2a Transporter in thetrans-Golgi Network and the Interaction with PIST in the Proximal Tubule

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Miguel A. Lanaspa ◽  
Yupanqui A. Caldas ◽  
Sophia Y. Breusegem ◽  
Ana Andrés-Hernando ◽  
Christina Cicerchi ◽  
...  
Keyword(s):  
Inorganic Phosphate ◽  
Culture Medium ◽  
Pdz Domain ◽  
Proximal Tubules ◽  
Opossum Kidney ◽  
Ok Cells ◽  
Pi Homeostasis ◽  
Pi Transport ◽  
Endosomal Transport ◽  
Golgi Network

Inorganic phosphate (Pi) homeostasis is maintained by the tight regulation of renal Pi excretion versus reabsorption rates that are in turn modulated by adjusting the number of Pi transporters (mainly NaPi-2a) in the proximal tubules. In response to some hormones and a high dietary Pi content, NaPi-2a is endocytosed and degraded in the lysosomes; however, we show here that some NaPi-2a molecules are targeted to thetrans-Golgi network (TGN) during the endocytosis. In the TGN, NaPi-2a interacts with PIST (PDZ-domain protein interacting specifically with TC10), a TGN-resident PDZ-domain-containing protein. The extension of the interaction is proportional to the expression of NaPi-2a in the TGN, and, consistent with that, it is increased with a high Pi diet. When overexpressed in opossum kidney (OK) cells, PIST retains NaPi-2a in the TGN and inhibits Na-dependent Pi transport. Overexpression of PIST also prevents the adaptation of OK cells to a low Pi culture medium. Our data supports the view that NaPi-2a is subjected to retrograde trafficking from the plasma membrane to the TGN using one of the machineries involved in endosomal transport and explains the reported expression of NaPi-2a in the TGN.

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