Genome-wide superior alleles, haplotypes and candidate genes associated with tolerance on sodic-dispersive soils in wheat (Triticum aestivum L.)

Abstract Key message The pleiotropic SNPs/haplotypes, overlapping genes (metal ion binding, photosynthesis), and homozygous/biallelic SNPs and transcription factors (HTH myb-type and BHLH) hold great potential for improving wheat yield potential on sodic-dispersive soils. Abstract Sodic-dispersive soils have multiple subsoil constraints including poor soil structure, alkaline pH and subsoil toxic elemental ion concentration, affecting growth and development in wheat. Tolerance is required at all developmental stages to enhance wheat yield potential on such soils. An in-depth investigation of genome-wide associations was conducted using a field phenotypic data of 206 diverse Focused Identification of Germplasm Strategy (FIGS) wheat lines for two consecutive years from different sodic and non-sodic plots and the exome targeted genotyping by sequencing (tGBS) assay. A total of 39 quantitative trait SNPs (QTSs), including 18 haplotypes were identified on chromosome 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 5A, 5D, 6B, 7A, 7B, 7D for yield and yield-components tolerance. Among these, three QTSs had common associations for multiple traits, indicating pleiotropism and four QTSs had close associations for multiple traits, within 32.38 Mb. The overlapping metal ion binding (Mn, Ca, Zn and Al) and photosynthesis genes and transcription factors (PHD-, Dof-, HTH myb-, BHLH-, PDZ_6-domain) identified are known to be highly regulated during germination, maximum stem elongation, anthesis, and grain development stages. The homozygous/biallelic SNPs having allele frequency above 30% were identified for yield and crop establishment/plants m−2. These SNPs correspond to HTH myb-type and BHLH transcription factors, brassinosteroid signalling pathway, kinase activity, ATP and chitin binding activity. These resources are valuable in haplotype-based breeding and genome editing to improve yield potential on sodic-dispersive soils.

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Genome-Wide Superior Alleles, Haplotypes and Candidate Genes Associated With Tolerance on Sodic-Dispersive Soils in Wheat (Triticum Aestivum L.)

10.21203/rs.3.rs-735264/v1 ◽

2021 ◽

Author(s):

Darshan Lal Sharma ◽

Roopali Bhoite ◽

Karyn Reeves ◽

Kerrie Forrest ◽

Rosemary Smith ◽

...

Keyword(s):

Transcription Factors ◽

Metal Ion ◽

Stem Elongation ◽

Wheat Yield ◽

Ion Concentration ◽

Yield Potential ◽

Multiple Traits ◽

Phenotypic Data ◽

Genome Wide ◽

Dispersive Soils

Abstract Sodic-dispersive soils have multiple subsoil constraints including poor soil structure, alkaline pH and subsoil toxic elemental ion concentration, affecting growth and development in wheat. Tolerance is required at all developmental stages to enhance wheat yield potential on such soils. An in-depth investigation of genome-wide associations was conducted using a field phenotypic data of 206 diverse Focused Identification of Germplasm Strategy (FIGS) wheat lines for two consecutive years from different sodic and non-sodic plots and the exome targeted genotyping by sequencing (tGBS) assay. A total of 39 quantitative trait SNPs (QTSs), including 18 haplotypes were identified on chromosome 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 5A, 5D, 6B, 7A, 7B, 7D for yield and yield-components tolerance. Among these, three QTSs had common associations for multiple traits, indicating pleiotropism and four QTSs had close associations for multiple traits, within 32.38 Mb. The overlapping metal ion binding (Mn, Ca, Zn and Al) and photosynthesis genes, and transcription factors (PHD-, Dof-, HTH myb-, BHLH-, PDZ_6-domain) identified are known to be highly regulated during germination, maximum stem elongation, anthesis, and grain development stages. The homozygous/biallelic SNPs having allele frequency above 30% were identified for yield and crop establishment/plants m-2. These SNPs correspond to HTH myb-type and BHLH transcription factors, brassinosteroid signaling pathway, kinase activity, ATP and chitin binding activity. These resources are valuable in haplotype-based breeding and genome editing to improve yield potential on sodic-dispersive soils.

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Faculty Opinions recommendation of Fusogenic supramolecular vesicle systems induced by metal ion binding to amphiphilic ligands.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1021994.251625 ◽

2004 ◽

Author(s):

Bradley Smith

Keyword(s):

Metal Ion ◽

Ion Binding ◽

Metal Ion Binding

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Photophysical Characterisation, Metal Ion Binding and Enantiomeric Recognition of Chiral Ligands Containing Phenazine Fluorophore

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc20040885 ◽

2004 ◽

Vol 69 (4) ◽

pp. 885-896 ◽

Cited By ~ 8

Author(s):

Luisa Stella Dolci ◽

Péter Huszthy ◽

Erika Samu ◽

Marco Montalti ◽

Luca Prodi ◽

...

Keyword(s):

Metal Ion ◽

Photophysical Properties ◽

Ion Binding ◽

Metal Ion Binding ◽

Ammonium Ions ◽

Enantiomerically Pure ◽

Binding Process ◽

High Affinity ◽

Enantiomeric Recognition ◽

Chiral Species

Enantiomerically pure dimethyl- and diisobutyl-substituted phenazino-18-crown-6 ligands bind metal and ammonium ions and also primary aralkylammonium perchlorates in acetonitrile with high affinity, causing pronounced changes in their luminescence properties. In addition, they show enantioselectivity towards chiral primary aralkylammonium perchlorates. The possibility to monitor the binding process by photoluminescence spectroscopy can gain ground for the design of very efficient enantioselective chemosensors for chiral species. The observed changes in the photophysical properties are also an important tool for understanding the interactions present in the adduct.

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Evidence for a polynuclear metal ion binding site in the catalytic domain of ribonuclease P RNA

The EMBO Journal ◽

10.1093/emboj/21.9.2253 ◽

2002 ◽

Vol 21 (9) ◽

pp. 2253-2262 ◽

Cited By ~ 35

Author(s):

E. L. Christian

Keyword(s):

Binding Site ◽

Metal Ion ◽

Catalytic Domain ◽

Ribonuclease P ◽

Ion Binding ◽

Metal Ion Binding ◽

Ribonuclease P Rna

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Enhanced Secretions of Algal Cell-Adhesion Molecules and Metal Ion-Binding Exoproteins Promote Self-Flocculation of Chlorella sp. Cultivated in Municipal Wastewater

Environmental Science & Technology ◽

10.1021/acs.est.1c01324 ◽

2021 ◽

Author(s):

Zhipeng Chen ◽

Shuang Qiu ◽

Ziwei Yu ◽

Mengting Li ◽

Shijian Ge

Keyword(s):

Cell Adhesion ◽

Adhesion Molecules ◽

Cell Adhesion Molecules ◽

Metal Ion ◽

Municipal Wastewater ◽

Algal Cell ◽

Ion Binding ◽

Metal Ion Binding ◽

Chlorella Sp

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Snapshots of a Non-Canonical RdRP in Action

Viruses ◽

10.3390/v13071260 ◽

2021 ◽

Vol 13 (7) ◽

pp. 1260

Author(s):

Diego S. Ferrero ◽

Michela Falqui ◽

Nuria Verdaguer

Keyword(s):

Metal Ion ◽

Rna Viruses ◽

Ion Binding ◽

Genome Replication ◽

Metal Ion Binding ◽

Insect Virus ◽

X Ray ◽

Template Strand ◽

Nucleotide Incorporation ◽

Elongation Process

RNA viruses typically encode their own RNA-dependent RNA polymerase (RdRP) to ensure genome replication and transcription. The closed “right hand” architecture of RdRPs encircles seven conserved structural motifs (A to G) that regulate the polymerization activity. The four palm motifs, arranged in the sequential order A to D, are common to all known template dependent polynucleotide polymerases, with motifs A and C containing the catalytic aspartic acid residues. Exceptions to this design have been reported in members of the Permutotetraviridae and Birnaviridae families of positive single stranded (+ss) and double-stranded (ds) RNA viruses, respectively. In these enzymes, motif C is located upstream of motif A, displaying a permuted C–A–B–D connectivity. Here we study the details of the replication elongation process in the non-canonical RdRP of the Thosea asigna virus (TaV), an insect virus from the Permutatetraviridae family. We report the X-ray structures of three replicative complexes of the TaV polymerase obtained with an RNA template-primer in the absence and in the presence of incoming rNTPs. The structures captured different replication events and allowed to define the critical interactions involved in: (i) the positioning of the acceptor base of the template strand, (ii) the positioning of the 3’-OH group of the primer nucleotide during RNA replication and (iii) the recognition and positioning of the incoming nucleotide. Structural comparisons unveiled a closure of the active site on the RNA template-primer binding, before rNTP entry. This conformational rearrangement that also includes the repositioning of the motif A aspartate for the catalytic reaction to take place is maintained on rNTP and metal ion binding and after nucleotide incorporation, before translocation.

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