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Sanchez DL, Samonte SOP, Alpuerto JBB, Croaker PA, Morales KY, Yang Y, Wilson LT, Tabien RE, Yan Z, Thomson MJ, Septiningsih EM. Phenotypic variation and genome-wide association studies of main culm panicle node number, maximum node production rate, and degree-days to heading in rice. BMC Genomics 2022; 23:390. [PMID: 35606708 PMCID: PMC9125873 DOI: 10.1186/s12864-022-08629-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 05/16/2022] [Indexed: 11/10/2022] Open
Abstract
Background Grain yield is a complex trait that results from interaction between underlying phenotypic traits and climatic, edaphic, and biotic variables. In rice, main culm panicle node number (MCPNN; the node number on which the panicle is borne) and maximum node production rate (MNPR; the number of leaves that emerge per degree-day > 10°C) are primary phenotypic plant traits that have significant positive direct effects on yield-related traits. Degree-days to heading (DDTH), which has a significant positive effect on grain yield, is influenced by the interaction between MCPNN and MNPR. The objective of this research is to assess the phenotypic variation of MCPNN, MNPR, and DDTH in a panel of diverse rice accessions, determine regions in the rice genome associated with these traits using genome-wide association studies (GWAS), and identify putative candidate genes that control these traits. Results Considerable variation was observed for the three traits in a 220-genotype diverse rice population. MCPNN ranged from 8.1 to 20.9 nodes in 2018 and from 9.9 to 21.0 nodes in 2019. MNPR ranged from 0.0097 to 0.0214 nodes/degree day > 10°C in 2018 and from 0.0108 to 0.0193 nodes/degree-day > 10°C in 2019. DDTH ranged from 713 to 2,345 degree-days > 10°C in 2018 and from 778 to 2,404 degree-days > 10°C in 2019. Thirteen significant (P < 2.91 x 10-7) trait-single nucleotide polymorphism (SNP) associations were identified using the multilocus mixed linear model for GWAS. Significant associations between MCPNN and three SNPs in chromosome 2 (S02_12032235, S02_11971745, and S02_12030176) were detected with both the 2018 and best linear unbiased prediction (BLUP) datasets. Nine SNPs in chromosome 6 (S06_1970442, S06_2310856, S06_2550351, S06_1968653, S06_2296852, S06_1968680, S06_1968681, S06_1970597, and S06_1970602) were significantly associated with MNPR in the 2019 dataset. One SNP in chromosome 11 (S11_29358169) was significantly associated with the DDTH in the BLUP dataset. Conclusions This study identifies SNP markers that are putatively associated with MCPNN, MNPR, and DDTH. Some of these SNPs were located within or near gene models, which identify possible candidate genes involved in these traits. Validation of the putative candidate genes through expression and gene editing analyses are necessary to confirm their roles in regulating MCPNN, MNPR, and DDTH. Identifying the underlying genetic basis for primary phenotypic traits MCPNN and MNPR could lead to the development of fast and efficient approaches for their estimation, such as marker-assisted selection and gene editing, which is essential in increasing breeding efficiency and enhancing grain yield in rice. On the other hand, DDTH is a resultant variable that is highly affected by nitrogen and water management, plant density, and several other factors. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08629-y.
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Affiliation(s)
- Darlene L Sanchez
- Texas A&M AgriLife Research Center at Beaumont, Beaumont, Texas, 77713, USA.
| | | | - Jasper Benedict B Alpuerto
- Texas A&M AgriLife Research Center at Beaumont, Beaumont, Texas, 77713, USA.,Bayer Research and Development Services (Bayer Crop Science), Chesterfield, Missouri, 63017, USA
| | - Peyton A Croaker
- Texas A&M AgriLife Research Center at Beaumont, Beaumont, Texas, 77713, USA
| | - Karina Y Morales
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, 77843, USA
| | - Yubin Yang
- Texas A&M AgriLife Research Center at Beaumont, Beaumont, Texas, 77713, USA
| | - Lloyd T Wilson
- Texas A&M AgriLife Research Center at Beaumont, Beaumont, Texas, 77713, USA
| | - Rodante E Tabien
- Texas A&M AgriLife Research Center at Beaumont, Beaumont, Texas, 77713, USA
| | - Zongbu Yan
- Texas A&M AgriLife Research Center at Beaumont, Beaumont, Texas, 77713, USA
| | - Michael J Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, 77843, USA
| | - Endang M Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, 77843, USA
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Ancient Origins of Cytoskeletal Crosstalk: Spectraplakin-like Proteins Precede the Emergence of Cortical Microtubule Stabilization Complexes as Crosslinkers. Int J Mol Sci 2022; 23:ijms23105594. [PMID: 35628404 PMCID: PMC9145010 DOI: 10.3390/ijms23105594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 11/17/2022] Open
Abstract
Adhesion between cells and the extracellular matrix (ECM) is one of the prerequisites for multicellularity, motility, and tissue specialization. Focal adhesions (FAs) are defined as protein complexes that mediate signals from the ECM to major components of the cytoskeleton (microtubules, actin, and intermediate filaments), and their mutual communication determines a variety of cellular processes. In this study, human cytoskeletal crosstalk proteins were identified by comparing datasets with experimentally determined cytoskeletal proteins. The spectraplakin dystonin was the only protein found in all datasets. Other proteins (FAK, RAC1, septin 9, MISP, and ezrin) were detected at the intersections of FAs, microtubules, and actin cytoskeleton. Homology searches for human crosstalk proteins as queries were performed against a predefined dataset of proteomes. This analysis highlighted the importance of FA communication with the actin and microtubule cytoskeleton, as these crosstalk proteins exhibit the highest degree of evolutionary conservation. Finally, phylogenetic analyses elucidated the early evolutionary history of spectraplakins and cortical microtubule stabilization complexes (CMSCs) as model representatives of the human cytoskeletal crosstalk. While spectraplakins probably arose at the onset of opisthokont evolution, the crosstalk between FAs and microtubules is associated with the emergence of metazoans. The multiprotein complexes contributing to cytoskeletal crosstalk in animals gradually gained in complexity from the onset of metazoan evolution.
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Persson K, Backman L. Structural and functional characterization of a plant alpha-actinin. FEBS Open Bio 2021. [PMID: 34110107 PMCID: PMC8329775 DOI: 10.1002/2211-5463.13222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/01/2021] [Accepted: 06/09/2021] [Indexed: 11/08/2022] Open
Abstract
The Australian tree malletwood (Rhodamnia argentea) is unique. The genome of malletwood is the only known plant genome that contains a gene coding for an α‐actinin‐like protein. Several organisms predating the animal‐plant bifurcation express an α‐actinin or α‐actinin‐like protein. Therefore, it appears that plants in general, but not malletwood, have lost the α‐actinin or α‐actinin‐like gene during evolution. In order to characterize its structure and function, we synthesized the gene and expressed the recombinant R. argentea protein. The results clearly show that this protein has all properties of genuine α‐actinin. The N‐terminal actin‐binding domain (ABD), with two calponin homology motifs, is very similar to the ABD of any α‐actinin. The C‐terminal calmodulin‐like domain, as well as the intervening rod domain, are also similar to the corresponding regions in other α‐actinins. The R. argentea α‐actinin‐like protein dimerises in solution and thereby can cross‐link actin filaments. Based on these results, we believe the R. argentea protein represents a genuine α‐actinin, making R. argentea unique in the plant world.
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Affiliation(s)
| | - Lars Backman
- Department of Chemistry, Umeå University, Sweden
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Yoon MY, Kim MY, Ha J, Lee T, Kim KD, Lee SH. QTL Analysis of Resistance to High-Intensity UV-B Irradiation in Soybean ( Glycine max [L.] Merr.). Int J Mol Sci 2019; 20:E3287. [PMID: 31277435 PMCID: PMC6651677 DOI: 10.3390/ijms20133287] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/01/2019] [Accepted: 07/03/2019] [Indexed: 11/17/2022] Open
Abstract
High-intensity ultraviolet-B (UV-B) irradiation is a complex abiotic stressor resulting in excessive light exposure, heat, and dehydration, thereby affecting crop yields. In the present study, we identified quantitative trait loci (QTLs) for resistance to high-intensity UV-B irradiation in soybean (Glycine max [L.]). We used a genotyping-by-sequencing approach using an F6 recombinant inbred line (RIL) population derived from a cross between Cheongja 3 (UV-B sensitive) and Buseok (UV-B resistant). We evaluated the degree of leaf damage by high-intensity UV-B radiation in the RIL population and identified four QTLs, UVBR12-1, 6-1, 10-1, and 14-1, for UV-B stress resistance, together explaining 20% of the observed phenotypic variation. The genomic regions containing UVBR12-1 and UVBR6-1 and their syntenic blocks included other known biotic and abiotic stress-related QTLs. The QTL with the highest logarithm of odds (LOD) score of 3.76 was UVBR12-1 on Chromosome 12, containing two genes encoding spectrin beta chain, brain (SPTBN, Glyma.12g088600) and bZIP transcription factor21/TGACG motif-binding 9 (bZIP TF21/TGA9, Glyma.12g088700). Their amino acid sequences did not differ between the mapping parents, but both genes were significantly upregulated by UV-B stress in Buseok but not in Cheongja 3. Among five genes in UVBR6-1 on Chromosome 6, Glyma.06g319700 (encoding a leucine-rich repeat family protein) had two nonsynonymous single nucleotide polymorphisms differentiating the parental lines. Our findings offer powerful genetic resources for efficient and precise breeding programs aimed at developing resistant soybean cultivars to multiple stresses. Furthermore, functional validation of the candidate genes will improve our understanding of UV-B stress defense mechanisms.
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Affiliation(s)
- Min Young Yoon
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Moon Young Kim
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
| | - Jungmin Ha
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
| | - Taeyoung Lee
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | | | - Suk-Ha Lee
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea.
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Ciska M, de la Espina SMD. Detection of Endogenous Nuclear Proteins in Plant Cells: Localizing Nuclear Matrix Constituent Proteins (NMCPs), the Plant Analogs of Lamins. Methods Mol Biol 2017; 1560:297-311. [PMID: 28155164 DOI: 10.1007/978-1-4939-6788-9_23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
At present, two complementary approaches are used for in situ protein visualization in plant nuclei. Imaging of transformed fluorescent proteins is the election tool for the analysis of protein movement and interaction. However, this methodology presents several drawbacks for the identification/localization of endogenous nuclear factors, such as over-expression or mislocalization of transformed proteins. In contrast, immunocytochemistry with specific antibodies represents a powerful tool for the localization of endogenous nuclear proteins at their "native" nuclear sub-compartments. In plant cells, the cell wall hampers antibody accessibility during immunocytochemical analysis thereby reducing the effectivity of the technique, particularly in the case of lowly expressed proteins. To overcome this problem in nuclear protein immunodetection, we developed a method based on the in vitro incubation of isolated nuclei with specific antibodies followed by imaging by confocal fluorescence or electron microscopy. Here we describe the application of this methodology to the localization of Nuclear Matrix Constituent Proteins (NMCP), the plant analogs of lamins, of the monocot Allium cepa, using antibodies raised against highly conserved regions of the proteins.
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Affiliation(s)
- Malgorzata Ciska
- Department of Cell and Molecular Biology, Biological Research Center, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
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Ciska M, Masuda K, Moreno Díaz de la Espina S. Lamin-like analogues in plants: the characterization of NMCP1 in Allium cepa. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:1553-64. [PMID: 23378381 PMCID: PMC3617829 DOI: 10.1093/jxb/ert020] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The nucleoskeleton of plants contains a peripheral lamina (also called plamina) and, even though lamins are absent in plants, their roles are still fulfilled in plant nuclei. One of the most intriguing topics in plant biology concerns the identity of lamin protein analogues in plants. Good candidates to play lamin functions in plants are the members of the NMCP (nuclear matrix constituent protein) family, which exhibit the typical tripartite structure of lamins. This paper describes a bioinformatics analysis and classification of the NMCP family based on phylogenetic relationships, sequence similarity and the distribution of conserved regions in 76 homologues. In addition, NMCP1 in the monocot Allium cepa characterized by its sequence and structure, biochemical properties, and subnuclear distribution and alterations in its expression throughout the root were identified. The results demonstrate that these proteins exhibit many similarities to lamins (structural organization, conserved regions, subnuclear distribution, and solubility) and that they may fulfil the functions of lamins in plants. These findings significantly advance understanding of the structural proteins of the plant lamina and nucleoskeleton and provide a basis for further investigation of the protein networks forming these structures.
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Affiliation(s)
- Malgorzata Ciska
- Cell and Molecular Biology Department, Centre of Biological Researches, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Kiyoshi Masuda
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Susana Moreno Díaz de la Espina
- Cell and Molecular Biology Department, Centre of Biological Researches, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
- To whom correspondence should be addressed. E-mail:
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Characterization of a 65 kDa NIF in the nuclear matrix of the monocot Allium cepa that interacts with nuclear spectrin-like proteins. Cell Biol Int 2012; 36:1097-105. [PMID: 22950797 DOI: 10.1042/cbi20120237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Plant cells have a well organized nucleus and nuclear matrix, but lack orthologues of the main structural components of the metazoan nuclear matrix. Although data is limited, most plant nuclear structural proteins are coiled-coil proteins, such as the NIFs (nuclear intermediate filaments) in Pisum sativum that cross-react with anti-intermediate filament and anti-lamin antibodies, form filaments 6-12 nm in diameter in vitro, and may play the role of lamins. We have investigated the conservation and features of NIFs in a monocot species, Allium cepa, and compared them with onion lamin-like proteins. Polyclonal antisera against the pea 65 kDa NIF were used in 1D and 2D Western blots, ICM (imunofluorescence confocal microscopy) and IEM (immunoelectron microscopy). Their presence in the nuclear matrix was analysed by differential extraction of nuclei, and their association with structural spectrin-like proteins by co-immunoprecipitation and co-localization in ICM. NIF is a conserved structural component of the nucleus and its matrix in monocots with Mr and pI values similar to those of pea 65 kDa NIF, which localized to the nuclear envelope, perichromatin domains and foci, and to the nuclear matrix, interacting directly with structural nuclear spectrin-like proteins. Its similarities with some of the proteins described as onion lamin-like proteins suggest that they are highly related or perhaps the same proteins.
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Simon DN, Wilson KL. The nucleoskeleton as a genome-associated dynamic 'network of networks'. Nat Rev Mol Cell Biol 2011; 12:695-708. [PMID: 21971041 DOI: 10.1038/nrm3207] [Citation(s) in RCA: 222] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In the cytosol, actin polymers, intermediate filaments and microtubules can anchor to cell surface adhesions and interlink to form intricate networks. This cytoskeleton is anchored to the nucleus through LINC (links the nucleoskeleton and cytoskeleton) complexes that span the nuclear envelope and in turn anchor to networks of filaments in the nucleus. The metazoan nucleoskeleton includes nuclear pore-linked filaments, A-type and B-type lamin intermediate filaments, nuclear mitotic apparatus (NuMA) networks, spectrins, titin, 'unconventional' polymers of actin and at least ten different myosin and kinesin motors. These elements constitute a poorly understood 'network of networks' that dynamically reorganizes during mitosis and is responsible for genome organization and integrity.
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Affiliation(s)
- Dan N Simon
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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