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Celebioglu B, Hart JP, Porch T, Griffiths P, Myers JR. Genome-Wide Association Study to Identify Possible Candidate Genes of Snap Bean Leaf and Pod Color. Genes (Basel) 2023; 14:2234. [PMID: 38137056 PMCID: PMC10742591 DOI: 10.3390/genes14122234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Color can be an indicator of plant health, quality, and productivity, and is useful to researchers to understand plant nutritional content in their studies. Color may be related to chlorophyll content and photosynthetic activity and provides information for those studying diseases and mineral nutrition because every nutrient deficiency and many diseases produce symptoms that affect color. In order to identify significant loci related to both leaf and pod color in a snap bean (Phaseolus vulgaris L.) diversity panel, a genome-wide association study (GWAS) was carried out. Leaf color in one and pod traits in multiple environments were characterized using a colorimeter. L*a*b* color data were recorded and used to calculate chroma (C*) and hue angle (H°). Leaves were evaluated at three positions (lower, middle, and upper) in the canopy and both pod exterior and interior colors were obtained. GWAS was conducted using two reference genomes that represent the Andean (G19833) and Middle American (5-593) domestication centers. Narrow sense heritabilities were calculated using the mixed linear model (MLM) method in genome association and prediction integrated tool (GAPIT), and significant single nucleotide polymorphisms (SNPs) for each color parameter were obtained using the Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) GWAS model with two principal components (PCAs). In comparison to pod color traits, narrow sense heritabilities of leaf traits were low and similar for both reference genomes. Generally, narrow sense heritability for all traits was highest in the lower, followed by middle, and then upper leaf positions. Heritability for both pod interior and exterior color traits was higher using the G19833 reference genome compared to 5-593 when evaluated by year and means across years. Forty-five significant SNPs associated with leaf traits and 872 associated with pods, totaling 917 significant SNPs were identified. Only one SNP was found in common for both leaf and pod traits on Pv03 in the 5-593 reference genome. One-hundred thirteen significant SNPs, 30 in leaves and 83 in pods had phenotypic variation explained (PVE) of 10% or greater. Fourteen SNPs (four from G19833 and ten from 5-593) with ≥10 PVE%, large SNP effect, and largest p-value for L* and H° pod exterior was identified on Pv01, Pv02, Pv03, and Pv08. More SNPs were associated with pod traits than with leaf traits. The pod interior did not exhibit colors produced by anthocyanins or flavonols which allowed the differentiation of potential candidate genes associated with chloroplast and photosynthetic activity compared to the pod exterior where candidate genes related to both flavonoids and photosynthesis affected color. Several SNPs were associated with known qualitative genes including the wax pod locus (y), persistent color (pc), purple pods (V), and two genes expressed in seeds but not previously reported to affect other plant tissues (B and J). An evaluation of significant SNPs within annotated genes found a number, within a 200 kb window, involved in both flavonoid and photosynthetic biosynthetic pathways.
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Affiliation(s)
- Burcu Celebioglu
- Department of Horticulture, Oregon State University, 4017 Ag & Life Science Bldg., Corvallis, OR 97331, USA;
| | - John P. Hart
- USDA-ARS, Tropical Agriculture Research Station (TARS), 2200 P. A. Campos Ave., Suite 201, Mayagüez, PR 00680, USA; (J.P.H.); (T.P.)
| | - Timothy Porch
- USDA-ARS, Tropical Agriculture Research Station (TARS), 2200 P. A. Campos Ave., Suite 201, Mayagüez, PR 00680, USA; (J.P.H.); (T.P.)
| | - Phillip Griffiths
- School of Integrated Plant Sciences, Horticulture Section, Cornell Agritech, 635 W. North St., Geneva, NY 14456, USA;
| | - James R. Myers
- Department of Horticulture, Oregon State University, 4017 Ag & Life Science Bldg., Corvallis, OR 97331, USA;
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Sandoval-Ibáñez O, Sharma A, Bykowski M, Borràs-Gas G, Behrendorff JBYH, Mellor S, Qvortrup K, Verdonk JC, Bock R, Kowalewska Ł, Pribil M. Curvature thylakoid 1 proteins modulate prolamellar body morphology and promote organized thylakoid biogenesis in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2021; 118:e2113934118. [PMID: 34654749 PMCID: PMC8594483 DOI: 10.1073/pnas.2113934118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 11/18/2022] Open
Abstract
The term "de-etiolation" refers to the light-dependent differentiation of etioplasts to chloroplasts in angiosperms. The underlying process involves reorganization of prolamellar bodies (PLBs) and prothylakoids into thylakoids, with concurrent changes in protein, lipid, and pigment composition, which together lead to the assembly of active photosynthetic complexes. Despite the highly conserved structure of PLBs among land plants, the processes that mediate PLB maintenance and their disassembly during de-etiolation are poorly understood. Among chloroplast thylakoid membrane-localized proteins, to date, only Curvature thylakoid 1 (CURT1) proteins were shown to exhibit intrinsic membrane-bending capacity. Here, we show that CURT1 proteins, which play a critical role in grana margin architecture and thylakoid plasticity, also participate in de-etiolation and modulate PLB geometry and density. Lack of CURT1 proteins severely perturbs PLB organization and vesicle fusion, leading to reduced accumulation of the light-dependent enzyme protochlorophyllide oxidoreductase (LPOR) and a delay in the onset of photosynthesis. In contrast, overexpression of CURT1A induces excessive bending of PLB membranes, which upon illumination show retarded disassembly and concomitant overaccumulation of LPOR, though without affecting greening or the establishment of photosynthesis. We conclude that CURT1 proteins contribute to the maintenance of the paracrystalline PLB morphology and are necessary for efficient and organized thylakoid membrane maturation during de-etiolation.
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Affiliation(s)
- Omar Sandoval-Ibáñez
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Copenhagen, Denmark
- Max Planck Institute of Molecular Plant Physiology, Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, 14476 Potsdam, Germany
| | - Anurag Sharma
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Copenhagen, Denmark
| | - Michał Bykowski
- Department of Plant Anatomy and Cytology, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, PL-02-096 Warsaw, Poland
| | - Guillem Borràs-Gas
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Copenhagen, Denmark
| | - James B Y H Behrendorff
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Copenhagen, Denmark
| | - Silas Mellor
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Copenhagen, Denmark
| | - Klaus Qvortrup
- Core Facility for Integrated Microscopy, The Panum Institute, Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Julian C Verdonk
- Horticulture and Product Physiology, Plant Sciences Group, Wageningen University, 6708 PD Wageningen, The Netherlands
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, 14476 Potsdam, Germany
| | - Łucja Kowalewska
- Department of Plant Anatomy and Cytology, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, PL-02-096 Warsaw, Poland;
| | - Mathias Pribil
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Copenhagen, Denmark;
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Santamarï A-Gï Mez J, Mariscal V, Luque I. Mechanisms for Protein Redistribution in Thylakoids of Anabaena During Cell Differentiation. Plant Cell Physiol 2018; 59:1860-1873. [PMID: 29878163 DOI: 10.1093/pcp/pcy103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 05/25/2018] [Indexed: 06/08/2023]
Abstract
Thylakoid membranes are far from being homogeneous in composition. On the contrary, compositional heterogeneity of lipid and protein content is well known to exist in these membranes. The mechanisms for the confinement of proteins at a particular membrane domain have started to be unveiled, but we are far from a thorough understanding, and many issues remain to be elucidated. During the differentiation of heterocysts in filamentous cyanobacteria of the Anabaena and Nostoc genera, thylakoids undergo a complete reorganization, separating into two membrane domains of different appearance and subcellular localization. Evidence also indicates different functionality and protein composition for these two membrane domains. In this work, we have addressed the mechanisms that govern the specific localization of proteins at a particular membrane domain. Two classes of proteins were distinguished according to their distribution in the thylakoids. Our results indicate that the specific accumulation of proteins of the CURVATURE THYLAKOID 1 (CURT1) family and proteins containing the homologous CAAD domain at subpolar honeycomb thylakoids is mediated by multiple mechanisms including a previously unnoticed phenomenon of thylakoid membrane migration.
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Affiliation(s)
- Javier Santamarï A-Gï Mez
- Instituto de Bioqu�mica Vegetal y Fotos�ntesis, CSIC and Universidad de Sevilla, Avda Am�rico Vespucio 49, Seville E-41092, Spain
| | - Vicente Mariscal
- Instituto de Bioqu�mica Vegetal y Fotos�ntesis, CSIC and Universidad de Sevilla, Avda Am�rico Vespucio 49, Seville E-41092, Spain
| | - Ignacio Luque
- Instituto de Bioqu�mica Vegetal y Fotos�ntesis, CSIC and Universidad de Sevilla, Avda Am�rico Vespucio 49, Seville E-41092, Spain
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Abstract
Thylakoids of land plants have a bipartite structure, consisting of cylindrical grana stacks, made of membranous discs piled one on top of the other, and stroma lamellae which are helically wound around the cylinders. Protein complexes predominantly located in the stroma lamellae and grana end membranes are either bulky [photosystem I (PSI) and the chloroplast ATP synthase (cpATPase)] or are involved in cyclic electron flow [the NAD(P)H dehydrogenase (NDH) and PGRL1-PGR5 heterodimers], whereas photosystem II (PSII) and its light-harvesting complex (LHCII) are found in the appressed membranes of the granum. Stacking of grana is thought to be due to adhesion between Lhcb proteins (LHCII or CP26) located in opposed thylakoid membranes. The grana margins contain oligomers of CURT1 proteins, which appear to control the size and number of grana discs in a dosage- and phosphorylation-dependent manner. Depending on light conditions, thylakoid membranes undergo dynamic structural changes that involve alterations in granum diameter and height, vertical unstacking of grana, and swelling of the thylakoid lumen. This plasticity is realized predominantly by reorganization of the supramolecular structure of protein complexes within grana stacks and by changes in multiprotein complex composition between appressed and non-appressed membrane domains. Reversible phosphorylation of LHC proteins (LHCPs) and PSII components appears to initiate most of the underlying regulatory mechanisms. An update on the roles of lipids, proteins, and protein complexes, as well as possible trafficking mechanisms, during thylakoid biogenesis and the de-etiolation process complements this review.
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Affiliation(s)
- Mathias Pribil
- Plant Molecular Biology, Department of Biology, Ludwig-Maximilians-University Munich (LMU), D-82152 Planegg-Martinsried, Germany
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