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Cho YB, Boyd RA, Ren Y, Lee MS, Jones SI, Ruiz-Vera UM, McGrath JM, Masters MD, Ort DR. Reducing chlorophyll levels in seed-filling stages results in higher seed nitrogen without impacting canopy carbon assimilation. PLANT, CELL & ENVIRONMENT 2024; 47:278-293. [PMID: 37828764 DOI: 10.1111/pce.14737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 10/14/2023]
Abstract
Chlorophyll is the major light-absorbing pigment for plant photosynthesis. While evolution has been selected for high chlorophyll content in leaves, previous work suggests that domesticated crops grown in modern high-density agricultural environments overinvest in chlorophyll production, thereby lowering light use and nitrogen use efficiency. To investigate the potential benefits of reducing chlorophyll levels, we created ethanol-inducible RNAi tobacco mutants that suppress Mg-chelatase subunit I (CHLI) with small RNA within 3 h of induction and reduce chlorophyll within 5 days in field conditions. We initiated chlorophyll reduction later in plant development to avoid the highly sensitive seedling stage and to allow young plants to have full green leaves to maximise light interception before canopy formation. This study demonstrated that leaf chlorophyll reduction >60% during seed-filling stages increased tobacco seed nitrogen concentration by as much as 17% while canopy photosynthesis, biomass and seed yields were maintained. These results indicate that time-specific reduction of chlorophyll could be a novel strategy that decouples the inverse relationship between yield and seed nitrogen by utilising saved nitrogen from the reduction of chlorophyll while maintaining full carbon assimilation capacity.
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Affiliation(s)
- Young B Cho
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ryan A Boyd
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yudong Ren
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Moon-Sub Lee
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Sarah I Jones
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ursula M Ruiz-Vera
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Justin M McGrath
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Michael D Masters
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Donald R Ort
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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Fan L, Hou Y, Zheng L, Shi H, Liu Z, Wang Y, Li S, Liu L, Guo M, Yang Z, Liu J. Characterization and fine mapping of a yellow leaf gene regulating chlorophyll biosynthesis and chloroplast development in cotton (Gossypium arboreum). Gene 2023; 885:147712. [PMID: 37579958 DOI: 10.1016/j.gene.2023.147712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/20/2023] [Accepted: 08/11/2023] [Indexed: 08/16/2023]
Abstract
Chlorophyll biosynthesis and chloroplast development are essential for photosynthesis and plant growth. Gossypium arboreum, a valuable source of genetic variation for cotton improvement, remains poorly studied for the mechanisms regulating chlorophyll biosynthesis and chloroplast development. Here we created a G. arboreum etiolated leaf and stuntedness (els) mutant that displayed a distinct yellow color of leaves, bracts and stems throughout the whole growth, where chlorophyll accumulation in leaves was reduced and chloroplast development was delayed. The GaCHLH gene, which encodes the H subunit of magnesium chelatase (Mg-chelatase), was screened by MutMap and KASP analysis. Compared to GaCHLH, the gene Gachlh of the mutant had a single nucleotide transition (G to A) at 1549 bp, which causes the substitution of a glycine (G) by a serine (S) at the 517th amino acid, resulting in an abnormal secondary structure of the Gachlh protein. GaCHLH-silenced SXY1 and ZM24 plants exhibited a lower GaCHLH expression level, a lower chlorophyll content, and the yellow-leaf phenotype. Gachlh expression affected the expression of key genes in the tetrapyrrole pathway. GaCHLH and Gachlh were located in the chloroplasts and that alteration of the mutation site did not affect the final target position. The BiFC assay result indicated that Gachlh could not bind to GaCHLD properly, which prevented the assembly of Mg-chelatase and thus led to the failure of chlorophyll synthesis. In this study, the Gachlh gene of G. arboreum els was finely localized and identified for the first time, providing new insights into the chlorophyll biosynthesis pathway in cotton.
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Affiliation(s)
- Liqiang Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Yan Hou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Lei Zheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Beijing 100081, China
| | - Huiyun Shi
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Zhao Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yuxuan Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Shengdong Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Le Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Mengzhen Guo
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute, Xinjiang Academy Agricultural and Reclamation Science, Shihezi 832003, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China.
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
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Li Y, Wang X, Zhang Q, Shen Y, Wang J, Qi S, Zhao P, Muhammad T, Islam MM, Zhan X, Liang Y. A mutation in SlCHLH encoding a magnesium chelatase H subunit is involved in the formation of yellow stigma in tomato (Solanum lycopersicum L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111466. [PMID: 36174799 DOI: 10.1016/j.plantsci.2022.111466] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Chlorophylls are ubiquitous pigments responsible for the green color in plants. Changes in the chlorophyll content have a significant impact on photosynthesis, plant growth and development. In this study, we used a yellow stigma mutant (ys) generated from a green stigma tomato WT by using ethylmethylsulfone (EMS)-induced mutagenesis. Compared with WT, the stigma of ys shows low chlorophyll content and impaired chloroplast ultrastructure. Through map-based cloning, the ys gene is localized to a 100 kb region on chromosome 4 between dCAPS596 and dCAPS606. Gene expression analysis and nonsynonymous SNP determination identified the Solyc04g015750, as the potential candidate gene, which encodes a magnesium chelatase H subunit (CHLH). In ys mutant, a single base C to T substitution in the SlCHLH gene results in the conversion of Serine into Leucine (Ser92Leu) at the N-terminal region. The functional complementation test shows that the SlCHLH from WT can rescue the green stigma phenotype of ys. In contrast, knockdown of SlCHLH in green stigma tomato AC, observed the yellow stigma phenotype at the stigma development stage. Overexpression of the mutant gene Slys in green stigma tomato AC results in the light green stigma. These results indicate that the mutation of the N-terminal S92 to Leu in SlCHLH is the main reason for the formation of the yellow stigma phenotype. Characterization of the ys mutant enriches the current knowledge of the tomato chlorophyll mutant library and provides a novel and effective tool for understanding the function of CHLH in tomato.
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Affiliation(s)
- Yushun Li
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, P.R. China; State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Shaanxi 712100, China.
| | - Xinyu Wang
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, P.R. China; State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Shaanxi 712100, China.
| | - Qinghua Zhang
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, P.R. China; State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Shaanxi 712100, China
| | - Yuanbo Shen
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, P.R. China; State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Shaanxi 712100, China.
| | - Jin Wang
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, P.R. China; State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Shaanxi 712100, China.
| | - Shiming Qi
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, P.R. China; State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Shaanxi 712100, China.
| | - Pan Zhao
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, P.R. China; State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Shaanxi 712100, China.
| | - Tayeb Muhammad
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, P.R. China; State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Shaanxi 712100, China; Directorate of Agriculture Extension, Merged Areas, Peshawar 25000, Khyber Pakhtunkhwa, Pakistan.
| | - Md Monirul Islam
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, P.R. China; State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Shaanxi 712100, China.
| | - Xiangqiang Zhan
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, P.R. China.
| | - Yan Liang
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, P.R. China; State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Shaanxi 712100, China.
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Acebron K, Salvatori N, Alberti G, Muller O, Peressotti A, Rascher U, Matsubara S. Elucidating the photosynthetic responses in chlorophyll-deficient soybean (Glycine max, L.) Cultivar. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2022. [DOI: 10.1016/j.jpap.2022.100152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Wang Y, Wang J, Chen L, Meng X, Zhen X, Liang Y, Han Y, Li H, Zhang B. Identification and function analysis of yellow-leaf mutant (YX-yl) of broomcorn millet. BMC PLANT BIOLOGY 2022; 22:463. [PMID: 36167497 PMCID: PMC9513943 DOI: 10.1186/s12870-022-03843-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/12/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND Broomcorn millet is highly tolerant to drought and barren soil. Changes in chlorophyll content directly affect leaf color, which subsequently leadsleading to poor photosynthetic performance and reduced crop yield. Herein, we isolated a yellow leaf mutant (YX-yl) using a forward genetics approach and evaluated its agronomic traits, photosynthetic pigment content, chloroplast ultrastructure, and chlorophyll precursors. Furthermore, the molecular mechanism of yellowing was explored using transcriptome sequencing. RESULTS The YX-yl mutant showed significantly decreased plant height and low yield. The leaves exhibited a yellow-green phenotype and poor photosynthetic capacity during the entire growth period. The content of chlorophyll a, chlorophyll b, and carotenoids in YX-yl leaves was lower than that in wild-type leaves. Chlorophyll precursor analysis results showed that chlorophyll biosynthesis in YX-yl was hindered by the conversion of porphobilinogen to protoporphyrin IX. Examination of chloroplast ultrastructure in the leaves revealed that the chloroplasts of YX-yl accumulated on one side of the cell. Moreover, the chloroplast structure of YX-yl was degraded. The inner and outer membranes of the chloroplasts could not be distinguished well. The numbers of grana and grana thylakoids in the chloroplasts were low. The transcriptome of the yellowing mutant YX-yl was sequenced and compared with that of the wild type. Nine chlorophyll-related genes with significantly different expression profiles were identified: PmUROD, PmCPO, PmGSAM, PmPBDG, PmLHCP, PmCAO, PmVDE, PmGluTR, and PmPNPT. The proteins encoded by these genes were located in the chloroplast, chloroplast membrane, chloroplast thylakoid membrane, and chloroplast matrix and were mainly involved in chlorophyll biosynthesis and redox-related enzyme regulation. CONCLUSIONS YX-yl is an ideal material for studying pigment metabolism mechanisms. Changes in the expression patterns of some genes between YX-yl and the wild type led to differences in chloroplast structures and enzyme activities in the chlorophyll biosynthesis pathway, ultimately resulting in a yellowing phenotype in the YX-yl mutant. Our findings provide an insight to the molecular mechanisms of leaf color formation and chloroplast development in broomcorn millet.
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Affiliation(s)
- Yushen Wang
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China, 030801
- Shanxi Key Laboratory of Germplasm Innovation and Molecular Breeding of Minor Crop, Taigu, Shanxi, China, 030801
- Ministerial and Provincial Co-Innovation Centre for Endemic Crops Production With High-Quality and Efficiency in Loess Plateau, Shanxi Agricultural University, Taigu, Shanxi, China, 030801
| | - Junjie Wang
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China, 030801
| | - Liqing Chen
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China, 030801
| | - Xiaowei Meng
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China, 030801
| | - Xiaoxi Zhen
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China, 030801
| | - Yinpei Liang
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China, 030801
| | - Yuanhuai Han
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China, 030801
- Shanxi Key Laboratory of Germplasm Innovation and Molecular Breeding of Minor Crop, Taigu, Shanxi, China, 030801
| | - Hongying Li
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China, 030801
| | - Bin Zhang
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China, 030801.
- Shanxi Key Laboratory of Germplasm Innovation and Molecular Breeding of Minor Crop, Taigu, Shanxi, China, 030801.
- Ministerial and Provincial Co-Innovation Centre for Endemic Crops Production With High-Quality and Efficiency in Loess Plateau, Shanxi Agricultural University, Taigu, Shanxi, China, 030801.
- Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, Shanxi, China, 030801.
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Xue Y, Dong H, Huang H, Li S, Shan X, Li H, Liu H, Xia D, Su S, Yuan Y. Mutation in Mg-Protoporphyrin IX Monomethyl Ester (Oxidative) Cyclase Gene ZmCRD1 Causes Chlorophyll-Deficiency in Maize. FRONTIERS IN PLANT SCIENCE 2022; 13:912215. [PMID: 35873969 PMCID: PMC9301084 DOI: 10.3389/fpls.2022.912215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/23/2022] [Indexed: 06/01/2023]
Abstract
Chlorophyll molecules are non-covalently associated with chlorophyll-binding proteins to harvest light and perform charge separation vital for energy conservation during photosynthetic electron transfer in photosynthesis for photosynthetic organisms. The present study characterized a pale-green leaf (pgl) maize mutant controlled by a single recessive gene causing chlorophyll reduction throughout the whole life cycle. Through positional mapping and complementation allelic test, Zm00001d008230 (ZmCRD1) with two missense mutations (p.A44T and p.T326M) was identified as the causal gene encoding magnesium-protoporphyrin IX monomethyl ester cyclase (MgPEC). Phylogenetic analysis of ZmCRD1 within and among species revealed that the p.T326M mutation was more likely to be causal. Subcellular localization showed that ZmCRD1 was targeted to chloroplasts. The pgl mutant showed a malformed chloroplast morphology and reduced number of starch grains in bundle sheath cells. The ZmCRD1 gene was mainly expressed in WT and mutant leaves, but the expression was reduced in the mutant. Most of the genes involved in chlorophyll biosynthesis, chlorophyll degradation, chloroplast development and photosynthesis were down-regulated in pgl. The photosynthetic capacity was limited along with developmental retardation and production reduction in pgl. These results confirmed the crucial role of ZmCRD1 in chlorophyll biosynthesis, chloroplast development and photosynthesis in maize.
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Lin N, Gao Y, Zhou Q, Ping X, Li J, Liu L, Yin J. Genetic mapping and physiological analysis of chlorophyll-deficient mutant in Brassica napus L. BMC PLANT BIOLOGY 2022; 22:244. [PMID: 35585493 PMCID: PMC9115954 DOI: 10.1186/s12870-022-03630-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Leaf color mutants have reduced photosynthetic efficiency, which has severely negative impacts on crop growth and economic product yield. There are different chlorophyll mutants in Arabidopsis and crops that can be used for genetic control and molecular mechanism studies of chlorophyll biosynthesis, chloroplast development and photoefficiency. Chlorophyll mutants in Brassica napus are mostly used for mapping and location research but are rarely used for physiological research. The chlorophyll-deficient mutant in this experiment were both genetically mapped and physiologically analyzed. RESULTS In this study, yellow leaf mutant of Brassica napus L. mutated by ethyl methyl sulfone (EMS) had significantly lower chlorophyll a, b and carotenoid contents than the wild type, and the net photosynthetic efficiency, stomatal conductance and transpiration rate were all significantly reduced. The mutant had sparse chloroplast distribution and weak autofluorescence. The granule stacks were reduced, and the shape was extremely irregular, with more broken stromal lamella. Transcriptome data analysis enriched the differentially expressed genes mainly in phenylpropane and sugar metabolism. The mutant was mapped to a 2.72 Mb region on A01 by using BSA-Seq, and the region was validated by SSR markers. CONCLUSIONS The mutant chlorophyll content and photosynthetic efficiency were significantly reduced compared with those of the wild type. Abnormal chloroplasts and thylakoids less connected to the stroma lamella appeared in the mutant. This work on the mutant will facilitate the process of cloning the BnaA01.cd gene and provide more genetic and physiological information concerning chloroplast development in Brassica napus.
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Affiliation(s)
- Na Lin
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, PR China
| | - Yumin Gao
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, PR China
| | - Qingyuan Zhou
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, PR China
| | - Xiaoke Ping
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, PR China
- Academy of Agricultural Sciences, Southwest University, Tiansheng Rd2#, Beibei, Chongqing, 400715, PR China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, PR China
- Academy of Agricultural Sciences, Southwest University, Tiansheng Rd2#, Beibei, Chongqing, 400715, PR China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, PR China
- Academy of Agricultural Sciences, Southwest University, Tiansheng Rd2#, Beibei, Chongqing, 400715, PR China
| | - Jiaming Yin
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, PR China.
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Salvatori N, Alberti G, Muller O, Peressotti A. Does Fluctuating Light Affect Crop Yield? A Focus on the Dynamic Photosynthesis of Two Soybean Varieties. FRONTIERS IN PLANT SCIENCE 2022; 13:862275. [PMID: 35557734 PMCID: PMC9085482 DOI: 10.3389/fpls.2022.862275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/30/2022] [Indexed: 06/15/2023]
Abstract
In natural environments, plants are exposed to variable light conditions, but photosynthesis has been mainly studied at steady state and this might overestimate carbon (C) uptake at the canopy scale. To better elucidate the role of light fluctuations on canopy photosynthesis, we investigated how the chlorophyll content, and therefore the different absorbance of light, would affect the quantum yield in fluctuating light conditions. For this purpose, we grew a commercial variety (Eiko) and a chlorophyll deficient mutant (MinnGold) either in fluctuating (F) or non-fluctuating (NF) light conditions with sinusoidal changes in irradiance. Two different light treatments were also applied: a low light treatment (LL; max 650 μmol m-2 s-1) and a high light treatment (HL; max 1,000 μmol m-2 s-1). Canopy gas exchanges were continuously measured throughout the experiment. We found no differences in C uptake in LL treatment, either under F or NF. Light fluctuations were instead detrimental for the chlorophyll deficient mutant in HL conditions only, while the green variety seemed to be well-adapted to them. Varieties adapted to fluctuating light might be identified to target the molecular mechanisms responsible for such adaptations.
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Affiliation(s)
- Nicole Salvatori
- Department of Life Sciences, University of Trieste, Trieste, Italy
- Department of Agricultural, Food, Environmental, and Animal Sciences, University of Udine, Udine, Italy
| | - Giorgio Alberti
- Department of Agricultural, Food, Environmental, and Animal Sciences, University of Udine, Udine, Italy
- Faculty of Science and Technology, Free University of Bolzano, South Tyrol, Italy
| | - Onno Muller
- Institute of Bio- and Geosciences Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Alessandro Peressotti
- Department of Agricultural, Food, Environmental, and Animal Sciences, University of Udine, Udine, Italy
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Salvatori N, Carteni F, Giannino F, Alberti G, Mazzoleni S, Peressotti A. A System Dynamics Approach to Model Photosynthesis at Leaf Level Under Fluctuating Light. FRONTIERS IN PLANT SCIENCE 2022; 12:787877. [PMID: 35154180 PMCID: PMC8833254 DOI: 10.3389/fpls.2021.787877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
Photosynthesis has been mainly studied under steady-state conditions even though this assumption results inadequate for assessing the biochemical responses to rapid variations occurring in natural environments. The combination of mathematical models with available data may enhance the understanding of the dynamic responses of plants to fluctuating environments and can be used to make predictions on how photosynthesis would respond to non-steady-state conditions. In this study, we present a leaf level System Dynamics photosynthesis model based and validated on an experiment performed on two soybean varieties, namely, the wild type Eiko and the chlorophyll-deficient mutant MinnGold, grown in constant and fluctuating light conditions. This mutant is known to have similar steady-state photosynthesis compared to the green wild type, but it is found to have less biomass at harvest. It has been hypothesized that this might be due to an unoptimized response to non-steady-state conditions; therefore, this mutant seems appropriate to investigate dynamic photosynthesis. The model explained well the photosynthetic responses of these two varieties to fluctuating and constant light conditions and allowed to make relevant conclusions on the different dynamic responses of the two varieties. Deviations between data and model simulations are mostly evident in the non-photochemical quenching (NPQ) dynamics due to the oversimplified combination of PsbS- and zeaxanthin-dependent kinetics, failing in finely capturing the NPQ responses at different timescales. Nevertheless, due to its simplicity, the model can provide the basis of an upscaled dynamic model at a plant level.
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Affiliation(s)
- Nicole Salvatori
- DI4A, Department of Agri-Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Fabrizio Carteni
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Francesco Giannino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Giorgio Alberti
- DI4A, Department of Agri-Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
- Faculty of Science and Technology, Free University of Bolzano, Bolzano, Italy
| | - Stefano Mazzoleni
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Alessandro Peressotti
- DI4A, Department of Agri-Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
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Wu CJ, Wang J, Zhu J, Ren J, Yang YX, Luo T, Xu LX, Zhou QH, Xiao XF, Zhou YX, Luo S. Molecular Characterization of Mg-Chelatase CHLI Subunit in Pea ( Pisum sativum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:821683. [PMID: 35145539 PMCID: PMC8821089 DOI: 10.3389/fpls.2022.821683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/03/2022] [Indexed: 05/28/2023]
Abstract
As a rate-limiting enzyme for chlorophyll biosynthesis, Mg-chelatase is a promising target for improving photosynthetic efficiency. It consists of CHLH, CHLD, and CHLI subunits. In pea (Pisum sativum L.), two putative CHLI genes (PsCHLI1 and PsCHLI2) were revealed recently by the whole genome sequencing, but their molecular features are not fully characterized. In this study, PsCHLI1 and PsCHLI2 cDNAs were identified by PCR-based cloning and sequencing. Phylogenetic analysis showed that PsCHLIs were derived from an ancient duplication in legumes. Both PsCHLIs were more highly expressed in leaves than in other organs and downregulated by abscisic acid and heat treatments, while PsCHLI1 was more highly expressed than PsCHLI2. PsCHLI1 and PsCHLI2 encode 422- and 417-amino acid proteins, respectively, which shared 82% amino acid identity and were located in chloroplasts. Plants with a silenced PsCHLI1 closely resembled PsCHLI1 and PsCHLI2 double-silenced plants, as both exhibited yellow leaves with barely detectable Mg-chelatase activity and chlorophyll content. Furthermore, plants with a silenced PsCHLI2 showed no obvious phenotype. In addition, the N-terminal fragment of PsCHLI1 (PsCHLI1N, Val63-Cys191) and the middle fragment of PsCHLI1 (PsCHLI1M, Gly192-Ser336) mediated the formation of homodimers and the interaction with CHLD, respectively, while active PsCHLI1 was only achieved by combining PsCHLI1N, PsCHLI1M, and the C-terminal fragment of PsCHLI1 (Ser337-Ser422). Taken together, PsCHLI1 is the key CHLI subunit, and its peptide fragments are essential for maintaining Mg-chelatase activity, which can be used to improve photosynthetic efficiency by manipulating Mg-chelatase in pea.
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Affiliation(s)
- Cai-jun Wu
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Jie Wang
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Jun Zhu
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Jing Ren
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - You-xin Yang
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Tao Luo
- Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Lu-xi Xu
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Qing-hong Zhou
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Xu-feng Xiao
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Yu-xin Zhou
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Sha Luo
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
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11
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Keller B, Zimmermann L, Rascher U, Matsubara S, Steier A, Muller O. Toward predicting photosynthetic efficiency and biomass gain in crop genotypes over a field season. PLANT PHYSIOLOGY 2022; 188:301-317. [PMID: 34662428 PMCID: PMC8774793 DOI: 10.1093/plphys/kiab483] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 09/13/2021] [Indexed: 05/19/2023]
Abstract
Photosynthesis acclimates quickly to the fluctuating environment in order to optimize the absorption of sunlight energy, specifically the photosynthetic photon fluence rate (PPFR), to fuel plant growth. The conversion efficiency of intercepted PPFR to photochemical energy (ɛe) and to biomass (ɛc) are critical parameters to describe plant productivity over time. However, they mask the link of instantaneous photochemical energy uptake under specific conditions, that is, the operating efficiency of photosystem II (Fq'/Fm'), and biomass accumulation. Therefore, the identification of energy- and thus resource-efficient genotypes under changing environmental conditions is impeded. We long-term monitored Fq'/Fm' at the canopy level for 21 soybean (Glycine max (L.) Merr.) and maize (Zea mays) genotypes under greenhouse and field conditions using automated chlorophyll fluorescence and spectral scans. Fq'/Fm' derived under incident sunlight during the entire growing season was modeled based on genotypic interactions with different environmental variables. This allowed us to cumulate the photochemical energy uptake and thus estimate ɛe noninvasively. ɛe ranged from 48% to 62%, depending on the genotype, and up to 9% of photochemical energy was transduced into biomass in the most efficient C4 maize genotype. Most strikingly, ɛe correlated with shoot biomass in seven independent experiments under varying conditions with up to r = 0.68. Thus, we estimated biomass production by integrating photosynthetic response to environmental stresses over the growing season and identified energy-efficient genotypes. This has great potential to improve crop growth models and to estimate the productivity of breeding lines or whole ecosystems at any time point using autonomous measuring systems.
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Affiliation(s)
- Beat Keller
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Lars Zimmermann
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
- Field Lab Campus Klein-Altendorf, University of Bonn, Rheinbach 53359, Germany
| | - Uwe Rascher
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Shizue Matsubara
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Angelina Steier
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Onno Muller
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
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12
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Cui Q, Huang J, Wu F, Li DZ, Zheng L, Hu G, Hu S, Zhang L. Biochemical and transcriptomic analyses reveal that critical genes involved in pigment biosynthesis influence leaf color changes in a new sweet osmanthus cultivar 'Qiannan Guifei'. PeerJ 2021; 9:e12265. [PMID: 34707941 PMCID: PMC8504463 DOI: 10.7717/peerj.12265] [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: 05/21/2020] [Accepted: 09/16/2021] [Indexed: 11/22/2022] Open
Abstract
Background Osmanthus fragrans (Oleaceae) is one of the most important ornamental plant species in China. Many cultivars with different leaf color phenotypes and good ornamental value have recently been developed. For example, a new cultivar ‘Qiannan Guifei’, presents a rich variety of leaf colors, which change from red to yellow-green and ultimately to green as leaves develop, making this cultivar valuable for landscaping. However, the biochemical characteristics and molecular mechanisms underlying leaf color changes of these phenotypes have not been elucidated. It has been hypothesized that the biosynthesis of different pigments in O. fragrans might change during leaf coloration. Here, we analyzed transcriptional changes in genes involved in chlorophyll (Chl), flavonoid, and carotenoid metabolic pathways and identified candidate genes responsible for leaf coloration in the new cultivar ‘Qiannan Guifei’. Methods Leaf samples were collected from ‘Qiannan Guifei’ plants at the red (R), yellow-green (YG) and green (G) leaf stages. We compared the different-colored leaves via leaf pigment concentrations, chloroplast ultrastructure, and transcriptomic data. We further analyzed differentially expressed genes (DEGs) involved in the Chl, flavonoid, and carotenoid metabolic pathways. In addition, we used qRT-PCR to validate expression patterns of the DEGs at the three stages. Results We found that, compared with those at the G stage, chloroplasts at the R and YG stages were less abundant and presented abnormal morphologies. Pigment analyses revealed that the leaves had higher flavonoid and anthocyanin levels at the R stage but lower Chl and carotenoid concentrations. Similarly, Chl and carotenoid concentrations were lower at the YG stage than at the G stage. By using transcriptomic sequencing, we further identified 61 DEGs involved in the three pigment metabolic pathways. Among these DEGs, seven structural genes (OfCHS, OfCHI, OfF3H, OfDFR, OfANS, OfUGT andOf3AT) involved in the flavonoid biosynthesis pathway were expressed at the highest level at the R stage, thereby increasing the biosynthesis of flavonoids, especially anthocyanins. Six putativeOfMYB genes, including three flavonoid-related activators and three repressors, were also highly expressed at the R stage, suggesting that they might coordinately regulate the accumulation of flavonoids, including anthocyanins. Additionally, expressions of the Chl biosynthesis-related genes OfHEMA, OfCHLG and OfCAO and the carotenoid biosynthesis-related genes OfHYB and OfZEP were upregulated from the R stage to the G stage, which increased the accumulation of Chl and carotenoids throughout leaf development. In summary, we screened the candidate genes responsible for the leaf color changes of ‘Qiannan Guifei’, improved current understanding of the regulatory mechanisms underlying leaf coloration and provided potential targets for future leaf color improvement in O. fragrans.
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Affiliation(s)
- Qi Cui
- School of Civil Engineering and Architecture, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
| | - Junhua Huang
- School of Civil Engineering and Architecture, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
| | - Fan Wu
- School of Civil Engineering and Architecture, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
| | - Dong-Ze Li
- School of Civil Engineering and Architecture, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
| | - Liqun Zheng
- School of Civil Engineering and Architecture, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
| | - Guang Hu
- School of Civil Engineering and Architecture, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
| | - Shaoqing Hu
- School of Civil Engineering and Architecture, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
| | - Lu Zhang
- School of Civil Engineering and Architecture, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
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13
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Eid A, Mohan C, Sanchez S, Wang D, Altpeter F. Multiallelic, Targeted Mutagenesis of Magnesium Chelatase With CRISPR/Cas9 Provides a Rapidly Scorable Phenotype in Highly Polyploid Sugarcane. Front Genome Ed 2021; 3:654996. [PMID: 34713257 PMCID: PMC8525377 DOI: 10.3389/fgeed.2021.654996] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/15/2021] [Indexed: 12/12/2022] Open
Abstract
Genome editing with sequence-specific nucleases, such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9), is revolutionizing crop improvement. Developing efficient genome-editing protocols for highly polyploid crops, including sugarcane (x = 10-13), remains challenging due to the high level of genetic redundancy in these plants. Here, we report the efficient multiallelic editing of magnesium chelatase subunit I (MgCh) in sugarcane. Magnesium chelatase is a key enzyme for chlorophyll biosynthesis. CRISPR/Cas9-mediated targeted co-mutagenesis of 49 copies/alleles of magnesium chelatase was confirmed via Sanger sequencing of cloned PCR amplicons. This resulted in severely reduced chlorophyll contents, which was scorable at the time of plant regeneration in the tissue culture. Heat treatment following the delivery of genome editing reagents elevated the editing frequency 2-fold and drastically promoted co-editing of multiple alleles, which proved necessary to create a phenotype that was visibly distinguishable from the wild type. Despite their yellow leaf color, the edited plants were established well in the soil and did not show noticeable growth retardation. This approach will facilitate the establishment of genome editing protocols for recalcitrant crops and support further optimization, including the evaluation of alternative RNA-guided nucleases to overcome the limitations of the protospacer adjacent motif (PAM) site or to develop novel delivery strategies for genome editing reagents.
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Affiliation(s)
- Ayman Eid
- Agronomy Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, United States
| | - Chakravarthi Mohan
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, United States
| | - Sara Sanchez
- Agronomy Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, United States
| | - Duoduo Wang
- Agronomy Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, United States
| | - Fredy Altpeter
- Agronomy Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
- Plant Molecular and Cellular Biology Program, Institute of Food and Agricultural Sciences, Gainesville, FL, United States
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14
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Slattery RA, Ort DR. Perspectives on improving light distribution and light use efficiency in crop canopies. PLANT PHYSIOLOGY 2021; 185:34-48. [PMID: 33631812 PMCID: PMC8133579 DOI: 10.1093/plphys/kiaa006] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/03/2020] [Indexed: 05/22/2023]
Abstract
Plant stands in nature differ markedly from most seen in modern agriculture. In a dense mixed stand, plants must vie for resources, including light, for greater survival and fitness. Competitive advantages over surrounding plants improve fitness of the individual, thus maintaining the competitive traits in the gene pool. In contrast, monoculture crop production strives to increase output at the stand level and thus benefits from cooperation to increase yield of the community. In choosing plants with higher yields to propagate and grow for food, humans may have inadvertently selected the best competitors rather than the best cooperators. Here, we discuss how this selection for competitiveness has led to overinvestment in characteristics that increase light interception and, consequently, sub-optimal light use efficiency in crop fields that constrains yield improvement. Decades of crop canopy modeling research have provided potential strategies for improving light distribution in crop canopies, and we review the current progress of these strategies, including balancing light distribution through reducing pigment concentration. Based on recent research revealing red-shifted photosynthetic pigments in algae and photosynthetic bacteria, we also discuss potential strategies for optimizing light interception and use through introducing alternative pigment types in crops. These strategies for improving light distribution and expanding the wavelengths of light beyond those traditionally defined for photosynthesis in plant canopies may have large implications for improving crop yield and closing the yield gap.
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Affiliation(s)
- Rebecca A Slattery
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Donald R Ort
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Departments of Plant Biology & Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Author for communication:
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15
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Eid A, Mohan C, Sanchez S, Wang D, Altpeter F. Multiallelic, Targeted Mutagenesis of Magnesium Chelatase With CRISPR/Cas9 Provides a Rapidly Scorable Phenotype in Highly Polyploid Sugarcane. Front Genome Ed 2021. [PMID: 34713257 DOI: 10.3389/fgeed.2021.65499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023] Open
Abstract
Genome editing with sequence-specific nucleases, such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9), is revolutionizing crop improvement. Developing efficient genome-editing protocols for highly polyploid crops, including sugarcane (x = 10-13), remains challenging due to the high level of genetic redundancy in these plants. Here, we report the efficient multiallelic editing of magnesium chelatase subunit I (MgCh) in sugarcane. Magnesium chelatase is a key enzyme for chlorophyll biosynthesis. CRISPR/Cas9-mediated targeted co-mutagenesis of 49 copies/alleles of magnesium chelatase was confirmed via Sanger sequencing of cloned PCR amplicons. This resulted in severely reduced chlorophyll contents, which was scorable at the time of plant regeneration in the tissue culture. Heat treatment following the delivery of genome editing reagents elevated the editing frequency 2-fold and drastically promoted co-editing of multiple alleles, which proved necessary to create a phenotype that was visibly distinguishable from the wild type. Despite their yellow leaf color, the edited plants were established well in the soil and did not show noticeable growth retardation. This approach will facilitate the establishment of genome editing protocols for recalcitrant crops and support further optimization, including the evaluation of alternative RNA-guided nucleases to overcome the limitations of the protospacer adjacent motif (PAM) site or to develop novel delivery strategies for genome editing reagents.
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Affiliation(s)
- Ayman Eid
- Agronomy Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, United States
| | - Chakravarthi Mohan
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, United States
| | - Sara Sanchez
- Agronomy Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, United States
| | - Duoduo Wang
- Agronomy Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, United States
| | - Fredy Altpeter
- Agronomy Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
- Plant Molecular and Cellular Biology Program, Institute of Food and Agricultural Sciences, Gainesville, FL, United States
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Liu M, Wang Y, Nie Z, Gai J, Bhat JA, Kong J, Zhao T. Double mutation of two homologous genes YL1 and YL2 results in a leaf yellowing phenotype in soybean [Glycine max (L.) Merr]. PLANT MOLECULAR BIOLOGY 2020; 103:527-543. [PMID: 32323129 DOI: 10.1007/s11103-020-01008-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 04/15/2020] [Indexed: 06/11/2023]
Abstract
KEY MESSAGE Two homologous, chloroplast located CAAX proteases were identified to be functional redundancy in determining soybean leaf color, and they probably play essential roles in regulating light harvesting and absorption during photosynthesis process. Leaf color mutants are ideal materials for studying photosynthesis and chlorophyll metabolism. The soybean [Glycine max (L.) Merr.] yellowing leaf (yl) variation is a recombinant mutant characterized by yellow foliage, which derived from the specific cross between green seed-coated and yellow seed-coated soybean varieties. Molecular cloning and subsequent gene silencing revealed that the yellow leaf trait of yl was controlled by two recessive nuclear genes, glyma11g04660 and glyma01g40650, named as YL1 and YL2 respectively, and the latter was confirmed to be same as the earlier reported green seed-coat gene G. Both YL1 and YL2 belonged to chloroplast-located proteases possessing Abi domain, and these genes were expressed in various tissues, especially in young leaves. In yl, the expression of YL1 and YL2 were suppressed in most tissues, and the young leaf of yl presented an increased maximal photochemical efficiency (Fv/Fm) as well as enhanced net photosynthesis activity (Pn), indicating that YL1 and YL2 are involved in light absorption regulation during photosynthesis process. Collectively, the identification and description of YL1 and YL2 in our study provides insights for the regulatory mechanism of photosynthesis process, and these findings will further assist to clarify the close relationship between photosynthesis and chlorophyll metabolism.
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Affiliation(s)
- Meifeng Liu
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Yaqi Wang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Zhixing Nie
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Junyi Gai
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Javaid Akhter Bhat
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Jiejie Kong
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Tuanjie Zhao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China.
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17
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Zhu X, Pan Y, Liu Z, Liu Y, Zhong D, Duan Z, Tian Z, Zhu B, Zhou G. Mutation of YL Results in a Yellow Leaf with Chloroplast RNA Editing Defect in Soybean. Int J Mol Sci 2020; 21:E4275. [PMID: 32560081 PMCID: PMC7348699 DOI: 10.3390/ijms21124275] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 01/12/2023] Open
Abstract
RNA editing plays a key role in organelle gene expression. Little is known about how RNA editing factors influence soybean plant development. Here, we report the isolation and characterization of a soybean yl (yellow leaf) mutant. The yl plants showed decreased chlorophyll accumulation, lower PS II activity, an impaired net photosynthesis rate, and an altered chloroplast ultrastructure. Fine mapping of YL uncovered a point mutation in Glyma.20G187000, which encodes a chloroplast-localized protein homologous to Arabidopsis thaliana (Arabidopsis) ORRM1. YL is mainly expressed in trifoliate leaves, and its deficiency affects the editing of multiple chloroplast RNA sites, leading to inferior photosynthesis in soybean. Taken together, these results demonstrate the importance of the soybean YL protein in chloroplast RNA editing and photosynthesis.
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Affiliation(s)
- Xiaowei Zhu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (Y.P.); (Z.L.); (Y.L.); (D.Z.); (Z.D.); (Z.T.)
- Horticulture Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Yi Pan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (Y.P.); (Z.L.); (Y.L.); (D.Z.); (Z.D.); (Z.T.)
| | - Zhi Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (Y.P.); (Z.L.); (Y.L.); (D.Z.); (Z.D.); (Z.T.)
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (Y.P.); (Z.L.); (Y.L.); (D.Z.); (Z.D.); (Z.T.)
| | - Deyi Zhong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (Y.P.); (Z.L.); (Y.L.); (D.Z.); (Z.D.); (Z.T.)
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zongbiao Duan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (Y.P.); (Z.L.); (Y.L.); (D.Z.); (Z.D.); (Z.T.)
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (Y.P.); (Z.L.); (Y.L.); (D.Z.); (Z.D.); (Z.T.)
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baoge Zhu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (Y.P.); (Z.L.); (Y.L.); (D.Z.); (Z.D.); (Z.T.)
| | - Guoan Zhou
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (Y.P.); (Z.L.); (Y.L.); (D.Z.); (Z.D.); (Z.T.)
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18
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Wang C, Zhang L, Li Y, Ali Buttar Z, Wang N, Xie Y, Wang C. Single Nucleotide Mutagenesis of the TaCHLI Gene Suppressed Chlorophyll and Fatty Acid Biosynthesis in Common Wheat Seedlings. FRONTIERS IN PLANT SCIENCE 2020; 11:97. [PMID: 32153608 PMCID: PMC7046076 DOI: 10.3389/fpls.2020.00097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/22/2020] [Indexed: 05/08/2023]
Abstract
Wheat (Triticum aestivum L.) is one of the most important crops in the world. Chlorophyll plays a vital role in plant development and crop improvement and further determines the crop productivity to a certain extent. The biosynthesis of chlorophyll remains a complex metabolic process, and fundamental biochemical discoveries have resulted from studies of plant mutants with altered leaf color. In this study, we identified a chlorophyll-deficiency mutant, referred to as chli, from the wheat cultivar Shaannong33 that exhibited an obvious pale-green leaf phenotype at the seedling stage, with significantly decreased accumulation of chlorophyll and its precursors, protoporphyrin IX and Mg-protoporphyrin IX. Interestingly, a higher protoporphyrin IX to Mg-protoporphyrin IX ratio was observed in chli. Lipid biosynthesis in chli leaves and seeds was also affected, with the mutant displaying significantly reduced total lipid content relative to Shaanong33. Genetic analysis indicated that the pale-green leaf phenotype was controlled by a single pair of recessive nuclear genes. Furthermore, sequence alignment revealed a single-nucleotide mutation (G664A) in the gene TraesCS7A01G480700.1, which encodes subunit I of the Mg-chelatase in plants. This single-nucleotide mutation resulted in an amino acid substitution (D221N) in the highly conserved domain of subunit I. As a result, mutant protein Tachli-7A lost the ability to interact with the normal protein TaCHLI-7A, as assessed by yeast two-hybrid assay. Meanwhile, Tachli-7A could not recover the chlorophyll deficiency phenotype of the Arabidopsis thaliana SALK_050029 mutant. Furthermore, we found that in Shaannong33, the protoporphyrin IX to Mg-protoporphyrin IX ratio was growth state-dependent and insensitive to environmental change. Overall, the mutation in Tachli-7A impaired the function of Mg-chelatase and blocked the conversion of protoporphyrin IX to Mg- protoporphyrin IX. Based on our results, the chli mutant represents a potentially useful resource for better understanding chlorophyll and lipid biosynthetic pathways in common wheat.
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Affiliation(s)
- Chaojie Wang
- College of Agronomy, Northwest A&F University, Yangling, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, China
| | - Lili Zhang
- College of Agronomy, Northwest A&F University, Yangling, China
| | - Yingzhuang Li
- College of Agronomy, Northwest A&F University, Yangling, China
| | | | - Na Wang
- College of Agronomy, Northwest A&F University, Yangling, China
| | - Yanzhou Xie
- College of Agronomy, Northwest A&F University, Yangling, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, China
| | - Chengshe Wang
- College of Agronomy, Northwest A&F University, Yangling, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, China
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19
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Keller B, Matsubara S, Rascher U, Pieruschka R, Steier A, Kraska T, Muller O. Genotype Specific Photosynthesis x Environment Interactions Captured by Automated Fluorescence Canopy Scans Over Two Fluctuating Growing Seasons. FRONTIERS IN PLANT SCIENCE 2019; 10:1482. [PMID: 31998328 PMCID: PMC6962999 DOI: 10.3389/fpls.2019.01482] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/25/2019] [Indexed: 05/19/2023]
Abstract
Photosynthesis reacts dynamic and in different time scales to changing conditions. Light and temperature acclimation balance photosynthetic processes in a complex interplay with the fluctuating environment. However, due to limitations in the measurements techniques, these acclimations are often described under steady-state conditions leading to inaccurate photosynthesis estimates in the field. Here we analyze the photosynthetic interaction with the fluctuating environment and canopy architecture over two seasons using a fully automated phenotyping system. We acquired over 700,000 chlorophyll fluorescence transients and spectral measurements under semi-field conditions in four crop species including 28 genotypes. As expected, the quantum efficiency of the photosystem II (Fv/Fm in the dark and Fq'/Fm' in the light) was determined by light intensity. It was further significantly affected by spectral indices representing canopy structure effects. In contrast, a newly established parameter, monitoring the efficiency of electron transport (Fr2/Fv in the dark respective Fr2'/Fq' in the light), was highly responsive to temperature (R2 up to 0.75). This parameter decreased with temperature and enabled the detection of cold tolerant species and genotypes. We demonstrated the ability to capture and model the dynamic photosynthesis response to the environment over entire growth seasons. The improved linkage of photosynthetic performance to canopy structure, temperature and cold tolerance offers great potential for plant breeding and crop growth modeling.
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Affiliation(s)
- Beat Keller
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Shizue Matsubara
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Uwe Rascher
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Roland Pieruschka
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Angelina Steier
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Thorsten Kraska
- Field Lab Campus Klein-Altendorf, University of Bonn, Rheinbach, Germany
| | - Onno Muller
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
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20
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Mao G, Wei H, Hu W, Ma Q, Zhang M, Wang H, Yu S. Fine mapping and molecular characterization of the virescent gene vsp in Upland cotton (Gossypium hirsutum). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2069-2086. [PMID: 30953093 DOI: 10.1007/s00122-019-03338-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/26/2019] [Indexed: 05/24/2023]
Abstract
The vsp gene was fine mapped to a 353.7-kb region, and a 201-bp deletion that affected chloroplast development and chlorophyll biosynthesis was found in the candidate gene GhPUR4. Virescent mutations can be used as marker traits in heterosis breeding and can also be used to research chloroplast development, chlorophyll biosynthesis and photosynthesis mechanisms. Here, we obtained a light-sensitive virescent mutant, vsp, that has reduced chlorophyll (Chl) content and abnormal chloroplast development. Then, the virescent space (vsp) gene in the vsp mutant was preliminarily mapped to a 38.32-Mb region of chromosome D04 using a high-density SNP genetic map with a total length of 5384.33 cM and 4472 bin markers. Furthermore, the vsp gene was narrowed down to a 353.7-kb region that contains 15 candidate genes using 484 virescent individuals from an F2 population. Sequence analysis of genes in this region showed that a 201-bp deletion was present in the Gh_D04G1108 (GhPUR4) gene in the vsp mutant. The 201-bp deletion of Gh_D04G1108 caused the deletion of 67 AAs in the GhPUR4 protein. Virus-induced gene silencing (VIGS) of GhPUR4 in normal plants caused reduced GhPUR4 gene expression levels, reduced Chl content, abnormal chloroplast development and virescent true leaves. This study could help us unravel the function of GhPUR4 in chloroplast development and Chl biosynthesis at the early developmental stages of the true leaves in cotton, which could promote the research and application of virescent mutations in cotton heterosis breeding.
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Affiliation(s)
- Guangzhi Mao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Wei Hu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Qiang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Meng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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Tang X, Wang Y, Zhang Y, Huang S, Liu Z, Fei D, Feng H. A missense mutation of plastid RPS4 is associated with chlorophyll deficiency in Chinese cabbage (Brassica campestris ssp. pekinensis). BMC PLANT BIOLOGY 2018; 18:130. [PMID: 29940850 PMCID: PMC6019835 DOI: 10.1186/s12870-018-1353-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 06/17/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Plastome mutants are ideal resources for elucidating the functions of plastid genes. Numerous studies have been conducted for the function of plastid genes in barley and tobacco; however, related information is limited in Chinese cabbage. RESULTS A chlorophyll-deficient mutant of Chinese cabbage that was derived by ethyl methanesulfonate treatment on isolated microspores showed uniformly pale green inner leaves and slow growth compared with that shown by the wild type "Fukuda 50' ('FT'). Genetic analysis revealed that cdm was cytoplasmically inherited. Physiological and ultrastructural analyses of cdm showed impaired photosynthesis and abnormal chloroplast development. Utilizing next generation sequencing, the complete plastomes of cdm and 'FT' were respectively re-mapped to the reference genome of Chinese cabbage, and an A-to-C base substitution with a mutation ratio higher than 99% was detected. The missense mutation of plastid ribosomal protein S4 led to valine substitution for glycine at residue 193. The expression level of rps4 was analyzed using quantitative real-time PCR and found lower in than in 'FT'. RNA gel-blot assays showed that the abundance of mature 23S rRNA, 16S rRNA, 5S rRNA, and 4.5S rRNA significantly decreased and that the processing of 23S, 16S rRNA, and 4.5S rRNA was seriously impaired, affecting the ribosomal function in cdm. CONCLUSIONS These findings indicated that cdm was a plastome mutant and that chlorophyll deficiency might be due to an A-to-C base substitution of the plastome-encoded rps4 that impaired the rRNA processing and affected the ribosomal function.
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Affiliation(s)
- Xiaoyan Tang
- College of Horticulture, Liaoning Key Lab of Genetics and Breeding for Cruciferous Vegetable Crops, Shenyang Agricultural University, Shenyang, Liaoning 110866 People’s Republic of China
| | - Yiheng Wang
- College of Horticulture, Liaoning Key Lab of Genetics and Breeding for Cruciferous Vegetable Crops, Shenyang Agricultural University, Shenyang, Liaoning 110866 People’s Republic of China
| | - Yun Zhang
- College of Horticulture, Liaoning Key Lab of Genetics and Breeding for Cruciferous Vegetable Crops, Shenyang Agricultural University, Shenyang, Liaoning 110866 People’s Republic of China
| | - Shengnan Huang
- College of Horticulture, Liaoning Key Lab of Genetics and Breeding for Cruciferous Vegetable Crops, Shenyang Agricultural University, Shenyang, Liaoning 110866 People’s Republic of China
| | - Zhiyong Liu
- College of Horticulture, Liaoning Key Lab of Genetics and Breeding for Cruciferous Vegetable Crops, Shenyang Agricultural University, Shenyang, Liaoning 110866 People’s Republic of China
| | - Danli Fei
- College of Horticulture, Liaoning Key Lab of Genetics and Breeding for Cruciferous Vegetable Crops, Shenyang Agricultural University, Shenyang, Liaoning 110866 People’s Republic of China
| | - Hui Feng
- College of Horticulture, Liaoning Key Lab of Genetics and Breeding for Cruciferous Vegetable Crops, Shenyang Agricultural University, Shenyang, Liaoning 110866 People’s Republic of China
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22
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Sakowska K, Alberti G, Genesio L, Peressotti A, Delle Vedove G, Gianelle D, Colombo R, Rodeghiero M, Panigada C, Juszczak R, Celesti M, Rossini M, Haworth M, Campbell BW, Mevy JP, Vescovo L, Cendrero-Mateo MP, Rascher U, Miglietta F. Leaf and canopy photosynthesis of a chlorophyll deficient soybean mutant. PLANT, CELL & ENVIRONMENT 2018; 41:1427-1437. [PMID: 29498070 DOI: 10.1111/pce.13180] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 02/19/2018] [Accepted: 02/20/2018] [Indexed: 05/22/2023]
Abstract
The photosynthetic, optical, and morphological characteristics of a chlorophyll-deficient (Chl-deficient) "yellow" soybean mutant (MinnGold) were examined in comparison with 2 green varieties (MN0095 and Eiko). Despite the large difference in Chl content, similar leaf photosynthesis rates were maintained in the Chl-deficient mutant by offsetting the reduced absorption of red photons by a small increase in photochemical efficiency and lower non-photochemical quenching. When grown in the field, at full canopy cover, the mutants reflected a significantly larger proportion of incoming shortwave radiation, but the total canopy light absorption was only slightly reduced, most likely due to a deeper penetration of light into the canopy space. As a consequence, canopy-scale gross primary production and ecosystem respiration were comparable between the Chl-deficient mutant and the green variety. However, total biomass production was lower in the mutant, which indicates that processes other than steady state photosynthesis caused a reduction in biomass accumulation over time. Analysis of non-photochemical quenching relaxation and gas exchange in Chl-deficient and green leaves after transitions from high to low light conditions suggested that dynamic photosynthesis might be responsible for the reduced biomass production in the Chl-deficient mutant under field conditions.
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Affiliation(s)
- Karolina Sakowska
- Institute of Ecology, University of Innsbruck, Sternwartestrasse 15, 6020, Innsbruck, Austria
- Department of Meteorology, Poznan University of Life Sciences, Piatkowska Street 94, 60-649, Poznan, Poland
- Sustainable Agro-Ecosystems and Bioresources Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Trento, Italy
| | - Giorgio Alberti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100, Udine, Italy
- Institute of Biometeorology, National Research Council (CNR-IBIMET), Via Caproni 8, 50145, Florence, Italy
| | - Lorenzo Genesio
- Institute of Biometeorology, National Research Council (CNR-IBIMET), Via Caproni 8, 50145, Florence, Italy
- Foxlab Joint CNR-FEM Initiative, Via E. Mach 1, 38010, San Michele all'Adige, Trento, Italy
| | - Alessandro Peressotti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100, Udine, Italy
| | - Gemini Delle Vedove
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100, Udine, Italy
| | - Damiano Gianelle
- Sustainable Agro-Ecosystems and Bioresources Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Trento, Italy
- Foxlab Joint CNR-FEM Initiative, Via E. Mach 1, 38010, San Michele all'Adige, Trento, Italy
| | - Roberto Colombo
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy
| | - Mirco Rodeghiero
- Sustainable Agro-Ecosystems and Bioresources Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Trento, Italy
| | - Cinzia Panigada
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy
| | - Radosław Juszczak
- Department of Meteorology, Poznan University of Life Sciences, Piatkowska Street 94, 60-649, Poznan, Poland
| | - Marco Celesti
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy
| | - Micol Rossini
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy
| | - Matthew Haworth
- Tree and Timber Institute, National Research Council (CNR-IVALSA), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Florence, Italy
| | | | - Jean-Philippe Mevy
- Institut Méditerranéen de Biodiversité et d'Ecologie Marine et Continentale (IMBE), Aix Marseille Université, Université Avigon, CNRS 7263/IRD 237, 3 Place Victor Hugo, 13331, Marseille Cedex 03, France
| | - Loris Vescovo
- Sustainable Agro-Ecosystems and Bioresources Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Trento, Italy
| | - M Pilar Cendrero-Mateo
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Leo-Brandt-Str, 52425, Jülich, Germany
| | - Uwe Rascher
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Leo-Brandt-Str, 52425, Jülich, Germany
| | - Franco Miglietta
- Institute of Biometeorology, National Research Council (CNR-IBIMET), Via Caproni 8, 50145, Florence, Italy
- Foxlab Joint CNR-FEM Initiative, Via E. Mach 1, 38010, San Michele all'Adige, Trento, Italy
- IMèRA, Institut D'Etudes Avancés de l'Universitè Aix-Marseille, 2 Place Le Verrier, 13004, Marseille, France
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23
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Wu H, Shi N, An X, Liu C, Fu H, Cao L, Feng Y, Sun D, Zhang L. Candidate Genes for Yellow Leaf Color in Common Wheat ( Triticum aestivum L.) and Major Related Metabolic Pathways according to Transcriptome Profiling. Int J Mol Sci 2018; 19:ijms19061594. [PMID: 29843474 PMCID: PMC6032196 DOI: 10.3390/ijms19061594] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/23/2018] [Accepted: 05/25/2018] [Indexed: 01/05/2023] Open
Abstract
The photosynthetic capacity and efficiency of a crop depends on the biosynthesis of photosynthetic pigments and chloroplast development. However, little is known about the molecular mechanisms of chloroplast development and chlorophyll (Chl) biosynthesis in common wheat because of its huge and complex genome. Ygm, a spontaneous yellow-green leaf color mutant of winter wheat, exhibits reduced Chl contents and abnormal chloroplast development. Thus, we searched for candidate genes associated with this phenotype. Comparative transcriptome profiling was performed using leaves from the yellow leaf color type (Y) and normal green color type (G) of the Ygm mutant progeny. We identified 1227 differentially expressed genes (DEGs) in Y compared with G (i.e., 689 upregulated genes and 538 downregulated genes). Gene ontology and pathway enrichment analyses indicated that the DEGs were involved in Chl biosynthesis (i.e., magnesium chelatase subunit H (CHLH) and protochlorophyllide oxidoreductase (POR) genes), carotenoid biosynthesis (i.e., β-carotene hydroxylase (BCH) genes), photosynthesis, and carbon fixation in photosynthetic organisms. We also identified heat shock protein (HSP) genes (sHSP, HSP70, HSP90, and DnaJ) and heat shock transcription factor genes that might have vital roles in chloroplast development. Quantitative RT-PCR analysis of the relevant DEGs confirmed the RNA-Seq results. Moreover, measurements of seven intermediate products involved in Chl biosynthesis and five carotenoid compounds involved in carotenoid-xanthophyll biosynthesis confirmed that CHLH and BCH are vital enzymes for the unusual leaf color phenotype in Y type. These results provide insights into leaf color variation in wheat at the transcriptional level.
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Affiliation(s)
- Huiyu Wu
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Narong Shi
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Xuyao An
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Cong Liu
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Hongfei Fu
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China.
| | - Li Cao
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Yi Feng
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Daojie Sun
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Lingli Zhang
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
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24
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Sandhu D, Coleman Z, Atkinson T, Rai KM, Mendu V. Genetics and Physiology of the Nuclearly Inherited Yellow Foliar Mutants in Soybean. FRONTIERS IN PLANT SCIENCE 2018; 9:471. [PMID: 29696030 PMCID: PMC5904354 DOI: 10.3389/fpls.2018.00471] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 03/26/2018] [Indexed: 05/27/2023]
Abstract
Plant photosynthetic pigments are important in harvesting the light energy and transfer of energy during photosynthesis. There are several yellow foliar mutants discovered in soybean and chromosomal locations for about half of them have been deduced. Viable-yellow mutants are capable of surviving with decreased photosynthesis, while lethal-yellow mutants die shortly after germination. In addition to the decreased chlorophyll content, other features associated with yellow mutants include altered Chl a and Chl b ratio, reduction in chloroplast size and number, lower levels of other photosynthetic pigments, inability of thylakoids to stack into granum, lack of lamellae to interconnect granum and reduced size of the light harvesting complex. For some yellow mutants, temperature and/or light play a critical role in the manifestation of phenotype. Although yellow foliar mutants are viewed as undesirable for crop production, there is the possibility of these mutants to create a positive impact by reducing the total amount of chlorophyll and diverting resources toward increased biochemical photosynthetic capacity leading to increased yield. Recent advances in model plants led to the isolation and characterization of various genes associated with yellow foliar phenotype. Knowledge gained from the model plants can be applied using homology based cloning approach to isolate genes in soybean and understanding the modes of actions of the involved proteins. Identifying and characterizing yellow foliar mutants will not only aid in understanding the biosynthetic pathways involved in the photosynthetic machinery, but may also provide ways to increase soybean productivity.
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Affiliation(s)
| | - Zachary Coleman
- Department of Biology, University of Wisconsin-Stevens Point, Stevens Point, WI, United States
| | - Taylor Atkinson
- Department of Biology, University of Wisconsin-Stevens Point, Stevens Point, WI, United States
| | - Krishan M. Rai
- Fiber and Biopolymer Research Institute, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
| | - Venugopal Mendu
- Fiber and Biopolymer Research Institute, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
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25
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Walker BJ, Drewry DT, Slattery RA, VanLoocke A, Cho YB, Ort DR. Chlorophyll Can Be Reduced in Crop Canopies with Little Penalty to Photosynthesis. PLANT PHYSIOLOGY 2018; 176:1215-1232. [PMID: 29061904 PMCID: PMC5813550 DOI: 10.1104/pp.17.01401] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 10/18/2017] [Indexed: 05/20/2023]
Abstract
The hypothesis that reducing chlorophyll content (Chl) can increase canopy photosynthesis in soybeans was tested using an advanced model of canopy photosynthesis. The relationship among leaf Chl, leaf optical properties, and photosynthetic biochemical capacity was measured in 67 soybean (Glycine max) accessions showing large variation in leaf Chl. These relationships were integrated into a biophysical model of canopy-scale photosynthesis to simulate the intercanopy light environment and carbon assimilation capacity of canopies with wild type, a Chl-deficient mutant (Y11y11), and 67 other mutants spanning the extremes of Chl to quantify the impact of variation in leaf-level Chl on canopy-scale photosynthetic assimilation and identify possible opportunities for improving canopy photosynthesis through Chl reduction. These simulations demonstrate that canopy photosynthesis should not increase with Chl reduction due to increases in leaf reflectance and nonoptimal distribution of canopy nitrogen. However, similar rates of canopy photosynthesis can be maintained with a 9% savings in leaf nitrogen resulting from decreased Chl. Additionally, analysis of these simulations indicate that the inability of Chl reductions to increase photosynthesis arises primarily from the connection between Chl and leaf reflectance and secondarily from the mismatch between the vertical distribution of leaf nitrogen and the light absorption profile. These simulations suggest that future work should explore the possibility of using reduced Chl to improve canopy performance by adapting the distribution of the "saved" nitrogen within the canopy to take greater advantage of the more deeply penetrating light.
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Affiliation(s)
- Berkley J Walker
- Global Change and Photosynthesis Research Unit, USDA/ARS, Urbana, Illinois 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
- Institute of Plant Biochemistry, Heinrich-Heine University, D-40225 Düsseldorf, Germany
| | - Darren T Drewry
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California 91109
- Joint Institute for Regional Earth System Science and Engineering, University of California, Los Angeles, California 90095
| | - Rebecca A Slattery
- Global Change and Photosynthesis Research Unit, USDA/ARS, Urbana, Illinois 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
- Department of Plant Biology, University of Illinois, Urbana, Illinois 61801
| | - Andy VanLoocke
- Global Change and Photosynthesis Research Unit, USDA/ARS, Urbana, Illinois 61801
- Department of Agronomy, Iowa State University, Ames, Iowa 50011
| | - Young B Cho
- Global Change and Photosynthesis Research Unit, USDA/ARS, Urbana, Illinois 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
| | - Donald R Ort
- Global Change and Photosynthesis Research Unit, USDA/ARS, Urbana, Illinois 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
- Department of Plant Biology, University of Illinois, Urbana, Illinois 61801
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26
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Ma Q, Li H, Zou Z, Arkorful E, Lv Q, Zhou Q, Chen X, Sun K, Li X. Transcriptomic analyses identify albino-associated genes of a novel albino tea germplasm 'Huabai 1'. HORTICULTURE RESEARCH 2018; 5:54. [PMID: 30302258 PMCID: PMC6165850 DOI: 10.1038/s41438-018-0053-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 05/05/2018] [Accepted: 05/21/2018] [Indexed: 05/16/2023]
Abstract
Albinism in shoots of tea plants is a common phenotypic expression which gives the tea infusion a pleasant umami taste. A novel natural albino mutant tea germplasm containing high amino acids content was found and named as 'Huabai 1'. 'Huabai 1' has white jade tender shoots under low temperature and turns green with increased temperature. In order to understand the molecular mechanism of color change in leaf of 'Huabai 1', transcriptome analysis was performed to identify albino-associated differentially expressed genes (DEGs). A total of 483 DEGs were identified from white shoots of 'Huabai 1' compared to its green shoots. There were 15 DEGs identified to be involved in phenylpropanoid biosynthesis, which account for the majority of characterized DEGs. The metabolites related to phenylpropanoid biosynthesis revealed similar expression pattern of DEGs. Furthermore, metabolic pathways such as ubiquonone, tyrosine, and flavonoid biosynthesis associated with phenylpropanoid biosynthesis could also contribute to the color change in 'Huabai 1' tender shoots. Protein-protein interaction analysis revealed a hub protein NEDD8 (CSA009575) which interacted with many regulated genes in spliceosome, nitrogen metabolism, phenylpropanoid biosynthesis, and other pathways. In conclusion, the findings in this study indicate that the color change of 'Huabai 1' tender shoots is a combined effect of phenylpropanoid biosynthesis pathway and other metabolic pathways including flavonoid biosynthesis in tea plants. Chlorophyll biosynthesis-related genes LHCII and SGR may also play some roles in color change of 'Huabai 1'.
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Affiliation(s)
- Qingping Ma
- College of Horticulture, Nanjing Agricultural University, Weigang No.1, 210095 Nanjing, China
| | - Huan Li
- College of Horticulture, Nanjing Agricultural University, Weigang No.1, 210095 Nanjing, China
| | - Zhongwei Zou
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, Manitoba R3T 2N2 Canada
| | - Emmanuel Arkorful
- College of Horticulture, Nanjing Agricultural University, Weigang No.1, 210095 Nanjing, China
| | - Qianru Lv
- College of Horticulture, Nanjing Agricultural University, Weigang No.1, 210095 Nanjing, China
| | - Qiongqiong Zhou
- College of Horticulture, Nanjing Agricultural University, Weigang No.1, 210095 Nanjing, China
| | - Xuan Chen
- College of Horticulture, Nanjing Agricultural University, Weigang No.1, 210095 Nanjing, China
| | - Kang Sun
- College of Horticulture, Nanjing Agricultural University, Weigang No.1, 210095 Nanjing, China
| | - Xinghui Li
- College of Horticulture, Nanjing Agricultural University, Weigang No.1, 210095 Nanjing, China
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Espina MJ, Ahmed CMS, Bernardini A, Adeleke E, Yadegari Z, Arelli P, Pantalone V, Taheri A. Development and Phenotypic Screening of an Ethyl Methane Sulfonate Mutant Population in Soybean. FRONTIERS IN PLANT SCIENCE 2018; 9:394. [PMID: 29651295 PMCID: PMC5884938 DOI: 10.3389/fpls.2018.00394] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 03/12/2018] [Indexed: 05/04/2023]
Abstract
Soybean is an important oil-producing crop in the Fabaceae family and there are increasing demands for soybean oil and other soybean products. Genetic improvement of soybean is needed to increase its production. In order to provide genetic diversity and resources for identifying important genes, a new ethyl methane sulfonate (EMS) mutagenized soybean population was generated using the newly released germplasm, JTN-5203 (maturity group V). Treatment of soybean seeds with 60 mM EMS concentration was found to be suitable for inducing mutation. A total of 1,820 M1 individuals were produced from 15,000 treated seeds. The resulting M2 population was planted in the field for phenotyping. After harvest, seed traits including total oil, protein, starch, moisture content, fatty acid and amino acid compositions were measured by NIR. Phenotypic variations observed in this population include changes in leaf morphology, plant architecture, seed compositions, and yield. Of most interest, we identified plants with increased amounts of total protein (50% vs. 41% for control) and plants with higher amounts of total oil (25% vs. 21.2% control). Similarly, we identified plants with increases in oleic acid content and decreases in linoleic acid and linolenic acid. This EMS mutant population will be used for further studies including screening for various traits such as amino acid pathways, allergens, phytic acids, and other important soybean agronomic traits. In addition, these mutant individuals will be evaluated in the next generation to assess the heritability. Beneficial traits from these mutants can be exploited for future soybean breeding programs. This germplasm can also be used for discovering novel mutant alleles and for functional gene expression analysis using reverse genetics tools such as TILLING.
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Affiliation(s)
- Mary J. Espina
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN, United States
| | - C. M. Sabbir Ahmed
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN, United States
| | - Angelina Bernardini
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN, United States
| | - Ekundayo Adeleke
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN, United States
| | - Zeinab Yadegari
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN, United States
| | - Prakash Arelli
- United States Department of Agriculture, Agricultural Research Service, Jackson, TN, United States
| | - Vince Pantalone
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
| | - Ali Taheri
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN, United States
- *Correspondence: Ali Taheri,
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Zhang D, Chang E, Yu X, Chen Y, Yang Q, Cao Y, Li X, Wang Y, Fu A, Xu M. Molecular Characterization of Magnesium Chelatase in Soybean [ Glycine max (L.) Merr.]. FRONTIERS IN PLANT SCIENCE 2018; 9:720. [PMID: 29971071 PMCID: PMC6018531 DOI: 10.3389/fpls.2018.00720] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 05/14/2018] [Indexed: 05/07/2023]
Abstract
Soybean (Glycine max) seed yields rely on the efficiency of photosynthesis, which is poorly understood in soybean. Chlorophyll, the major light harvesting pigment, is crucial for chloroplast biogenesis and photosynthesis. Magnesium chelatase catalyzes the insertion of Mg2+ into protoporphyrin IX in the first committed and key regulatory step of chlorophyll biosynthesis. It consists of three types of subunits, ChlI, ChlD, and ChlH. To gain a better knowledge of chlorophyll biosynthesis in soybean, we analyzed soybean Mg-chelatase subunits and their encoding genes. Soybean genome harbors 4 GmChlI genes, 2 GmChlD genes, and 3 GmChlH genes, likely evolved from two rounds of gene duplication events. The qRT-PCR analysis revealed that GmChlI, GmChlD, and GmChlH genes predominantly expressed in photosynthetic tissues, but the expression levels among paralogs are different. In silicon promoter analyses revealed these genes harbor different cis-regulatory elements in their promoter regions, suggesting they could differentially respond to various environmental and developmental signals. Subcellular localization analyses illustrated that GmChlI, GmChlD, and GmChlH isoforms are all localized in chloroplast, consistent with their functions. Yeast two hybrid and bimolecular fluorescence complementation (BiFC) assays showed each isoform has a potential to be assembled into the Mg-chelatase holocomplex. We expressed each GmChlI, GmChlD, and GmChlH isoform in Arabidopsis corresponding mutants, and results showed that 4 GmChlI and 2 GmChlD isoforms and GmChlH1 could rescue the severe phenotype of Arabidopsis mutants, indicating that they maintain normal biochemical functions in vivo. However, GmChlH2 and GmChlH3 could not completely rescue the chlorotic phenotype of Arabidopsis gun5-2 mutant, suggesting that the functions of these two proteins could be different from GmChlH1. Considering the differences shown on primary sequences, biochemical functions, and gene expression profiles, we conclude that the paralogs of each soybean Mg-chelatase subunit have diverged more or less during evolution. Soybean could have developed a complex regulatory mechanism to control chlorophyll content to adapt to different developmental and environmental situations.
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Fine mapping and candidate gene analysis of the virescent gene v 1 in Upland cotton (Gossypium hirsutum). Mol Genet Genomics 2017; 293:249-264. [PMID: 29052764 DOI: 10.1007/s00438-017-1383-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 10/13/2017] [Indexed: 01/12/2023]
Abstract
The young leaves of virescent mutants are yellowish and gradually turn green as the plants reach maturity. Understanding the genetic basis of virescent mutants can aid research of the regulatory mechanisms underlying chloroplast development and chlorophyll biosynthesis, as well as contribute to the application of virescent traits in crop breeding. In this study, fine mapping was employed, and a recessive gene (v 1) from a virescent mutant of Upland cotton was narrowed to an 84.1-Kb region containing ten candidate genes. The GhChlI gene encodes the cotton Mg-chelatase I subunit (CHLI) and was identified as the candidate gene for the virescent mutation using gene annotation. BLAST analysis showed that the GhChlI gene has two copies, Gh_A10G0282 and Gh_D10G0283. Sequence analysis indicated that the coding region (CDS) of GhChlI is 1269 bp in length, with three predicted exons and one non-synonymous nucleotide mutation (G1082A) in the third exon of Gh_D10G0283, with an amino acid (AA) substitution of arginine (R) to lysine (K). GhChlI-silenced TM-1 plants exhibited a lower GhChlI expression level, a lower chlorophyll content, and the virescent phenotype. Analysis of upstream regulatory elements and expression levels of GhChlI showed that the expression quantity of GhChlI may be normal, and with the development of the true leaf, the increase in the Gh_A10G0282 dosage may partially make up for the deficiency of Gh_D10G0283 in the v 1 mutant. Phylogenetic analysis and sequence alignment revealed that the protein sequence encoded by the third exon of GhChlI is highly conserved across diverse plant species, in which AA substitutions among the completely conserved residues frequently result in changes in leaf color in various species. These results suggest that the mutation (G1082A) within the GhChlI gene may cause a functional defect of the GhCHLI subunit and thus the virescent phenotype in the v1 mutant. The GhChlI mutation not only provides a tool for understanding the associations of CHLI protein function and the chlorophyll biosynthesis pathway but also has implications for cotton breeding.
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Patil G, Mian R, Vuong T, Pantalone V, Song Q, Chen P, Shannon GJ, Carter TC, Nguyen HT. Molecular mapping and genomics of soybean seed protein: a review and perspective for the future. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1975-1991. [PMID: 28801731 PMCID: PMC5606949 DOI: 10.1007/s00122-017-2955-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/26/2017] [Indexed: 05/16/2023]
Abstract
KEY MESSAGE Genetic improvement of soybean protein meal is a complex process because of negative correlation with oil, yield, and temperature. This review describes the progress in mapping and genomics, identifies knowledge gaps, and highlights the need of integrated approaches. Meal protein derived from soybean [Glycine max (L) Merr.] seed is the primary source of protein in poultry and livestock feed. Protein is a key factor that determines the nutritional and economical value of soybean. Genetic improvement of soybean seed protein content is highly desirable, and major quantitative trait loci (QTL) for soybean protein have been detected and repeatedly mapped on chromosomes (Chr.) 20 (LG-I), and 15 (LG-E). However, practical breeding progress is challenging because of seed protein content's negative genetic correlation with seed yield, other seed components such as oil and sucrose, and interaction with environmental effects such as temperature during seed development. In this review, we discuss rate-limiting factors related to soybean protein content and nutritional quality, and potential control factors regulating seed storage protein. In addition, we describe advances in next-generation sequencing technologies for precise detection of natural variants and their integration with conventional and high-throughput genotyping technologies. A syntenic analysis of QTL on Chr. 15 and 20 was performed. Finally, we discuss comprehensive approaches for integrating protein and amino acid QTL, genome-wide association studies, whole-genome resequencing, and transcriptome data to accelerate identification of genomic hot spots for allele introgression and soybean meal protein improvement.
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Affiliation(s)
- Gunvant Patil
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Rouf Mian
- Soybean and Nitrogen Fixation Unit, USDA-ARS, Raleigh, NC, 27607, USA.
| | - Tri Vuong
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Vince Pantalone
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996-4561, USA
| | - Qijian Song
- Agricultural Research Service, Department of Agriculture United States, Beltsville, MD, 20705, USA
| | - Pengyin Chen
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Grover J Shannon
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Tommy C Carter
- Soybean and Nitrogen Fixation Unit, USDA-ARS, Raleigh, NC, 27607, USA
| | - Henry T Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
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Zhu J, Chen J, Gao F, Xu C, Wu H, Chen K, Si Z, Yan H, Zhang T. Rapid mapping and cloning of the virescent-1 gene in cotton by bulked segregant analysis-next generation sequencing and virus-induced gene silencing strategies. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4125-4135. [PMID: 28922761 PMCID: PMC5853531 DOI: 10.1093/jxb/erx240] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Map-based gene cloning is a vital strategy for the identification of the quantitative trait loci or genes underlying important agronomic traits. The conventional map-based cloning method is powerful but generally time-consuming and labor-intensive. In this context, we introduce an improved bulked segregant analysis method in combination with a virus-induced gene silencing (VIGS) strategy for rapid and reliable gene mapping, identification and functional verification. This method was applied to a multiple recessive marker line of upland cotton, Texas 582 (T582), and identified unique genomic positions harboring mutant loci, showing the reliability and efficacy of this method. The v1 locus was further fine-mapped. Only one gene, GhCHLI, which encodes one of the subunits of Mg chelatase, was differentially down-regulated in T582 compared with TM-1. A point mutation occurred in the AAA+ conserved region of GhCHLI and led to an amino acid substitution. Suppression of its expression by VIGS in TM-1 resulted in a yellow blade phenotype that was similar to T582. This integrated approach provides a paradigm for the rapid mapping and identification of the candidate genes underlying the genetic traits in plants with large and complex genomes in the future.
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Affiliation(s)
- Jiankun Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Jiedan Chen
- Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang 310029, China
| | - Fengkai Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Chenyu Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Huaitong Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Kun Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Zhanfeng Si
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Hu Yan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Tianzhen Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
- Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang 310029, China
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Slattery RA, VanLoocke A, Bernacchi CJ, Zhu XG, Ort DR. Photosynthesis, Light Use Efficiency, and Yield of Reduced-Chlorophyll Soybean Mutants in Field Conditions. FRONTIERS IN PLANT SCIENCE 2017; 8:549. [PMID: 28458677 PMCID: PMC5394119 DOI: 10.3389/fpls.2017.00549] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 03/27/2017] [Indexed: 05/20/2023]
Abstract
Reducing chlorophyll (chl) content may improve the conversion efficiency of absorbed photosynthetically active radiation into biomass and therefore yield in dense monoculture crops by improving light penetration and distribution within the canopy. The effects of reduced chl on leaf and canopy photosynthesis and photosynthetic efficiency were studied in two reportedly robust reduced-chl soybean mutants, Y11y11 and y9y9, in comparison to the wild-type (WT) "Clark" cultivar. Both mutants were characterized during the 2012 growing season whereas only the Y11y11 mutant was characterized during the 2013 growing season. Chl deficiency led to greater rates of leaf-level photosynthesis per absorbed photon early in the growing season when mutant chl content was ∼35% of the WT, but there was no effect on photosynthesis later in the season when mutant leaf chl approached 50% of the WT. Transient benefits of reduced chl at the leaf level did not translate to improvements in canopy-level processes. Reduced pigmentation in these mutants was linked to lower water use efficiency, which may have dampened any photosynthetic benefits of reduced chl, especially since both growing seasons experienced significant drought conditions. These results, while not confirming our hypothesis or an earlier published study in which the Y11y11 mutant significantly outyielded the WT, do demonstrate that soybean significantly overinvests in chl. Despite a >50% chl reduction, there was little negative impact on biomass accumulation or yield, and the small negative effects present were likely due to pleiotropic effects of the mutation. This outcome points to an opportunity to reinvest nitrogen and energy resources that would otherwise be used in pigment-proteins into increasing biochemical photosynthetic capacity, thereby improving canopy photosynthesis and biomass production.
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Affiliation(s)
- Rebecca A. Slattery
- Department of Plant Biology, University of Illinois at Urbana-Champaign, UrbanaIL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, UrbanaIL, USA
| | - Andy VanLoocke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, UrbanaIL, USA
- Global Change and Photosynthesis Research Unit, United States Department of Agriculture, UrbanaIL, USA
| | - Carl J. Bernacchi
- Department of Plant Biology, University of Illinois at Urbana-Champaign, UrbanaIL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, UrbanaIL, USA
- Global Change and Photosynthesis Research Unit, United States Department of Agriculture, UrbanaIL, USA
| | - Xin-Guang Zhu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, UrbanaIL, USA
- Chinese Academy of Sciences–German Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Donald R. Ort
- Department of Plant Biology, University of Illinois at Urbana-Champaign, UrbanaIL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, UrbanaIL, USA
- Global Change and Photosynthesis Research Unit, United States Department of Agriculture, UrbanaIL, USA
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Li Z, Jiang L, Ma Y, Wei Z, Hong H, Liu Z, Lei J, Liu Y, Guan R, Guo Y, Jin L, Zhang L, Li Y, Ren Y, He W, Liu M, Htwe NMPS, Liu L, Guo B, Song J, Tan B, Liu G, Li M, Zhang X, Liu B, Shi X, Han S, Hua S, Zhou F, Yu L, Li Y, Wang S, Wang J, Chang R, Qiu L. Development and utilization of a new chemically-induced soybean library with a high mutation density . JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:60-74. [PMID: 27774740 PMCID: PMC5248594 DOI: 10.1111/jipb.12505] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/20/2016] [Indexed: 05/20/2023]
Abstract
Mutagenized populations have provided important materials for introducing variation and identifying gene function in plants. In this study, an ethyl methanesulfonate (EMS)-induced soybean (Glycine max) population, consisting of 21,600 independent M2 lines, was developed. Over 1,000 M4 (5) families, with diverse abnormal phenotypes for seed composition, seed shape, plant morphology and maturity that are stably expressed across different environments and generations were identified. Phenotypic analysis of the population led to the identification of a yellow pigmentation mutant, gyl, that displayed significantly decreased chlorophyll (Chl) content and abnormal chloroplast development. Sequence analysis showed that gyl is allelic to MinnGold, where a different single nucleotide polymorphism variation in the Mg-chelatase subunit gene (ChlI1a) results in golden yellow leaves. A cleaved amplified polymorphic sequence marker was developed and may be applied to marker-assisted selection for the golden yellow phenotype in soybean breeding. We show that the newly developed soybean EMS mutant population has potential for functional genomics research and genetic improvement in soybean.
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Gao M, Hu L, Li Y, Weng Y. The chlorophyll-deficient golden leaf mutation in cucumber is due to a single nucleotide substitution in CsChlI for magnesium chelatase I subunit. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1961-73. [PMID: 27435733 DOI: 10.1007/s00122-016-2752-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/02/2016] [Indexed: 05/19/2023]
Abstract
The cucumber chlorophyll-deficient golden leaf mutation is due to a single nucleotide substitution in the CsChlI gene for magnesium chelatase I subunit which plays important roles in the chlorophyll biosynthesis pathway. The Mg-chelatase catalyzes the insertion of Mg(2+) into the protoporphyrin IX in the chlorophyll biosynthesis pathway, which is a protein complex encompassing three subunits CHLI, CHLD, and CHLH. Chlorophyll-deficient mutations in genes encoding the three subunits have played important roles in understanding the structure, function and regulation of this important enzyme. In an EMS mutagenesis population, we identified a chlorophyll-deficient mutant C528 with golden leaf color throughout its development which was viable and able to set fruits and seeds. Segregation analysis in multiple populations indicated that this leaf color mutation was recessively inherited and the green color showed complete dominance over golden color. Map-based cloning identified CsChlI as the candidate gene for this mutation which encoded the CHLI subunit of cucumber Mg-chelatase. The 1757-bp CsChlI gene had three exons and a single nucleotide change (G to A) in its third exon resulted in an amino acid substitution (G269R) and the golden leaf color in C528. This mutation occurred in the highly conserved nucleotide-binding domain of the CHLI protein in which chlorophyll-deficient mutations have been frequently identified. The mutant phenotype, CsChlI expression pattern and the mutated residue in the CHLI protein suggested the mutant allele in C528 is unique among mutations identified so far in different species. This golden leaf mutant not only has its potential in cucumber breeding, but also provides a useful tool in understanding the CHLI function and its regulation in the chlorophyll biosynthesis pathway as well as chloroplast development.
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Affiliation(s)
- Meiling Gao
- College of Life Science, Agriculture and Forestry, Qiqihar University, Qiqihar, 161006, China.
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA.
| | - Liangliang Hu
- Horticulture College, Northwest A&F University, Yangling, 712100, China
| | - Yuhong Li
- Horticulture College, Northwest A&F University, Yangling, 712100, China
| | - Yiqun Weng
- College of Life Science, Agriculture and Forestry, Qiqihar University, Qiqihar, 161006, China.
- Vegetable Crops Research Unit, USDA-ARS, 1575 Linden Drive, Madison, WI, 53706, USA.
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Dhanapal AP, Ray JD, Singh SK, Hoyos-Villegas V, Smith JR, Purcell LC, Fritschi FB. Genome-wide association mapping of soybean chlorophyll traits based on canopy spectral reflectance and leaf extracts. BMC PLANT BIOLOGY 2016; 16:174. [PMID: 27488358 PMCID: PMC4973047 DOI: 10.1186/s12870-016-0861-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 07/26/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Chlorophyll is a major component of chloroplasts and a better understanding of the genetic basis of chlorophyll in soybean [Glycine max (L.) Merr.] might contribute to improving photosynthetic capacity and yield in regions with adverse environmental conditions. A collection of 332 diverse soybean genotypes were grown in 2 years (2009 and 2010) and chlorophyll a (eChl_A), chlorophyll b (eChl_B), and total chlorophyll (eChl_T) content as well as chlorophyll a/b ratio (eChl_R) in leaf tissues were determined by extraction and spectrometric determination. Total chlorophyll was also derived from canopy spectral reflectance measurements using a model of wavelet transformed spectra (tChl_T) as well as with a spectral reflectance index (iChl_T). RESULTS A genome-wide associating mapping approach was employed using 31,253 single nucleotide polymorphisms (SNPs) to identify loci associated with the extract based eChl_A, eChl_B, eChl_R and eChl_T measurements and the two canopy spectral reflectance-based methods (tChl_T and iChl_T). A total of 23 (14 loci), 15 (7 loci) and 14 SNPs (10 loci) showed significant association with eChl_A, eChl_B and eChl_R respectively. A total of 52 unique SNPs were significantly associated with total chlorophyll content based on at least one of the three approaches (eChl_T, tChl_T and iChl_T) and likely tagged 27 putative loci for total chlorophyll content, four of which were indicated by all three approaches. CONCLUSIONS Results presented here show that markers for chlorophyll traits can be identified in soybean using both extract-based and canopy spectral reflectance-based phenotypes, and confirm that high-throughput phenotyping-amenable canopy spectral reflectance measurements can be used for association mapping.
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Affiliation(s)
| | - Jeffery D. Ray
- Crop Genetics Research Unit, USDA-ARS, 141 Experiment Station Road, Stoneville, MS 38776 USA
| | | | | | - James R. Smith
- Crop Genetics Research Unit, USDA-ARS, 141 Experiment Station Road, Stoneville, MS 38776 USA
| | - Larry C. Purcell
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72704 USA
| | - Felix B. Fritschi
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
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Slattery RA, Grennan AK, Sivaguru M, Sozzani R, Ort DR. Light sheet microscopy reveals more gradual light attenuation in light-green versus dark-green soybean leaves. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4697-709. [PMID: 27329746 PMCID: PMC4973739 DOI: 10.1093/jxb/erw246] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Light wavelengths preferentially absorbed by chlorophyll (chl) often display steep absorption gradients. This over-saturates photosynthesis in upper chloroplasts and deprives lower chloroplasts of blue and red light. Reducing chl content could create a more even leaf light distribution and thereby increase leaf light-use efficiency and overall canopy photosynthesis. This was tested on soybean cultivar 'Clark' (WT) and a near-isogenic chl b deficient mutant, Y11y11, grown in controlled environment chambers and in the field. Light attenuation was quantified using a novel approach involving light sheet microscopy. Leaf adaxial and abaxial surfaces were illuminated separately with blue, red, and green wavelengths, and chl fluorescence was detected orthogonally to the illumination plane. Relative fluorescence was significantly greater in deeper layers of the Y11y11 mesophyll than in WT, with the greatest differences in blue, then red, and finally green light when illuminated from the adaxial surface. Modeled relative photosynthesis based on chlorophyll profiles and Beer's Law predicted less steep gradients in mutant relative photosynthesis rates compared to WT. Although photosynthetic light-use efficiency was greater in the field-grown mutant with ~50% lower chl, light-use efficiency was lower in the mutant when grown in chambers where chl was ~80% reduced. This difference is probably due to pleiotropic effects of the mutation that accompany very severe reductions in chlorophyll and may warrant further testing in other low-chl lines.
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Affiliation(s)
- Rebecca A Slattery
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA
| | - Aleel K Grennan
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA
| | - Mayandi Sivaguru
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, 2115 Gardner Hall, Box 7612, Raleigh, NC 27695, USA
| | - Donald R Ort
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA Global Change and Photosynthesis Research Unit, United States Department of Agriculture, 1206 West Gregory Drive, Urbana, IL 61801, USA
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Campbell BW, Stupar RM. Soybean (Glycine max) Mutant and Germplasm Resources: Current Status and Future Prospects. ACTA ACUST UNITED AC 2016; 1:307-327. [PMID: 30775866 DOI: 10.1002/cppb.20015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Genetic bottlenecks during domestication and modern breeding limited the genetic diversity of soybean (Glycine max (L.) Merr.). Therefore, expanding and diversifying soybean genetic resources is a major priority for the research community. These resources, consisting of natural and induced genetic variants, are valuable tools for improving soybean and furthering soybean biological knowledge. During the twentieth century, researchers gathered a wealth of genetic variation in the forms of landraces, Glycine soja accessions, Glycine tertiary germplasm, and the U.S. Department of Agriculture (USDA) Type and Isoline Collections. During the twenty-first century, soybean researchers have added several new genetic and genomic resources. These include the reference genome sequence, genotype data for the USDA soybean germplasm collection, next-generation mapping populations, new irradiation and transposon-based mutagenesis populations, and designer nuclease platforms for genome engineering. This paper briefly surveys the publicly accessible soybean genetic resources currently available or in development and provides recommendations for developing such genetic resources in the future. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Benjamin W Campbell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota
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Anderson JE, Michno JM, Kono TJY, Stec AO, Campbell BW, Curtin SJ, Stupar RM. Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants. BMC Biotechnol 2016; 16:41. [PMID: 27176220 PMCID: PMC4866027 DOI: 10.1186/s12896-016-0271-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/04/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The safety of mutagenized and genetically transformed plants remains a subject of scrutiny. Data gathered and communicated on the phenotypic and molecular variation induced by gene transfer technologies will provide a scientific-based means to rationally address such concerns. In this study, genomic structural variation (e.g. large deletions and duplications) and single nucleotide polymorphism rates were assessed among a sample of soybean cultivars, fast neutron-derived mutants, and five genetically transformed plants developed through Agrobacterium based transformation methods. RESULTS On average, the number of genes affected by structural variations in transgenic plants was one order of magnitude less than that of fast neutron mutants and two orders of magnitude less than the rates observed between cultivars. Structural variants in transgenic plants, while rare, occurred adjacent to the transgenes, and at unlinked loci on different chromosomes. DNA repair junctions at both transgenic and unlinked sites were consistent with sequence microhomology across breakpoints. The single nucleotide substitution rates were modest in both fast neutron and transformed plants, exhibiting fewer than 100 substitutions genome-wide, while inter-cultivar comparisons identified over one-million single nucleotide polymorphisms. CONCLUSIONS Overall, these patterns provide a fresh perspective on the genomic variation associated with high-energy induced mutagenesis and genetically transformed plants. The genetic transformation process infrequently results in novel genetic variation and these rare events are analogous to genetic variants occurring spontaneously, already present in the existing germplasm, or induced through other types of mutagenesis. It remains unclear how broadly these results can be applied to other crops or transformation methods.
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Affiliation(s)
- Justin E Anderson
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Jean-Michel Michno
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Thomas J Y Kono
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Adrian O Stec
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Benjamin W Campbell
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Shaun J Curtin
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Robert M Stupar
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA.
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