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Li X, Tian J, Chen X, Liao H. Bioengineering and management for efficient and sustainable utilization of phosphorus in crops. Curr Opin Biotechnol 2024; 90:103180. [PMID: 39241658 DOI: 10.1016/j.copbio.2024.103180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 07/25/2024] [Accepted: 08/02/2024] [Indexed: 09/09/2024]
Abstract
Phosphorus (P) is an essential macronutrient for plant growth, but low P availability in soils is also a primary constraint to crop production. To meet the increasing demands for food, P fertilizer applications have been increased, causing the accumulation of surplus P in soils, which has led to the frequency and magnitude of associated risk effects on agroecosystems. Finding solutions for efficient and sustainable crop P utilization is, therefore, an urgent priority. This review summarizes recent progress in bioengineering approaches to improving crop P efficiency and highlights that modifying root architecture in P-deficient soils and reducing P accumulation in grains in soils with P surplus could offer a way forward for improving P use efficiency.
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Affiliation(s)
- Xinxin Li
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiang Tian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Root Biology Center, South China Agricultural University, Guangzhou 510642, China
| | - Xinping Chen
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Hong Liao
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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2
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Yang B, Tan Z, Yan J, Zhang K, Ouyang Z, Fan R, Lu Y, Zhang Y, Yao X, Zhao H, Wang X, Lu S, Guo L. Phospholipase-mediated phosphate recycling during plant leaf senescence. Genome Biol 2024; 25:199. [PMID: 39075580 PMCID: PMC11285201 DOI: 10.1186/s13059-024-03348-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 07/23/2024] [Indexed: 07/31/2024] Open
Abstract
BACKGROUND Phosphorus is a macronutrient necessary for plant growth and development and its availability and efficient use affect crop yields. Leaves are the largest tissue that uses phosphorus in plants, and membrane phospholipids are the main source of cellular phosphorus usage. RESULTS Here we identify a key process for plant cellular phosphorus recycling mediated by membrane phospholipid hydrolysis during leaf senescence. Our results indicate that over 90% of lipid phosphorus, accounting for more than one-third of total cellular phosphorus, is recycled from senescent leaves before falling off the plants. Nonspecific phospholipase C4 (NPC4) and phospholipase Dζ2 (PLDζ2) are highly induced during leaf senescence, and knockouts of PLDζ2 and NPC4 decrease the loss of membrane phospholipids and delay leaf senescence. Conversely, overexpression of PLDζ2 and NPC4 accelerates the loss of phospholipids and leaf senescence, promoting phosphorus remobilization from senescent leaves to young tissues and plant growth. We also show that this phosphorus recycling process in senescent leaves mediated by membrane phospholipid hydrolysis is conserved in plants. CONCLUSIONS These results indicate that PLDζ2- and NPC4-mediated membrane phospholipid hydrolysis promotes phosphorus remobilization from senescent leaves to growing tissues and that the phospholipid hydrolysis-mediated phosphorus recycling improves phosphorus use efficiency in plants.
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Affiliation(s)
- Bao Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Department of Biology, University of Missouri, St. Louis, MO, 63121, USA
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Zengdong Tan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Yazhouwan National Laboratory, Sanya, 572025, Hainan, China
| | - Jiayu Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Ke Zhang
- Department of Biology, University of Missouri, St. Louis, MO, 63121, USA
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Zhewen Ouyang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Ruyi Fan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yefei Lu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yuting Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Yazhouwan National Laboratory, Sanya, 572025, Hainan, China
| | - Xuan Yao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Yazhouwan National Laboratory, Sanya, 572025, Hainan, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xuemin Wang
- Department of Biology, University of Missouri, St. Louis, MO, 63121, USA
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
- Yazhouwan National Laboratory, Sanya, 572025, Hainan, China.
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3
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Yang X, Liu C, Liang C, Wang T, Tian J. The Phosphorus-Iron Nexus: Decoding the Nutrients Interaction in Soil and Plant. Int J Mol Sci 2024; 25:6992. [PMID: 39000100 PMCID: PMC11241702 DOI: 10.3390/ijms25136992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 06/25/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024] Open
Abstract
Phosphorus (P) and iron (Fe) are two essential mineral nutrients in plant growth. It is widely observed that interactions of P and Fe could influence their availability in soils and affect their homeostasis in plants, which has received significant attention in recent years. This review presents a summary of latest advances in the activation of insoluble Fe-P complexes by soil properties, microorganisms, and plants. Furthermore, we elucidate the physiological and molecular mechanisms underlying how plants adapt to Fe-P interactions. This review also discusses the current limitations and presents potential avenues for promoting sustainable agriculture through the optimization of P and Fe utilization efficiency in crops.
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Affiliation(s)
| | | | | | - Tianqi Wang
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (X.Y.); (C.L.); (C.L.); (J.T.)
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4
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Hu D, Cui R, Wang K, Yang Y, Wang R, Zhu H, He M, Fan Y, Wang L, Wang L, Chu S, Zhang J, Zhang S, Yang Y, Zhai X, Lü H, Zhang D, Wang J, Kong F, Yu D, Zhang H, Zhang D. The Myb73-GDPD2-GA2ox1 transcriptional regulatory module confers phosphate deficiency tolerance in soybean. THE PLANT CELL 2024; 36:2176-2200. [PMID: 38345432 PMCID: PMC11132883 DOI: 10.1093/plcell/koae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 02/07/2024] [Indexed: 05/30/2024]
Abstract
Phosphorus is indispensable in agricultural production. An increasing food supply requires more efficient use of phosphate due to limited phosphate resources. However, how crops regulate phosphate efficiency remains largely unknown. Here, we identified a major quantitative trait locus, qPE19, that controls 7 low-phosphate (LP)-related traits in soybean (Glycine max) through linkage mapping and genome-wide association studies. We identified the gene responsible for qPE19 as GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE2 (GmGDPD2), and haplotype 5 represents the optimal allele favoring LP tolerance. Overexpression of GmGDPD2 significantly affects hormone signaling and improves root architecture, phosphate efficiency and yield-related traits; conversely, CRISPR/Cas9-edited plants show decreases in these traits. GmMyb73 negatively regulates GmGDPD2 by directly binding to its promoter; thus, GmMyb73 negatively regulates LP tolerance. GmGDPD2 physically interacts with GA 2-oxidase 1 (GmGA2ox1) in the plasma membrane, and overexpressing GmGA2ox1 enhances LP-associated traits, similar to GmGDPD2 overexpression. Analysis of double mutants for GmGDPD2 and GmGA2ox1 demonstrated that GmGDPD2 regulates LP tolerance likely by influencing auxin and gibberellin dose-associated cell division in the root. These results reveal a regulatory module that plays a major role in regulating LP tolerance in soybeans and is expected to be utilized to develop phosphate-efficient varieties to enhance soybean production, particularly in phosphate-deficient soils.
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Affiliation(s)
- Dandan Hu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Ruifan Cui
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Ke Wang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Yuming Yang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Ruiyang Wang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Hongqing Zhu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Mengshi He
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Yukun Fan
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Le Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Li Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Shanshan Chu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Jinyu Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Shanshan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Yifei Yang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Xuhao Zhai
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Haiyan Lü
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Dandan Zhang
- State Key Laboratory of Agricultural Microbiology, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinshe Wang
- Zhengzhou National Subcenter for Soybean Improvement, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Fanjiang Kong
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Hengyou Zhang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
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Yang B, Li J, Yan J, Zhang K, Ouyang Z, Lu Y, Wei H, Li Q, Yao X, Lu S, Hong Y, Wang X, Guo L. Non-specific phospholipase C4 hydrolyzes phosphosphingolipids and phosphoglycerolipids and promotes rapeseed growth and yield. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2421-2436. [PMID: 37642157 DOI: 10.1111/jipb.13560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 08/28/2023] [Indexed: 08/31/2023]
Abstract
Phosphorus is a major nutrient vital for plant growth and development, with a substantial amount of cellular phosphorus being used for the biosynthesis of membrane phospholipids. Here, we report that NON-SPECIFIC PHOSPHOLIPASE C4 (NPC4) in rapeseed (Brassica napus) releases phosphate from phospholipids to promote growth and seed yield, as plants with altered NPC4 levels showed significant changes in seed production under different phosphate conditions. Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9)-mediated knockout of BnaNPC4 led to elevated accumulation of phospholipids and decreased growth, whereas overexpression (OE) of BnaNPC4 resulted in lower phospholipid contents and increased plant growth and seed production. We demonstrate that BnaNPC4 hydrolyzes phosphosphingolipids and phosphoglycerolipids in vitro, and plants with altered BnaNPC4 function displayed changes in their sphingolipid and glycerolipid contents in roots, with a greater change in glycerolipids than sphingolipids in leaves, particularly under phosphate deficiency conditions. In addition, BnaNPC4-OE plants led to the upregulation of genes involved in lipid metabolism, phosphate release, and phosphate transport and an increase in free inorganic phosphate in leaves. These results indicate that BnaNPC4 hydrolyzes phosphosphingolipids and phosphoglycerolipids in rapeseed to enhance phosphate release from membrane phospholipids and promote growth and seed production.
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Affiliation(s)
- Bao Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianwu Li
- Department of Biology, University of Missouri, St. Louis, MO, 63121, USA
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Jiayu Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ke Zhang
- Department of Biology, University of Missouri, St. Louis, MO, 63121, USA
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Zhewen Ouyang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yefei Lu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huili Wei
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Xuan Yao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yueyun Hong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuemin Wang
- Department of Biology, University of Missouri, St. Louis, MO, 63121, USA
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, 572025, China
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6
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Hu D, Khan IU, Wang J, Shi X, Jiang X, Qi S, Dai Z, Mao H, Du D. Invasive Wedelia trilobata Performs Better Than Its Native Congener in Various Forms of Phosphorous in Different Growth Stages. PLANTS (BASEL, SWITZERLAND) 2023; 12:3051. [PMID: 37687298 PMCID: PMC10490449 DOI: 10.3390/plants12173051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/10/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023]
Abstract
At present, many hypotheses have been proposed to explain the mechanism of alien plants' successful invasion; the resource fluctuations hypothesis indicates that nutrient availability is a main abiotic factor driving the invasion of alien plants. Higher phosphorus utilization and absorption efficiency might be one of the important reasons for alien plants successful invasion. Wedelia trilobata, one of the notorious invasive weeds in China, possesses a strong ability to continue their development under infertile habitats. In this study, firstly, W. trilobata and its native congener, W. chinensis, were grown in various phosphorus forms to test their absorption efficiency of phosphorus. Secondly, the different responses of W. trilobata and W. chinensis to the insoluble phosphorus in three growth stages (at 30, 60, and 150 days cultivation) were also tested. The results showed that the growth rate, root morphology, and phosphorus absorption efficiency of W. trilobata under various insoluble, organic, or low phosphorus conditions were significantly higher than that of W. chinensis. During the short-term cultivation period (30 d), the growth of W. trilobata under insoluble and low phosphorus treatments had no significant difference, and the growth of W. trilobata in insoluble phosphorus treatment also had no significant effect in long-term cultivation (60 and 150 d). However, the growth of W. chinensis in each period under the conditions of insoluble and low phosphorus was significantly inhibited throughout these three growth stages. Therefore, invasive W. trilobata had a higher phosphorus utilization efficiency than its native congener. This study could explain how invasive W. trilobata performs under nutrient-poor habitats, while also providing favorable evidence for the resource fluctuations hypothesis.
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Affiliation(s)
- Die Hu
- School of Agricultural Engineering, Jiangsu University, Zhenjiang 212013, China; (D.H.); (J.W.); (X.J.); (H.M.)
| | - Irfan Ullah Khan
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; (I.U.K.); (X.S.); (Z.D.); (D.D.)
| | - Jiahao Wang
- School of Agricultural Engineering, Jiangsu University, Zhenjiang 212013, China; (D.H.); (J.W.); (X.J.); (H.M.)
| | - Xinning Shi
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; (I.U.K.); (X.S.); (Z.D.); (D.D.)
| | - Xinqi Jiang
- School of Agricultural Engineering, Jiangsu University, Zhenjiang 212013, China; (D.H.); (J.W.); (X.J.); (H.M.)
| | - Shanshan Qi
- School of Agricultural Engineering, Jiangsu University, Zhenjiang 212013, China; (D.H.); (J.W.); (X.J.); (H.M.)
| | - Zhicong Dai
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; (I.U.K.); (X.S.); (Z.D.); (D.D.)
- Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Hanping Mao
- School of Agricultural Engineering, Jiangsu University, Zhenjiang 212013, China; (D.H.); (J.W.); (X.J.); (H.M.)
| | - Daolin Du
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; (I.U.K.); (X.S.); (Z.D.); (D.D.)
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Zhang K, Gao W, Zhou Y, Zhao H, Xia Y, Zhang M, Bo Y, Lyu X, Hu Z, Yang J, Zhang M. Allelic variations of ClACO gene improve nitrogen uptake via ethylene-mediated root architecture in watermelon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:199. [PMID: 37624448 DOI: 10.1007/s00122-023-04448-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023]
Abstract
KEY MESSAGE The ClACO gene encoding 1-aminocyclopropane-1-carboxylate oxidase enabled highly efficient 15N uptake in watermelon. Nitrogen is one of the most essential nutrient elements that play a pivotal role in regulating plant growth and development for crop productivity. Elucidating the genetic basis of high nitrogen uptake is the key to improve nitrogen use efficiency for sustainable agricultural productivity. Whereas previous researches on nitrogen absorption process are mainly focused on a few model plants or crops. To date, the causal genes that determine the efficient nitrogen uptake of watermelon have not been mapped and remains largely unknown. Here, we fine-mapped the 1-aminocyclopropane-1-carboxylate oxidase (ClACO) gene associated with nitrogen uptake efficiency in watermelon via bulked segregant analysis (BSA). The variations in the ClACO gene led to the changes of gene expression levels between two watermelon accessions with different nitrogen uptake efficiencies. Intriguingly, in terms of the transcript abundance of ClACO, it was concomitant with significant differences in ethylene evolutions in roots and root architectures between the two accessions and among the different genotypic offsprings of the recombinant BC2F1(ZJU132)-18. These findings suggest that ethylene as a negative regulator altered nitrogen uptake efficiency in watermelon by controlling root development. In conclusion, our current study will provide valuable target gene for precise breeding of 'green' watermelon varieties with high-nitrogen uptake efficiencies.
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Affiliation(s)
- Kejia Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Wei Gao
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yimei Zhou
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Haoshun Zhao
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yuelin Xia
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Mengyi Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | | | - Xiaolong Lyu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China.
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Khan F, Siddique AB, Shabala S, Zhou M, Zhao C. Phosphorus Plays Key Roles in Regulating Plants' Physiological Responses to Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2023; 12:2861. [PMID: 37571014 PMCID: PMC10421280 DOI: 10.3390/plants12152861] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023]
Abstract
Phosphorus (P), an essential macronutrient, plays a pivotal role in the growth and development of plants. However, the limited availability of phosphorus in soil presents significant challenges for crop productivity, especially when plants are subjected to abiotic stresses such as drought, salinity and extreme temperatures. Unraveling the intricate mechanisms through which phosphorus participates in the physiological responses of plants to abiotic stresses is essential to ensure the sustainability of agricultural production systems. This review aims to analyze the influence of phosphorus supply on various aspects of plant growth and plant development under hostile environmental conditions, with a special emphasis on stomatal development and operation. Furthermore, we discuss recently discovered genes associated with P-dependent stress regulation and evaluate the feasibility of implementing P-based agricultural practices to mitigate the adverse effects of abiotic stress. Our objective is to provide molecular and physiological insights into the role of P in regulating plants' tolerance to abiotic stresses, underscoring the significance of efficient P use strategies for agricultural sustainability. The potential benefits and limitations of P-based strategies and future research directions are also discussed.
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Affiliation(s)
- Fahad Khan
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (F.K.); (A.B.S.); (M.Z.)
| | - Abu Bakar Siddique
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (F.K.); (A.B.S.); (M.Z.)
| | - Sergey Shabala
- School of Biological Science, University of Western Australia, Crawley, WA 6009, Australia;
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (F.K.); (A.B.S.); (M.Z.)
| | - Chenchen Zhao
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (F.K.); (A.B.S.); (M.Z.)
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Hale B, Ratnayake S, Flory A, Wijeratne R, Schmidt C, Robertson AE, Wijeratne AJ. Gene regulatory network inference in soybean upon infection by Phytophthora sojae. PLoS One 2023; 18:e0287590. [PMID: 37418376 PMCID: PMC10328377 DOI: 10.1371/journal.pone.0287590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 06/07/2023] [Indexed: 07/09/2023] Open
Abstract
Phytophthora sojae is a soil-borne oomycete and the causal agent of Phytophthora root and stem rot (PRR) in soybean (Glycine max [L.] Merrill). Yield losses attributed to P. sojae are devastating in disease-conducive environments, with global estimates surpassing 1.1 million tonnes annually. Historically, management of PRR has entailed host genetic resistance (both vertical and horizontal) complemented by disease-suppressive cultural practices (e.g., oomicide application). However, the vast expansion of complex and/or diverse P. sojae pathotypes necessitates developing novel technologies to attenuate PRR in field environments. Therefore, the objective of the present study was to couple high-throughput sequencing data and deep learning to elucidate molecular features in soybean following infection by P. sojae. In doing so, we generated transcriptomes to identify differentially expressed genes (DEGs) during compatible and incompatible interactions with P. sojae and a mock inoculation. The expression data were then used to select two defense-related transcription factors (TFs) belonging to WRKY and RAV families. DNA Affinity Purification and sequencing (DAP-seq) data were obtained for each TF, providing putative DNA binding sites in the soybean genome. These bound sites were used to train Deep Neural Networks with convolutional and recurrent layers to predict new target sites of WRKY and RAV family members in the DEG set. Moreover, we leveraged publicly available Arabidopsis (Arabidopsis thaliana) DAP-seq data for five TF families enriched in our transcriptome analysis to train similar models. These Arabidopsis data-based models were used for cross-species TF binding site prediction on soybean. Finally, we created a gene regulatory network depicting TF-target gene interactions that orchestrate an immune response against P. sojae. Information herein provides novel insight into molecular plant-pathogen interaction and may prove useful in developing soybean cultivars with more durable resistance to P. sojae.
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Affiliation(s)
- Brett Hale
- Molecular Biosciences Graduate Program, Arkansas State University, State University, AR, United States of America
- Arkansas Biosciences Institute, Arkansas State University, State University, AR, United States of America
- College of Science and Mathematics, Arkansas State University, State University, AR, United States of America
| | - Sandaruwan Ratnayake
- Arkansas Biosciences Institute, Arkansas State University, State University, AR, United States of America
- College of Science and Mathematics, Arkansas State University, State University, AR, United States of America
| | - Ashley Flory
- Arkansas Biosciences Institute, Arkansas State University, State University, AR, United States of America
| | | | - Clarice Schmidt
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States of America
| | - Alison E. Robertson
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States of America
| | - Asela J. Wijeratne
- Arkansas Biosciences Institute, Arkansas State University, State University, AR, United States of America
- College of Science and Mathematics, Arkansas State University, State University, AR, United States of America
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10
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Wang R, Liu X, Zhu H, Yang Y, Cui R, Fan Y, Zhai X, Yang Y, Zhang S, Zhang J, Hu D, Zhang D. Transcription factors GmERF1 and GmWRKY6 synergistically regulate low phosphorus tolerance in soybean. PLANT PHYSIOLOGY 2023; 192:1099-1114. [PMID: 36932694 PMCID: PMC10231356 DOI: 10.1093/plphys/kiad170] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 06/01/2023]
Abstract
Soybean (Glycine max) is a major grain and oil crop worldwide, but low phosphorus (LP) in soil severely limits the development of soybean production. Dissecting the regulatory mechanism of the phosphorus (P) response is crucial for improving the P use efficiency of soybean. Here, we identified a transcription factor, GmERF1 (ethylene response factor 1), that is mainly expressed in soybean root and localized in the nucleus. Its expression is induced by LP stress and differs substantially in extreme genotypes. The genomic sequences of 559 soybean accessions suggested that the allelic variation of GmERF1 has undergone artificial selection, and its haplotype is significantly related to LP tolerance. GmERF1 knockout or RNA interference resulted in significant increases in root and P uptake efficiency traits, while the overexpression of GmERF1 produced an LP-sensitive phenotype and affected the expression of 6 LP stress-related genes. In addition, GmERF1 directly interacted with GmWRKY6 to inhibit transcription of GmPT5 (phosphate transporter 5), GmPT7, and GmPT8, which affects plant P uptake and use efficiency under LP stress. Taken together, our results show that GmERF1 can affect root development by regulating hormone levels, thus promoting P absorption in soybean, and provide a better understanding of the role of GmERF1 in soybean P signal transduction. The favorable haplotypes from wild soybean will be conducive to the molecular breeding of high P use efficiency in soybean.
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Affiliation(s)
- Ruiyang Wang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiaoqian Liu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongqing Zhu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Yuming Yang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Ruifan Cui
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Yukun Fan
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Xuhao Zhai
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Yifei Yang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Shanshan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Jinyu Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Dandan Hu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
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11
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Chen Z, Wang L, Cardoso JA, Zhu S, Liu G, Rao IM, Lin Y. Improving phosphorus acquisition efficiency through modification of root growth responses to phosphate starvation in legumes. FRONTIERS IN PLANT SCIENCE 2023; 14:1094157. [PMID: 36844096 PMCID: PMC9950756 DOI: 10.3389/fpls.2023.1094157] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Phosphorus (P) is one of the essential macronutrients for plant growth and development, and it is an integral part of the major organic components, including nucleic acids, proteins and phospholipids. Although total P is abundant in most soils, a large amount of P is not easily absorbed by plants. Inorganic phosphate (Pi) is the plant-available P, which is generally immobile and of low availability in soils. Hence, Pi starvation is a major constraint limiting plant growth and productivity. Enhancing plant P efficiency can be achieved by improving P acquisition efficiency (PAE) through modification of morpho-physiological and biochemical alteration in root traits that enable greater acquisition of external Pi from soils. Major advances have been made to dissect the mechanisms underlying plant adaptation to P deficiency, especially for legumes, which are considered important dietary sources for humans and livestock. This review aims to describe how legume root growth responds to Pi starvation, such as changes in the growth of primary root, lateral roots, root hairs and cluster roots. In particular, it summarizes the various strategies of legumes to confront P deficiency by regulating root traits that contribute towards improving PAE. Within these complex responses, a large number of Pi starvation-induced (PSI) genes and regulators involved in the developmental and biochemical alteration of root traits are highlighted. The involvement of key functional genes and regulators in remodeling root traits provides new opportunities for developing legume varieties with maximum PAE needed for regenerative agriculture.
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Affiliation(s)
- Zhijian Chen
- Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Linjie Wang
- Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | | | - Shengnan Zhu
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, China
| | - Guodao Liu
- Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Idupulapati M. Rao
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
| | - Yan Lin
- Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou, China
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12
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Yang Y, Wang R, Wang L, Cui R, Zhang H, Che Z, Hu D, Chu S, Jiao Y, Yu D, Zhang D. GmEIL4 enhances soybean (Glycine max) phosphorus efficiency by improving root system development. PLANT, CELL & ENVIRONMENT 2023; 46:592-606. [PMID: 36419232 DOI: 10.1111/pce.14497] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 11/01/2022] [Accepted: 11/22/2022] [Indexed: 06/16/2023]
Abstract
Phosphorus (P) deficiency seriously affects plant growth and development and ultimately limits the quality and yield of crops. Here, a new P efficiency-related major quantitative trait locus gene, GmEIL4 (encoding an ethylene-insensitive 3-like 1 protein), was cloned at qP2, which was identified by linkage analysis and genome-wide association study across four environments. Overexpressing GmEIL4 significantly improved the P uptake efficiency by increasing the number, length and surface area of lateral roots of hairy roots in transgenic soybeans, while interfering with GmEIL4 resulted in poor root phenotypic characteristics compared with the control plants under low P conditions. Interestingly, we found that GmEIL4 interacted with EIN3-binding F box protein 1 (GmEBF1), which may regulate the root response to low P stress. We conclude that the expression of GmEIL4 was induced by low-P stress and that overexpressing GmEIL4 improved P accumulation by regulating root elongation and architecture. Analysis of allele variation of GmEIL4 in 894 soybean accessions suggested that GmEIL4 is undergoing artificial selection during soybean evolution, which will benefit soybean production. Together, this study further elucidates how plants respond to low P stress by modifying root structure and provides insight into the great potential of GmEIL4 in crop P-efficient breeding.
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Affiliation(s)
- Yuming Yang
- Department of Agriculture, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Ruiyang Wang
- Department of Agriculture, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Li Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, China
| | - Ruifan Cui
- Department of Agriculture, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Hengyou Zhang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | | | - Dandan Hu
- Department of Agriculture, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Shanshan Chu
- Department of Agriculture, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Yongqing Jiao
- Department of Agriculture, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Deyue Yu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, China
| | - Dan Zhang
- Department of Agriculture, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
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13
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Du H, Fang C, Li Y, Kong F, Liu B. Understandings and future challenges in soybean functional genomics and molecular breeding. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:468-495. [PMID: 36511121 DOI: 10.1111/jipb.13433] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Soybean (Glycine max) is a major source of plant protein and oil. Soybean breeding has benefited from advances in functional genomics. In particular, the release of soybean reference genomes has advanced our understanding of soybean adaptation to soil nutrient deficiencies, the molecular mechanism of symbiotic nitrogen (N) fixation, biotic and abiotic stress tolerance, and the roles of flowering time in regional adaptation, plant architecture, and seed yield and quality. Nevertheless, many challenges remain for soybean functional genomics and molecular breeding, mainly related to improving grain yield through high-density planting, maize-soybean intercropping, taking advantage of wild resources, utilization of heterosis, genomic prediction and selection breeding, and precise breeding through genome editing. This review summarizes the current progress in soybean functional genomics and directs future challenges for molecular breeding of soybean.
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Affiliation(s)
- Haiping Du
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Chao Fang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Yaru Li
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Baohui Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
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14
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Yang T, Yang S, Chen Z, Tan Y, Bol R, Duan H, He J. Global transcriptomic analysis reveals candidate genes associated with different phosphorus acquisition strategies among soybean varieties. FRONTIERS IN PLANT SCIENCE 2022; 13:1080014. [PMID: 36600925 PMCID: PMC9806128 DOI: 10.3389/fpls.2022.1080014] [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: 10/25/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Introduction Soybean adapts to phosphorus-deficient soils through three important phosphorus acquisition strategies, namely altered root conformation, exudation of carboxylic acids, and symbiosis with clumping mycorrhizal fungi. However, the trade-offs and regulatory mechanisms of these three phosphorus acquisition strategies in soybean have not been researched. Methods In this study, we investigated the responses of ten different soybean varieties to low soil phosphorus availability by determining biomass, phosphorus accumulation, root morphology, exudation, and mycorrhizal colonization rate. Furthermore, the molecular regulatory mechanisms underlying root phosphorus acquisition strategies were examined among varieties with different low-phosphorus tolerance using transcriptome sequencing and weighted gene co-expression network analysis. Results and discussion The results showed that two types of phosphorus acquisition strategies-"outsourcing" and "do-it-yourself"-were employed by soybean varieties under low phosphorus availability. The "do-it-yourself" varieties, represented by QD11, Zh30, and Sd, obtained sufficient phosphorus by increasing their root surface area and secreting carboxylic acids. In contrast, the "outsourcing" varieties, represented by Zh301, Zh13, and Hc6, used increased symbiosis with mycorrhizae to obtain phosphorus owing to their large root diameters. Transcriptome analysis showed that the direction of acetyl-CoA metabolism could be the dividing line between the two strategies of soybean selection. ERF1 and WRKY1 may be involved in the regulation of phosphorus acquisition strategies for soybeans grown under low P environments. These findings will enhance our understanding of phosphorus acquisition strategies in soybeans. In addition, they will facilitate the development of breeding strategies that are more flexible to accommodate a variety of production scenarios in agriculture under low phosphorus environments.
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Affiliation(s)
- Tongli Yang
- College of Agriculture, Guizhou University, Guiyang, China
| | - Songhua Yang
- College of Agriculture, Guizhou University, Guiyang, China
- Agricultural Ecological Environment and Resources Protection Station of Bijie Agricultural and Rural Bureau, Guiyang, China
| | - Zhu Chen
- College of Agriculture, Guizhou University, Guiyang, China
| | - Yuechen Tan
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Roland Bol
- Institute of Bio- and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, Germany
- School of Natural Sciences, Environment Centre Wales, Bangor University, Bangor, United Kingdom
| | - Honglang Duan
- Institute for Forest Resources & Environment of Guizhou, College of Forestry, Guizhou University, Guiyang, China
| | - Jin He
- College of Agriculture, Guizhou University, Guiyang, China
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15
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Fan K, Sze CC, Li MW, Lam HM. Roles of non-coding RNAs in the hormonal and nutritional regulation in nodulation and nitrogen fixation. FRONTIERS IN PLANT SCIENCE 2022; 13:997037. [PMID: 36330261 PMCID: PMC9623164 DOI: 10.3389/fpls.2022.997037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Symbiotic nitrogen fixation is an important component in the nitrogen cycle and is a potential solution for sustainable agriculture. It is the result of the interactions between the plant host, mostly restricted to legume species, and the rhizobial symbiont. From the first encounter between the host and the symbiont to eventual successful nitrogen fixation, there are delicate processes involved, such as nodule organogenesis, rhizobial infection thread progression, differentiation of the bacteroid, deregulation of the host defense systems, and reallocation of resources. All these processes are tightly regulated at different levels. Recent evidence revealed that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), participate in these processes by controlling the transcription and translation of effector genes. In general, ncRNAs are functional transcripts without translation potential and are important gene regulators. MiRNAs, negative gene regulators, bind to the target mRNAs and repress protein production by causing the cleavage of mRNA and translational silencing. LncRNAs affect the formation of chromosomal loops, DNA methylation, histone modification, and alternative splicing to modulate gene expression. Both lncRNAs and circRNAs could serve as target mimics of miRNA to inhibit miRNA functions. In this review, we summarized and discussed the current understanding of the roles of ncRNAs in legume nodulation and nitrogen fixation in the root nodule, mainly focusing on their regulation of hormone signal transduction, the autoregulation of nodulation (AON) pathway and nutrient homeostasis in nodules. Unraveling the mediation of legume nodulation by ncRNAs will give us new insights into designing higher-performance leguminous crops for sustainable agriculture.
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16
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Xu H, Zhang H, Fan Y, Wang R, Cui R, Liu X, Chu S, Jiao Y, Zhang X, Zhang D. The purple acid phosphatase GmPAP17 predominantly enhances phosphorus use efficiency in soybean. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 320:111283. [PMID: 35643608 DOI: 10.1016/j.plantsci.2022.111283] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/04/2022] [Accepted: 04/07/2022] [Indexed: 06/15/2023]
Abstract
Purple acid phosphatase (PAP) is an important plant acid phosphatase, which can secrete to the rhizosphere to decompose organophosphorus, promote phosphorus use efficiency, plant growth and development. However, little is known about the functions of intracellular PAP in plants, especially for soybean. Our previous study integrating QTL mapping and transcriptome analysis identified an promising low phosphorus (LP)-induced gene GmPAP17. Here, we determined that GmPAP17 was mainly expressed in roots and had a strong response to LP stress. Furthermore, and the relative expression in the root of LP tolerant genotypes NN94-156 was significantly greater than that of LP sensitive genotype Bogao after LP stress treatment. The overexpression of GmPAP17 significantly enhanced both acid phosphatase activity and growth performance of hairy roots under LP stress condition, it was vice versa for RNAi interference of GmPAP17, indicating that GmPAP17 plays an important role in P use efficiency. Moreover, yeast two-hybrid and bimolecular fluorescence complementation analysis showed that GmRAP2.2 was involved in the regulation network of GmPAP17. Taken together, our results suggest that GmPAP17 is a novel plant PAP that functions in the adaptation of soybean to LP stress, possibly through its involvement in P recycling in plants.
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Affiliation(s)
- Huanqing Xu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Hengyou Zhang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Yukun Fan
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Ruiyang Wang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Ruifan Cui
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiaoqian Liu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shanshan Chu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Yongqing Jiao
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Xingguo Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.
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Wang Q, Du W, Yu W, Zhang W, Huang F, Cheng H, Yu D. Genome-wide association analysis discovered new loci and candidate genes associated with low-phosphorus tolerance based on shoot mineral elements concentrations in soybean. Mol Genet Genomics 2022; 297:843-858. [PMID: 35441900 DOI: 10.1007/s00438-022-01895-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/31/2022] [Indexed: 10/18/2022]
Abstract
Phosphorus (P) deficiency is one of the major limitations for soybean production. Moreover, it has been well reported P and other mineral elements function interdependently or antagonistically to control nutrients homeostasis in plants. Thus, it is urgently needed to understand the genetic mechanism of the accumulation of mineral elements in response to low-P stress. In this study, to identify single nucleotide polymorphisms (SNPs) and candidate genes controlling the accumulation of mineral elements suffering low-P stress in seedling stage of soybean plants, we measured concentrations of mineral elements, including P, Zn, Fe, Mn, Mg and Ca, in shoots of 211 soybean accessions under normal phosphorus (+P) and low phosphorus (-P) conditions in two hydroponic experiments. And genome-wide association study (GWAS) using high density NJAU 355K SoySNP array and concentrations of five of these mineral elements except P was performed. A total of 36 SNPs distributed on 13 chromosomes were identified to be significantly associated with low-P tolerance, and nine SNPs on chromosome 10 formed a SNP cluster. Meanwhile, the candidate gene GmFeB1 was found to serve as a negative regulator element involved in soybean P metabolism and the haplotype1 (Hap1) of GmFeB1 showed significantly higher shoot Fe concentration under -P condition than that of Hap2. In summary, we uncover 36 SNPs significantly associated with shoot mineral elements concentrations under different P conditions and a soybean low-P related gene GmFeB1, which will provide additional genetic information for soybean low-P tolerance and new gene resources for P-efficient soybean varieties breeding.
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Affiliation(s)
- Qing Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenkai Du
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenqing Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weihao Zhang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fang Huang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hao Cheng
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China.
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18
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Wang Q, Du W, Zhang S, Yu W, Wang J, Zhang C, Zhang H, Huang F, Cheng H, Yu D. Functional study and elite haplotype identification of soybean phosphate starvation response transcription factors GmPHR14 and GmPHR32. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:29. [PMID: 37309533 PMCID: PMC10248592 DOI: 10.1007/s11032-022-01301-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/22/2022] [Indexed: 06/14/2023]
Abstract
Phosphorus (P) is one of the important mineral elements required for plant growth and development. However, because of the low mobility in soil, P deficiency has been an important factor limiting soybean production. Here, we identified 14 PHR (phosphate starvation response) genes in soybean genome and verified that two previously unreported GmPHR members, GmPHR14 and GmPHR32, were involved in low-P stress tolerance in soybean. GmPHR14 and GmPHR32 were present in two diverged branches of the phylogenic tree. Both genes were highly expressed in roots and root nodules and were induced by P deficiency. GmPHR14 and GmPHR32 both were expressed in the nucleus. The 211 amino acids in the N terminus of GmPHR32 were found to be required for the transcriptional activity. Overexpressing GmPHR14 or GmPHR32 in soybean hairy roots significantly increased roots and shoots dry weight under low-P condition, and overexpressing GmPHR14 additionally significantly increased roots P concentration under low-P condition. GmPHR14 and GmPHR32 were polymorphic in soybean population and the elite haplotype2 (Hap2) for both genes was preferentially present in improved cultivars and showed significantly higher shoots dry weight under low-P condition than the other two haplotypes. These results suggested GmPHR14 and GmPHR32 both positively regulated low-P responses in soybean, and would shed light on the molecular mechanism of low-P stress tolerance. Furthermore, the identified elite haplotypes would be useful in P-efficient soybean breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01301-z.
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Affiliation(s)
- Qing Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Wenkai Du
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shixi Zhang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Wenqing Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jiao Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Cankui Zhang
- Department of Agronomy, Purdue University, West Lafayette, IN 47907 USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907 USA
| | - Hengyou Zhang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 China
| | - Fang Huang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Hao Cheng
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
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19
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Mo X, Liu G, Zhang Z, Lu X, Liang C, Tian J. Mechanisms Underlying Soybean Response to Phosphorus Deficiency through Integration of Omics Analysis. Int J Mol Sci 2022; 23:4592. [PMID: 35562981 PMCID: PMC9105353 DOI: 10.3390/ijms23094592] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/14/2022] [Accepted: 04/18/2022] [Indexed: 12/17/2022] Open
Abstract
Low phosphorus (P) availability limits soybean growth and yield. A set of potential strategies for plant responses to P deficiency have been elucidated in the past decades, especially in model plants such as Arabidopsis thaliana and rice (Oryza sativa). Recently, substantial efforts focus on the mechanisms underlying P deficiency improvement in legume crops, especially in soybeans (Glycine max). This review summarizes recent advances in the morphological, metabolic, and molecular responses of soybean to phosphate (Pi) starvation through the combined analysis of transcriptomics, proteomics, and metabolomics. Furthermore, we highlight the functions of the key factors controlling root growth and P homeostasis, base on which, a P signaling network in soybean was subsequently presumed. This review also discusses current barriers and depicts perspectives in engineering soybean cultivars with high P efficiency.
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Affiliation(s)
| | | | | | | | - Cuiyue Liang
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (X.M.); (G.L.); (Z.Z.); (X.L.)
| | - Jiang Tian
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (X.M.); (G.L.); (Z.Z.); (X.L.)
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20
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Hibbert L, Taylor G. Improving phosphate use efficiency in the aquatic crop watercress (Nasturtium officinale). HORTICULTURE RESEARCH 2022; 9:uhac011. [PMID: 35147194 PMCID: PMC8969064 DOI: 10.1093/hr/uhac011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Watercress is a nutrient-dense leafy green crop, traditionally grown in aquatic outdoor systems and increasingly seen as well-suited for indoor hydroponic systems. However, there is concern that this crop has a detrimental impact on the environment through direct phosphate additions causing environmental pollution. Phosphate-based fertilisers are supplied to enhanced crop yield, but their use may contribute to eutrophication of waterways downstream of traditional watercress farms. One option is to develop a more phosphate use efficient (PUE) crop. This review identifies the key traits for this aquatic crop (the ideotype), for future selection, marker development and breeding. Traits identified as important for PUE are (i) increased root surface area through prolific root branching and adventitious root formation, (ii) aerenchyma formation and root hair growth. Functional genomic traits for improved PUE are (iii) efficacious phosphate remobilisation and scavenging strategies and (iv) the use of alternative metabolic pathways. Key genomic targets for this aquatic crop are identified as: PHT phosphate transporter genes, global transcriptional regulators such as those of the SPX family and genes involved in galactolipid and sulfolipid biosynthesis such as MGD2/3, PECP1, PSR2, PLDζ1/2 and SQD2. Breeding for enhanced PUE in watercress will be accelerated by improved molecular genetic resources such as a full reference genome sequence that is currently in development.
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Affiliation(s)
- Lauren Hibbert
- School of Biological Sciences, University of Southampton, Southampton, Hampshire, SO17 1BJ, UK
- Department of Plant Sciences, UC Davis, Davis, CA, 95616, USA
| | - Gail Taylor
- School of Biological Sciences, University of Southampton, Southampton, Hampshire, SO17 1BJ, UK
- Department of Plant Sciences, UC Davis, Davis, CA, 95616, USA
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21
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Zhang M, Liu S, Wang Z, Yuan Y, Zhang Z, Liang Q, Yang X, Duan Z, Liu Y, Kong F, Liu B, Ren B, Tian Z. Progress in soybean functional genomics over the past decade. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:256-282. [PMID: 34388296 PMCID: PMC8753368 DOI: 10.1111/pbi.13682] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 05/24/2023]
Abstract
Soybean is one of the most important oilseed and fodder crops. Benefiting from the efforts of soybean breeders and the development of breeding technology, large number of germplasm has been generated over the last 100 years. Nevertheless, soybean breeding needs to be accelerated to meet the needs of a growing world population, to promote sustainable agriculture and to address future environmental changes. The acceleration is highly reliant on the discoveries in gene functional studies. The release of the reference soybean genome in 2010 has significantly facilitated the advance in soybean functional genomics. Here, we review the research progress in soybean omics (genomics, transcriptomics, epigenomics and proteomics), germplasm development (germplasm resources and databases), gene discovery (genes that are responsible for important soybean traits including yield, flowering and maturity, seed quality, stress resistance, nodulation and domestication) and transformation technology during the past decade. At the end, we also briefly discuss current challenges and future directions.
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Affiliation(s)
- Min Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Zhao Wang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yaqin Yuan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhifang Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qianjin Liang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xia Yang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zongbiao Duan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Baohui Liu
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Bo Ren
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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22
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Liu X, Yang Y, Wang R, Cui R, Xu H, Sun C, Wang J, Zhang H, Chen H, Zhang D. GmWRKY46, a WRKY transcription factor, negatively regulates phosphorus tolerance primarily through modifying root morphology in soybean. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 315:111148. [PMID: 35067311 DOI: 10.1016/j.plantsci.2021.111148] [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: 08/26/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 05/18/2023]
Abstract
Phosphorus (P) deficiency affects soybean growth and development, resulting in significant reduction of yields. However, the regulatory mechanism of P deficiency tolerance in soybean is still largely unclear. WRKY transcription factors are a family of regulators involved in a variety of abiotic stresses in plants while rarely reported in P deficiency. Here, we demonstrated that a soybean GmWRKY46 gene, belonging to group III of WRKY TF family, was involved in the regulation of P deficiency tolerance in soybean. The expression of GmWRKY46 in low P sensitive soybean varieties was significantly higher than that in tolerant soybean varieties. It was primarily expressed in roots and strongly induced by P deprivation. GmWRKY46 was localized in the nucleus. Compared with the control expressing the empty vector, overexpression of GmWRKY46 in soybean hairy roots exhibited more sensitive phenotypes to low P stress, while the RNA interfered GmWRKY46 significantly enhanced P deficiency tolerance by increasing the proliferation, elongation and P absorption efficiency of hairy roots. Expression patterns of a number of P-responsive genes (GmPht1;1, GmPht1;4, GmPTF1, GmACP1, GmPAP21 and GmExpansin-A7) were altered in both overexpression and gene silenced plants. The results provided a novel insight into how soybean responds to low P stress and new gene that may be used to improve soybean low P tolerance through gene editing approach.
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Affiliation(s)
- Xiaoqian Liu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yuming Yang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Ruiyang Wang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Ruifan Cui
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Huanqing Xu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Chongyuan Sun
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jinshe Wang
- Zhengzhou National Subcenter for Soybean Improvement, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Hengyou Zhang
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, Chinese Academy of Sciences, Harbin, 150081, China
| | - Huatao Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
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23
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Ren G, Yang B, Cui M, Yu H, Fan X, Dai Z, Sun J, Li G, Zhang H, Du D. Additive effects of warming and nitrogen addition on the performance and competitiveness of invasive Solidago canadensis L. FRONTIERS IN PLANT SCIENCE 2022; 13:1017554. [PMID: 36407577 PMCID: PMC9671518 DOI: 10.3389/fpls.2022.1017554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/14/2022] [Indexed: 05/04/2023]
Abstract
Changes in temperature and nitrogen (N) deposition determine the growth and competitive dominance of both invasive and native plants. However, a paucity of experimental evidence limits understanding of how these changes influence plant invasion. Therefore, we conducted a greenhouse experiment in which invasive Solidago canadensis L. was planted in mixed culture with native Artemisia argyi Levl. et Van under combined conditions of warming and N addition. Our results show that due to the strong positive effect of nitrogen addition, the temperature increases and nitrogen deposition interaction resulted in greatly enhanced species performance. Most of the relative change ratios (RCR) of phenotypic traits differences between S. canadensis and A. argyi occur in the low invasion stage, and six of eight traits had higher RCR in response to N addition and/or warming in native A. argyi than in invasive S. canadensis. Our results also demonstrate that the effects of the warming and nitrogen interaction on growth-related traits and competitiveness of S. canadensis and A. argyi were usually additive rather than synergistic or antagonistic. This conclusion suggests that the impact of warming and nitrogen deposition on S. canadensis can be inferred from single factor studies. Further, environmental changes did not modify the competitive relationship between invasive S. canadensis and native A. argyi but the relative yield of S. canadensis was significantly greater than A. argyi. This finding indicated that we can rule out the influence of environmental changes such as N addition and warming which makes S. canadensis successfully invade new habitats through competition. Correlation analysis showed that invasive S. canadensis may be more inclined to mobilize various characteristics to strengthen competition during the invasion process, which will facilitate S. canadensis becoming the superior competitor in S. canadensis-A. argyi interactions. These findings contribute to our understanding of the spreading of invasive plants such as S. canadensis under climate change and help identify potential precautionary measures that could prevent biological invasions.
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Affiliation(s)
- Guangqian Ren
- Institute of Environment and Ecology, Academy of Environmental Health and Ecological Security, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, China
| | - Bin Yang
- Institute of Environment and Ecology, Academy of Environmental Health and Ecological Security, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Miaomiao Cui
- Institute of Environment and Ecology, Academy of Environmental Health and Ecological Security, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Haochen Yu
- Institute of Environment and Ecology, Academy of Environmental Health and Ecological Security, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Xue Fan
- Institute of Environment and Ecology, Academy of Environmental Health and Ecological Security, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Zhicong Dai
- Institute of Environment and Ecology, Academy of Environmental Health and Ecological Security, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, China
| | - Jianfan Sun
- Institute of Environment and Ecology, Academy of Environmental Health and Ecological Security, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Guanlin Li
- Institute of Environment and Ecology, Academy of Environmental Health and Ecological Security, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Haiyan Zhang
- School of Inspection and Testing Certification, Changzhou Vocational Institute of Engineering, Changzhou, China
| | - Daolin Du
- Institute of Environment and Ecology, Academy of Environmental Health and Ecological Security, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, China
- *Correspondence: Daolin Du,
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24
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Xu H, Guo Y, Qiu L, Ran Y. Progress in Soybean Genetic Transformation Over the Last Decade. FRONTIERS IN PLANT SCIENCE 2022; 13:900318. [PMID: 35755694 PMCID: PMC9231586 DOI: 10.3389/fpls.2022.900318] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 05/11/2022] [Indexed: 05/13/2023]
Abstract
Soybean is one of the important food, feed, and biofuel crops in the world. Soybean genome modification by genetic transformation has been carried out for trait improvement for more than 4 decades. However, compared to other major crops such as rice, soybean is still recalcitrant to genetic transformation, and transgenic soybean production has been hampered by limitations such as low transformation efficiency and genotype specificity, and prolonged and tedious protocols. The primary goal in soybean transformation over the last decade is to achieve high efficiency and genotype flexibility. Soybean transformation has been improved by modifying tissue culture conditions such as selection of explant types, adjustment of culture medium components and choice of selection reagents, as well as better understanding the transformation mechanisms of specific approaches such as Agrobacterium infection. Transgenesis-based breeding of soybean varieties with new traits is now possible by development of improved protocols. In this review, we summarize the developments in soybean genetic transformation to date, especially focusing on the progress made using Agrobacterium-mediated methods and biolistic methods over the past decade. We also discuss current challenges and future directions.
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Affiliation(s)
- Hu Xu
- Tianjin Genovo Biotechnology Co., Ltd., Tianjin, China
| | - Yong Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijuan Qiu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Lijuan Qiu,
| | - Yidong Ran
- Tianjin Genovo Biotechnology Co., Ltd., Tianjin, China
- Yidong Ran,
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25
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Bechtaoui N, Rabiu MK, Raklami A, Oufdou K, Hafidi M, Jemo M. Phosphate-Dependent Regulation of Growth and Stresses Management in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:679916. [PMID: 34777404 PMCID: PMC8581177 DOI: 10.3389/fpls.2021.679916] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 09/28/2021] [Indexed: 05/22/2023]
Abstract
The importance of phosphorus in the regulation of plant growth function is well studied. However, the role of the inorganic phosphate (Pi) molecule in the mitigation of abiotic stresses such as drought, salinity, heavy metal, heat, and acid stresses are poorly understood. We revisited peer-reviewed articles on plant growth characteristics that are phosphorus (P)-dependently regulated under the sufficient-P and low/no-P starvation alone or either combined with one of the mentioned stress. We found that the photosynthesis rate and stomatal conductance decreased under Pi-starved conditions. The total chlorophyll contents were increased in the P-deficient plants, owing to the lack of Pi molecules to sustain the photosynthesis functioning, particularly, the Rubisco and fructose-1,6-bisphosphatase function. The dry biomass of shoots, roots, and P concentrations were significantly reduced under Pi starvation with marketable effects in the cereal than in the legumes. To mitigate P stress, plants activate alternative regulatory pathways, the Pi-dependent glycolysis, and mitochondrial respiration in the cytoplasm. Plants grown under well-Pi supplementation of drought stress exhibited higher dry biomass of shoots than the no-P treated ones. The Pi supply to plants grown under heavy metals stress reduced the metal concentrations in the leaves for the cadmium (Cd) and lead (Pb), but could not prevent them from absorbing heavy metals from soils. To detoxify from heavy metal stress, plants enhance the catalase and ascorbate peroxidase activity that prevents lipid peroxidation in the leaves. The HvPIP and PHO1 genes were over-expressed under both Pi starvation alone and Pi plus drought, or Pi plus salinity stress combination, implying their key roles to mediate the stress mitigations. Agronomy Pi-based interventions to increase Pi at the on-farm levels were discussed. Revisiting the roles of P in growth and its better management in agricultural lands or where P is supplemented as fertilizer could help the plants to survive under abiotic stresses.
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Affiliation(s)
- Noura Bechtaoui
- AgroBiosciences Program, University Mohammed VI Polytechnic (UM6P), Benguerir, Morocco
| | - Muhammad Kabir Rabiu
- AgroBiosciences Program, University Mohammed VI Polytechnic (UM6P), Benguerir, Morocco
- Centre for Dryland Agriculture, Bayero University, Kano, Nigeria
| | - Anas Raklami
- Laboratory of Microbial Biotechnology, Agrosciences, and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakech, Morocco
| | - Khalid Oufdou
- AgroBiosciences Program, University Mohammed VI Polytechnic (UM6P), Benguerir, Morocco
- Laboratory of Microbial Biotechnology, Agrosciences, and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakech, Morocco
| | - Mohamed Hafidi
- AgroBiosciences Program, University Mohammed VI Polytechnic (UM6P), Benguerir, Morocco
- Laboratory of Microbial Biotechnology, Agrosciences, and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakech, Morocco
| | - Martin Jemo
- AgroBiosciences Program, University Mohammed VI Polytechnic (UM6P), Benguerir, Morocco
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26
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Li C, Li K, Zheng M, Liu X, Ding X, Gai J, Yang S. Gm6PGDH1, a Cytosolic 6-Phosphogluconate Dehydrogenase, Enhanced Tolerance to Phosphate Starvation by Improving Root System Development and Modifying the Antioxidant System in Soybean. FRONTIERS IN PLANT SCIENCE 2021; 12:704983. [PMID: 34484268 PMCID: PMC8414836 DOI: 10.3389/fpls.2021.704983] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Phosphorus plays an important role in plant growth and development, and is an important limiting factor for crop yield. Although previous studies have shown that 6-phosphogluconate dehydrogenase (6PGDH) plays an important role in plant resistance to adversity, its response to low phosphorus (P) stress remains unknown. In this study, we reported the cloning and characterization of a cytosolic 6PGDH gene, Gm6PGDH1, which enhanced the tolerance to phosphate (Pi) starvation by improving root system development and modifying the antioxidant system in transgenic plants. Gm6PGDH1 was highly expressed in the root at full bloom stage, and strongly induced by Pi starvation. The results from intact soybean composite plant and soybean plant, both containing a Gm6PGDH1-overexpressing construct, showed that Gm6PGDH1 was involved in root system development, and subsequently affected P uptake under Pi-deficient conditions. Meanwhile, the accumulation of reactive oxygen species (ROS) in the root tip of transgenic soybean was reduced, and the activity of ROS-scavenging enzymes was enhanced compared with those of the wild type under Pi-deficient conditions. Interestingly, we found that the overexpression of Gm6PGDH1 weakened the response of several other important Pi-answer genes to Pi starvation, such as some purple acid phosphatases (PAPs) and redox-related genes. In addition, the results from a virus-induced gene silencing (VIGS) indicated that Gm6PGDH1 might have functional redundancy in soybean, and the results from a heterogeneous transformation system showed that overexpressing Gm6PGDH1 also enhanced tolerance to Pi starvation in transgenic Arabidopsis. Together, these results suggested the great potential of Gm6PGDH1 in crop breeding for low Pi tolerance.
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Affiliation(s)
- Cheng Li
- Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, National Center for Soybean Improvement, Soybean Research Institute, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Kangning Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Ministry of Agriculture (MOA) Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing, China
| | - Mingming Zheng
- Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, National Center for Soybean Improvement, Soybean Research Institute, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Xinyi Liu
- Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, National Center for Soybean Improvement, Soybean Research Institute, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Xianlong Ding
- Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, National Center for Soybean Improvement, Soybean Research Institute, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Junyi Gai
- Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, National Center for Soybean Improvement, Soybean Research Institute, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Shouping Yang
- Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, National Center for Soybean Improvement, Soybean Research Institute, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
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Zhang J, Xu H, Yang Y, Zhang X, Huang Z, Zhang D. Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting soybean genotypes subjected to phosphate starvation. BMC Genomics 2021; 22:433. [PMID: 34107875 PMCID: PMC8191232 DOI: 10.1186/s12864-021-07750-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 05/27/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Phosphorus (P) is essential for plant growth and development, and low-phosphorus (LP) stress is a major factor limiting the growth and yield of soybean. Long noncoding RNAs (lncRNAs) have recently been reported to be key regulators in the responses of plants to stress conditions, but the mechanism through which LP stress mediates the biogenesis of lncRNAs in soybean remains unclear. RESULTS In this study, to explore the response mechanisms of lncRNAs to LP stress, we used the roots of two representative soybean genotypes that present opposite responses to P deficiency, namely, a P-sensitive genotype (Bogao) and a P-tolerant genotype (NN94156), for the construction of RNA sequencing (RNA-seq) libraries. In total, 4,166 novel lncRNAs, including 525 differentially expressed (DE) lncRNAs, were identified from the two genotypes at different P levels. GO and KEGG analyses indicated that numerous DE lncRNAs might be involved in diverse biological processes related to phosphate, such as lipid metabolic processes, catalytic activity, cell membrane formation, signal transduction, and nitrogen fixation. Moreover, lncRNA-mRNA-miRNA and lncRNA-mRNA networks were constructed, and the results identified several promising lncRNAs that might be highly valuable for further analysis of the mechanism underlying the response of soybean to LP stress. CONCLUSIONS These results revealed that LP stress can significantly alter the genome-wide profiles of lncRNAs, particularly those of the P-sensitive genotype Bogao. Our findings increase the understanding of and provide new insights into the function of lncRNAs in the responses of soybean to P stress.
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Affiliation(s)
- Jinyu Zhang
- School of Life Science and Technology, Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, 453003 China
| | - Huanqing Xu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002 China
| | - Yuming Yang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002 China
| | - Xiangqian Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002 China
| | - Zhongwen Huang
- School of Life Science and Technology, Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, 453003 China
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002 China
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28
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Liu X, Chu S, Sun C, Xu H, Zhang J, Jiao Y, Zhang D. Genome-wide identification of low phosphorus responsive microRNAs in two soybean genotypes by high-throughput sequencing. Funct Integr Genomics 2020; 20:825-838. [PMID: 33009591 DOI: 10.1007/s10142-020-00754-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 01/24/2023]
Abstract
MicroRNAs (miRNAs) have been reported to be correlated with various stress responses in soybean, but only a few miRNAs have been demonstrated to respond to low phosphorus (LP) stress. To unravel the response mechanisms of miRNAs to low-P stress, the roots of two representative soybean genotypes with different P efficiency, Nannong94-156 (a LP-tolerant genotype) and Bogao (a LP-sensitive genotype), were used for the construction of RNA sequencing (RNA-seq) libraries under low/normal-P treatment by high-throughput sequencing. In total, 603 existing miRNAs and 1699 novel miRNAs belonging to 248 and 1582 families in all samples were identified, respectively. Among these miRNAs, 777 miRNAs were differentially expressed (DE) across different P levels and genotypes. Furthermore, putative targets of DE miRNAs were predicted, and these miRNAs mainly targeted ERF (ethylene responsive factor), auxin response factors (ARF), zinc finger protein, MYB, and NAC domain transcription factors. Gene ontology (GO) analysis showed that targets of DE miRNAs were significantly enriched in binding, metabolic processes, biological regulation, response to stress, and phosphorus metabolic processes. In addition, the expression profiles of chosen P-responsive miRNAs and target genes were validated by quantitative real-time PCR (qRT-PCR). Our study focused on genome-wide miRNA identification in two representative soybean genotypes under low-P stress. Overall, the DE miRNAs across different P levels and genotypes and their putative target genes will provide useful information for further study of miRNAs mediating low-P response and facilitate improvements in soybean breeding.
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Affiliation(s)
- Xiaoqian Liu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Shanshan Chu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Chongyuan Sun
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Huanqing Xu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jinyu Zhang
- Henan Institute of Science and Technology, Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, 453003, China
| | - Yongqing Jiao
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
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29
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Chu S, Zhang X, Yu K, Lv L, Sun C, Liu X, Zhang J, Jiao Y, Zhang D. Genome-Wide Analysis Reveals Dynamic Epigenomic Differences in Soybean Response to Low-Phosphorus Stress. Int J Mol Sci 2020; 21:E6817. [PMID: 32957498 PMCID: PMC7555642 DOI: 10.3390/ijms21186817] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/12/2020] [Accepted: 09/15/2020] [Indexed: 01/23/2023] Open
Abstract
Low-phosphorus (low-P) stress has a significant limiting effect on crop yield and quality. Although the molecular mechanisms of the transcriptional level responsible for the low-P stress response have been studied in detail, the underlying epigenetic mechanisms in gene regulation remain largely unknown. In this study, we evaluated the changes in DNA methylation, gene expression and small interfering RNAs (siRNAs) abundance genome-wide in response to low-P stress in two representative soybean genotypes with different P-efficiencies. The DNA methylation levels were slightly higher under low-P stress in both genotypes. Integrative methylation and transcription analysis suggested a complex regulatory relationship between DNA methylation and gene expression that may be associated with the type, region, and extent of methylation. Association analysis of low-P-induced differential methylation and gene expression showed that transcriptional alterations of a small part of genes were associated with methylation changes. Dynamic methylation alterations in transposable element (TE) regions in the CHH methylation context correspond with changes in the amount of siRNA under low-P conditions, indicating an important role of siRNAs in modulating TE activity by guiding CHH methylation in TE regions. Together, these results could help to elucidate the epigenetic regulation mechanisms governing the responses of plants to abiotic stresses.
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Affiliation(s)
- Shanshan Chu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (S.C.); (X.Z.); (K.Y.); (L.L.); (C.S.); (X.L.); (Y.J.)
| | - Xiangqian Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (S.C.); (X.Z.); (K.Y.); (L.L.); (C.S.); (X.L.); (Y.J.)
| | - Kaiye Yu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (S.C.); (X.Z.); (K.Y.); (L.L.); (C.S.); (X.L.); (Y.J.)
| | - Lingling Lv
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (S.C.); (X.Z.); (K.Y.); (L.L.); (C.S.); (X.L.); (Y.J.)
| | - Chongyuan Sun
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (S.C.); (X.Z.); (K.Y.); (L.L.); (C.S.); (X.L.); (Y.J.)
| | - Xiaoqian Liu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (S.C.); (X.Z.); (K.Y.); (L.L.); (C.S.); (X.L.); (Y.J.)
| | - Jinyu Zhang
- Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang 453003, China;
| | - Yongqing Jiao
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (S.C.); (X.Z.); (K.Y.); (L.L.); (C.S.); (X.L.); (Y.J.)
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (S.C.); (X.Z.); (K.Y.); (L.L.); (C.S.); (X.L.); (Y.J.)
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