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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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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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3
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Mahmoud A, Qi R, Chi X, Liao N, Malangisha GK, Ali A, Moustafa-Farag M, Yang J, Zhang M, Hu Z. Integrated Bulk Segregant Analysis, Fine Mapping, and Transcriptome Revealed QTLs and Candidate Genes Associated with Drought Adaptation in Wild Watermelon. Int J Mol Sci 2023; 25:65. [PMID: 38203237 PMCID: PMC10779233 DOI: 10.3390/ijms25010065] [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: 10/07/2023] [Revised: 12/07/2023] [Accepted: 12/09/2023] [Indexed: 01/12/2024] Open
Abstract
Drought stress has detrimental effects on crop productivity worldwide. A strong root system is crucial for maintaining water and nutrients uptake under drought stress. Wild watermelons possess resilient roots with excellent drought adaptability. However, the genetic factors controlling this trait remain uninvestigated. In this study, we conducted a bulk segregant analysis (BSA) on an F2 population consisting of two watermelon genotypes, wild and domesticated, which differ in their lateral root development under drought conditions. We identified two quantitative trait loci (qNLR_Dr. Chr01 and qNLR_Dr. Chr02) associated with the lateral root response to drought. Furthermore, we determined that a small region (0.93 Mb in qNLR_Dr. Chr01) is closely linked to drought adaptation through quantitative trait loci (QTL) validation and fine mapping. Transcriptome analysis of the parent roots under drought stress revealed unique effects on numerous genes in the sensitive genotype but not in the tolerant genotype. By integrating BSA, fine mapping, and the transcriptome, we identified six genes, namely L-Ascorbate Oxidase (AO), Cellulose Synthase-Interactive Protein 1 (CSI1), Late Embryogenesis Abundant Protein (LEA), Zinc-Finger Homeodomain Protein 2 (ZHD2), Pericycle Factor Type-A 5 (PFA5), and bZIP transcription factor 53-like (bZIP53-like), that might be involved in the drought adaptation. Our findings provide valuable QTLs and genes for marker-assisted selection in improving water-use efficiency and drought tolerance in watermelon. They also lay the groundwork for the genetic manipulation of drought-adapting genes in watermelon and other Cucurbitacea species.
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Affiliation(s)
- Ahmed Mahmoud
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
- Horticulture Research Institute, Agricultural Research Center, 9 Cairo University St, Giza 12619, Egypt;
| | - Rui Qi
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
| | - Xiaolu Chi
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
| | - Nanqiao Liao
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
| | - Guy Kateta Malangisha
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
| | - Abid Ali
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
| | - Mohamed Moustafa-Farag
- Horticulture Research Institute, Agricultural Research Center, 9 Cairo University St, Giza 12619, Egypt;
| | - Jinghua Yang
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Mingfang Zhang
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Zhongyuan Hu
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
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Li P, Ma X, Wang J, Yao L, Li B, Meng Y, Si E, Yang K, Shang X, Zhang X, Wang H. Integrated Analysis of Metabolome and Transcriptome Reveals Insights for Low Phosphorus Tolerance in Wheat Seedling. Int J Mol Sci 2023; 24:14840. [PMID: 37834288 PMCID: PMC10573437 DOI: 10.3390/ijms241914840] [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: 09/04/2023] [Revised: 09/23/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Low phosphorus (LP) stress leads to a significant reduction in wheat yield, primarily in the reduction of biomass, the number of tillers and spike grains, the delay in heading and flowering, and the inhibition of starch synthesis and grouting. However, the differences in regulatory pathway responses to low phosphorus stress among different wheat genotypes are still largely unknown. In this study, metabolome and transcriptome analyses of G28 (LP-tolerant) and L143 (LP-sensitive) wheat varieties after 72 h of normal phosphorus (CK) and LP stress were performed. A total of 181 and 163 differentially accumulated metabolites (DAMs) were detected for G28CK vs. G28LP and L143CK vs. L143LP, respectively. Notably, the expression of pilocarpine (C07474) in G28CK vs. G28LP was significantly downregulated 4.77-fold, while the expression of neochlorogenic acid (C17147) in L143CK vs. L143LP was significantly upregulated 2.34-fold. A total of 4023 differentially expressed genes (DEGs) were acquired between G28 and L143, of which 1120 DEGs were considered as the core DEGs of LP tolerance of wheat after LP treatment. The integration of metabolomics and transcriptomic data further revealed that the LP tolerance of wheat was closely related to 15 metabolites and 18 key genes in the sugar and amino acid metabolism pathway. The oxidative phosphorylation pathway was enriched to four ATPases, two cytochrome c reductase genes, and fumaric acid under LP treatment. Moreover, PHT1;1, TFs (ARFA, WRKY40, MYB4, MYB85), and IAA20 genes were related to the Pi starvation stress of wheat roots. Therefore, the differences in LP tolerance of different wheat varieties were related to energy metabolism, amino acid metabolism, phytohormones, and PHT proteins, and precisely regulated by the levels of various molecular pathways to adapt to Pi starvation stress. Taken together, this study may help to reveal the complex regulatory process of wheat adaptation to Pi starvation and provide new genetic clues for further study on improving plant Pi utilization efficiency.
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Affiliation(s)
- Pengcheng Li
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, 730070, China; (P.L.); (X.M.)
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaole Ma
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, 730070, China; (P.L.); (X.M.)
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Juncheng Wang
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, 730070, China; (P.L.); (X.M.)
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Lirong Yao
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, 730070, China; (P.L.); (X.M.)
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Baochun Li
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, 730070, China; (P.L.); (X.M.)
- Department of Botany, College of Life Sciences and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yaxiong Meng
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, 730070, China; (P.L.); (X.M.)
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Erjing Si
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, 730070, China; (P.L.); (X.M.)
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Ke Yang
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, 730070, China; (P.L.); (X.M.)
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Xunwu Shang
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Xueyong Zhang
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, 730070, China; (P.L.); (X.M.)
| | - Huajun Wang
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, 730070, China; (P.L.); (X.M.)
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
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5
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Wan X, Yao G, Wang K, Liu Y, Wang F, Jiang H. Transcriptomic Analysis of the Response of the Toxic Dinoflagellate Prorocentrum lima to Phosphorous Limitation. Microorganisms 2023; 11:2216. [PMID: 37764060 PMCID: PMC10535992 DOI: 10.3390/microorganisms11092216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/26/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
Some dinoflagellates cause harmful algal blooms, releasing toxic secondary metabolites, to the detriment of marine ecosystems and human health. Phosphorus (P) is a limiting macronutrient for dinoflagellate growth in the ocean. Previous studies have been focused on the physiological response of dinoflagellates to ambient P changes. However, the whole-genome's molecular mechanisms are poorly understood. In this study, RNA-Seq was utilized to compare the global gene expression patterns of a marine diarrheic shellfish poisoning (DSP) toxin-producing dinoflagellate, Prorocentrum lima, grown in inorganic P-replete and P-deficient conditions. A total of 148 unigenes were significantly up-regulated, and 30 unigenes were down-regulated under 1/4 P-limited conditions, while 2708 unigenes were significantly up-regulated, and 284 unigenes were down-regulated under 1/16 P-limited conditions. KEGG enrichment analysis of the differentially expressed genes shows that genes related to ribosomal proteins, glycolysis, fatty acid biosynthesis, phagosome formation, and ubiquitin-mediated proteolysis are found to be up-regulated, while most of the genes related to photosynthesis are down-regulated. Further analysis shows that genes encoding P transporters, organic P utilization, and endocytosis are significantly up-regulated in the P-limited cells, indicating a strong ability of P. lima to utilize dissolved inorganic P as well as intracellular organic P. These transcriptomic data are further corroborated by biochemical and physiological analyses, which reveals that under P deficiency, cellular contents of starch, lipid, and toxin increase, while photosynthetic efficiency declines. Our results indicate that has P. lima evolved diverse strategies to acclimatize to low P environments. The accumulation of carbon sources and DSP toxins could provide protection for P. lima to cope with adverse environmental conditions.
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Affiliation(s)
| | | | | | | | | | - Hui Jiang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China; (X.W.); (G.Y.); (K.W.); (Y.L.); (F.W.)
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6
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Chen C, Zhang Y, Liu Y, Cui J, He X, Wu Y, Yue L, Zhang J, Ding M, Yi Z, Fang X. Joint QTL Mapping and Transcriptome Sequencing Analysis Reveal Candidate Seed-Shattering-Related Genes in Common Buckwheat. Int J Mol Sci 2023; 24:10013. [PMID: 37373161 DOI: 10.3390/ijms241210013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Common buckwheat (Fagopyrum esculentum M.) is an important traditional miscellaneous grain crop. However, seed-shattering is a significant problem in common buckwheat. To investigate the genetic architecture and genetic regulation of seed-shattering in common buckwheat, we constructed a genetic linkage map using the F2 population of Gr (green-flower mutant and shattering resistance) and UD (white flower and susceptible to shattering), which included eight linkage groups with 174 loci, and detected seven QTLs of pedicel strength. RNA-seq analysis of pedicel in two parents revealed 214 differentially expressed genes DEGs that play roles in phenylpropanoid biosynthesis, vitamin B6 metabolism, and flavonoid biosynthesis. Weighted gene co-expression network analysis (WGCNA) was performed and screened out 19 core hub genes. Untargeted GC-MS analysis detected 138 different metabolites and conjoint analysis screened out 11 DEGs, which were significantly associated with differential metabolites. Furthermore, we identified 43 genes in the QTLs, of which six genes had high expression levels in the pedicel of common buckwheat. Finally, 21 candidate genes were screened out based on the above analysis and gene function. Our results provided additional knowledge for the identification and functions of causal candidate genes responsible for the variation in seed-shattering and would be an invaluable resource for the genetic dissection of common buckwheat resistance-shattering molecular breeding.
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Affiliation(s)
- Chuyi Chen
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Yuke Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Institute of Advanced Agricultural Sciences, Peking University, Weifang 261000, China
| | - Yang Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Jingbin Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Xingxing He
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Yichao Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Linqing Yue
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Jian Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Mengqi Ding
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Zelin Yi
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Xiaomei Fang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
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7
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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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8
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Kayoumu M, Iqbal A, Muhammad N, Li X, Li L, Wang X, Gui H, Qi Q, Ruan S, Guo R, Zhang X, Song M, Dong Q. Phosphorus Availability Affects the Photosynthesis and Antioxidant System of Contrasting Low-P-Tolerant Cotton Genotypes. Antioxidants (Basel) 2023; 12:antiox12020466. [PMID: 36830024 PMCID: PMC9952849 DOI: 10.3390/antiox12020466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/08/2023] [Accepted: 02/11/2023] [Indexed: 02/17/2023] Open
Abstract
Phosphorus (P) is an essential macronutrient, and an important component of plant metabolism. However, little is known about the effects of low P availability on P absorption, the photosynthetic electron transport chain, and the antioxidant system in cotton. This study used cotton genotypes (sensitive FJA and DLNTDH and tolerant BX014 and LuYuan343) with contrasting low-P tolerance in a hydroponic experiment under 15 µM, 50 µM, and 500 μM P concentrations. The results showed that low P availability reduced plant development and leaf area, shoot length, and dry weight in FJA and DLNADH, compared to BX014 and LuYuan343. The low P availability decreased the gas-exchange parameters such as the net photosynthetic rate, transpiration rate, and stomatal conductance, and increased the intercellular CO2 concentration. Chlorophyll a fluorescence demonstrated that the leaves' absorption and trapped-energy flux were largely steady. In contrast, considerable gains in absorption and trapped-energy flux per reaction center resulted from decreases in the electron transport per reaction center under low-P conditions. In addition, low P availability reduced the activities of antioxidant enzymes and increased the content of malondialdehyde in the cotton genotypes, especially in FJA and DLNTDH. Moreover, low P availability reduced the activity of PEPC and generated a decline in the content of ATP and NADPH. Our research can provide a theoretical physiological basis for the growth and tolerance of cotton under low-P conditions.
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Affiliation(s)
- Mirezhatijiang Kayoumu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology/School of Agricultural Sciences, Zhengzhou University, Anyang 455000, China
| | - Asif Iqbal
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology/School of Agricultural Sciences, Zhengzhou University, Anyang 455000, China
- Western Agricultural Research Center of Chinese Academy of Agricultural Sciences, Changji 831100, China
- Department of Agriculture, Hazara University, Mansehra 21120, Pakistan
| | - Noor Muhammad
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology/School of Agricultural Sciences, Zhengzhou University, Anyang 455000, China
| | - Xiaotong Li
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology/School of Agricultural Sciences, Zhengzhou University, Anyang 455000, China
| | - Leilei Li
- Rice Cultivation Laboratory, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiangru Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology/School of Agricultural Sciences, Zhengzhou University, Anyang 455000, China
| | - Huiping Gui
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology/School of Agricultural Sciences, Zhengzhou University, Anyang 455000, China
| | - Qian Qi
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology/School of Agricultural Sciences, Zhengzhou University, Anyang 455000, China
| | - Sijia Ruan
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology/School of Agricultural Sciences, Zhengzhou University, Anyang 455000, China
| | - Ruishi Guo
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology/School of Agricultural Sciences, Zhengzhou University, Anyang 455000, China
| | - Xiling Zhang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology/School of Agricultural Sciences, Zhengzhou University, Anyang 455000, China
- Correspondence: (X.Z.); (M.S.); (Q.D.); Tel.: +86-0372-2562-308 (Q.D.)
| | - Meizhen Song
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology/School of Agricultural Sciences, Zhengzhou University, Anyang 455000, China
- Western Agricultural Research Center of Chinese Academy of Agricultural Sciences, Changji 831100, China
- Correspondence: (X.Z.); (M.S.); (Q.D.); Tel.: +86-0372-2562-308 (Q.D.)
| | - Qiang Dong
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology/School of Agricultural Sciences, Zhengzhou University, Anyang 455000, China
- Western Agricultural Research Center of Chinese Academy of Agricultural Sciences, Changji 831100, China
- Correspondence: (X.Z.); (M.S.); (Q.D.); Tel.: +86-0372-2562-308 (Q.D.)
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9
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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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10
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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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11
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Hou F, Zhang N, Ma L, An L, Zhou X, Zou C, Yang C, Pan G, Lübberstedt T, Shen Y. ZmbZIP54 and ZmFDX5 cooperatively regulate maize seedling tolerance to lead by mediating ZmPRP1 transcription. Int J Biol Macromol 2023; 224:621-633. [PMID: 36273546 DOI: 10.1016/j.ijbiomac.2022.10.151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/14/2022] [Accepted: 10/17/2022] [Indexed: 11/05/2022]
Abstract
Extensive lead (Pb) accumulation in plants exerts toxic effects on plant growth and development and enters the human food chain. Combining linkage mapping, transcriptome analysis, and association studies, we cloned the ZmbZIP54 transcription factor, which confers maize tolerance to Pb. Combined overexpression and knockdown confirmed that ZmbZIP54 mitigates Pb toxicity in maize by alleviating Pb absorption into the roots. Yeast one-hybrid and dual-luciferase assays revealed that ZmbZIP54 binds to the ZmPRP1 promoter and promotes its transcription. Yeast two-hybrid and bimolecular fluorescence complementation assays indicated that ZmFdx5 interacts with ZmbZIP54 in the nucleus. ZmFdx5 acts as a switch that controls the regulation of ZmPRP1 expression by ZmbZIP54 when maize encounters Pb stress. Furthermore, we revealed that variation in the 5'-UTR of ZmbZIP54 affects its expression level under Pb stress and contributes to the difference in Pb tolerance among maize lines. Finally, we proposed a model to summarize the role of ZmbZIP54 in Pb tolerance, which involves the cooperative effect of ZmbZIP54 and ZmFdx5 on the ZmPRP1 transcription in maize response to Pb. This study provides novel insights into the development of Pb-tolerant maize varieties and bioremediation of Pb-contaminated soils.
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Affiliation(s)
- Fengxia Hou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Na Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Langlang Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Lijun An
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xun Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Chaoying Zou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Cong Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Guangtang Pan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | | | - Yaou Shen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China.
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12
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Genetic approaches for assessment of phosphorus use efficiency in groundnut (Arachis hypogaea L.). Sci Rep 2022; 12:21552. [PMID: 36513706 PMCID: PMC9747966 DOI: 10.1038/s41598-022-24016-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 11/08/2022] [Indexed: 12/15/2022] Open
Abstract
Production of phosphorus efficient genotypes in groundnut can improve and also reduces environmental pollution. Identification of P-efficient groundnut genotypes is a need of the hour to sustain in P-deficient soils. The pot experiment showed significant differences between genotypes (G) and treatments (T) for all the traits and G × T interaction for majority of traits. The G × T × Y interaction effects were also significant for all the traits except leaf P% (LP%), leaf acid phosphatase (LAP) and root dry weight (RDW). In lysimeter experiment, the effect of G, T and G × T were significant for leaf dry weight (LDW), stem dry weight (SDW), total transpiration (TT) and transpiration efficiency (TE). For traits, LDW, SDW, TT, TE, ICGV 00351 and ICGS 76; for SDW, TT, ICGV 02266 are best performers under both P-sufficient and deficient conditions. Based on P-efficiency indices and surrogate traits of P-uptake, ICGV's 02266, 05155, 00308, 06040 and 06146 were considered as efficient P-responding genotypes. From GGE biplot, ICGV 06146 under P-deficient and TAG 24 under both P-sufficient and deficient conditions are portrayed as best performer. ICGV 06146 was identified as stable pod yielder and a promising genotype for P-deficient soils. The genotypes identified in this study can be used as a parent in developing mapping population to decipher the genetics and to devleop groundnut breeding lines suitable to P-deficient soils.
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13
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Jianing G, Yuhong G, Yijun G, Rasheed A, Qian Z, Zhiming X, Mahmood A, Shuheng Z, Zhuo Z, Zhuo Z, Xiaoxue W, Jian W. Improvement of heat stress tolerance in soybean ( Glycine max L), by using conventional and molecular tools. FRONTIERS IN PLANT SCIENCE 2022; 13:993189. [PMID: 36226280 PMCID: PMC9549248 DOI: 10.3389/fpls.2022.993189] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/23/2022] [Indexed: 06/12/2023]
Abstract
The soybean is a significant legume crop, providing several vital dietary components. Extreme heat stress negatively affects soybean yield and quality, especially at the germination stage. Continuous change in climatic conditions is threatening the global food supply and food security. Therefore, it is a critical need of time to develop heat-tolerant soybean genotypes. Different molecular techniques have been developed to improve heat stress tolerance in soybean, but until now complete genetic mechanism of soybean is not fully understood. Various molecular methods, like quantitative trait loci (QTL) mapping, genetic engineering, transcription factors (TFs), transcriptome, and clustered regularly interspaced short palindromic repeats (CRISPR), are employed to incorporate heat tolerance in soybean under the extreme conditions of heat stress. These molecular techniques have significantly improved heat stress tolerance in soybean. Besides this, we can also use specific classical breeding approaches and different hormones to reduce the harmful consequences of heat waves on soybean. In future, integrated use of these molecular tools would bring significant results in developing heat tolerance in soybean. In the current review, we have presented a detailed overview of the improvement of heat tolerance in soybean and highlighted future prospective. Further studies are required to investigate different genetic factors governing the heat stress response in soybean. This information would be helpful for future studies focusing on improving heat tolerance in soybean.
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Affiliation(s)
- Guan Jianing
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Gai Yuhong
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Guan Yijun
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Adnan Rasheed
- College of Life Sciences, Changchun Normal University, Changchun, China
| | - Zhao Qian
- College of Life Sciences, Changchun Normal University, Changchun, China
| | - Xie Zhiming
- College of Life Sciences, Baicheng Normal University, Baicheng, China
| | - Athar Mahmood
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Zhang Shuheng
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Zhang Zhuo
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Zhao Zhuo
- College of Life Sciences, Jilin Normal University, Changchun, China
| | - Wang Xiaoxue
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Wei Jian
- College of Life Sciences, Changchun Normal University, Changchun, China
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14
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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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15
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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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16
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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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17
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Omomowo OI, Babalola OO. Constraints and Prospects of Improving Cowpea Productivity to Ensure Food, Nutritional Security and Environmental Sustainability. FRONTIERS IN PLANT SCIENCE 2021; 12:751731. [PMID: 34745184 PMCID: PMC8570086 DOI: 10.3389/fpls.2021.751731] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/30/2021] [Indexed: 05/23/2023]
Abstract
Providing safe and secure food for an increasing number of people globally is challenging. Coping with such a human population by merely applying the conventional agricultural production system has not proved to be agro-ecologically friendly; nor is it sustainable. Cowpea (Vigna unguiculata (L) Walp) is a multi-purpose legume. It consists of high-quality protein for human consumption, and it is rich in protein for livestock fodder. It enriches the soil in that it recycles nutrients through the fixation of nitrogen in association with nodulating bacteria. However, the productivity of this multi-functional, indigenous legume that is of great value to African smallholder farmers and the rural populace, and also to urban consumers and entrepreneurs, is limited. Because cowpea is of strategic importance in Africa, there is a need to improve on its productivity. Such endeavors in Africa are wrought with challenges that include drought, salinity, the excessive demand among farmers for synthetic chemicals, the repercussions of climate change, declining soil nutrients, microbial infestations, pest issues, and so forth. Nevertheless, giant strides have already been made and there have already been improvements in adopting sustainable and smart biotechnological approaches that are favorably influencing the production costs of cowpea and its availability. As such, the prospects for a leap in cowpea productivity in Africa and in the enhancement of its genetic gain are good. Potential and viable means for overcoming some of the above-mentioned production constraints would be to focus on the key cowpea producer nations in Africa and to encourage them to embrace biotechnological techniques in an integrated approach to enhance for sustainable productivity. This review highlights the spectrum of constraints that limit the cowpea yield, but looks ahead of the constraints and seeks a way forward to improve cowpea productivity in Africa. More importantly, this review investigates applications and insights concerning mechanisms of action for implementing eco-friendly biotechnological techniques, such as the deployment of bio inoculants, applying climate-smart agricultural (CSA) practices, agricultural conservation techniques, and multi-omics smart technology in the spheres of genomics, transcriptomics, proteomics, and metabolomics, for improving cowpea yields and productivity to achieve sustainable agro-ecosystems, and ensuring their stability.
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Affiliation(s)
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
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Zhang H, Hu Z, Yang Y, Liu X, Lv H, Song BH, An YQC, Li Z, Zhang D. Transcriptome profiling reveals the spatial-temporal dynamics of gene expression essential for soybean seed development. BMC Genomics 2021; 22:453. [PMID: 34134624 PMCID: PMC8207594 DOI: 10.1186/s12864-021-07783-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Seeds are the economic basis of oilseed crops, especially soybeans, the most widely cultivated oilseed crop worldwide. Seed development is accompanied by a multitude of diverse cellular processes, and revealing the underlying regulatory activities is critical for seed improvement. RESULTS In this study, we profiled the transcriptomes of developing seeds at 20, 25, 30, and 40 days after flowering (DAF), as these stages represent critical time points of seed development from early to full development. We identified a set of highly abundant genes and highlighted the importance of these genes in supporting nutrient accumulation and transcriptional regulation for seed development. We identified 8925 differentially expressed genes (DEGs) that exhibited temporal expression patterns over the course and expression specificities in distinct tissues, including seeds and nonseed tissues (roots, stems, and leaves). Genes specific to nonseed tissues might have tissue-associated roles, with relatively low transcript abundance in developing seeds, suggesting their spatially supportive roles in seed development. Coexpression network analysis identified several underexplored genes in soybeans that bridge tissue-specific gene modules. CONCLUSIONS Our study provides a global view of gene activities and biological processes critical for seed formation in soybeans and prioritizes a set of genes for further study. The results of this study help to elucidate the mechanism controlling seed development and storage reserves.
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Affiliation(s)
- Hengyou Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Zhenbin Hu
- Department of Biology, Saint Louis University, St. Louis, MO, USA
| | - Yuming Yang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaoqian Liu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Haiyan Lv
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Bao-Hua Song
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Yong-Qiang Charles An
- US Department of Agriculture, Agricultural Research Service, Midwest Area, Plant Genetics Research Unit at Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Zhimin Li
- 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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19
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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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Fatiukha A, Deblieck M, Klymiuk V, Merchuk-Ovnat L, Peleg Z, Ordon F, Fahima T, Korol A, Saranga Y, Krugman T. Genomic Architecture of Phenotypic Plasticity in Response to Water Stress in Tetraploid Wheat. Int J Mol Sci 2021; 22:ijms22041723. [PMID: 33572141 PMCID: PMC7915520 DOI: 10.3390/ijms22041723] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 01/12/2023] Open
Abstract
Phenotypic plasticity is one of the main mechanisms of adaptation to abiotic stresses via changes in critical developmental stages. Altering flowering phenology is a key evolutionary strategy of plant adaptation to abiotic stresses, to achieve the maximum possible reproduction. The current study is the first to apply the linear regression residuals as drought plasticity scores while considering the variation in flowering phenology and traits under non-stress conditions. We characterized the genomic architecture of 17 complex traits and their drought plasticity scores for quantitative trait loci (QTL) mapping, using a mapping population derived from a cross between durum wheat (Triticum turgidum ssp. durum) and wild emmer wheat (T. turgidum ssp. dicoccoides). We identified 79 QTLs affected observed traits and their plasticity scores, of which 33 reflected plasticity in response to water stress and exhibited epistatic interactions and/or pleiotropy between the observed and plasticity traits. Vrn-B3 (TaTF1) residing within an interval of a major drought-escape QTL was proposed as a candidate gene. The favorable alleles for most of the plasticity QTLs were contributed by wild emmer wheat, demonstrating its high potential for wheat improvement. Our study presents a new approach for the quantification of plant adaptation to various stresses and provides new insights into the genetic basis of wheat complex traits under water-deficit stress.
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Affiliation(s)
- Andrii Fatiukha
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Mathieu Deblieck
- Julius Kühn-Institut (JKI) Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, 06484 Quedlinburg, Germany; (M.D.); (F.O.)
| | - Valentyna Klymiuk
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Lianne Merchuk-Ovnat
- R. H. Smith Institute of Plant Science & Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (L.M.-O.); (Z.P.); (Y.S.)
| | - Zvi Peleg
- R. H. Smith Institute of Plant Science & Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (L.M.-O.); (Z.P.); (Y.S.)
| | - Frank Ordon
- Julius Kühn-Institut (JKI) Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, 06484 Quedlinburg, Germany; (M.D.); (F.O.)
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Abraham Korol
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Yehoshua Saranga
- R. H. Smith Institute of Plant Science & Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (L.M.-O.); (Z.P.); (Y.S.)
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Correspondence: ; Tel.: +972-04-8240783
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21
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Laoué J, Depardieu C, Gérardi S, Lamothe M, Bomal C, Azaiez A, Gros-Louis MC, Laroche J, Boyle B, Hammerbacher A, Isabel N, Bousquet J. Combining QTL Mapping and Transcriptomics to Decipher the Genetic Architecture of Phenolic Compounds Metabolism in the Conifer White Spruce. FRONTIERS IN PLANT SCIENCE 2021; 12:675108. [PMID: 34079574 PMCID: PMC8166253 DOI: 10.3389/fpls.2021.675108] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/08/2021] [Indexed: 05/05/2023]
Abstract
Conifer forests worldwide are becoming increasingly vulnerable to the effects of climate change. Although the production of phenolic compounds (PCs) has been shown to be modulated by biotic and abiotic stresses, the genetic basis underlying the variation in their constitutive production level remains poorly documented in conifers. We used QTL mapping and RNA-Seq to explore the complex polygenic network underlying the constitutive production of PCs in a white spruce (Picea glauca) full-sib family for 2 years. QTL detection was performed for nine PCs and differentially expressed genes (DEGs) were identified between individuals with high and low PC contents for five PCs exhibiting stable QTLs across time. A total of 17 QTLs were detected for eight metabolites, including one major QTL explaining up to 91.3% of the neolignan-2 variance. The RNA-Seq analysis highlighted 50 DEGs associated with phenylpropanoid biosynthesis, several key transcription factors, and a subset of 137 genes showing opposite expression patterns in individuals with high levels of the flavonoids gallocatechin and taxifolin glucoside. A total of 19 DEGs co-localized with QTLs. Our findings represent a significant step toward resolving the genomic architecture of PC production in spruce and facilitate the functional characterization of genes and transcriptional networks responsible for differences in constitutive production of PCs in conifers.
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Affiliation(s)
- Justine Laoué
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
- *Correspondence: Justine Laoué
| | - Claire Depardieu
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Sébastien Gérardi
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Manuel Lamothe
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Claude Bomal
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Aïda Azaiez
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Marie-Claude Gros-Louis
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Jérôme Laroche
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Brian Boyle
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Almuth Hammerbacher
- Department of Zoology, Entomology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Nathalie Isabel
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
- Jean Bousquet
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22
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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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Reddy VRP, Das S, Dikshit HK, Mishra GP, Aski M, Meena SK, Singh A, Pandey R, Singh MP, Tripathi K, Gore PG, Priti, Bhagat TK, Kumar S, Nair R, Sharma TR. Genome-Wide Association Analysis for Phosphorus Use Efficiency Traits in Mungbean ( Vigna radiata L. Wilczek) Using Genotyping by Sequencing Approach. FRONTIERS IN PLANT SCIENCE 2020; 11:537766. [PMID: 33193476 PMCID: PMC7658405 DOI: 10.3389/fpls.2020.537766] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 09/18/2020] [Indexed: 10/10/2023]
Abstract
Mungbean (Vigna radiata L. Wilczek) is an annual grain legume crop affected by low availability of phosphorus. Phosphorus deficiency mainly affects the growth and development of plants along with changes in root morphology and increase in root-to-shoot ratio. Deciphering the genetic basis of phosphorus use efficiency (PUE) traits can benefit our understanding of mungbean tolerance to low-phosphorus condition. To address this issue, 144 diverse mungbean genotypes were evaluated for 12 PUE traits under hydroponics with optimum- and low-phosphorus levels. The broad sense heritability of traits ranged from 0.63 to 0.92 and 0.58 to 0.92 under optimum- and low-phosphorus conditions, respectively. This study, reports for the first time such a large number of genome wide Single nucleotide polymorphisms (SNPs) (76,160) in mungbean. Further, genome wide association study was conducted using 55,634 SNPs obtained by genotyping-by-sequencing method. The results indicated that total 136 SNPs shared by both GLM and MLM models were associated with tested PUE traits under different phosphorus regimes. We have identified SNPs with highest p value (-log10(p)) for some traits like, TLA and RDW with p value (-log10(p)) of more than 6.0 at LP/OP and OP condition. We have identified nine SNPs (three for TLA and six for RDW trait) which was found to be present in chromosomes 8, 4, and 7. One SNP present in Vradi07g06230 gene contains zinc finger CCCH domain. In total, 71 protein coding genes were identified, of which 13 genes were found to be putative candidate genes controlling PUE by regulating nutrient uptake and root architectural development pathways in mungbean. Moreover, we identified three potential candidate genes VRADI11G08340, VRADI01G05520, and VRADI04G10750 with missense SNPs in coding sequence region, which results in significant variation in protein structure at tertiary level. The identified SNPs and candidate genes provide the essential information for genetic studies and marker-assisted breeding program for improving low-phosphorus tolerance in mungbean.
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Affiliation(s)
| | - Shouvik Das
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Harsh Kumar Dikshit
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Gyan Prakash Mishra
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Muraleedhar Aski
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Surendra Kumar Meena
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Division of Basic Science, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Akanksha Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Amity Institute of Organic Agriculture, Amity University, Noida, India
| | - Renu Pandey
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Madan Pal Singh
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Kuldeep Tripathi
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Padmavati Ganpat Gore
- Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Priti
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Shiv Kumar
- Biodiversity and Integrated Gene Management Program, International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
| | | | - Tilak Raj Sharma
- Division of Crop Science, Indian Council of Agricultural Research, New Delhi, India
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Yu K, Wang J, Sun C, Liu X, Xu H, Yang Y, Dong L, Zhang D. High-density QTL mapping of leaf-related traits and chlorophyll content in three soybean RIL populations. BMC PLANT BIOLOGY 2020; 20:470. [PMID: 33050902 PMCID: PMC7556954 DOI: 10.1186/s12870-020-02684-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 10/04/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Leaf size and shape, which affect light capture, and chlorophyll content are important factors affecting photosynthetic efficiency. Genetic variation of these components significantly affects yield potential and seed quality. Identification of the genetic basis for these traits and the relationship between them is of great practical significance for achieving ideal plant architecture and high photosynthetic efficiency for improved yield. RESULTS Here, we undertook a large-scale linkage mapping study using three mapping populations to determine the genetic interplay between soybean leaf-related traits and chlorophyll content across two environments. Correlation analysis revealed a significant negative correlation between leaf size and shape, while both traits were positively correlated with chlorophyll content. This phenotypic relationship was verified across the three mapping populations as determined by principal component analysis, suggesting that these traits are under the control of complex and interrelated genetic components. The QTLs for leaf-related traits and chlorophyll are partly shared, which further supports the close genetic relationship between the two traits. The largest-effect major loci, q20, was stably identified across all population and environments and harbored the narrow leaflet gene Gm-JAG1 (Ln/ln), which is a key regulator of leaflet shape in soybean. CONCLUSION Our results uncover several major QTLs (q4-1, q4-2, q11, q13, q18 and q20) and its candidate genes specific or common to leaf-related traits and chlorophyll, and also show a complex epistatic interaction between the two traits. The SNP markers closely linked to these valuable QTLs could be used for molecular design breeding with improved plant architecture, photosynthetic capacity and even yield.
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Affiliation(s)
- Kaiye Yu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Agronomy College, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Jinshe Wang
- Zhengzhou National Subcenter for Soybean Improvement, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan China
| | - Chongyuan Sun
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Agronomy College, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Xiaoqian Liu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Agronomy College, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Huanqing Xu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Agronomy College, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Yuming Yang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Agronomy College, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Lidong Dong
- School of Life Sciences, Guangzhou University, Guangzhou, 510006 Guangdong China
| | - Dan Zhang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Agronomy College, Henan Agricultural University, Zhengzhou, 450002 Henan China
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25
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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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Zhang H, Yang Y, Sun C, Liu X, Lv L, Hu Z, Yu D, Zhang D. Up-regulating GmETO1 improves phosphorus uptake and use efficiency by promoting root growth in soybean. PLANT, CELL & ENVIRONMENT 2020; 43:2080-2094. [PMID: 32515009 DOI: 10.1111/pce.13816] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 05/26/2020] [Indexed: 05/21/2023]
Abstract
Soybean is a high inorganic phosphate (Pi) demanding crop; its production is strongly suppressed when Pi is deficient in soil. However, the regulatory mechanism of Pi deficiency tolerance in soybean is still largely unclear. Here, our findings highlighted the pivotal role of the ethylene-associated pathway in soybean tolerance to Pi deficiency by comparatively studying transcriptome changes between a representative Pi-deficiency-tolerant soybean genotype NN94156 and a sensitive genotype Bogao under different Pi supplies. By further integrating high-confident linkage and association mapping, we identified that Ethylene-Overproduction Protein 1 (GmETO1), an essential ethylene-biosynthesis regulator, underlies the major quantitative trait locus (QTL) q14-2 controlling Pi uptake. GmETO1 was also the representative member of ETO1 family members that was strongly induced by Pi deficiency. Overexpressing GmETO1 significantly enhanced Pi deficiency tolerance by increasing proliferation and elongation of hairy roots, Pi uptake and use efficiency, and conversely, silencing of GmETO1 led to opposite findings. We further demonstrated that Pi-deficiency inducible genes critical for root morphological and physiological traits including GmACP1/2, Pht1;4, Expansin-A7 and Root Primordium Defective 1 functioned downstream of GmETO1. Our study provides comprehensive insight into the complex regulatory mechanism of Pi deficiency tolerance in soybean and a potential way to genetically improve soybean low-Pi tolerance.
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Affiliation(s)
- Hengyou Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- The Donald Danforth Plant Science Center, St. Louis, Missouri, USA
| | - Yuming Yang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Chongyuan Sun
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xiaoqian Liu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Lingling Lv
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Zhenbin Hu
- The Donald Danforth Plant Science Center, St. Louis, Missouri, USA
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
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Gautier AT, Cochetel N, Merlin I, Hevin C, Lauvergeat V, Vivin P, Mollier A, Ollat N, Cookson SJ. Scion genotypes exert long distance control over rootstock transcriptome responses to low phosphate in grafted grapevine. BMC PLANT BIOLOGY 2020; 20:367. [PMID: 32746781 PMCID: PMC7398338 DOI: 10.1186/s12870-020-02578-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/26/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND Grafting is widely used in horticulture and rootstocks are known to modify scion growth and adaptation to soil conditions. However, the role of scion genotype in regulating rootstock development and functioning has remained largely unexplored. In this study, reciprocal grafts of two grapevine genotypes were produced as well as the corresponding homo-graft controls. These plants were subjected to a low phosphate (LP) treatment and transcriptome profiling by RNA sequencing was done on root samples collected 27 h after the onset of the LP treatment. RESULTS A set of transcripts responsive to the LP treatment in all scion/rootstock combinations was identified. Gene expression patterns associated with genetic variation in response to LP were identified by comparing the response of the two homo-grafts. In addition, the scion was shown to modify root transcriptome responses to LP in a rootstock dependent manner. A weighted gene co-expression network analysis identified modules of correlated genes; the analysis of the association of these modules with the phosphate treatment, and the scion and rootstock genotype identified potential hub genes. CONCLUSIONS This study provides insights into the response of grafted grapevine to phosphate supply and identifies potential shoot-to-root signals that could vary between different grapevine genotypes.
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Affiliation(s)
- Antoine T Gautier
- EGFV, Bordeaux Sciences Agro, INRAE, Univ. Bordeaux, ISVV, 33882, Villenave d'Ornon, France
- Crop Production and Biostimulation Laboratory, Université Libre de Bruxelles, Campus Plaine, B-1050, Brussels, Belgium
| | - Noé Cochetel
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Isabelle Merlin
- EGFV, Bordeaux Sciences Agro, INRAE, Univ. Bordeaux, ISVV, 33882, Villenave d'Ornon, France
| | - Cyril Hevin
- EGFV, Bordeaux Sciences Agro, INRAE, Univ. Bordeaux, ISVV, 33882, Villenave d'Ornon, France
| | - Virginie Lauvergeat
- EGFV, Bordeaux Sciences Agro, INRAE, Univ. Bordeaux, ISVV, 33882, Villenave d'Ornon, France
| | - Philippe Vivin
- EGFV, Bordeaux Sciences Agro, INRAE, Univ. Bordeaux, ISVV, 33882, Villenave d'Ornon, France
| | - Alain Mollier
- ISPA, Bordeaux Sciences Agro, INRAE, 33140, Villenave d'Ornon, France
| | - Nathalie Ollat
- EGFV, Bordeaux Sciences Agro, INRAE, Univ. Bordeaux, ISVV, 33882, Villenave d'Ornon, France
| | - Sarah J Cookson
- EGFV, Bordeaux Sciences Agro, INRAE, Univ. Bordeaux, ISVV, 33882, Villenave d'Ornon, France.
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O'Rourke JA, McCabe CE, Graham MA. Dynamic gene expression changes in response to micronutrient, macronutrient, and multiple stress exposures in soybean. Funct Integr Genomics 2020; 20:321-341. [PMID: 31655948 PMCID: PMC7152590 DOI: 10.1007/s10142-019-00709-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/11/2019] [Accepted: 08/08/2019] [Indexed: 12/22/2022]
Abstract
Preserving crop yield is critical for US soybean production and the global economy. Crop species have been selected for increased yield for thousands of years with individual lines selected for improved performance in unique environments, constraints not experienced by model species such as Arabidopsis. This selection likely resulted in novel stress adaptations, unique to crop species. Given that iron deficiency is a perennial problem in the soybean growing regions of the USA and phosphate deficiency looms as a limitation to global agricultural production, nutrient stress studies in crop species are critically important. In this study, we directly compared whole-genome expression responses of leaves and roots to iron (Fe) and phosphate (Pi) deficiency, representing a micronutrient and macronutrient, respectively. Conducting experiments side by side, we observed soybean responds to both nutrient deficiencies within 24 h. While soybean responds largely to -Fe deficiency, it responds strongly to Pi resupply. Though the timing of the responses was different, both nutrient stress signals used the same molecular pathways. Our study is the first to demonstrate the speed and diversity of the soybean stress response to multiple nutrient deficiencies. We also designed the study to examine gene expression changes in response to multiple stress events. We identified 865 and 3375 genes that either altered their direction of expression after a second stress exposure or were only differentially expressed after a second stress event. Understanding the molecular underpinnings of these responses in crop species could have major implications for improving stress tolerance and preserving yield.
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Affiliation(s)
- Jamie A O'Rourke
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, 50011, USA.
- Department of Agronomy, Iowa State University, 1567 Agronomy Hall, Ames, IA, 50011, USA.
| | - Chantal E McCabe
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, 50011, USA
| | - Michelle A Graham
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, 50011, USA
- Department of Agronomy, Iowa State University, 1567 Agronomy Hall, Ames, IA, 50011, USA
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Lv L, Yu K, Lü H, Zhang X, Liu X, Sun C, Xu H, Zhang J, He X, Zhang D. Transcriptome-wide identification of novel circular RNAs in soybean in response to low-phosphorus stress. PLoS One 2020; 15:e0227243. [PMID: 31961887 PMCID: PMC6974154 DOI: 10.1371/journal.pone.0227243] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/16/2019] [Indexed: 02/07/2023] Open
Abstract
Low-phosphorus (LP) stress is a major factor limiting the growth and yield of soybean. Circular RNAs (circRNAs) are novel noncoding RNAs that play a crucial role in plant responses to abiotic stress. However, how LP stress mediates the biogenesis of circRNAs in soybean remains unclear. Here, to explore the response mechanisms of circRNAs to LP stress, the roots of two representative soybean genotypes with different P-use efficiency, Bogao (a LP-sensitive genotype) and Nannong 94156 (a LP-tolerant genotype), were used for the construction of RNA sequencing (RNA-seq) libraries and circRNA identification. In total, 371 novel circRNA candidates, including 120 significantly differentially expressed (DE) circRNAs, were identified across different P levels and genotypes. More DE circRNAs were significantly regulated by LP stress in Bogao than in NN94156, suggesting that the tolerant genotype was less affected by LP stress than the sensitive genotype was; in other words, NN94156 may have a better ability to maintain P homeostasis under LP stress. Moreover, a positive correlation was observed between the expression patterns of P stress-induced circRNAs and their circRNA-host genes. Gene Ontology (GO) enrichment analysis of these circRNA-host genes and microRNA (miRNA)-targeted genes indicated that these DE circRNAs were involved mainly in defense responses, ADP binding, nucleoside binding, organic substance catabolic processes, oxidoreductase activity, and signal transduction. Together, our results revealed that LP stress can significantly alter the genome-wide profiles of circRNAs and indicated that the regulation of circRNAs was both genotype and environment specific in response to LP stress. LP-induced circRNAs might provide a rich resource for LP-responsive circRNA candidates for future studies.
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Affiliation(s)
- Lingling Lv
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Kaiye Yu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Haiyan Lü
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xiangqian Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xiaoqian Liu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Chongyuan Sun
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Huanqing Xu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jinyu Zhang
- Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
| | - Xiaohui He
- Smart City Institute, Zhengzhou University, Zhengzhou, China
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
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Sulieman S, Kusano M, Ha CV, Watanabe Y, Abdalla MA, Abdelrahman M, Kobayashi M, Saito K, Mühling KH, Tran LSP. Divergent metabolic adjustments in nodules are indispensable for efficient N 2 fixation of soybean under phosphate stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 289:110249. [PMID: 31623782 DOI: 10.1016/j.plantsci.2019.110249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 07/18/2019] [Accepted: 08/30/2019] [Indexed: 06/10/2023]
Abstract
The main objective of the present study was to characterize the symbiotic N2 fixation (SNF) capacity and to elucidate the underlying mechanisms for low-Pi acclimation in soybean plants grown in association with two Bradyrhizobium diazoefficiens strains which differ in SNF capacity (USDA110 vs. CB1809). In comparison with the USDA110-soybean, the CB1809-soybean association revealed a greater SNF capacity in response to Pi starvation, as evidenced by relative higher plant growth and higher expression levels of the nifHDK genes. This enhanced Pi acclimation was partially related to the efficient utilization to the overall carbon (C) budget of symbiosis in the CB1809-induced nodules compared with that of the USDA110-induced nodules under low-Pi provision. In contrast, the USDA110-induced nodules favored other metabolic acclimation mechanisms that expend substantial C cost, and consequently cause negative implications on nodule C expenditure during low-Pi conditions. Fatty acids, phytosterols and secondary metabolites are characterized among the metabolic pathways involved in nodule acclimation under Pi starvation. While USDA110-soybean association performed better under Pi sufficiency, it is very likely that the CB1809-soybean association is better acclimatized to cope with Pi deficiency owing to the more effective functional plasticity and lower C cost associated with these nodular metabolic arrangements.
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Affiliation(s)
- Saad Sulieman
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan; Institute of Plant Nutrition and Soil Science, Kiel University, Hermann-Rodewald-Straße 2, 24118 Kiel, Germany; Department of Agronomy, Faculty of Agriculture, University of Khartoum, 13314 Shambat, Khartoum North, Sudan
| | - Miyako Kusano
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Chien Van Ha
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Yasuko Watanabe
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Muna Ali Abdalla
- Institute of Plant Nutrition and Soil Science, Kiel University, Hermann-Rodewald-Straße 2, 24118 Kiel, Germany; Department of Food Science and Technology, Faculty of Agriculture, University of Khartoum, 13314 Shambat, Khartoum North, Sudan
| | - Mostafa Abdelrahman
- Arid Land Research Center, Tottori University, Tottori 680-0001, Japan; Botany Department, Faculty of Science, Aswan University, Aswan 81528, Egypt
| | - Makoto Kobayashi
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Kazuki Saito
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan; Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan
| | - Karl H Mühling
- Institute of Plant Nutrition and Soil Science, Kiel University, Hermann-Rodewald-Straße 2, 24118 Kiel, Germany
| | - Lam-Son Phan Tran
- Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang, Viet Nam; Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan.
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31
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Zhang D, Zhang H, Hu Z, Chu S, Yu K, Lv L, Yang Y, Zhang X, Chen X, Kan G, Tang Y, An YQC, Yu D. Artificial selection on GmOLEO1 contributes to the increase in seed oil during soybean domestication. PLoS Genet 2019; 15:e1008267. [PMID: 31291251 PMCID: PMC6645561 DOI: 10.1371/journal.pgen.1008267] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 07/22/2019] [Accepted: 06/22/2019] [Indexed: 11/19/2022] Open
Abstract
Increasing seed oil content is one of the most important breeding goals for soybean due to a high global demand for edible vegetable oil. However, genetic improvement of seed oil content has been difficult in soybean because of the complexity of oil metabolism. Determining the major variants and molecular mechanisms conferring oil accumulation is critical for substantial oil enhancement in soybean and other oilseed crops. In this study, we evaluated the seed oil contents of 219 diverse soybean accessions across six different environments and dissected the underlying mechanism using a high-resolution genome-wide association study (GWAS). An environmentally stable quantitative trait locus (QTL), GqOil20, significantly associated with oil content was identified, accounting for 23.70% of the total phenotypic variance of seed oil across multiple environments. Haplotype and expression analyses indicate that an oleosin protein-encoding gene (GmOLEO1), colocated with a leading single nucleotide polymorphism (SNP) from the GWAS, was significantly correlated with seed oil content. GmOLEO1 is predominantly expressed during seed maturation, and GmOLEO1 is localized to accumulated oil bodies (OBs) in maturing seeds. Overexpression of GmOLEO1 significantly enriched smaller OBs and increased seed oil content by 10.6% compared with those of control seeds. A time-course transcriptomics analysis between transgenic and control soybeans indicated that GmOLEO1 positively enhanced oil accumulation by affecting triacylglycerol metabolism. Our results also showed that strong artificial selection had occurred in the promoter region of GmOLEO1, which resulted in its high expression in cultivated soybean relative to wild soybean, leading to increased seed oil accumulation. The GmOLEO1 locus may serve as a direct target for both genetic engineering and selection for soybean oil improvement.
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Affiliation(s)
- Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Hengyou Zhang
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Zhenbin Hu
- Department of Agronomy, Kansas State University, Manhattan, Kansas, United States of America
| | - Shanshan Chu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Kaiye Yu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Lingling Lv
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Yuming Yang
- 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, China
| | - Xiangqian Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xi Chen
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Guizhen Kan
- 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, China
| | - Yang Tang
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Yong-Qiang Charles An
- USDA-ARS, Plant Genetics Research Unit at Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - 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, China
- School of Life Sciences, Guangzhou University, Guangzhou, China
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32
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Li Q, Shen Y, Guo L, Wang H, Zhang Y, Fan C, Zheng Y. The EIL transcription factor family in soybean: Genome-wide identification, expression profiling and genetic diversity analysis. FEBS Open Bio 2019; 9:629-642. [PMID: 30984538 PMCID: PMC6443860 DOI: 10.1002/2211-5463.12596] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 12/28/2018] [Accepted: 01/14/2019] [Indexed: 11/15/2022] Open
Abstract
The ETHYLENE INSENSITIVE3-LIKE (EIL) transcription factor family plays a critical role in the ethylene signaling pathway, which regulates a broad spectrum of plant growth and developmental processes, as well as defenses to myriad stresses. Although genome-wide analysis of this family has been carried out for several plant species, no comprehensive analysis of the EIL gene family in soybean has been reported so far. Furthermore, there are few studies on the functions of EIL genes in soybean. In this study, we identified 12 soybean (Gm) EIL genes, which we divided into three groups based on their phylogenetic relationships. We then detected their duplication status and found that most of the GmEIL genes have duplicated copies derived from two whole-genome duplication events. These duplicated genes underwent strong negative selection during evolution. We further analyzed the transcript profiles of GmEIL genes using the transcriptome data and found that their spatio-temporal and stress expression patterns varied considerably. For example, GmEIL1-GmEIL5 were found to be strongly expressed in almost every sample, while GmEIL8-GmEIL12 exhibited low expression, or were not expressed at all. Additionally, these genes showed different responses to dehydration, salinity and phosphate starvation. Finally, we surveyed genetic variations of these genes in 302 resequenced wild soybeans, landraces and improved soybean cultivars. Our data showed that most GmEIL genes are well conserved, and are not modified in domesticated or improved cultivars. Together, these findings provide a potentially valuable resource for characterizing the GmEIL gene family and lay the basis for further elucidation of their molecular mechanisms.
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Affiliation(s)
- Qing Li
- College of Life Sciences and OceanographyShenzhen UniversityChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong ProvinceCollege of Optoelectronic EngineeringShenzhen UniversityChina
| | - Yanting Shen
- Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Luqin Guo
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
| | - Hong Wang
- College of Life Sciences and OceanographyShenzhen UniversityChina
| | - Yu Zhang
- College of Life Sciences and OceanographyShenzhen UniversityChina
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
| | - Chengming Fan
- Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Yihong Zheng
- College of Life Sciences and OceanographyShenzhen UniversityChina
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Broekgaarden C, Pelgrom KTB, Bucher J, van Dam NM, Grosser K, Pieterse CMJ, van Kaauwen M, Steenhuis G, Voorrips RE, de Vos M, Vosman B, Worrich A, van Wees SCM. Combining QTL mapping with transcriptome and metabolome profiling reveals a possible role for ABA signaling in resistance against the cabbage whitefly in cabbage. PLoS One 2018; 13:e0206103. [PMID: 30399182 PMCID: PMC6219772 DOI: 10.1371/journal.pone.0206103] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/05/2018] [Indexed: 11/18/2022] Open
Abstract
Whiteflies are among the world's most significant agricultural pests and chemical insecticides are extensively used to reduce crop damage to acceptable levels. However, nearly all insecticides pose a threat to the environment and alternative control methods, such as breeding of crop varieties that are inherently insect-resistant, are needed. Previously, a strong source of plant-age dependent resistance to the cabbage whitefly (Aleyrodes proletella) has been identified in the modern white cabbage (Brassica oleracea var. capitata) variety Rivera. However, nothing is known about the molecular mechanisms or the genes involved in this resistance. In the present study, a multidisciplinary approach combining transcriptome and metabolome profiling with genetic mapping was used to identify the molecular players of whitefly resistance in cabbage. Transcriptome profiles of young (susceptible) and older (resistant) Rivera plants were analyzed using RNA sequencing. While many genes involved in general processes were differentially expressed between both ages, several defense-related processes were overrepresented in the transcriptome profile of older plants. Hormone measurements revealed that jasmonic acid (JA) levels decreased upon whitefly infestation at both plant ages. Interestingly, abscisic acid (ABA) levels showed contrasting effects in response to whitefly infestation: ABA levels were reduced in young plants but induced in older plants upon whitefly feeding. Auxin levels were significantly lower in older plants compared with young plants, independent of whitefly presence, while glucosinolate levels were higher. Additionally, whitefly performance was monitored in an F2 population derived from a cross between Rivera and the susceptible white cabbage variety Christmas Drumhead. Significant QTL intervals were mapped on chromosome 2 and 9 for oviposition rate and whitefly adult survival, respectively. Several genes that were higher expressed in older plants and located in the identified QTL intervals were orthologous to Arabidopsis genes that have been related to ABA signaling, suggesting a role for ABA in the regulation of resistance towards whiteflies. Our results show that combining different omics approaches is a useful strategy to identify candidate genes underlying insect resistance.
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Affiliation(s)
- Colette Broekgaarden
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, the Netherlands
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands
- Keygene N.V., Wageningen, the Netherlands
| | - Koen T. B. Pelgrom
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Johan Bucher
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Nicole M. van Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Friedrich Schiller University Jena, Institute of Biodiversity, Jena, Germany
| | - Katharine Grosser
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Friedrich Schiller University Jena, Institute of Biodiversity, Jena, Germany
| | - Corné M. J. Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, the Netherlands
| | - Martijn van Kaauwen
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Greet Steenhuis
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Roeland E. Voorrips
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands
| | | | - Ben Vosman
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Anja Worrich
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Friedrich Schiller University Jena, Institute of Biodiversity, Jena, Germany
| | - Saskia C. M. van Wees
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, the Netherlands
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Cai Z, Cheng Y, Xian P, Ma Q, Wen K, Xia Q, Zhang G, Nian H. Acid phosphatase gene GmHAD1 linked to low phosphorus tolerance in soybean, through fine mapping. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1715-1728. [PMID: 29754326 DOI: 10.1007/s00122-018-3109-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 05/07/2018] [Indexed: 05/06/2023]
Abstract
KEY MESSAGE Map-based cloning identified GmHAD1, a gene which encodes a HAD-like acid phosphatase, associated with soybean tolerance to low phosphorus stress. Phosphorus (P) deficiency in soils is a major limiting factor for crop growth worldwide. Plants may adapt to low phosphorus (LP) conditions via changes to root morphology, including the number, length, orientation, and branching of the principal root classes. To elucidate the genetic mechanisms for LP tolerance in soybean, quantitative trait loci (QTL) related to root morphology responses to LP were identified via hydroponic experiments. In total, we identified 14 major loci associated with these traits in a RIL population. The log-likelihood scores ranged from 2.81 to 7.43, explaining 4.23-13.98% of phenotypic variance. A major locus on chromosome 08, named qP8-2, was co-localized with an important P efficiency QTL (qPE8), containing phosphatase genes GmACP1 and GmACP2. Another major locus on chromosome 10 named qP10-2 explained 4.80-13.98% of the total phenotypic variance in root morphology. The qP10-2 contains GmHAD1, a gene which encodes an acid phosphatase. In the transgenic soybean hairy roots, GmHAD1 overexpression increased P efficiency by 8.4-16.5% relative to the control. Transgenic Arabidopsis plants had higher biomass than wild-type plants across both short- and long-term P reduction. These results suggest that GmHAD1, an acid phosphatase gene, improved the utilization of organic phosphate by soybean and Arabidopsis plants.
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Affiliation(s)
- Zhandong Cai
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Yanbo Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Peiqi Xian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Qibin Ma
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Ke Wen
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Qiuju Xia
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518086, People's Republic of China
| | - Gengyun Zhang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518086, People's Republic of China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
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Zeng H, Zhang X, Zhang X, Pi E, Xiao L, Zhu Y. Early Transcriptomic Response to Phosphate Deprivation in Soybean Leaves as Revealed by RNA-Sequencing. Int J Mol Sci 2018; 19:E2145. [PMID: 30041471 PMCID: PMC6073939 DOI: 10.3390/ijms19072145] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/17/2018] [Accepted: 07/17/2018] [Indexed: 01/15/2023] Open
Abstract
Low phosphate (Pi) availability is an important limiting factor affecting soybean production. However, the underlying molecular mechanisms responsible for low Pi stress response and tolerance remain largely unknown, especially for the early signaling events under low Pi stress. Here, a genome-wide transcriptomic analysis in soybean leaves treated with a short-term Pi-deprivation (24 h) was performed through high-throughput RNA sequencing (RNA-seq) technology. A total of 533 loci were found to be differentially expressed in response to Pi deprivation, including 36 mis-annotated loci and 32 novel loci. Among the differentially expressed genes (DEGs), 303 were induced and 230 were repressed by Pi deprivation. To validate the reliability of the RNA-seq data, 18 DEGs were randomly selected and analyzed by quantitative RT-PCR (reverse transcription polymerase chain reaction), which exhibited similar fold changes with RNA-seq. Enrichment analyses showed that 29 GO (Gene Ontology) terms and 8 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were significantly enriched in the up-regulated DEGs and 25 GO terms and 16 KEGG pathways were significantly enriched in the down-regulated DEGs. Some DEGs potentially involved in Pi sensing and signaling were up-regulated by short-term Pi deprivation, including five SPX-containing genes. Some DEGs possibly associated with water and nutrient uptake, hormonal and calcium signaling, protein phosphorylation and dephosphorylation and cell wall modification were affected at the early stage of Pi deprivation. The cis-elements of PHO (phosphatase) element, PHO-like element and P responsive element were present more frequently in promoter regions of up-regulated DEGs compared to that of randomly-selected genes in the soybean genome. Our transcriptomic data showed an intricate network containing transporters, transcription factors, kinases and phosphatases, hormone and calcium signaling components is involved in plant responses to early Pi deprivation.
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Affiliation(s)
- Houqing Zeng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
| | - Xiajun Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
| | - Xin Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
| | - Erxu Pi
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
| | - Liang Xiao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yiyong Zhu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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Chu S, Li H, Zhang X, Yu K, Chao M, Han S, Zhang D. Physiological and Proteomics Analyses Reveal Low-Phosphorus Stress Affected the Regulation of Photosynthesis in Soybean. Int J Mol Sci 2018; 19:E1688. [PMID: 29882786 PMCID: PMC6032344 DOI: 10.3390/ijms19061688] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/01/2018] [Accepted: 06/04/2018] [Indexed: 12/22/2022] Open
Abstract
Previous studies have revealed a significant genetic relationship between phosphorus (P)-efficiency and photosynthesis-related traits in soybean. In this study, we used proteome profiling in combination with expression analysis, biochemical investigations, and leaf ultrastructural analysis to identify the underlying physiological and molecular responses. The expression analysis and ultrastructural analysis showed that the photosynthesis key genes were decreased at transcript levels and the leaf mesophyll and chloroplast were severely damaged after low-P stress. Approximately 55 protein spots showed changes under low-P condition by mass spectrometry, of which 17 were involved in various photosynthetic processes. Further analysis revealed the depression of photosynthesis caused by low-P stress mainly involves the regulation of leaf structure, adenosine triphosphate (ATP) synthesis, absorption and transportation of CO₂, photosynthetic electron transport, production of assimilatory power, and levels of enzymes related to the Calvin cycle. In summary, our findings indicated that the existence of a stringent relationship between P supply and the genomic control of photosynthesis in soybean. As an important strategy to protect soybean photosynthesis, P could maintain the stability of cell structure, up-regulate the enzymes’ activities, recover the process of photosystem II (PSII), and induce the expression of low-P responsive genes and proteins.
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Affiliation(s)
- Shanshan Chu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.
| | - Hongyan Li
- 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.
| | - Kaiye Yu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.
| | - Maoni Chao
- Henan Institute of Science and Technology, Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang 453003, China.
| | - Suoyi Han
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences, 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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de Abreu E Lima F, Li K, Wen W, Yan J, Nikoloski Z, Willmitzer L, Brotman Y. Unraveling lipid metabolism in maize with time-resolved multi-omics data. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:1102-1115. [PMID: 29385634 DOI: 10.1111/tpj.13833] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 01/03/2018] [Accepted: 01/04/2018] [Indexed: 05/19/2023]
Abstract
Maize is the cereal crop with the highest production worldwide, and its oil is a key energy resource. Improving the quantity and quality of maize oil requires a better understanding of lipid metabolism. To predict the function of maize genes involved in lipid biosynthesis, we assembled transcriptomic and lipidomic data sets from leaves of B73 and the high-oil line By804 in two distinct time-series experiments. The integrative analysis based on high-dimensional regularized regression yielded lipid-transcript associations indirectly validated by Gene Ontology and promoter motif enrichment analyses. The co-localization of lipid-transcript associations using the genetic mapping of lipid traits in leaves and seedlings of a B73 × By804 recombinant inbred line population uncovered 323 genes involved in the metabolism of phospholipids, galactolipids, sulfolipids and glycerolipids. The resulting association network further supported the involvement of 50 gene candidates in modulating levels of representatives from multiple acyl-lipid classes. Therefore, the proposed approach provides high-confidence candidates for experimental testing in maize and model plant species.
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Affiliation(s)
| | - Kun Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
| | - Weiwei Wen
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
| | - Zoran Nikoloski
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam, Germany
| | - Lothar Willmitzer
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Yariv Brotman
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel
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38
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Transcriptome Dataset of Soybean (Glycine max) Grown under Phosphorus-Deficient and -Sufficient Conditions. DATA 2017. [DOI: 10.3390/data2020017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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