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Lin S, Zhang W, Wang G, Hu Y, Zhong X, Tang G. Physiological Regulation of Photosynthetic-Related Indices, Antioxidant Defense, and Proline Anabolism on Drought Tolerance of Wild Soybean ( Glycine soja L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:880. [PMID: 38592877 PMCID: PMC10975085 DOI: 10.3390/plants13060880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/13/2024] [Accepted: 03/13/2024] [Indexed: 04/11/2024]
Abstract
Wild soybean (Glycine soja L.), drought-tolerant cultivar Tiefeng 31 (Glycine max L.), and drought-sensitive cultivar Fendou 93 (Glycine max L.) were used as materials to investigate the drought tolerance mechanism after 72 h 2.5 M PEG 8000 (osmotic potential -0.54 MPa)-simulated drought stress at the seedling stage. The results indicated that the leaves of the G. soja did not wilt under drought stress. However, both the drought-tolerant and drought-sensitive cultivated soybean cultivars experienced varying degrees of leaf wilt. Notably, the drought-sensitive cultivated soybean cultivars exhibited severe leaf wilt after the drought stress. Drought stress was determined to have a significant impact on the dry matter of the above-ground part of the drought-sensitive cultivar Fendou 93, followed by the drought-tolerant cultivar Tiefeng 31, with the lowest reduction observed in G. soja. Furthermore, the presence of drought stress resulted in the closure of leaf stomata. G. soja exhibited the highest proportion of stomatal opening per unit area, followed by the drought-tolerant cultivar Tiefeng 31, while the drought-sensitive cultivar Fendou 93 displayed the lowest percentage. Photosynthesis-related indexes, including photosynthetic rate, intercellular CO2, transpiration rate, and stomatal conductance, decreased in Fendou 93 and Tiefeng 31 after drought stress, but increased in G. soja. In terms of the antioxidant scavenging system, lower accumulation of malondialdehyde (MDA) was observed in G. soja and Tiefeng 31, along with higher activities of superoxide dismutase (SOD, EC 1.15.1.1) and catalase (CAT, EC 1.11.1.6) to counteract excess reactive oxygen species and maintain cell membrane integrity. In contrast, the drought-sensitive cultivar Fendou 93 had higher MDA content and higher activities of ascorbate peroxidase (APX, EC 1.11.1.11) and peroxidase (POD, 1.11.1.7). G. soja and Tiefeng 31 also exhibited less accumulation of osmolytes, including soluble sugar, soluble protein, and free proline content. The activities of δ-OAT, ProDH, and P5CS, key enzymes in proline anabolism, showed an initial increase under drought stress, followed by a decrease, and then an increase again at the end of drought stress in G. soja. Before drought stress, Tiefeng 31 had higher activities of ProDH and P5CS, which decreased with prolonged drought stress. Fendou 93 experienced an increase in the activities of δ-OAT, ProDH, and P5CS under drought stress. The δ-OAT gene expression levels were up-regulated in all three germplasms. The expression levels of the P5CS gene in Fendou 93 and Tiefeng 31 were down-regulated, while G. soja showed no significant change. The expression of the P5CR gene and ProDH gene was down-regulated in Fendou 93 and Tiefeng 31, but up-regulated in G. soja. This indicates that proline content is regulated at both the transcription and translation levels.
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Affiliation(s)
- Song Lin
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Zhejiang University, Hangzhou 310058, China; (S.L.); (Y.H.); (X.Z.)
| | - Weimei Zhang
- Lishui Institute of Agriculture and Forest Science, Lishui 323000, China;
| | - Guifeng Wang
- Bureau of Agriculture and Rural Affairs of Lianyungang City, Lianyungang 222001, China;
| | - Yunxiang Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Zhejiang University, Hangzhou 310058, China; (S.L.); (Y.H.); (X.Z.)
| | - Xuanbo Zhong
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Zhejiang University, Hangzhou 310058, China; (S.L.); (Y.H.); (X.Z.)
| | - Guixiang Tang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Zhejiang University, Hangzhou 310058, China; (S.L.); (Y.H.); (X.Z.)
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Yu B, Chao DY, Zhao Y. How plants sense and respond to osmotic stress. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:394-423. [PMID: 38329193 DOI: 10.1111/jipb.13622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/09/2024]
Abstract
Drought is one of the most serious abiotic stresses to land plants. Plants sense and respond to drought stress to survive under water deficiency. Scientists have studied how plants sense drought stress, or osmotic stress caused by drought, ever since Charles Darwin, and gradually obtained clues about osmotic stress sensing and signaling in plants. Osmotic stress is a physical stimulus that triggers many physiological changes at the cellular level, including changes in turgor, cell wall stiffness and integrity, membrane tension, and cell fluid volume, and plants may sense some of these stimuli and trigger downstream responses. In this review, we emphasized water potential and movements in organisms, compared putative signal inputs in cell wall-containing and cell wall-free organisms, prospected how plants sense changes in turgor, membrane tension, and cell fluid volume under osmotic stress according to advances in plants, animals, yeasts, and bacteria, summarized multilevel biochemical and physiological signal outputs, such as plasma membrane nanodomain formation, membrane water permeability, root hydrotropism, root halotropism, Casparian strip and suberin lamellae, and finally proposed a hypothesis that osmotic stress responses are likely to be a cocktail of signaling mediated by multiple osmosensors. We also discussed the core scientific questions, provided perspective about the future directions in this field, and highlighted the importance of robust and smart root systems and efficient source-sink allocations for generating future high-yield stress-resistant crops and plants.
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Affiliation(s)
- Bo Yu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, The Chinese Academy of Sciences, Shanghai, 200032, China
- Key Laboratory of Plant Carbon Capture, The Chinese Academy of Sciences, Shanghai, 200032, China
| | - Dai-Yin Chao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, The Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Zhao
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, The Chinese Academy of Sciences, Shanghai, 200032, China
- Key Laboratory of Plant Carbon Capture, The Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Kiryushkin AS, Ilina EL, Kiikova TY, Pawlowski K, Demchenko KN. Do DEEPER ROOTING 1 Homologs Regulate the Lateral Root Slope Angle in Cucumber ( Cucumis sativus)? Int J Mol Sci 2024; 25:1975. [PMID: 38396652 PMCID: PMC10888659 DOI: 10.3390/ijms25041975] [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: 12/12/2023] [Revised: 01/28/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
The architecture of the root system is fundamental to plant productivity. The rate of root growth, the density of lateral roots, and the spatial structure of lateral and adventitious roots determine the developmental plasticity of the root system in response to changes in environmental conditions. One of the genes involved in the regulation of the slope angle of lateral roots is DEEPER ROOTING 1 (DRO1). Its orthologs and paralogs have been identified in rice, Arabidopsis, and several other species. However, nothing is known about the formation of the slope angle of lateral roots in species with the initiation of lateral root primordia within the parental root meristem. To address this knowledge gap, we identified orthologs and paralogs of the DRO1 gene in cucumber (Cucumis sativus) using a phylogenetic analysis of IGT protein family members. Differences in the transcriptional response of CsDRO1, CsDRO1-LIKE1 (CsDRO1L1), and CsDRO1-LIKE2 (CsDRO1L2) to exogenous auxin were analyzed. The results showed that only CsDRO1L1 is auxin-responsive. An analysis of promoter-reporter fusions demonstrated that the CsDRO1, CsDRO1L1, and CsDRO1L2 genes were expressed in the meristem in cell files of the central cylinder, endodermis, and cortex; the three genes displayed different expression patterns in cucumber roots with only partial overlap. A knockout of individual CsDRO1, CsDRO1L1, and CsDRO1L2 genes was performed via CRISPR/Cas9 gene editing. Our study suggests that the knockout of individual genes does not affect the slope angle formation during lateral root primordia development in the cucumber parental root.
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Affiliation(s)
- Alexey S. Kiryushkin
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia; (A.S.K.); (E.L.I.)
| | - Elena L. Ilina
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia; (A.S.K.); (E.L.I.)
| | - Tatyana Y. Kiikova
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia; (A.S.K.); (E.L.I.)
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden
| | - Kirill N. Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia; (A.S.K.); (E.L.I.)
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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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5
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Wang W, Liu H, Xie Y, King GJ, White PJ, Zou J, Xu F, Shi L. Rapid identification of a major locus qPRL-C06 affecting primary root length in Brassica napus by QTL-seq. ANNALS OF BOTANY 2023; 131:569-583. [PMID: 36181516 PMCID: PMC10147330 DOI: 10.1093/aob/mcac123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 09/30/2022] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Brassica napus is one of the most important oilseed crops worldwide. Seed yield of B. napus significantly correlates with the primary root length (PRL). The aims of this study were to identify quantitative trait loci (QTLs) for PRL in B. napus. METHODS QTL-seq and conventional QTL mapping were jointly used to detect QTLs associated with PRL in a B. napus double haploid (DH) population derived from a cross between 'Tapidor' and 'Ningyou 7'. The identified major locus was confirmed and resolved by an association panel of B. napus and an advanced backcross population. RNA-seq analysis of two long-PRL lines (Tapidor and TN20) and two short-PRL lines (Ningyou 7 and TN77) was performed to identify differentially expressed genes in the primary root underlying the target QTLs. KEY RESULTS A total of 20 QTLs impacting PRL in B. napus grown at a low phosphorus (P) supply were found by QTL-seq. Eight out of ten QTLs affecting PRL at a low P supply discovered by conventional QTL mapping could be detected by QTL-seq. The locus qPRL-C06 identified by QTL-seq was repeatedly detected at both an optimal P supply and a low P supply by conventional QTL mapping. This major constitutive QTL was further confirmed by regional association mapping. qPRL-C06 was delimited to a 0.77 Mb genomic region on chromosome C06 using an advanced backcross population. A total of 36 candidate genes within qPRL-C06 were identified that showed variations in coding sequences and/or exhibited significant differences in mRNA abundances in primary root between the long-PRL and short-PRL lines, including five genes involved in phytohormone biosynthesis and signaling. CONCLUSIONS These results both demonstrate the power of the QTL-seq in rapid QTL detection for root traits and will contribute to marker-assisted selective breeding of B. napus cultivars with increased PRL.
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Affiliation(s)
- Wei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Haijiang Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiwen Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Graham John King
- Southern Cross Plant Science, Southern Cross University, Lismore NSW 2480, Australia
| | - Philip John White
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
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Karnatam KS, Chhabra G, Saini DK, Singh R, Kaur G, Praba UP, Kumar P, Goyal S, Sharma P, Ranjan R, Sandhu SK, Kumar R, Vikal Y. Genome-Wide Meta-Analysis of QTLs Associated with Root Traits and Implications for Maize Breeding. Int J Mol Sci 2023; 24:ijms24076135. [PMID: 37047112 PMCID: PMC10093813 DOI: 10.3390/ijms24076135] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 04/14/2023] Open
Abstract
Root system architecture (RSA), also known as root morphology, is critical in plant acquisition of soil resources, plant growth, and yield formation. Many QTLs associated with RSA or root traits in maize have been identified using several bi-parental populations, particularly in response to various environmental factors. In the present study, a meta-analysis of QTLs associated with root traits was performed in maize using 917 QTLs retrieved from 43 mapping studies published from 1998 to 2020. A total of 631 QTLs were projected onto a consensus map involving 19,714 markers, which led to the prediction of 68 meta-QTLs (MQTLs). Among these 68 MQTLs, 36 MQTLs were validated with the marker-trait associations available from previous genome-wide association studies for root traits. The use of comparative genomics approaches revealed several gene models conserved among the maize, sorghum, and rice genomes. Among the conserved genomic regions, the ortho-MQTL analysis uncovered 20 maize MQTLs syntenic to 27 rice MQTLs for root traits. Functional analysis of some high-confidence MQTL regions revealed 442 gene models, which were then subjected to in silico expression analysis, yielding 235 gene models with significant expression in various tissues. Furthermore, 16 known genes viz., DXS2, PHT, RTP1, TUA4, YUC3, YUC6, RTCS1, NSA1, EIN2, NHX1, CPPS4, BIGE1, RCP1, SKUS13, YUC5, and AW330564 associated with various root traits were present within or near the MQTL regions. These results could aid in QTL cloning and pyramiding in developing new maize varieties with specific root architecture for proper plant growth and development under optimum and abiotic stress conditions.
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Affiliation(s)
- Krishna Sai Karnatam
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141001, India
| | - Gautam Chhabra
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141001, India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana 141001, India
| | - Rajveer Singh
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141001, India
| | - Gurwinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141001, India
| | - Umesh Preethi Praba
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141001, India
| | - Pankaj Kumar
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141001, India
| | - Simran Goyal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141001, India
| | - Priti Sharma
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141001, India
| | - Rumesh Ranjan
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana 141001, India
| | - Surinder K Sandhu
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana 141001, India
| | - Ramesh Kumar
- Indian Institute of Maize Research, Ludhiana 141001, India
| | - Yogesh Vikal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141001, India
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7
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Alahakoon D, Fennell A. Genetic analysis of grapevine root system architecture and loci associated gene networks. FRONTIERS IN PLANT SCIENCE 2023; 13:1083374. [PMID: 36816477 PMCID: PMC9932984 DOI: 10.3389/fpls.2022.1083374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/29/2022] [Indexed: 06/18/2023]
Abstract
Own-rooted grapevines and grapevine rootstocks are vegetatively propagated from cuttings and have an adventitious root system. Unraveling the genetic underpinnings of the adventitious root system architecture (RSA) is important for improving own-rooted and grafted grapevine sustainability for a changing climate. Grapevine RSA genetic analysis was conducted in an Vitis sp. 'VRS-F2' population. Nine root morphology, three total root system morphology, and two biomass traits that contribute to root anchorage and water and nutrient uptake were phenotyped. Quantitative trait loci (QTL) analysis was performed using a high density integrated GBS and rhAmpSeq genetic map. Thirty-one QTL were detected for eleven of the RSA traits (surface area, root volume, total root length, fresh weight, number of tips, forks or links, longest root and average root diameter, link length, and link surface area) revealing many small effects. Several QTL were colocated on chromosomes 1, 9, 13, 18, and 19. QTL with identical peak positions on chromosomes 1 or 13 were enriched for AP2-EREBP, AS2, C2C2-CO, HMG, and MYB transcription factors, and QTL on chromosomes 9 or 13 were enriched for the ALFIN-LIKE transcription factor and regulation of autophagy pathways. QTL modeling for individual root traits identified eight models explaining 13.2 to 31.8% of the phenotypic variation. 'Seyval blanc' was the grandparent contributing to the allele models that included a greater surface area, total root length, and branching (number of forks and links) traits promoting a greater root density. In contrast, V. riparia 'Manitoba 37' contributed the allele for greater average branch length (link length) and diameter, promoting a less dense elongated root system with thicker roots. LATERAL ORGAN BOUNDARY DOMAIN (LBD or AS2/LOB) and the PROTODERMAL FACTOR (PFD2 and ANL2) were identified as important candidate genes in the enriched pathways underlying the hotspots for grapevine adventitious RSA. The combined QTL hotspot and trait modeling identified transcription factors, cell cycle and circadian rhythm genes with a known role in root cell and epidermal layer differentiation, lateral root development and cortex thickness. These genes are candidates for tailoring grapevine root system texture, density and length in breeding programs.
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Affiliation(s)
| | - Anne Fennell
- Agronomy, Horticulture, and Plant Science Department, South Dakota State University, Brookings, SD, United States
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8
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Moraga C, Sanchez E, Ferrarini MG, Gutierrez RA, Vidal EA, Sagot MF. BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data. Gigascience 2022; 11:6773084. [PMID: 36283679 PMCID: PMC9596168 DOI: 10.1093/gigascience/giac093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/08/2021] [Accepted: 09/15/2022] [Indexed: 11/04/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that are key players in the regulation of gene expression. In the past decade, with the increasing accessibility of high-throughput sequencing technologies, different methods have been developed to identify miRNAs, most of which rely on preexisting reference genomes. However, when a reference genome is absent or is not of high quality, such identification becomes more difficult. In this context, we developed BrumiR, an algorithm that is able to discover miRNAs directly and exclusively from small RNA (sRNA) sequencing (sRNA-seq) data. We benchmarked BrumiR with datasets encompassing animal and plant species using real and simulated sRNA-seq experiments. The results demonstrate that BrumiR reaches the highest recall for miRNA discovery, while at the same time being much faster and more efficient than the state-of-the-art tools evaluated. The latter allows BrumiR to analyze a large number of sRNA-seq experiments, from plants or animal species. Moreover, BrumiR detects additional information regarding other expressed sequences (sRNAs, isomiRs, etc.), thus maximizing the biological insight gained from sRNA-seq experiments. Additionally, when a reference genome is available, BrumiR provides a new mapping tool (BrumiR2reference) that performs an a posteriori exhaustive search to identify the precursor sequences. Finally, we also provide a machine learning classifier based on a random forest model that evaluates the sequence-derived features to further refine the prediction obtained from the BrumiR-core. The code of BrumiR and all the algorithms that compose the BrumiR toolkit are freely available at https://github.com/camoragaq/BrumiR.
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Affiliation(s)
| | - Evelyn Sanchez
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingenieria y Tecnologia, Universidad Mayor, 8580745 Santiago, Chile,Agencia Nacional de Investigación y Desarrollo–Millennium Science Initiative Program, Millennium Institute for Integrative Biology iBio, 7500565 Santiago, Chile
| | - Mariana Galvão Ferrarini
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France,Inria Lyon Centre, ERABLE team, 56 Bd Niels Bohr, 69100 Villeurbanne, France,Université de Lyon, INSA-Lyon, INRA, BF2i, UMR0203, Villeurbanne F-69621, France
| | - Rodrigo A Gutierrez
- Agencia Nacional de Investigación y Desarrollo–Millennium Science Initiative Program, Millennium Institute for Integrative Biology iBio, 7500565 Santiago, Chile,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile , 8331010 Santiago, Chile,Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation, Instituto de Ecología y Biodiversidad, 8370415 Santiago, Chile
| | - Elena A Vidal
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingenieria y Tecnologia, Universidad Mayor, 8580745 Santiago, Chile,Agencia Nacional de Investigación y Desarrollo–Millennium Science Initiative Program, Millennium Institute for Integrative Biology iBio, 7500565 Santiago, Chile,Escuela de Biotecnología, Facultad de Ciencias, Ingenieria y Tecnologia, Universidad Mayor, 8580745 Santiago, Chile
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9
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Mahmoud A, Qi R, Zhao H, Yang H, Liao N, Ali A, Malangisha GK, Ma Y, Zhang K, Zhou Y, Xia Y, Lyu X, Yang J, Zhang M, Hu Z. An allelic variant in the ACS7 gene promotes primary root growth in watermelon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3357-3373. [PMID: 35980402 DOI: 10.1007/s00122-022-04173-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Gene mining in a C. lanatus × C. amarus population revealed one gene, ACS7, linked to primary root elongation in watermelon. Watermelon is a xerophytic crop characterized by a long primary root and robust lateral roots. Therefore, watermelon serves as an excellent model for studying root elongation and development. However, the genetic mechanism underlying the primary root elongation in watermelon remains unknown. Herein, through bulk segregant analysis we identified a genetic locus, qPRL.Chr03, controlling primary root length (PRL) using two different watermelon species (Citrullus lanatus and Citrullus amarus) that differ in their root architecture. Fine mapping revealed that xaa-Pro dipeptidase and 1-aminocyclopropane-1-carboxylate synthase 7 (ACS7) are candidate regulators of the primary root growth. Allelic variation in the delimited region among 193 watermelon accessions indicated that the long-root alleles might only exist in C. amarus. Interestingly, the discrepancy in PRL among the C. amarus accessions was clearly associated with a nonsynonymous single nucleotide polymorphism variant within the ACS7 gene. The ACS7 expression and ethylene levels in the primary root tips suggested that ethylene is a negative regulator of root elongation in watermelon, as supported by the application of 1-aminocyclopropane-1-carboxylate (ACC, the ethylene precursor) or 2-aminoethoxyvinyl glycine (AVG, an ACS inhibitor). To the best of our knowledge, these findings provide the first description of the genetic basis of root elongation in watermelon. The detected markers of the ACS7 gene will facilitate marker-assisted selection for the PRL trait to improve water and nutrient use efficacy in watermelon and beyond.
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Affiliation(s)
- Ahmed Mahmoud
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- Agriculture Research Center, Horticulture Research Institute, 9 Gmaa St, Giza, 12619, Egypt
| | - Rui Qi
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China
| | - Haoshun Zhao
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Haiyang Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Nanqiao Liao
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Abid Ali
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Guy Kateta Malangisha
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Yuyuan Ma
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Kejia Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Yimei Zhou
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Yuelin Xia
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Xiaolong Lyu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China.
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China.
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China.
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China.
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10
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Liu W, Chen T, Liu Y, Le QT, Wang R, Lee H, Xiong L. The Plastidial DIG5 Protein Affects Lateral Root Development by Regulating Flavonoid Biosynthesis and Auxin Transport in Arabidopsis. Int J Mol Sci 2022; 23:ijms231810642. [PMID: 36142550 PMCID: PMC9501241 DOI: 10.3390/ijms231810642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/08/2022] [Accepted: 09/11/2022] [Indexed: 11/16/2022] Open
Abstract
To reveal the mechanisms underlying root adaptation to drought stress, we isolated and characterized an Arabidopsis mutant, dig5 (drought inhibition of lateral root growth 5), which exhibited increased sensitivity to the phytohormone abscisic acid (ABA) for the inhibition of lateral root growth. The dig5 mutant also had fewer lateral roots under normal conditions and the aerial parts were yellowish with a lower level of chlorophylls. The mutant seedlings also displayed phenotypes indicative of impaired auxin transport, such as abnormal root curling, leaf venation defects, absence of apical hook formation, and reduced hypocotyl elongation in darkness. Auxin transport assays with [3H]-labeled indole acetic acid (IAA) confirmed that dig5 roots were impaired in polar auxin transport. Map-based cloning and complementation assays indicated that the DIG5 locus encodes a chloroplast-localized tRNA adenosine deaminase arginine (TADA) that is involved in chloroplast protein translation. The levels of flavonoids, which are naturally occurring auxin transport inhibitors in plants, were significantly higher in dig5 roots than in the wild type roots. Further investigation showed that flavonoid biosynthetic genes were upregulated in dig5. Introduction of the flavonoid biosynthetic mutation transparent testa 4 (tt4) into dig5 restored the lateral root growth of dig5. Our study uncovers an important role of DIG5/TADA in retrogradely controlling flavonoid biosynthesis and lateral root development. We suggest that the DIG5-related signaling pathways, triggered likely by drought-induced chlorophyll breakdown and leaf senescence, may potentially help the plants to adapt to drought stress through optimizing the root system architecture.
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Affiliation(s)
- Wei Liu
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- High-Tech Research Center, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Tao Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Yajie Liu
- Department of Biology, Hong Kong Baptist University, Kowloon Tang, Hong Kong, China
| | - Quang Tri Le
- Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 136-713, Korea
| | - Ruigang Wang
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot 010010, China
| | - Hojoung Lee
- Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 136-713, Korea
| | - Liming Xiong
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Department of Biology, Hong Kong Baptist University, Kowloon Tang, Hong Kong, China
- State Key Laboratory for Agribiotechnology, Chinese University of Hong Kong, Hong Kong, China
- Correspondence:
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11
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The Pyla-1 Natural Accession of Arabidopsis thaliana Shows Little Nitrate-Induced Plasticity of Root Development. NITROGEN 2022. [DOI: 10.3390/nitrogen3030029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Optimizing root system architecture is a strategy for coping with soil fertility, such as low nitrogen input. An ample number of Arabidopsis thaliana natural accessions have set the foundation for studies on mechanisms that regulate root morphology. This report compares the Columbia-0 (Col-0) reference and Pyla-1 (Pyl-1) from a coastal zone in France, known for having the tallest sand dune in Europe. Seedlings were grown on vertical agar plates with different nitrate concentrations. The lateral root outgrowth of Col-0 was stimulated under mild depletion and repressed under nitrate enrichment. The Pyl-1 produced a long primary root and any or very few visible lateral roots across the nitrate supplies. This could reflect an adaptation to sandy soil conditions, where the primary root grows downwards to the lower strata to take up water and mobile soil resources without elongating the lateral roots. Microscopic observations revealed similar densities of lateral root primordia in both accessions. The Pyl-1 maintained the ability to initiate lateral root primordia. However, the post-initiation events seemed to be critical in modulating the lateral-root-less phenotype. In Pyl-1, the emergence of primordia through the primary root tissues was slowed, and newly formed lateral roots stayed stunted. In brief, Pyl-1 is a fascinating genotype for studying the nutritional influences on lateral root development.
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12
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Hamann K, Meier MC, Lewis NS, Carim AI. Plastic Morphological Response to Spectral Shifts during Inorganic Phototropic Growth. JACS AU 2022; 2:865-874. [PMID: 35557752 PMCID: PMC9088297 DOI: 10.1021/jacsau.1c00588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 06/15/2023]
Abstract
Plants exhibit phototropism in which growth is directed toward sunlight and demonstrate morphological plasticity in response to changes in the spectral distribution of the incident illumination. Inorganic phototropic growth via template-free, light-directed electrochemical deposition of semiconductor material can spontaneously generate highly ordered mesostructures with anisotropic, nanoscale lamellar features that exhibit a pitch proportional to the wavelength (λ) of the stimulating illumination. In this work, Se-Te films were generated via a two-step inorganic phototropic growth process using a series of narrowband light-emitting diode sources with discrete output wavelengths (λ0 ≠ λ1). Analogous to the plasticity observed in plants, changes in illumination wavelength from λ0 to λ1 resulted in morphological changes including feature branching, termination, and/or fusion along the growth direction. The interfacial feature pitch changed with the growth duration, in some cases in a notably nonmonotonic fashion, and eventually matched that obtained for growth using only λ1. Simulated morphologies generated by modeling light-material interactions at the growth interface closely matched the evolved structures observed experimentally, indicating that the characteristics of the optical stimulation produce the observed plastic response during inorganic phototropic growth. Examination of the interfacial electric field modulation for λ1 illumination of simplified structures, representative of those generated experimentally, revealed the interfacial light scattering and concentration behavior that directed phototropic growth away from equilibrium, as well as the emergent nature of the phenomena that reestablish equilibrium.
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Affiliation(s)
- Kathryn
R. Hamann
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Madeline C. Meier
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Nathan S. Lewis
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
- Beckman
Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Azhar I. Carim
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
- Beckman
Institute, California Institute of Technology, Pasadena, California 91125, United States
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13
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Templalexis D, Tsitsekian D, Liu C, Daras G, Šimura J, Moschou P, Ljung K, Hatzopoulos P, Rigas S. Potassium transporter TRH1/KUP4 contributes to distinct auxin-mediated root system architecture responses. PLANT PHYSIOLOGY 2022; 188:1043-1060. [PMID: 34633458 PMCID: PMC8825323 DOI: 10.1093/plphys/kiab472] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/07/2021] [Indexed: 05/09/2023]
Abstract
In plants, auxin transport and development are tightly coupled, just as hormone and growth responses are intimately linked in multicellular systems. Here we provide insights into uncoupling this tight control by specifically targeting the expression of TINY ROOT HAIR 1 (TRH1), a member of plant high-affinity potassium (K+)/K+ uptake/K+ transporter (HAK/KUP/KT) transporters that facilitate K+ uptake by co-transporting protons, in Arabidopsis root cell files. Use of this system pinpointed specific root developmental responses to acropetal versus basipetal auxin transport. Loss of TRH1 function shows TRHs and defective root gravitropism, associated with auxin imbalance in the root apex. Cell file-specific expression of TRH1 in the central cylinder rescued trh1 root agravitropism, whereas positional TRH1 expression in peripheral cell layers, including epidermis and cortex, restored trh1 defects. Applying a system-level approach, the role of RAP2.11 and ROOT HAIR DEFECTIVE-LIKE 5 transcription factors (TFs) in root hair development was verified. Furthermore, ERF53 and WRKY51 TFs were overrepresented upon restoration of root gravitropism supporting involvement in gravitropic control. Auxin has a central role in shaping root system architecture by regulating multiple developmental processes. We reveal that TRH1 jointly modulates intracellular ionic gradients and cell-to-cell polar auxin transport to drive root epidermal cell differentiation and gravitropic response. Our results indicate the developmental importance of HAK/KUP/KT proton-coupled K+ transporters.
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Affiliation(s)
- Dimitris Templalexis
- Department of Biotechnology, Agricultural University of Athens, Athens 118 55, Greece
| | - Dikran Tsitsekian
- Department of Biotechnology, Agricultural University of Athens, Athens 118 55, Greece
| | - Chen Liu
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-756 61, Sweden
| | - Gerasimos Daras
- Department of Biotechnology, Agricultural University of Athens, Athens 118 55, Greece
| | - Jan Šimura
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå SE-901 83, Sweden
| | - Panagiotis Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-756 61, Sweden
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion GR 70 013, Greece
- Department of Biology, University of Crete, Heraklion GR 71 500, Greece
| | - Karin Ljung
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå SE-901 83, Sweden
| | | | - Stamatis Rigas
- Department of Biotechnology, Agricultural University of Athens, Athens 118 55, Greece
- Author for communication:
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14
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Li H, Chen H, Chen L, Wang C. The Role of Hydrogen Sulfide in Plant Roots during Development and in Response to Abiotic Stress. Int J Mol Sci 2022; 23:ijms23031024. [PMID: 35162947 PMCID: PMC8835357 DOI: 10.3390/ijms23031024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 12/31/2022] Open
Abstract
Hydrogen sulfide (H2S) is regarded as a “New Warrior” for managing plant stress. It also plays an important role in plant growth and development. The regulation of root system architecture (RSA) by H2S has been widely recognized. Plants are dependent on the RSA to meet their water and nutritional requirements. They are also partially dependent on the RSA for adapting to environment change. Therefore, a good understanding of how H2S affects the RSA could lead to improvements in both crop function and resistance to environmental change. In this review, we summarized the regulating effects of H2S on the RSA in terms of primary root growth, lateral and adventitious root formation, root hair development, and the formation of nodules. We also discussed the genes involved in the regulation of the RSA by H2S, and the relationships with other signal pathways. In addition, we discussed how H2S regulates root growth in response to abiotic stress. This review could provide a comprehensive understanding of the role of H2S in roots during development and under abiotic stress.
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Affiliation(s)
- Hua Li
- College of Life Science, Henan Agricultural University, Zhengzhou 450002, China; (H.C.); (L.C.)
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian 271018, China
- Correspondence: (H.L.); (C.W.)
| | - Hongyu Chen
- College of Life Science, Henan Agricultural University, Zhengzhou 450002, China; (H.C.); (L.C.)
| | - Lulu Chen
- College of Life Science, Henan Agricultural University, Zhengzhou 450002, China; (H.C.); (L.C.)
| | - Chenyang Wang
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University,
Zhengzhou 450002, China
- Correspondence: (H.L.); (C.W.)
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15
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Li C, Li L, Reynolds MP, Wang J, Chang X, Mao X, Jing R. Recognizing the hidden half in wheat: root system attributes associated with drought tolerance. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5117-5133. [PMID: 33783492 DOI: 10.1093/jxb/erab124] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/15/2021] [Indexed: 05/09/2023]
Abstract
Improving drought tolerance in wheat is crucial for maintaining productivity and food security. Roots are responsible for the uptake of water from soil, and a number of root traits are associated with drought tolerance. Studies have revealed many quantitative trait loci and genes controlling root development in plants. However, the genetic dissection of root traits in response to drought in wheat is still unclear. Here, we review crop root traits associated with drought, key genes governing root development in plants, and quantitative trait loci and genes regulating root system architecture under water-limited conditions in wheat. Deep roots, optimal root length density and xylem diameter, and increased root surface area are traits contributing to drought tolerance. In view of the diverse environments in which wheat is grown, the balance among root and shoot traits, as well as individual and population performance, are discussed. The known functions of key genes provide information for the genetic dissection of root development of wheat in a wide range of conditions, and will be beneficial for molecular marker development, marker-assisted selection, and genetic improvement in breeding for drought tolerance.
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Affiliation(s)
- Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | | | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoping Chang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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16
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The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators. Cells 2021; 10:cells10071665. [PMID: 34359847 PMCID: PMC8303113 DOI: 10.3390/cells10071665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/15/2021] [Accepted: 06/28/2021] [Indexed: 12/20/2022] Open
Abstract
Auxin plays a dual role in growth regulation and, depending on the tissue and concentration of the hormone, it can either promote or inhibit division and expansion processes in plants. Recent studies have revealed that, beyond transcriptional reprogramming, alternative auxin-controlled mechanisms regulate root growth. Here, we explored the impact of different concentrations of the synthetic auxin NAA that establish growth-promoting and -repressing conditions on the root tip proteome and phosphoproteome, generating a unique resource. From the phosphoproteome data, we pinpointed (novel) growth regulators, such as the RALF34-THE1 module. Our results, together with previously published studies, suggest that auxin, H+-ATPases, cell wall modifications and cell wall sensing receptor-like kinases are tightly embedded in a pathway regulating cell elongation. Furthermore, our study assigned a novel role to MKK2 as a regulator of primary root growth and a (potential) regulator of auxin biosynthesis and signalling, and suggests the importance of the MKK2 Thr31 phosphorylation site for growth regulation in the Arabidopsis root tip.
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17
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Zhou C, Zhang Y, Liu W, Zha L, Shao M, Li B. Light Quality Affected the Growth and Root Organic Carbon and Autotoxin Secretions of Hydroponic Lettuce. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1542. [PMID: 33187202 PMCID: PMC7696194 DOI: 10.3390/plants9111542] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 11/16/2022]
Abstract
Light is a crucial environmental signal and photosynthetic energy for plant growth, development, and primary and secondary metabolism. To explore the effects of light quality on the growth and root exudates of hydroponic lettuce (Lactuca sativa L.), white LED (W, control) and four the mixtures of red (R) and blue (B) LED with different R/B light intensity ratios (R/B = 2, 2R1B; R/B = 3, 3R1B; R/B = 4, 4R1B; and R/B = 8, 8R1B) were designed. The results showed that the biomass of lettuce under 8R1B and W treatments was higher than that under other light quality treatments. The photosynthetic rate (Pn) under red and blue light was significantly higher than that of white light. Total root length, root surface area, and root volume were the highest under 8R1B. 4R1B treatment significant increased root activity by 68.6% compared with W. In addition, total organic carbon (TOC) content, TOC content/shoot dry weight, TOC content/root dry weight, and TOC content/root surface area were the highest under 4R1B. Moreover, 8R1B treatment reduced the concentration of benzoic acid and salicylic acid, and the secretion ability of benzoic acid and salicylic acid by per unit root surface area and accumulation by per unit shoot dry weight. In addition, 2R1B and 3R1B reduced the secretion ability of gallic acid and tannic acid by per unit root surface area and accumulation by per unit shoot dry weight. In conclusion, this study showed that the secretion of autotoxins could be reduced through the mediation of red and blue light composition of LEDs in a plant factory. In terms of autotoxin secretion reduction efficiency and yield performance of lettuce, 8R1B light regime is recommended for practical use.
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Affiliation(s)
- Chengbo Zhou
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.Z.); (Y.Z.); (L.Z.); (M.S.); (B.L.)
- Key Lab of Energy Conservation and Waste Management of Agricultural Structures, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Yubin Zhang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.Z.); (Y.Z.); (L.Z.); (M.S.); (B.L.)
- Key Lab of Energy Conservation and Waste Management of Agricultural Structures, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Wenke Liu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.Z.); (Y.Z.); (L.Z.); (M.S.); (B.L.)
- Key Lab of Energy Conservation and Waste Management of Agricultural Structures, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Lingyan Zha
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.Z.); (Y.Z.); (L.Z.); (M.S.); (B.L.)
- Key Lab of Energy Conservation and Waste Management of Agricultural Structures, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Mingjie Shao
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.Z.); (Y.Z.); (L.Z.); (M.S.); (B.L.)
- Key Lab of Energy Conservation and Waste Management of Agricultural Structures, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Baoshi Li
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.Z.); (Y.Z.); (L.Z.); (M.S.); (B.L.)
- Key Lab of Energy Conservation and Waste Management of Agricultural Structures, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
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18
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Kumar V, Vogelsang L, Schmidt RR, Sharma SS, Seidel T, Dietz KJ. Remodeling of Root Growth Under Combined Arsenic and Hypoxia Stress Is Linked to Nutrient Deprivation. FRONTIERS IN PLANT SCIENCE 2020; 11:569687. [PMID: 33193499 PMCID: PMC7644957 DOI: 10.3389/fpls.2020.569687] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/06/2020] [Indexed: 05/29/2023]
Abstract
Root architecture responds to environmental stress. Stress-induced metabolic and nutritional changes affect the endogenous root development program. Transcriptional and translational changes realize the switch between stem cell proliferation and cell differentiation, lateral root or root hair formation and root functionality for stress acclimation. The current work explores the effects of stress combination of arsenic toxicity (As) and hypoxia (Hpx) on root development in Arabidopsis thaliana. As revealed previously, combined As and Hpx treatment leads to severe nutritional disorder evident from deregulation of root transcriptome and plant mineral contents. Both As and Hpx were identified to pose stress-specific constraints on root development that lead to unique root growth phenotype under their combination. Besides inhibition of root apical meristem (RAM) activity under all stresses, As induced lateral root growth while root hair density and lengths were strongly increased by Hpx and HpxAs-treatments. A dual stimulation of phosphate (Pi)-starvation response was observed for HpxAs-treated plant roots; however, the response under HpxAs aligned more with Hpx than As. Transcriptional evidence along with biochemical data suggests involvement of PHOSPHATE STARVATION RESPONSE 1; PHR1-dependent systemic signaling. Pi metabolism-related transcripts in close association with cellular iron homeostasis modulate root development under HpxAs. Early redox potential changes in meristematic cells, differential ROS accumulation in root hair zone cell layers and strong deregulation of NADPH oxidases, NADPH-dependent oxidoreductases and peroxidases signify a role of redox and ROS signaling in root architecture remodeling under HpxAs. Differential aquaporin expression suggests transmembrane ROS transport to regulate root hair induction and growth. Reorganization of energy metabolism through NO-dependent alternate oxidase, lactate fermentation, and phosphofructokinase seems crucial under HpxAs. TOR and SnRK-signaling network components were potentially involved in control of sustainable utilization of available energy reserves for root hair growth under combined stress as well as recovery on reaeration. Findings are discussed in context of combined stress-induced signaling in regulation of root development in contrast to As and Hpx alone.
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Affiliation(s)
- Vijay Kumar
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, University of Bielefeld, Bielefeld, Germany
- Department of Biosciences, Himachal Pradesh University, Shimla, India
| | - Lara Vogelsang
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, University of Bielefeld, Bielefeld, Germany
| | - Romy R. Schmidt
- Department of Plant Biotechnology, Faculty of Biology, University of Bielefeld, Bielefeld, Germany
| | - Shanti S. Sharma
- Department of Botany, School of Life Sciences, Sikkim University, Gangtok, India
| | - Thorsten Seidel
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, University of Bielefeld, Bielefeld, Germany
| | - Karl-Josef Dietz
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, University of Bielefeld, Bielefeld, Germany
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Deja-Muylle A, Parizot B, Motte H, Beeckman T. Exploiting natural variation in root system architecture via genome-wide association studies. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2379-2389. [PMID: 31957786 DOI: 10.1093/jxb/eraa029] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 01/17/2020] [Indexed: 05/26/2023]
Abstract
Root growth and development has become an important research topic for breeders and researchers based on a growing need to adapt plants to changing and more demanding environmental conditions worldwide. Over the last few years, genome-wide association studies (GWASs) became an important tool to identify the link between traits in the field and their genetic background. Here we give an overview of the current literature concerning GWASs performed on root system architecture (RSA) in plants. We summarize which root traits and approaches have been used for GWAS, mentioning their respective success rate towards a successful gene discovery. Furthermore, we zoom in on the current technical hurdles in root phenotyping and GWAS, and discuss future possibilities in this field of research.
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Affiliation(s)
- Agnieszka Deja-Muylle
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Boris Parizot
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hans Motte
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Tom Beeckman
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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20
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Chang W, Guo Y, Zhang H, Liu X, Guo L. Same Actor in Different Stages: Genes in Shoot Apical Meristem Maintenance and Floral Meristem Determinacy in Arabidopsis. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00089] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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21
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Micro-scale interactions between Arabidopsis root hairs and soil particles influence soil erosion. Commun Biol 2020; 3:164. [PMID: 32246054 PMCID: PMC7125084 DOI: 10.1038/s42003-020-0886-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 03/11/2020] [Indexed: 01/24/2023] Open
Abstract
Soil is essential for sustaining life on land. Plant roots play a crucial role in stabilising soil and minimising erosion, although these mechanisms are still not completely understood. Consequently, identifying and breeding for plant traits to enhance erosion resistance is challenging. Root hair mutants in Arabidopsis thaliana were studied using three different quantitative methods to isolate their effect on root-soil cohesion. We present compelling evidence that micro-scale interactions of root hairs with surrounding soil increase soil cohesion and reduce erosion. Arabidopsis seedlings with root hairs were more difficult to detach from soil, compost and sterile gel media than those with hairless roots, and it was 10-times harder to erode soil from roots with than without hairs. We also developed a model that can consistently predict the impact root hairs make to soil erosion resistance. Our study thus provides new insight into the mechanisms by which roots maintain soil stability. Sarah De Baets et al. investigate the effect of root hair abundance on root-substrate cohesion and experimental soil erosion in Arabidopsis. They find that plants with root hairs are more difficult to detach from soil and are better able to prevent soil erosion than root hairless plants and present a model to predict the impact of root hairs on soil erosion resistance.
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22
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Spatial regulation of resource allocation in response to nutritional availability. J Theor Biol 2020; 486:110078. [PMID: 31734241 DOI: 10.1016/j.jtbi.2019.110078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 11/08/2019] [Accepted: 11/11/2019] [Indexed: 01/31/2023]
Abstract
It is critical for a living organism to appropriately allocate resources among its organs, or within a specific organ, because available resources are generally limited. For example, in response to the nutritional environment of their soil, plants regulate resource allocation in their roots in order to plastically change their root system architecture (RSA) for efficiently absorbing nutrients. However, it is still not understood why and how RSA is adaptively controlled. Therefore, we modeled and investigated the spatial regulation of resource allocation, focusing on RSA in response to nutrient availability, and provided analytical solutions to the optimal strategy in the case of simple fitness functions. We first showed that our model could explain the experimental evidence where root growth is maximized at the optimal nutrient concentration under the homogeneous condition. Next, we extended our model to incorporate the spatial heterogeneity of nutrient availability. This extended model revealed that growth suppression by systemic control is required for adapting to high nutrient conditions, whereas growth promotion by local control is sufficient for adaptation to low-nutrient environments. This evidence predicts that systemic control can be evolved in the presence of excessive amounts of nutrition, consistent with the 'N-supply' systemic signal that is observed experimentally. Furthermore, our model can also explain various experimental results using nitrogen nutrition. Our model provides a theoretical basis for understanding the spatial regulation of adaptive resource allocation in response to nutritional environment.
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Nelissen H, Gonzalez N. Understanding plant organ growth: a multidisciplinary field. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:7-10. [PMID: 31725876 DOI: 10.1093/jxb/erz448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 09/27/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Gent, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark, Gent, Belgium
| | - Nathalie Gonzalez
- INRA, UMR1332 Biologie du fruit et Pathologie, INRA Bordeaux Aquitaine, CS20032, F-33882, Villenave d'Ornon cedex, France
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24
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Feigl G, Molnár Á, Szőllősi R, Ördög A, Törőcsik K, Oláh D, Bodor A, Perei K, Kolbert Z. Zinc-induced root architectural changes of rhizotron-grown B. napus correlate with a differential nitro-oxidative response. Nitric Oxide 2019; 90:55-65. [PMID: 31271864 DOI: 10.1016/j.niox.2019.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 06/27/2019] [Accepted: 06/28/2019] [Indexed: 12/24/2022]
Abstract
Roots have a noteworthy plasticity: due to different stress conditions their architecture can change to favour seedling vigour and yield stability. The development of the root system is regulated by a complex and diverse signalling network, which besides hormonal factors, includes reactive oxygen (ROS) - and nitrogen species (RNS). The delicate balance of the endogenous signal system can be affected by various environmental stimuli, such as the excess of essential heavy metals, like zinc (Zn). Zn at low concentration, is able to induce the morphological and physiological adaptation of the root system, but in excess it exerts toxic effects on plants. In this study the effect of a low, growth-inducing, and a high, growth inhibiting Zn concentrations on the early development of Brassica napus (L.) root architecture and the underlying nitro-oxidative mechanisms were studied in a soil-filled rhizotron system. The growth-inhibiting Zn treatment resulted in elevated protein tyrosine nitration due to the imbalance in ROS and RNS homeostasis, however its pattern was not changed compared to the control. This nitro-oxidative stress was accompanied by serious changes in the cell wall composition and decrease in the cell proliferation and viability, due to the high Zn uptake and disturbed microelement homeostasis in the root tips. During the positive root growth response, a tyrosine nitration-pattern reorganisation was observed; there were no substantial changes in ROS and RNS balance and the viability and proliferation of the root tips' meristematic zone decreased to a lesser extent, as a result of a lower Zn uptake. The obtained results suggest that Zn in different amounts triggers different root growth responses accompanied by distinct changes in the pattern and strength of tyrosine nitration, proposing that nitrosative processes have an important role in the stress-induced root growth responses.
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Affiliation(s)
- Gábor Feigl
- Department of Plant Biology, University of Szeged, H6726, Szeged, Közép Fasor 52, Hungary.
| | - Árpád Molnár
- Department of Plant Biology, University of Szeged, H6726, Szeged, Közép Fasor 52, Hungary.
| | - Réka Szőllősi
- Department of Plant Biology, University of Szeged, H6726, Szeged, Közép Fasor 52, Hungary.
| | - Attila Ördög
- Department of Plant Biology, University of Szeged, H6726, Szeged, Közép Fasor 52, Hungary.
| | - Kitti Törőcsik
- Department of Plant Biology, University of Szeged, H6726, Szeged, Közép Fasor 52, Hungary.
| | - Dóra Oláh
- Department of Plant Biology, University of Szeged, H6726, Szeged, Közép Fasor 52, Hungary.
| | - Attila Bodor
- Department of Biotechnology, University of Szeged, H6726, Szeged, Közép Fasor 52, Hungary; Institute of Environmental and Technological Sciences, University of Szeged, H6726, Szeged, Közép Fasor 52, Hungary.
| | - Katalin Perei
- Department of Biotechnology, University of Szeged, H6726, Szeged, Közép Fasor 52, Hungary; Institute of Environmental and Technological Sciences, University of Szeged, H6726, Szeged, Közép Fasor 52, Hungary.
| | - Zsuzsanna Kolbert
- Department of Plant Biology, University of Szeged, H6726, Szeged, Közép Fasor 52, Hungary.
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25
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Crombez H, Motte H, Beeckman T. Tackling Plant Phosphate Starvation by the Roots. Dev Cell 2019; 48:599-615. [PMID: 30861374 DOI: 10.1016/j.devcel.2019.01.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 10/16/2018] [Accepted: 12/31/2018] [Indexed: 12/17/2022]
Abstract
Plant responses to phosphate deprivation encompass a wide range of strategies, varying from altering root system architecture, entering symbiotic interactions to excreting root exudates for phosphorous release, and recycling of internal phosphate. These processes are tightly controlled by a complex network of proteins that are specifically upregulated upon phosphate starvation. Although the different effects of phosphate starvation have been intensely studied, the full extent of its contribution to altered root system architecture remains unclear. In this review, we focus on the effect of phosphate starvation on the developmental processes that shape the plant root system and their underlying molecular pathways.
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Affiliation(s)
- Hanne Crombez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent 9052, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, Ghent 9052, Belgium
| | - Hans Motte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent 9052, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, Ghent 9052, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent 9052, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, Ghent 9052, Belgium.
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26
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ANAC032 regulates root growth through the MYB30 gene regulatory network. Sci Rep 2019; 9:11358. [PMID: 31388054 PMCID: PMC6684591 DOI: 10.1038/s41598-019-47822-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/24/2019] [Indexed: 01/03/2023] Open
Abstract
Reactive oxygen species (ROS) play important roles as root growth regulators. We previously reported a comprehensive transcriptomic atlas, which we named ROS-map, that revealed ROS-responsible genes in Arabidopsis root tips. By using ROS-map, we have characterised an early ROS response key transcription factor, MYB30, as a regulator of root cell elongation under ROS signals. However, there are other ROS-responsible transcription factors which have the potential to regulate root growth. In the present study, we characterised the function of another early ROS-responsible transcription factor, ANAC032, that was selected from ROS-map. Overexpression of ANAC032 fused with the transcriptional activation domain, VP16, inhibited root growth, especially decreasing cell elongation. By transcriptome analysis, we revealed that ANAC032 regulated many stress-responsible genes in the roots. Intriguingly, ANAC032 upregulated MYB30 and its target genes. The upregulation of MYB30 target genes was completely abolished in the ANAC032-VP16x2 OX and ANAC032 estradiol-inducible line in myb30-2 mutants. Moreover, root growth inhibition was alleviated in ANAC032-OX in myb30-2 mutants. Overall, we characterised an upstream transcription factor, ANAC032, of the MYB30 transcriptional cascade which is a key regulator for root cell elongation under ROS signalling.
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27
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Michniewicz M, Ho CH, Enders TA, Floro E, Damodaran S, Gunther LK, Powers SK, Frick EM, Topp CN, Frommer WB, Strader LC. TRANSPORTER OF IBA1 Links Auxin and Cytokinin to Influence Root Architecture. Dev Cell 2019; 50:599-609.e4. [PMID: 31327740 DOI: 10.1016/j.devcel.2019.06.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/29/2019] [Accepted: 06/14/2019] [Indexed: 10/26/2022]
Abstract
Developmental processes that control root system architecture are critical for soil exploration by plants, allowing for uptake of water and nutrients. Conversion of the auxin precursor indole-3-butyric acid (IBA) to active auxin (indole-3-acetic acid; IAA) modulates lateral root formation. However, mechanisms governing IBA-to-IAA conversion have yet to be elucidated. We identified TRANSPORTER OF IBA1 (TOB1) as a vacuolar IBA transporter that limits lateral root formation. Moreover, TOB1, which is transcriptionally regulated by the phytohormone cytokinin, is necessary for the ability of cytokinin to exert inhibitory effects on lateral root production. The increased production of lateral roots in tob1 mutants, TOB1 transport of IBA into the vacuole, and cytokinin-regulated TOB1 expression provide a mechanism linking cytokinin signaling and IBA contribution to the auxin pool to tune root system architecture.
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Affiliation(s)
- Marta Michniewicz
- Department of Biology, Washington University, St. Louis, MO 63130, USA
| | - Cheng-Hsun Ho
- Institute for Molecular Physiology, Heinrich Heine Universität Düsseldorf, Institute for Biotransformative Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan; Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Tara A Enders
- Department of Biology, Washington University, St. Louis, MO 63130, USA
| | - Eric Floro
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Suresh Damodaran
- Department of Biology, Washington University, St. Louis, MO 63130, USA
| | - Lauren K Gunther
- Department of Biology, Washington University, St. Louis, MO 63130, USA
| | - Samantha K Powers
- Department of Biology, Washington University, St. Louis, MO 63130, USA
| | - Elizabeth M Frick
- Department of Biology, Washington University, St. Louis, MO 63130, USA
| | | | - Wolf B Frommer
- Institute for Molecular Physiology, Heinrich Heine Universität Düsseldorf, Institute for Biotransformative Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
| | - Lucia C Strader
- Department of Biology, Washington University, St. Louis, MO 63130, USA; Center for Engineering MechanoBiology, Washington University, St. Louis, MO 63130, USA; Center for Science & Engineering of Living Systems, Washington University, St. Louis, MO 63130, USA.
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28
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Colchado-López J, Cervantes RC, Rosas U. A Linear Model to Describe Branching and Allometry in Root Architecture. PLANTS (BASEL, SWITZERLAND) 2019; 8:plants8070218. [PMID: 31336829 PMCID: PMC6681317 DOI: 10.3390/plants8070218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 06/26/2019] [Accepted: 07/08/2019] [Indexed: 05/31/2023]
Abstract
Root architecture is a complex structure that comprises multiple traits of the root phenotype. Novel platforms and models have been developed to better understand root architecture. In this methods paper, we introduce a novel allometric model, named rhizochron index (m), which describes lateral root (LR) branching and elongation patterns across the primary root (PR). To test our model, we obtained data from 16 natural accessions of Arabidopsis thaliana at three stages of early root development to measure conventional traits of root architecture (e.g., PR and LR length), and extracted the rhizochron index (m). In addition, we tested previously published datasets to assess the utility of the rhizochron index (m) to distinguish mutants and environmental effects on root architecture. Our results indicate that rhizochron index (m) is useful to distinguish the natural variations of root architecture between A. thaliana accessions, but not across early stages of root development. Correlation analyses in these accessions showed that m is a novel trait that partially captures information from other root architecture traits such as total lateral root length, and the ratio between lateral root and primary root lengths. Moreover, we found that the rhizochron index was useful to distinguish ABA effect on root architecture, as well as the mutant pho1 phenotype. We propose the rhizochron index (m) as a new feature of the root architectural system to be considered, in addition to conventional traits in future investigations.
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Affiliation(s)
- Joel Colchado-López
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | - R Cristian Cervantes
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | - Ulises Rosas
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico.
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29
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Tang L, Hamid Y, Sahito ZA, Gurajala HK, He Z, Yang X. Effects of CO 2 application coupled with endophyte inoculation on rhizosphere characteristics and cadmium uptake by Sedum alfredii Hance in response to cadmium stress. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 239:287-298. [PMID: 30913479 DOI: 10.1016/j.jenvman.2019.03.084] [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: 11/05/2018] [Revised: 03/14/2019] [Accepted: 03/16/2019] [Indexed: 06/09/2023]
Abstract
Comparative impact of CO2 application and endophyte inoculation was investigated on the growth, rhizosphere characteristics, and cadmium (Cd) absorption of two ecotypes of Sedum alfredii Hance in response to Cd stress under hydroponic or rhizo-box culture conditions. The results showed that both CO2 application and endophyte inoculation significantly (P < 0.05) promoted plant growth (fresh weight and dry weight), improved root morphological properties (SRL, SRA, SRV, ARD and RTN) and exudation (pH, TOC, TN, soluble sugar and organic acids), changed Cd uptake and distribution of both ecotypes of S. alfredii. Meanwhile soil total and DTPA extractable Cd in rhizo-box decreased by biofortification treatments. Superposition biofortification exhibits utmost improvement for the above mentioned parameters, and has potential for enhancing phytoremediation efficiency of hyperaccumulator and sustaining regular growth of non-hyperaccumulator in Cd contaminated soils.
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Affiliation(s)
- Lin Tang
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Yasir Hamid
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Zulfiqar Ali Sahito
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Hanumanth Kumar Gurajala
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Zhenli He
- University of Florida, Institute of Food and Agricultural Sciences, Indian River Research and Education Center, Fort Pierce, Florida, 34945, United States
| | - Xiaoe Yang
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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30
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Evolution of Deeper Rooting 1-like homoeologs in wheat entails the C-terminus mutations as well as gain and loss of auxin response elements. PLoS One 2019; 14:e0214145. [PMID: 30947257 PMCID: PMC6448822 DOI: 10.1371/journal.pone.0214145] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/07/2019] [Indexed: 11/19/2022] Open
Abstract
Root growth angle (RGA) in response to gravity controlled by auxin is a pertinent target trait for obtainment of higher yield in cereals. But molecular basis of this root architecture trait remain obscure in wheat and barley. We selected four cultivars two each for wheat and barley to unveil the molecular genetic mechanism of Deeper Rooting 1-like gene which controls RGA in rice leading to higher yield under drought imposition. Morphological analyses revealed a deeper and vertically oriented root growth in “NARC 2009” variety of wheat than “Galaxy” and two other barley cultivars “Scarlet” and “ISR42-8”. Three new homoeologs designated as TaANDRO1-like, TaBNDRO1-like and TaDNDRO1-like corresponding to A, B and D genomes of wheat could be isolated from “NARC 2009”. Due to frameshift and intronization/exonization events the gene structures of these paralogs exhibit variations in size. DRO1-like genes with five distinct domains prevail in diverse plant phyla from mosses to angiosperms but in lower plants their differentiation from LAZY, NGR and TAC1 (root and shoot angle genes) is enigmatic. Instead of IGT as denominator motif of this family, a new C-terminus motif WxxTD in the V-domain is proposed as family specific motif. The EAR-like motif IVLEM at the C-terminus of the TaADRO1-like and TaDDRO1-like that diverged to KLHTLIPNK in TaBDRO1-like and HvDRO1-like is the hallmark of these proteins. Split-YFP and yeast two hybrid assays complemented the interaction of TaDRO1-like with TOPLESS—a repressor of auxin regulated root promoting genes in plants—through IVLEM/KLHTLIPNK motif. Quantitative RT-PCR revealed abundance of DRO1-like RNA in root tips and spikelets while transcript signals were barely detectable in shoot and leaf tissues. Interestingly, wheat exhibited stronger expression of TaBDRO1-like than barley (HvDRO1-like), but TaBDRO1-like was the least expressing among three paralogs. The underlying cause of this expression divergence seems to be the presence of AuxRE motif TGTCTC and core TGTC with a coupling AuxRE-like motif ATTTTCTT proximal to the transcriptional start site in TaBDRO1-like and HvDRO1-like promoters. This is evident from binding of ARF1 to TGTCTC and TGTC motifs of TaBDRO1-like as revealed by yeast one-hybrid assay. Thus, evolution of DRO1-like wheat homoeologs might incorporate the C-terminus mutations as well as gain and loss of AuxREs and other cis-regulatory elements during expression divergence. Since root architecture is an important target trait for wheat crop improvement, therefore DRO1-like genes have potential applications in plant breeding for enhancement of plant productivity by the use of modern genome editing approaches.
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31
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Zhou M, Sng NJ, LeFrois CE, Paul AL, Ferl RJ. Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by spaceflight in Arabidopsis thaliana. BMC Genomics 2019; 20:205. [PMID: 30866818 PMCID: PMC6416986 DOI: 10.1186/s12864-019-5554-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/21/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Plants adapted to diverse environments on Earth throughout their evolutionary history, and developed mechanisms to thrive in a variety of terrestrial habitats. When plants are grown in the novel environment of spaceflight aboard the International Space Station (ISS), an environment completely outside their evolutionary history, they respond with unique alterations to their gene expression profile. Identifying the genes important for physiological adaptation to spaceflight and dissecting the biological processes and pathways engaged by plants during spaceflight has helped reveal spaceflight adaptation, and has furthered understanding of terrestrial growth processes. However, the underlying regulatory mechanisms responsible for these changes in gene expression patterns are just beginning to be explored. Epigenetic modifications, such as DNA methylation at position five in cytosine, has been shown to play a role in the physiological adaptation to adverse terrestrial environments, and may play a role in spaceflight as well. RESULTS Whole Genome Bisulfite Sequencing of DNA of Arabidopsis grown on the ISS from seed revealed organ-specific patterns of differential methylation compared to ground controls. The overall levels of methylation in CG, CHG, and CHH contexts were similar between flight and ground DNA, however, thousands of specifically differentially methylated cytosines were discovered, and there were clear organ-specific differences in methylation patterns. Spaceflight leaves had higher methylation levels in CHG and CHH contexts within protein-coding genes in spaceflight; about a fifth of the leaf genes were also differentially regulated in spaceflight, almost half of which were associated with reactive oxygen signaling. CONCLUSIONS The physiological adaptation of plants to spaceflight is likely nuanced by epigenomic modification. This is the first examination of differential genomic methylation from plants grown completely in the spaceflight environment of the ISS in plant growth hardware developed for informing exploration life support strategies. Yet even in this optimized plant habitat, plants respond as if stressed. These data suggest that gene expression associated with physiological adaptation to spaceflight is regulated in part by methylation strategies similar to those engaged with familiar terrestrial stress responses. The differential methylation maps generated here provide a useful reference for elucidating the layers of regulation of spaceflight responses.
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Affiliation(s)
- Mingqi Zhou
- 0000 0004 1936 8091grid.15276.37Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL USA ,0000 0004 1936 8091grid.15276.37Horticultural Sciences Department, University of Florida, Gainesville, FL USA
| | - Natasha J. Sng
- 0000 0004 1936 8091grid.15276.37Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL USA ,0000 0004 1936 8091grid.15276.37Horticultural Sciences Department, University of Florida, Gainesville, FL USA
| | - Collin E. LeFrois
- 0000 0004 1936 8091grid.15276.37Horticultural Sciences Department, University of Florida, Gainesville, FL USA
| | - Anna-Lisa Paul
- 0000 0004 1936 8091grid.15276.37Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL USA ,0000 0004 1936 8091grid.15276.37Horticultural Sciences Department, University of Florida, Gainesville, FL USA
| | - Robert J. Ferl
- 0000 0004 1936 8091grid.15276.37Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL USA ,0000 0004 1936 8091grid.15276.37Horticultural Sciences Department, University of Florida, Gainesville, FL USA ,0000 0004 1936 8091grid.15276.37Interdisciplinary Center for Biotechnology, University of Florida, Gainesville, FL USA
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Prince SJ, Valliyodan B, Ye H, Yang M, Tai S, Hu W, Murphy M, Durnell LA, Song L, Joshi T, Liu Y, Van de Velde J, Vandepoele K, Grover Shannon J, Nguyen HT. Understanding genetic control of root system architecture in soybean: Insights into the genetic basis of lateral root number. PLANT, CELL & ENVIRONMENT 2019; 42:212-229. [PMID: 29749073 DOI: 10.1111/pce.13333] [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: 12/31/2017] [Accepted: 03/26/2018] [Indexed: 05/04/2023]
Abstract
Developing crops with better root systems is a promising strategy to ensure productivity in both optimum and stress environments. Root system architectural traits in 397 soybean accessions were characterized and a high-density single nucleotide polymorphisms (SNPs)-based genome-wide association study was performed to identify the underlying genes associated with root structure. SNPs associated with root architectural traits specific to landraces and elite germplasm pools were detected. Four loci were detected in landraces for lateral root number (LRN) and distribution of root thickness in diameter Class I with a major locus on chromosome 16. This major loci was detected in the coding region of unknown protein, and subsequent analyses demonstrated that root traits are affected with mutated haplotypes of the gene. In elite germplasm pool, 3 significant SNPs in alanine-glyoxalate aminotransferase, Leucine-Rich Repeat receptor/No apical meristem, and unknown functional genes were found to govern multiple traits including root surface area and volume. However, no major loci were detected for LRN in elite germplasm. Nucleotide diversity analysis found evidence of selective sweeps around the landraces LRN gene. Soybean accessions with minor and mutated allelic variants of LRN gene were found to perform better in both water-limited and optimal field conditions.
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Affiliation(s)
- Silvas J Prince
- Division of Plant Sciences, University of Missouri, Columbia, 65211, MO, USA
- Noble Research Institute, Ardmore, 73401, OK, USA
| | - Babu Valliyodan
- Division of Plant Sciences, University of Missouri, Columbia, 65211, MO, USA
| | - Heng Ye
- Division of Plant Sciences, University of Missouri, Columbia, 65211, MO, USA
| | - Ming Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Wushu Hu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Mackensie Murphy
- Division of Plant Sciences, University of Missouri, Columbia, 65211, MO, USA
| | - Lorellin A Durnell
- Division of Plant Sciences, University of Missouri, Columbia, 65211, MO, USA
| | - Li Song
- Division of Plant Sciences, University of Missouri, Columbia, 65211, MO, USA
- Institutes of Agricultural Science and Technology Development, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Trupti Joshi
- Department of Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology and Office of Research, School of Medicine, University of Missouri, Columbia, MO, USA
| | - Yang Liu
- Department of Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Jan Van de Velde
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium
| | - J Grover Shannon
- Division of Plant Sciences, University of Missouri, Columbia, 65211, MO, USA
| | - Henry T Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, 65211, MO, USA
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Ristova D, Giovannetti M, Metesch K, Busch W. Natural genetic variation shapes root system responses to phytohormones in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:468-481. [PMID: 30030851 PMCID: PMC6220887 DOI: 10.1111/tpj.14034] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 06/13/2018] [Accepted: 07/02/2018] [Indexed: 05/21/2023]
Abstract
Plants adjust their architecture by modulating organ growth. This ability is largely dependent on phytohormones. While responses to phytohormones have been studied extensively, it remains unclear to which extent and how these responses are modulated in non-reference strains. Here, we assess variation of root traits upon treatment with auxin, cytokinin and abscisic acid (ABA) in 192 Arabidopsis accessions. We identify common response patterns, uncover the extent of their modulation by specific genotypes, and find that the Col-0 reference accession is not a good representative of the species in this regard. We conduct genome-wide association studies and identify 114 significant associations, most of them relating to ABA treatment. The numerous ABA candidate genes are not enriched for known ABA-associated genes, indicating that we largely uncovered unknown players. Overall, our study provides a comprehensive view of the diversity of hormone responses in the Arabidopsis thaliana species, and shows that variation of genes that are yet mostly not associated with such a role to determine natural variation of the response to phytohormones.
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Affiliation(s)
- Daniela Ristova
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr. Bohr‐Gasse 3Vienna1030Austria
| | - Marco Giovannetti
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr. Bohr‐Gasse 3Vienna1030Austria
| | - Kristina Metesch
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr. Bohr‐Gasse 3Vienna1030Austria
| | - Wolfgang Busch
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr. Bohr‐Gasse 3Vienna1030Austria
- Salk Institute for Biological StudiesPlant Molecular and Cellular Biology Laboratory, and Integrative Biology Laboratory10010 N Torrey Pines RdLa JollaCA92037USA
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Nimmo HG. Entrainment of Arabidopsis roots to the light:dark cycle by light piping. PLANT, CELL & ENVIRONMENT 2018; 41:1742-1748. [PMID: 29314066 DOI: 10.1111/pce.13137] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 12/12/2017] [Indexed: 06/07/2023]
Abstract
Correct operation of the plant circadian clock is crucial for optimal growth and development. Recent evidence has shown that the plant clock is tissue specific and potentially hierarchical, implying that there are signalling mechanisms that can synchronise the clock in different tissues. Here, I have addressed the mechanism that allows the shoot and root clocks to be synchronised in light:dark cycles but not in continuous light. Luciferase imaging data from 2 different Arabidopsis accessions with 2 different markers show that the period of the root clock is much less sensitive to blue light than to red light. Decapitated roots were imaged either in darkness or with the top section of root tissue exposed to light. Exposure to red light reduced the period of the root tissue maintained in darkness, whereas exposure to blue light did not. The data indicate that light can be piped through root tissue to affect the circadian period of tissue in darkness. I propose that the synchronisation of shoots and roots in light:dark cycles is achieved by light piping from shoots to roots.
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Affiliation(s)
- Hugh G Nimmo
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK
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Manzano C, Pallero-Baena M, Silva-Navas J, Navarro Neila S, Casimiro I, Casero P, Garcia-Mina JM, Baigorri R, Rubio L, Fernandez JA, Norris M, Ding Y, Moreno-Risueno MA, Del Pozo JC. A light-sensitive mutation in Arabidopsis LEW3 reveals the important role of N-glycosylation in root growth and development. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5103-5116. [PMID: 29106622 DOI: 10.1093/jxb/erx324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Plant roots have the potential capacity to grow almost indefinitely if meristematic and lateral branching is sustained. In a genetic screen we identified an Arabidopsis mutant showing limited root growth (lrg1) due to defects in cell division and elongation in the root meristem. Positional cloning determined that lrg1 affects an alpha-1,2-mannosyltransferase gene, LEW3, involved in protein N-glycosylation. The lrg1 mutation causes a synonymous substitution that alters the correct splicing of the fourth intron in LEW3, causing a mix of wild-type and truncated protein. LRG1 RNA missplicing in roots and short root phenotypes in lrg1 are light-intensity dependent. This mutation disrupts a GC-base pair in a three-base-pair stem with a four-nucleotide loop, which seems to be necessary for correct LEW3 RNA splicing. We found that the lrg1 short root phenotype correlates with high levels of reactive oxygen species and low pH in the apoplast. Proteomic analyses of N-glycosylated proteins identified GLU23/PYK10 and PRX34 as N-glycosylation targets of LRG1 activity. The lrg1 mutation reduces the positive interaction between Arabidopsis and Serendipita indica. A prx34 mutant showed a significant reduction in root growth, which is additive to lrg1. Taken together our work highlights the important role of N-glycosylation in root growth and development.
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Affiliation(s)
- Concepción Manzano
- Centro de Biotecnología y Genómica de Plantas (CBGP) INIA-UPM. Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria. Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Mercedes Pallero-Baena
- Facultad de Ciencias. Dept. de Anatomía, Biología Celular y Zoología. Universidad de Extremadura. 06006-Badajoz, Spain
| | - J Silva-Navas
- Centro de Biotecnología y Genómica de Plantas (CBGP) INIA-UPM. Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria. Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Sara Navarro Neila
- Centro de Biotecnología y Genómica de Plantas (CBGP) INIA-UPM. Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria. Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Ilda Casimiro
- Facultad de Ciencias. Dept. de Anatomía, Biología Celular y Zoología. Universidad de Extremadura. 06006-Badajoz, Spain
| | - Pedro Casero
- Facultad de Ciencias. Dept. de Anatomía, Biología Celular y Zoología. Universidad de Extremadura. 06006-Badajoz, Spain
| | - Jose M Garcia-Mina
- Departamento de Biología Ambiental, Grupo BACh. Facultad de Ciencias. Universidad de Navarra31008 Pamplona, Spain
| | - Roberto Baigorri
- Departamento de Biología Ambiental, Grupo BACh. Facultad de Ciencias. Universidad de Navarra 31008 Pamplona, Spain
- Technical and Development Department, Timac Agro-Grupo Roullier, c/Barrio Féculas s/n, 31580 Lodosa, Navarra, Spain
| | - Lourdes Rubio
- Departamento de Biología Vegetal (Fisiología Vegetal). Facultad de Ciencias. Universidad de Málaga. Campus de Teatinos S/N. 29071 Málaga, Spain
| | - Jose A Fernandez
- Departamento de Biología Vegetal (Fisiología Vegetal). Facultad de Ciencias. Universidad de Málaga. Campus de Teatinos S/N. 29071 Málaga, Spain
| | - Matthew Norris
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Miguel A Moreno-Risueno
- Centro de Biotecnología y Genómica de Plantas (CBGP) INIA-UPM. Universidad Politécnica de Madrid. Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Juan C Del Pozo
- Centro de Biotecnología y Genómica de Plantas (CBGP) INIA-UPM. Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria. Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
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Michaud O, Fiorucci AS, Xenarios I, Fankhauser C. Local auxin production underlies a spatially restricted neighbor-detection response in Arabidopsis. Proc Natl Acad Sci U S A 2017; 114:7444-7449. [PMID: 28652343 PMCID: PMC5514730 DOI: 10.1073/pnas.1702276114] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Competition for light triggers numerous developmental adaptations known as the "shade-avoidance syndrome" (SAS). Important molecular events underlying specific SAS responses have been identified. However, in natural environments light is often heterogeneous, and it is currently unknown how shading affecting part of a plant leads to local responses. To study this question, we analyzed upwards leaf movement (hyponasty), a rapid adaptation to neighbor proximity, in Arabidopsis We show that manipulation of the light environment at the leaf tip triggers a hyponastic response that is restricted to the treated leaf. This response is mediated by auxin synthesized in the blade and transported to the petiole. Our results suggest that a strong auxin response in the vasculature of the treated leaf and auxin signaling in the epidermis mediate leaf elevation. Moreover, the analysis of an auxin-signaling mutant reveals signaling bifurcation in the control of petiole elongation versus hyponasty. Our work identifies a mechanism for a local shade response that may pertain to other plant adaptations to heterogeneous environments.
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Affiliation(s)
- Olivier Michaud
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Anne-Sophie Fiorucci
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Ioannis Xenarios
- Swiss Institute of Bioinformatics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Christian Fankhauser
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland;
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Merchuk-Ovnat L, Fahima T, Ephrath JE, Krugman T, Saranga Y. Ancestral QTL Alleles from Wild Emmer Wheat Enhance Root Development under Drought in Modern Wheat. FRONTIERS IN PLANT SCIENCE 2017; 8:703. [PMID: 28536586 PMCID: PMC5422550 DOI: 10.3389/fpls.2017.00703] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 04/18/2017] [Indexed: 05/17/2023]
Abstract
A near-isogenic line (NIL-7A-B-2), introgressed with a quantitative trait locus (QTL) on chromosome 7AS from wild emmer wheat (Triticum turgidum ssp. dicoccoides) into the background of bread wheat (T. aestivum L.) cv. BarNir, was recently developed and studied in our lab. NIL-7A-B-2 exhibited better productivity and photosynthetic capacity than its recurrent parent across a range of environments. Here we tested the hypothesis that root-system modifications play a major role in NIL-7A-B-2's agronomical superiority. Root-system architecture (dry matter and projected surface area) and shoot parameters of NIL-7A-B-2 and 'BarNir' were evaluated at 40, 62, and 82 days after planting (DAP) in a sand-tube experiment, and root tip number was assessed in a 'cigar-roll' seedling experiment, both under well-watered and water-limited (WL) treatments. At 82 DAP, under WL treatment, NIL-7A-B-2 presented greater investment in deep roots (depth 40-100 cm) than 'BarNir,' with the most pronounced effect recorded in the 60-80 cm soil depth (60 and 40% increase for root dry matter and surface area, respectively). NIL-7A-B-2 had significantly higher root-tip numbers (∼48%) per plant than 'BarNir' under both treatments. These results suggest that the introgression of 7AS QTL from wild emmer wheat induced a deeper root system under progressive water stress, which may enhance abiotic stress resistance and productivity of domesticated wheat.
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Affiliation(s)
- Lianne Merchuk-Ovnat
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of JerusalemRehovot, Israel
| | - Tzion Fahima
- Institute of Evolution, University of HaifaHaifa, Israel
| | - Jhonathan E. Ephrath
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the NegevBeersheba, Israel
| | - Tamar Krugman
- Institute of Evolution, University of HaifaHaifa, Israel
| | - Yehoshua Saranga
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of JerusalemRehovot, Israel
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Guseman JM, Webb K, Srinivasan C, Dardick C. DRO1 influences root system architecture in Arabidopsis and Prunus species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:1093-1105. [PMID: 28029738 DOI: 10.1111/tpj.13470] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 12/12/2016] [Accepted: 12/16/2016] [Indexed: 05/18/2023]
Abstract
Roots provide essential uptake of water and nutrients from the soil, as well as anchorage and stability for the whole plant. Root orientation, or angle, is an important component of the overall architecture and depth of the root system; however, little is known about the genetic control of this trait. Recent reports in Oryza sativa (rice) identified a role for DEEPER ROOTING 1 (DRO1) in influencing the orientation of the root system, leading to positive changes in grain yields under water-limited conditions. Here we found that DRO1 and DRO1-related genes are present across diverse plant phyla, and fall within the IGT gene family. The IGT family also includes TAC1 and LAZY1, which are known to affect the orientation of lateral shoots. Consistent with a potential role in root development, DRO1 homologs in Arabidopsis and peach showed root-specific expression. Promoter-reporter constructs revealed that AtDRO1 is predominantly expressed in both the root vasculature and root tips, in a distinct developmental pattern. Mutation of AtDRO1 led to more horizontal lateral root angles. Overexpression of AtDRO1 under a constitutive promoter resulted in steeper lateral root angles, as well as shoot phenotypes including upward leaf curling, shortened siliques and narrow lateral branch angles. A conserved C-terminal EAR-like motif found in IGT genes was required for these ectopic phenotypes. Overexpression of PpeDRO1 in Prunus domestica (plum) led to deeper-rooting phenotypes. Collectively, these data indicate a potential application for DRO1-related genes to alter root architecture for drought avoidance and improved resource use.
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Affiliation(s)
- Jessica M Guseman
- USDA-ARS Appalachian Fruit Research Station, 2217 Wiltshire Rd., Kearneysville, WV, 25430, USA
| | - Kevin Webb
- USDA-ARS Appalachian Fruit Research Station, 2217 Wiltshire Rd., Kearneysville, WV, 25430, USA
| | - Chinnathambi Srinivasan
- USDA-ARS Appalachian Fruit Research Station, 2217 Wiltshire Rd., Kearneysville, WV, 25430, USA
| | - Chris Dardick
- USDA-ARS Appalachian Fruit Research Station, 2217 Wiltshire Rd., Kearneysville, WV, 25430, USA
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Möller BK, Xuan W, Beeckman T. Dynamic control of lateral root positioning. CURRENT OPINION IN PLANT BIOLOGY 2017; 35:1-7. [PMID: 27649449 DOI: 10.1016/j.pbi.2016.09.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/30/2016] [Accepted: 09/01/2016] [Indexed: 05/25/2023]
Abstract
In dicot root systems, lateral roots are in general regularly spaced along the longitudinal axis of the primary root to facilitate water and nutrient uptake. Recently, recurrent programmed cell death in the root cap of the growing root has been implicated in lateral root spacing. The root cap contains an auxin source that modulates lateral root patterning. Periodic release of auxin by dying root cap cells seems to trigger lateral root specification at regular intervals. However, it is currently unclear through which molecular mechanisms auxin restricts lateral root specification to specific cells along the longitudinal and radial axes of the root, or how environmental signals impact this process.
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Affiliation(s)
- Barbara K Möller
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
| | - Wei Xuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Weigang No. 1, Nanjing 210095, PR China
| | - Tom Beeckman
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium.
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Secco D, Bouain N, Rouached A, Prom-U-Thai C, Hanin M, Pandey AK, Rouached H. Phosphate, phytate and phytases in plants: from fundamental knowledge gained in Arabidopsis to potential biotechnological applications in wheat. Crit Rev Biotechnol 2017; 37:898-910. [PMID: 28076998 DOI: 10.1080/07388551.2016.1268089] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Phosphorus (P) is an essential macronutrient for all living organisms. In plants, P is taken up from the rhizosphere by the roots mainly as inorganic phosphate (Pi), which is required in large and sufficient quantities to maximize crop yields. In today's agricultural society, crop yield is mostly ensured by the excessive use of Pi fertilizers, a costly practice neither eco-friendly or sustainable. Therefore, generating plants with improved P use efficiency (PUE) is of major interest. Among the various strategies employed to date, attempts to engineer genetically modified crops with improved capacity to utilize phytate (PA), the largest soil P form and unfortunately not taken up by plants, remains a key challenge. To meet these challenges, we need a better understanding of the mechanisms regulating Pi sensing, signaling, transport and storage in plants. In this review, we summarize the current knowledge on these aspects, which are mainly gained from investigations conducted in Arabidopsis thaliana, and we extended it to those available on an economically important crop, wheat. Strategies to enhance the PA use, through the use of bacterial or fungal phytases and other attempts of reducing seed PA levels, are also discussed. We critically review these data in terms of their potential for use as a technology for genetic manipulation of PUE in wheat, which would be both economically and environmentally beneficial.
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Affiliation(s)
- David Secco
- a Biochimie et Physiologie Moléculaire des Plantes , CNRS, INRA, Montpellier SupAgro, UM , Montpellier , France
| | - Nadia Bouain
- a Biochimie et Physiologie Moléculaire des Plantes , CNRS, INRA, Montpellier SupAgro, UM , Montpellier , France
| | - Aida Rouached
- a Biochimie et Physiologie Moléculaire des Plantes , CNRS, INRA, Montpellier SupAgro, UM , Montpellier , France
| | - Chanakan Prom-U-Thai
- b Agronomy Division, Department of Plant and Soil Sciences, Faculty of Agriculture , Chiang Mai University , Chiang Mai , Thailand
| | - Moez Hanin
- c Laboratoire de Biotechnologie et Amélioration des Plantes , Centre de Biotechnologie de Sfax , Sfax , Tunisie
| | - Ajay K Pandey
- d Department of Biotechnology, C-127 , National Agri-Food Biotechnology Institute , Punjab , India
| | - Hatem Rouached
- a Biochimie et Physiologie Moléculaire des Plantes , CNRS, INRA, Montpellier SupAgro, UM , Montpellier , France.,b Agronomy Division, Department of Plant and Soil Sciences, Faculty of Agriculture , Chiang Mai University , Chiang Mai , Thailand.,c Laboratoire de Biotechnologie et Amélioration des Plantes , Centre de Biotechnologie de Sfax , Sfax , Tunisie
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Van Dingenen J, Blomme J, Gonzalez N, Inzé D. Plants grow with a little help from their organelle friends. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:6267-6281. [PMID: 27815330 DOI: 10.1093/jxb/erw399] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Chloroplasts and mitochondria are indispensable for plant development. They not only provide energy and carbon sources to cells, but also have evolved to become major players in a variety of processes such as amino acid metabolism, hormone biosynthesis and cellular signalling. As semi-autonomous organelles, they contain a small genome that relies largely on nuclear factors for its maintenance and expression. An intensive crosstalk between the nucleus and the organelles is therefore essential to ensure proper functioning, and the nuclear genes encoding organellar proteins involved in photosynthesis and oxidative phosphorylation are obviously crucial for plant growth. Organ growth is determined by two main cellular processes: cell proliferation and cell expansion. Here, we review how plant growth is affected in mutants of organellar proteins that are differentially expressed during leaf and root development. Our findings indicate a clear role for organellar proteins in plant organ growth, primarily during cell proliferation. However, to date, the role of the nuclear-encoded organellar proteins in the cellular processes driving organ growth has not been investigated in much detail. We therefore encourage researchers to extend their phenotypic characterization beyond macroscopic features in order to get a better view on how chloroplasts and mitochondria regulate the basic processes of cell proliferation and cell expansion, essential to driving growth.
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Affiliation(s)
- Judith Van Dingenen
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Jonas Blomme
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Nathalie Gonzalez
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
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Araya T, von Wirén N, Takahashi H. CLE peptide signaling and nitrogen interactions in plant root development. PLANT MOLECULAR BIOLOGY 2016; 91:607-615. [PMID: 26994997 DOI: 10.1007/s11103-016-0472-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 03/11/2016] [Indexed: 06/05/2023]
Abstract
The CLAVATA signaling pathway is essential for the regulation of meristem activities in plants. This signaling pathway consists of small signaling peptides of the CLE family interacting with CLAVATA1 and leucine-rich repeat receptor-like kinases (LRR-RLKs). The peptide-receptor relationships determine the specificities of CLE-dependent signals controlling stem cell fate and differentiation that are critical for the establishment and maintenance of shoot and root apical meristems. Plants root systems are highly organized into three-dimensional structures for successful anchoring and uptake of water and mineral nutrients from the soil environment. Recent studies have provided evidence that CLE peptides and CLAVATA signaling pathways play pivotal roles in the regulation of lateral root development and systemic autoregulation of nodulation (AON) integrated with nitrogen (N) signaling mechanisms. Integrations of CLE and N signaling pathways through shoot-root vascular connections suggest that N demand modulates morphological control mechanisms and optimize N uptake as well as symbiotic N fixation in roots.
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Affiliation(s)
- Takao Araya
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466, Gatersleben, Germany
| | - Nicolaus von Wirén
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466, Gatersleben, Germany
| | - Hideki Takahashi
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI, 48824, USA.
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43
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Roberts I, Smith S, Stes E, De Rybel B, Staes A, van de Cotte B, Njo MF, Dedeyne L, Demol H, Lavenus J, Audenaert D, Gevaert K, Beeckman T, De Smet I. CEP5 and XIP1/CEPR1 regulate lateral root initiation in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4889-99. [PMID: 27296247 PMCID: PMC4983111 DOI: 10.1093/jxb/erw231] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Roots explore the soil for water and nutrients through the continuous production of lateral roots. Lateral roots are formed at regular distances in a steadily elongating organ, but how future sites for lateral root formation become established is not yet understood. Here, we identified C-TERMINALLY ENCODED PEPTIDE 5 (CEP5) as a novel, auxin-repressed and phloem pole-expressed signal assisting in the formation of lateral roots. In addition, based on genetic and expression data, we found evidence for the involvement of its proposed receptor, XYLEM INTERMIXED WITH PHLOEM 1 (XIP1)/CEP RECEPTOR 1 (CEPR1), during the process of lateral root initiation. In conclusion, we report here on the existence of a peptide ligand-receptor kinase interaction that impacts lateral root initiation. Our results represent an important step towards the understanding of the cellular communication implicated in the early phases of lateral root formation.
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Affiliation(s)
- Ianto Roberts
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Genetics, Ghent University, B-9052 Ghent, Belgium
| | - Stephanie Smith
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - Elisabeth Stes
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Genetics, Ghent University, B-9052 Ghent, Belgium Medical Biotechnology Center, VIB, B-9000 Ghent, Belgium Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Bert De Rybel
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Genetics, Ghent University, B-9052 Ghent, Belgium
| | - An Staes
- Medical Biotechnology Center, VIB, B-9000 Ghent, Belgium Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Brigitte van de Cotte
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Genetics, Ghent University, B-9052 Ghent, Belgium
| | - Maria Fransiska Njo
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Genetics, Ghent University, B-9052 Ghent, Belgium
| | - Lise Dedeyne
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Genetics, Ghent University, B-9052 Ghent, Belgium
| | - Hans Demol
- Medical Biotechnology Center, VIB, B-9000 Ghent, Belgium Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Julien Lavenus
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Genetics, Ghent University, B-9052 Ghent, Belgium
| | - Dominique Audenaert
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Genetics, Ghent University, B-9052 Ghent, Belgium
| | - Kris Gevaert
- Medical Biotechnology Center, VIB, B-9000 Ghent, Belgium Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Genetics, Ghent University, B-9052 Ghent, Belgium
| | - Ive De Smet
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Genetics, Ghent University, B-9052 Ghent, Belgium Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK Centre for Plant Integrative Biology, University of Nottingham, Loughborough LE12 5RD, UK
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44
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Kunert KJ, Vorster BJ, Fenta BA, Kibido T, Dionisio G, Foyer CH. Drought Stress Responses in Soybean Roots and Nodules. FRONTIERS IN PLANT SCIENCE 2016; 7:1015. [PMID: 27462339 PMCID: PMC4941547 DOI: 10.3389/fpls.2016.01015] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/27/2016] [Indexed: 05/18/2023]
Abstract
Drought is considered to be a major threat to soybean production worldwide and yet our current understanding of the effects of drought on soybean productively is largely based on studies on above-ground traits. Although the roots and root nodules are important sensors of drought, the responses of these crucial organs and their drought tolerance features remain poorly characterized. The symbiotic interaction between soybean and rhizobia facilitates atmospheric nitrogen fixation, a process that provides essential nitrogen to support plant growth and development. Symbiotic nitrogen fixation is important for sustainable agriculture, as it sustains plant growth on nitrogen-poor soils and limits fertilizer use for crop nitrogen nutrition. Recent developments have been made in our understanding of the drought impact on soybean root architecture and nodule traits, as well as underpinning transcriptome, proteome and also emerging metabolome information, with a view to improve the selection of more drought-tolerant soybean cultivars and rhizobia in the future. We conclude that the direct screening of root and nodule traits in the field as well as identification of genes, proteins and also metabolites involved in such traits will be essential in order to gain a better understanding of the regulation of root architecture, bacteroid development and lifespan in relation to drought tolerance in soybean.
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Affiliation(s)
- Karl J. Kunert
- Department Plant Production and Soil Science, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Barend J. Vorster
- Department Plant Production and Soil Science, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Berhanu A. Fenta
- Melkassa Agricultural Research Centre, Ethiopian Institute of Agricultural ResearchAdama, Ethiopia
| | - Tsholofelo Kibido
- Department Plant Production and Soil Science, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Giuseppe Dionisio
- Faculty of Science and Technology, Research Centre Flakkebjerg, Department of Molecular Biology and Genetics, Aarhus UniversityAarhus, Denmark
| | - Christine H. Foyer
- Centre for Plant Sciences, School of Biology, Faculty of Biological Sciences, University of LeedsLeeds, UK
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van Dam NM, Bouwmeester HJ. Metabolomics in the Rhizosphere: Tapping into Belowground Chemical Communication. TRENDS IN PLANT SCIENCE 2016; 21:256-265. [PMID: 26832948 DOI: 10.1016/j.tplants.2016.01.008] [Citation(s) in RCA: 252] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/18/2015] [Accepted: 01/06/2016] [Indexed: 05/19/2023]
Abstract
The rhizosphere is densely populated with a variety of organisms. Interactions between roots and rhizosphere community members are mostly achieved via chemical communication. Root exudates contain an array of primary and secondary plant metabolites that can attract, deter, or kill belowground insect herbivores, nematodes, and microbes, and inhibit competing plants. Metabolomics of root exudates can potentially help us to better understand this chemical dialogue. The main limitations are the proper sampling of the exudate, the sensitivity of the metabolomics platforms, and the multivariate data analysis to identify causal relations. Novel technologies may help to generate a spatially explicit metabolome of the root and its exudates at a scale that is relevant for the rhizosphere community.
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Affiliation(s)
- Nicole M van Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany; Institute of Ecology, Friedrich Schiller University Jena, Dornburger-Str. 159, 07743 Jena, Germany; Molecular Interaction Ecology, Institute of Water and Wetland Research (IWWR), Radboud University, PO Box 9010, Nijmegen, GL 6500, The Netherlands.
| | - Harro J Bouwmeester
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, Wageningen, PB 6708, The Netherlands.
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46
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Smakowska E, Kong J, Busch W, Belkhadir Y. Organ-specific regulation of growth-defense tradeoffs by plants. CURRENT OPINION IN PLANT BIOLOGY 2016; 29:129-37. [PMID: 26802804 DOI: 10.1016/j.pbi.2015.12.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/07/2015] [Accepted: 12/08/2015] [Indexed: 05/22/2023]
Abstract
Plants grow while also defending themselves against phylogenetically unrelated pathogens. Because defense and growth are both costly programs, a plant's success in colonizing resource-scarce environments requires tradeoffs between the two. Here, we summarize efforts aimed at understanding how plants use iterative tradeoffs to modulate differential organ growth when defenses are elicited. First, we focus on shoots to illustrate how light, in conjunction with the growth hormone gibberellin (GA) and the defense hormone jasmonic acid (JA), act to finely regulate defense and growth programs in this organ. Second, we expand on the regulation of growth-defense trade-offs in the root, a less well-studied topic despite the critical role of this organ in acquiring resources in an environment deeply entrenched with disparate populations of microbes.
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Affiliation(s)
- Elwira Smakowska
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr Gasse 3, Vienna 1030, Austria
| | - Jixiang Kong
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr Gasse 3, Vienna 1030, Austria
| | - Wolfgang Busch
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr Gasse 3, Vienna 1030, Austria
| | - Youssef Belkhadir
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr Gasse 3, Vienna 1030, Austria.
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47
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Dun X, Tao Z, Wang J, Wang X, Liu G, Wang H. Comparative Transcriptome Analysis of Primary Roots of Brassica napus Seedlings with Extremely Different Primary Root Lengths Using RNA Sequencing. FRONTIERS IN PLANT SCIENCE 2016; 7:1238. [PMID: 27594860 PMCID: PMC4990598 DOI: 10.3389/fpls.2016.01238] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/04/2016] [Indexed: 05/18/2023]
Abstract
Primary root (PR) development is a crucial developmental process that is essential for plant survival. The elucidation of the PR transcriptome provides insight into the genetic mechanism controlling PR development in crops. In this study, we performed a comparative transcriptome analysis to investigate the genome-wide gene expression profiles of the seedling PRs of four Brassica napus genotypes that were divided into two groups, short group (D43 and D61), and long group (D69 and D72), according to their extremely different primary root lengths (PRLs). The results generated 55,341,366-64,631,336 clean reads aligned to 62,562 genes (61.9% of the current annotated genes) in the B. napus genome. We provide evidence that at least 44,986 genes are actively expressed in the B. napus PR. The majority of the genes that were expressed during seedling PR development were associated with metabolism, cellular processes, response to stimulus, biological regulation, and signaling. Using a pairwise comparison approach, 509 differentially expressed genes (DEGs; absolute value of log2 fold-change ≥1 and p ≤ 0.05) between the long and short groups were revealed, including phytohormone-related genes, protein kinases and phosphatases, oxygenase, cytochrome P450 proteins, etc. Combining GO functional category, KEGG, and MapMan pathway analyses indicated that the DEGs involved in cell wall metabolism, carbohydrate metabolism, lipid metabolism, secondary metabolism, protein modification and degradation, hormone pathways and signaling pathways were the main causes of the observed PRL differences. We also identified 16 differentially expressed transcription factors (TFs) involved in PR development. Taken together, these transcriptomic datasets may serve as a foundation for the identification of candidate genes and may provide valuable information for understanding the molecular and cellular events related to PR development.
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48
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Ha CV, Watanabe Y, Tran UT, Le DT, Tanaka M, Nguyen KH, Seki M, Nguyen DV, Tran LSP. Comparative analysis of root transcriptomes from two contrasting drought-responsive Williams 82 and DT2008 soybean cultivars under normal and dehydration conditions. FRONTIERS IN PLANT SCIENCE 2015; 6:551. [PMID: 26300889 PMCID: PMC4528160 DOI: 10.3389/fpls.2015.00551] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 07/06/2015] [Indexed: 05/04/2023]
Abstract
The economically important DT2008 and the model Williams 82 (W82) soybean cultivars were reported to have differential drought-tolerant degree to dehydration and drought, which was associated with root trait. Here, we used 66K Affymetrix Soybean Array GeneChip to compare the root transcriptomes of DT2008 and W82 seedlings under normal, as well as mild (2 h treatment) and severe (10 h treatment) dehydration conditions. Out of the 38172 soybean genes annotated with high confidence, 822 (2.15%) and 632 (1.66%) genes showed altered expression by dehydration in W82 and DT2008 roots, respectively, suggesting that a larger machinery is required to be activated in the drought-sensitive W82 cultivar to cope with the stress. We also observed that long-term dehydration period induced expression change of more genes in soybean roots than the short-term one, independently of the genotypes. Furthermore, our data suggest that the higher drought tolerability of DT2008 might be attributed to the higher number of genes induced in DT2008 roots than in W82 roots by early dehydration, and to the expression changes of more genes triggered by short-term dehydration than those by prolonged dehydration in DT2008 roots vs. W82 roots. Differentially expressed genes (DEGs) that could be predicted to have a known function were further analyzed to gain a basic understanding on how soybean plants respond to dehydration for their survival. The higher drought tolerability of DT2008 vs. W82 might be attributed to differential expression in genes encoding osmoprotectant biosynthesis-, detoxification- or cell wall-related proteins, kinases, transcription factors and phosphatase 2C proteins. This research allowed us to identify genetic components that contribute to the improved drought tolerance of DT2008, as well as provide a useful genetic resource for in-depth functional analyses that ultimately leads to development of soybean cultivars with improved tolerance to drought.
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Affiliation(s)
- Chien Van Ha
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- National Key Laboratory for Plant Cell Technology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural ScienceHanoi, Vietnam
| | - Yasuko Watanabe
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Uyen Thi Tran
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Dung Tien Le
- National Key Laboratory for Plant Cell Technology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural ScienceHanoi, Vietnam
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Kien Huu Nguyen
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- National Key Laboratory for Plant Cell Technology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural ScienceHanoi, Vietnam
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- CREST, Japan Science and Technology AgencyKawaguchi, Japan
| | - Dong Van Nguyen
- National Key Laboratory for Plant Cell Technology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural ScienceHanoi, Vietnam
| | - Lam-Son Phan Tran
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- *Correspondence: Lam-Son Phan Tran, Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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