501
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Giri J, Bhosale R, Huang G, Pandey BK, Parker H, Zappala S, Yang J, Dievart A, Bureau C, Ljung K, Price A, Rose T, Larrieu A, Mairhofer S, Sturrock CJ, White P, Dupuy L, Hawkesford M, Perin C, Liang W, Peret B, Hodgman CT, Lynch J, Wissuwa M, Zhang D, Pridmore T, Mooney SJ, Guiderdoni E, Swarup R, Bennett MJ. Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate. Nat Commun 2018; 9:1408. [PMID: 29650967 PMCID: PMC5897452 DOI: 10.1038/s41467-018-03850-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/16/2018] [Indexed: 11/09/2022] Open
Abstract
Root traits such as root angle and hair length influence resource acquisition particularly for immobile nutrients like phosphorus (P). Here, we attempted to modify root angle in rice by disrupting the OsAUX1 auxin influx transporter gene in an effort to improve rice P acquisition efficiency. We show by X-ray microCT imaging that root angle is altered in the osaux1 mutant, causing preferential foraging in the top soil where P normally accumulates, yet surprisingly, P acquisition efficiency does not improve. Through closer investigation, we reveal that OsAUX1 also promotes root hair elongation in response to P limitation. Reporter studies reveal that auxin response increases in the root hair zone in low P environments. We demonstrate that OsAUX1 functions to mobilize auxin from the root apex to the differentiation zone where this signal promotes hair elongation when roots encounter low external P. We conclude that auxin and OsAUX1 play key roles in promoting root foraging for P in rice. Plant root architecture can adapt to different nutrient conditions in the soil. Here Giri et al. show that the rice auxin influx carrier AUX1 mobilizes auxin from the root apex to the differentiation zone and promotes root hair elongation when roots encounter low external phosphate.
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Affiliation(s)
- Jitender Giri
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Rahul Bhosale
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Guoqiang Huang
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University, Shanghai, China
| | - Bipin K Pandey
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Helen Parker
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Susan Zappala
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Jing Yang
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University, Shanghai, China
| | - Anne Dievart
- CIRAD, UMR AGAP, F34398, Montpellier, Cedex 5, France
| | | | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden
| | - Adam Price
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Terry Rose
- Japan International Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan.,Southern Cross Plant Science, Southern Cross University, Lismore, NSW, 2480, Australia
| | - Antoine Larrieu
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Stefan Mairhofer
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,School of Computer Science, University of Nottingham, Jubilee Campus, Nottingham, NG8 1BB, UK
| | - Craig J Sturrock
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Philip White
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Lionel Dupuy
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | | | | | - Wanqi Liang
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University, Shanghai, China
| | - Benjamin Peret
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Charlie T Hodgman
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Jonathan Lynch
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,Department of Plant Science, The Pennsylvania State University, 102 Tyson Building, University Park, PA, 16802, USA
| | - Matthias Wissuwa
- Japan International Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - Dabing Zhang
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University, Shanghai, China.,University of Adelaide-SJTU Joint Centre for Agriculture and Health, University of Adelaide, Waite Campus, Urrbrae, SA, Australia
| | - Tony Pridmore
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,School of Computer Science, University of Nottingham, Jubilee Campus, Nottingham, NG8 1BB, UK
| | - Sacha J Mooney
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | | | - Ranjan Swarup
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Malcolm J Bennett
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.
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502
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Sreeman SM, Vijayaraghavareddy P, Sreevathsa R, Rajendrareddy S, Arakesh S, Bharti P, Dharmappa P, Soolanayakanahally R. Introgression of Physiological Traits for a Comprehensive Improvement of Drought Adaptation in Crop Plants. Front Chem 2018; 6:92. [PMID: 29692985 PMCID: PMC5903164 DOI: 10.3389/fchem.2018.00092] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 03/14/2018] [Indexed: 11/23/2022] Open
Abstract
Burgeoning population growth, industrial demand, and the predicted global climate change resulting in erratic monsoon rains are expected to severely limit fresh water availability for agriculture both in irrigated and rainfed ecosystems. In order to remain food and nutrient secure, agriculture research needs to focus on devising strategies to save water in irrigated conditions and to develop superior cultivars with improved water productivity to sustain yield under rainfed conditions. Recent opinions accruing in the scientific literature strongly favor the adoption of a "trait based" crop improvement approach for increasing water productivity. Traits associated with maintenance of positive tissue turgor and maintenance of increased carbon assimilation are regarded as most relevant to improve crop growth rates under water limiting conditions and to enhance water productivity. The advent of several water saving agronomic practices notwithstanding, a genetic enhancement strategy of introgressing distinct physiological, morphological, and cellular mechanisms on to a single elite genetic background is essential for achieving a comprehensive improvement in drought adaptation in crop plants. The significant progress made in genomics, though would provide the necessary impetus, a clear understanding of the "traits" to be introgressed is the most essential need of the hour. Water uptake by a better root architecture, water conservation by preventing unproductive transpiration are crucial for maintaining positive tissue water relations. Improved carbon assimilation associated with carboxylation capacity and mesophyll conductance is important in sustaining crop growth rates under water limited conditions. Besides these major traits, we summarize the available information in literature on classifying various drought adaptive traits. We provide evidences that Water-Use Efficiency when introgressed with moderately higher transpiration, would significantly enhance growth rates and water productivity in rice through an improved photosynthetic capacity.
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Affiliation(s)
| | | | - Rohini Sreevathsa
- ICAR-National Research Centre for Plant Biotechnology, New Delhi, India
| | - Sowmya Rajendrareddy
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
| | - Smitharani Arakesh
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
| | - Pooja Bharti
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
| | - Prathibha Dharmappa
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
| | - Raju Soolanayakanahally
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
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503
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Mackill DJ, Khush GS. IR64: a high-quality and high-yielding mega variety. RICE (NEW YORK, N.Y.) 2018; 11:18. [PMID: 29629479 PMCID: PMC5890005 DOI: 10.1186/s12284-018-0208-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/14/2018] [Indexed: 05/05/2023]
Abstract
High-yielding varieties developed in the 1960s and 1970s at the International Rice Research Institute (IRRI) and elsewhere benefited farmers and the public, ultimately increasing yields and reducing the cost of rice to consumers. Most of these varieties, however, did not have the optimum cooking quality that was possessed by many of the traditional varieties they replaced. In 1985, the IRRI-developed indica variety IR64 was released in the Philippines. In addition to its high yield, early maturity and disease resistance, it had excellent cooking quality, matching that of the best varieties available. These merits resulted in its rapid spread and cultivation on over 10 million ha in the two decades after it was released. It has intermediate amylose content and gelatinization temperature, and good taste. It is resistant to blast and bacterial blight diseases, and to brown planthopper. Because of its success as a variety, it has been used extensively in scientific studies and has been well-characterized genetically. Many valuable genes have been introduced into IR64 through backcross breeding and it has been used in thousands of crosses. Its area of cultivation has declined in the past 10 years, but it has been replaced by a new generation of high-quality varieties that are mostly its progeny or relatives. Continued basic studies on IR64 and related varieties should help in unraveling the complex genetic control of yield and other desirable traits that are prized by rice farmers and consumers.
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Affiliation(s)
- David J Mackill
- Mars, Inc. and Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Gurdev S Khush
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
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504
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Canto CDLF, Kalogiros DI, Ptashnyk M, George TS, Waugh R, Bengough AG, Russell J, Dupuy LX. Morphological and genetic characterisation of the root system architecture of selected barley recombinant chromosome substitution lines using an integrated phenotyping approach. J Theor Biol 2018; 447:84-97. [PMID: 29559229 DOI: 10.1016/j.jtbi.2018.03.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/12/2018] [Accepted: 03/13/2018] [Indexed: 11/27/2022]
Abstract
Discoveries on the genetics of resource acquisition efficiency are limited by the ability to measure plant roots in sufficient number and with adequate genotypic variability. This paper presents a root phenotyping study that explores ways to combine live imaging and computer algorithms for model-based extraction of root growth parameters. The study is based on a subset of barley Recombinant Chromosome Substitution Lines (RCSLs) and a combinatorial approach was designed for fast identification of the regions of the genome that contribute the most to variations in root system architecture (RSA). Results showed there was a strong genotypic variation in root growth parameters within the set of genotypes studied. The chromosomal regions associated with primary root growth differed from the regions of the genome associated with changes in lateral root growth. The concepts presented here are discussed in the context of identifying root QTL and its potential to assist breeding for novel crops with improved root systems.
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Affiliation(s)
- C De La Fuente Canto
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom ; School of Life Sciences, University of Dundee, Dundee DD2 1PP, United Kingdom
| | - D I Kalogiros
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom ; School of Science and Engineering, University of Dundee, Dundee DD2 1PP, United Kingdom
| | - M Ptashnyk
- School of Science and Engineering, University of Dundee, Dundee DD2 1PP, United Kingdom
| | - T S George
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - R Waugh
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - A G Bengough
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom ; School of Science and Engineering, University of Dundee, Dundee DD2 1PP, United Kingdom
| | - J Russell
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - L X Dupuy
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom .
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505
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Suralta RR, Niones JM, Kano-Nakata M, Thi Tran T, Mitsuya S, Yamauchi A. Plasticity in nodal root elongation through the hardpan triggered by rewatering during soil moisture fluctuation stress in rice. Sci Rep 2018. [PMID: 29531273 PMCID: PMC5847610 DOI: 10.1038/s41598-018-22809-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Rainfed lowland (RFL) rice fields have hardpans and experience soil moisture fluctuations (SMF) stress, which influence root system development. Here, we clarify the expression and timing of the plasticity in nodal root elongation through the hardpan under SMF and its contribution to shoot growth using a shallow-rooting IR64 and its deep-rooting introgression line, YTH304. Under SMF, soil moisture content had negative relationship with soil penetration resistance, regardless of hardpan bulk densities. YTH304 had greater root system below the hardpan than IR64 in hardpan with 1.50 but not in 1.70 g cm-3 bulk density (BD). YTH304 had greater plasticity in nodal root elongation through the hardpan than IR64 under SMF, which was clearly expressed during rewatering. YTH304 also had greater soil water uptake below the hardpan during drought and greater shoot growth than IR64. The results imply that deep root system development during SMF was due to the plasticity in nodal root elongation through the hardpan expressed during rewatering rather than during drought periods. This is against the long standing belief that active root elongation through the hardpan happens during drought. This also implies a need to revisit current root screening methods to identify rice lines with good hardpan penetration ability.
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Affiliation(s)
- Roel Rodriguez Suralta
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464 8601, Japan.,Crop Biotechnology Center, Philippine Rice Research Institute, Maligaya, Science City of Muñoz, Nueva Ecija, 3119, Philippines
| | - Jonathan Manito Niones
- Crop Biotechnology Center, Philippine Rice Research Institute, Maligaya, Science City of Muñoz, Nueva Ecija, 3119, Philippines
| | - Mana Kano-Nakata
- International Cooperation Center for Agricultural Education, Nagoya University, Nagoya, 464 8601, Japan
| | - Thiem Thi Tran
- Faculty of Agronomy, Vietnam National University of Agriculture, Trauquy, Gialam, Hanoi, Vietnam
| | - Shiro Mitsuya
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464 8601, Japan
| | - Akira Yamauchi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464 8601, Japan.
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506
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Shi R, Junker A, Seiler C, Altmann T. Phenotyping roots in darkness: disturbance-free root imaging with near infrared illumination. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:400-411. [PMID: 32290980 DOI: 10.1071/fp17262] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 10/30/2017] [Indexed: 06/11/2023]
Abstract
Root systems architecture (RSA) and size properties are essential determinants of plant performance and need to be assessed in high-throughput plant phenotyping platforms. Thus, we tested a concept that involves near-infrared (NIR) imaging of roots growing along surfaces of transparent culture vessels using special long pass filters to block their exposure to visible light. Two setups were used to monitor growth of Arabidopsis, rapeseed, barley and maize roots upon exposure to white light, filter-transmitted radiation or darkness: root growth direction was analysed (1) through short-term cultivation on agar plates, and (2) using soil-filled transparent pots to monitor long-term responses. White light-triggered phototropic responses were detected for Arabidopsis in setup 1, and for rapeseed, barley and maize roots in setups 1 and 2, whereas light effects could be avoided by use of the NIR filter thus confirming its suitability to mimic darkness. NIR image-derived 'root volume' values correlated well with root dry weight. The root system fractions visible at the different pot sides and in different zones revealed species- and genotype-dependent variation of spatial root distribution and other RSA traits. Following this validated concept, root imaging setups may be integrated into shoot phenotyping facilities in order to enable root system analysis in the context of whole-plant performance investigations.
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Affiliation(s)
- Rongli Shi
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Astrid Junker
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Christiane Seiler
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Thomas Altmann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
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507
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Genome-wide association study to identify candidate loci and genes for Mn toxicity tolerance in rice. PLoS One 2018; 13:e0192116. [PMID: 29425206 PMCID: PMC5806864 DOI: 10.1371/journal.pone.0192116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/18/2018] [Indexed: 11/19/2022] Open
Abstract
Manganese (Mn) is an essential micro-nutrient for plants, but flooded rice fields can accumulate high levels of Mn2+ leading to Mn toxicity. Here, we present a genome-wide association study (GWAS) to identify candidate loci conferring Mn toxicity tolerance in rice (Oryza sativa L.). A diversity panel of 288 genotypes was grown in hydroponic solutions in a greenhouse under optimal and toxic Mn concentrations. We applied a Mn toxicity treatment (5 ppm Mn2+, 3 weeks) at twelve days after transplanting. Mn toxicity caused moderate damage in rice in terms of biomass loss and symptom formation despite extremely high shoot Mn concentrations ranging from 2.4 to 17.4 mg g-1. The tropical japonica subpopulation was more sensitive to Mn toxicity than other subpopulations. Leaf damage symptoms were significantly correlated with Mn uptake into shoots. Association mapping was conducted for seven traits using 416741 single nucleotide polymorphism (SNP) markers using a mixed linear model, and detected six significant associations for the traits shoot manganese concentration and relative shoot length. Candidate regions contained genes coding for a heavy metal transporter, peroxidase precursor and Mn2+ ion binding proteins. The significant marker SNP-2.22465867 caused an amino acid change in a gene (LOC_Os02g37170) with unknown function. This study demonstrated significant natural variation in rice for Mn toxicity tolerance and the possibility of using GWAS to unravel genetic factors responsible for such complex traits.
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508
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Bin Rahman ANMR, Zhang J. Preferential Geographic Distribution Pattern of Abiotic Stress Tolerant Rice. RICE (NEW YORK, N.Y.) 2018; 11:10. [PMID: 29423779 PMCID: PMC5805671 DOI: 10.1186/s12284-018-0202-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 01/17/2018] [Indexed: 05/06/2023]
Abstract
Crop productivity and stability of the food system are threatened by climate change, mainly through the effects of predicted abiotic stresses. Despite extensive research on abiotic stress tolerance in the past decades, the successful translation of these research to fields/farmers is scarce. The impelling demand of climate resilient varieties, and the poor translation of research into the field despite the availability of high throughput technologies lead us to critically analyse a neglected aspect of current abiotic stress tolerance research. Although environmental factors play the most important role in the development of adaptive traits of plants, most abiotic stress tolerance research ignores eco-geographic aspects of highly stress tolerant accessions. In this review, we critically examined the geographic distribution pattern of highly tolerant rice accessions of all major abiotic stresses along with one micronutrient deficiency. Remarkably, we identified a shared geographic distribution pattern of highly tolerant accessions for all abiotic stresses including zinc deficiency despite the sparseness of highly tolerant accessions. The majority of these tolerant accessions predominately originated from Bangladesh centred narrow geographic region. We therefore analysed the climatic and agro-ecological features of Bangladesh. Considering the threat of climate change on global food security and poverty, urgent concerted research efforts are necessary for the development of climate resilient rice varieties utilizing the technological advancement, know-hows, and the preferential distribution pattern of abiotic stress tolerant rice.
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Affiliation(s)
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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509
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Fine Mapping of QUICK ROOTING 1 and 2, Quantitative Trait Loci Increasing Root Length in Rice. G3-GENES GENOMES GENETICS 2018; 8:727-735. [PMID: 29279303 PMCID: PMC5919730 DOI: 10.1534/g3.117.300147] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The volume that the root system can occupy is associated with the efficiency of water and nutrient uptake from soil. Genetic improvement of root length, which is a limiting factor for root distribution, is necessary for increasing crop production. In this report, we describe identification of two quantitative trait loci (QTLs) for maximal root length, QUICK ROOTING 1 (QRO1) on chromosome 2 and QRO2 on chromosome 6, in cultivated rice (Oryza sativa L.). We measured the maximal root length in 26 lines carrying chromosome segments from the long-rooted upland rice cultivar Kinandang Patong in the genetic background of the short-rooted lowland cultivar IR64. Five lines had longer roots than IR64. By rough mapping of the target regions in BC4F2 populations, we detected putative QTLs for maximal root length on chromosomes 2, 6, and 8. To fine-map these QTLs, we used BC4F3 recombinant homozygous lines. QRO1 was mapped between markers RM5651 and RM6107, which delimit a 1.7-Mb interval on chromosome 2, and QRO2 was mapped between markers RM20495 and RM3430-1, which delimit an 884-kb interval on chromosome 6. Both QTLs may be promising gene resources for improving root system architecture in rice.
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510
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Chen D, Chai S, McIntyre CL, Xue GP. Overexpression of a predominantly root-expressed NAC transcription factor in wheat roots enhances root length, biomass and drought tolerance. PLANT CELL REPORTS 2018; 37:225-237. [PMID: 29079898 DOI: 10.1007/s00299-017-2224-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 10/05/2017] [Indexed: 05/10/2023]
Abstract
TaRNAC1 is a constitutively and predominantly root-expressed NAC transcription factor. TaRNAC1 overexpression in wheat roots confers increased root length, biomass and drought tolerance and improved grain yield under water limitation. A large and deep root system is an important trait for yield sustainability of dryland cereal crops in drought-prone environments. This study investigated the role of a predominantly root-expressed NAC transcription factor from wheat (TaRNAC1) in the root growth. Expression analysis showed that TaRNAC1 was a constitutively expressed gene with high level expression in the roots and was not drought-upregulated. Overexpression of TaRNAC1 in wheat using a predominantly root-expressed promoter resulted in increased root length and biomass observed at the early growth stage and a marked increase in the maturity root biomass with dry root weight of > 70% higher than that of the wild type plants. Analysis of some root growth-related genes revealed that the expression level of GA3-ox2, which encodes GIBBERELLIN 3-OXIDASE catalysing the conversion of inactive gibberellin (GA) to active GA, was elevated in the roots of transgenic wheat. TaRNAC1 overexpressing transgenic wheat showed more dehydration tolerance under polyethylene glycol (PEG) treatment and produced more aboveground biomass and grain under water-limited conditions than the wild type plants. These data suggest that TaRNAC1 may play a role in root growth and be used as a molecular tool for potential enlargement of root system in wheat.
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Affiliation(s)
- Dandan Chen
- College of Agronomy, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, People's Republic of China
- CSIRO Agriculture and Food, 306 Carmody Rd., St Lucia, QLD, 4067, Australia
| | - Shoucheng Chai
- College of Agronomy, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - C Lynne McIntyre
- CSIRO Agriculture and Food, 306 Carmody Rd., St Lucia, QLD, 4067, Australia
| | - Gang-Ping Xue
- CSIRO Agriculture and Food, 306 Carmody Rd., St Lucia, QLD, 4067, Australia.
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511
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Casartelli A, Riewe D, Hubberten HM, Altmann T, Hoefgen R, Heuer S. Exploring traditional aus-type rice for metabolites conferring drought tolerance. RICE (NEW YORK, N.Y.) 2018; 11:9. [PMID: 29372429 PMCID: PMC5785456 DOI: 10.1186/s12284-017-0189-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/22/2017] [Indexed: 05/07/2023]
Abstract
BACKGROUND Traditional varieties and landraces belonging to the aus-type group of rice (Oryza sativa L.) are known to be highly tolerant to environmental stresses, such as drought and heat, and are therefore recognized as a valuable genetic resource for crop improvement. Using two aus-type (Dular, N22) and two drought intolerant irrigated varieties (IR64, IR74) an untargeted metabolomics analysis was conducted to identify drought-responsive metabolites associated with tolerance. RESULTS The superior drought tolerance of Dular and N22 compared with the irrigated varieties was confirmed by phenotyping plants grown to maturity after imposing severe drought stress in a dry-down treatment. Dular and N22 did not show a significant reduction in grain yield compared to well-watered control plants, whereas the intolerant varieties showed a significant reduction in both, total spikelet number and grain yield. The metabolomics analysis was conducted with shoot and root samples of plants at the tillering stage at the end of the dry-down treatment. The data revealed an overall higher accumulation of N-rich metabolites (amino acids and nucleotide-related metabolites allantoin and uridine) in shoots of the tolerant varieties. In roots, the aus-type varieties were characterised by a higher reduction of metabolites representative of glycolysis and the TCA cycle, such as malate, glyceric acid and glyceric acid-3-phosphate. On the other hand, the oligosaccharide raffinose showed a higher fold increase in both, shoots and roots of the sensitive genotypes. The data further showed that, for certain drought-responsive metabolites, differences between the contrasting rice varieties were already evident under well-watered control conditions. CONCLUSIONS The drought tolerance-related metabolites identified in the aus-type varieties provide a valuable set of protective compounds and an entry point for assessing genetic diversity in the underlying pathways for developing drought tolerant rice and other crops.
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Affiliation(s)
- Alberto Casartelli
- School of Agriculture, Food and Wine, Waite Campus, The University of Adelaide, Adelaide, SA Australia
| | - David Riewe
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Berlin, Germany
| | | | - Thomas Altmann
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Berlin, Germany
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Sigrid Heuer
- School of Agriculture, Food and Wine, Waite Campus, The University of Adelaide, Adelaide, SA Australia
- Rothamsted Research, Harpenden, UK
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512
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Wang L, Guo M, Li Y, Ruan W, Mo X, Wu Z, Sturrock CJ, Yu H, Lu C, Peng J, Mao C. LARGE ROOT ANGLE1, encoding OsPIN2, is involved in root system architecture in rice. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:385-397. [PMID: 29294052 PMCID: PMC5853395 DOI: 10.1093/jxb/erx427] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 11/13/2017] [Indexed: 05/17/2023]
Abstract
Root system architecture is very important for plant growth and crop yield. It is essential for nutrient and water uptake, anchoring, and mechanical support. Root growth angle (RGA) is a vital constituent of root system architecture and is used as a parameter for variety evaluation in plant breeding. However, little is known about the underlying molecular mechanisms that determine root growth angle in rice (Oryza sativa). In this study, a rice mutant large root angle1 (lra1) was isolated and shown to exhibit a large RGA and reduced sensitivity to gravity. Genome resequencing and complementation assays identified OsPIN2 as the gene responsible for the mutant phenotypes. OsPIN2 was mainly expressed in roots and the base of shoots, and showed polar localization in the plasma membrane of root epidermal and cortex cells. OsPIN2 was shown to play an important role in mediating root gravitropic responses in rice and was essential for plants to produce normal RGAs. Taken together, our findings suggest that OsPIN2 plays an important role in root gravitropic responses and determining the root system architecture in rice by affecting polar auxin transport in the root tip.
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Affiliation(s)
- Lingling Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Mengxue Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Wenyuan Ruan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xiaorong Mo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhongchang Wu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Craig J Sturrock
- The Hounsfield Facility, School of Biosciences, University of Nottingham, Nottingham, UK
| | - Hao Yu
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore
| | - Chungui Lu
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Nottingham, UK
| | - Jinrong Peng
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chuanzao Mao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
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513
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Solis J, Gutierrez A, Mangu V, Sanchez E, Bedre R, Linscombe S, Baisakh N. Genetic Mapping of Quantitative Trait Loci for Grain Yield under Drought in Rice under Controlled Greenhouse Conditions. Front Chem 2018; 5:129. [PMID: 29359127 PMCID: PMC5766644 DOI: 10.3389/fchem.2017.00129] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 12/20/2017] [Indexed: 02/05/2023] Open
Abstract
Drought stress is a constant threat to rice production worldwide. Most modern rice cultivars are sensitive to drought, and the effect is severe at the reproductive stage. Conventional breeding for drought resistant (DR) rice varieties is slow and limited due to the quantitative nature of the DR traits. Identification of genes (QTLs)/markers associated with DR traits is a prerequisite for marker-assisted breeding. Grain yield is the most important trait and to this end drought yield QTLs have been identified under field conditions. The present study reports identification of drought yield QTLs under controlled conditions without confounding effects of other factors prevalent under natural conditions. A linkage map covering 1,781.5 cM with an average resolution of 9.76 cM was constructed using an F2 population from a cross between two Japonica cultivars, Cocodrie (drought sensitive) and Vandana (drought tolerant) with 213 markers distributed over 12 rice chromosomes. A subset of 59 markers (22 genic SSRs and 37 SNPs) derived from the transcriptome of the parents were also placed in the map. Single marker analysis using 187 F2 : 3 progeny identified 6 markers distributed on chromosomes 1, 5, and 8 to be associated with grain yield under drought (GYD). Composite interval mapping identified six genomic regions/quantitative trait loci (QTL) on chromosome 1, 5, 8, and 9 to be associated with GYD. QTLs located on chromosome 1 (qGYD1.2, qGYD1.3), chromosome 5 (qGYD5.1) and chromosome 8 (qGYD8.1) were contributed by Vandana alleles, whereas the QTLs, qGYD1.1 and qQYD9.1 were contributed by Cocodrie alelles. The additive positive phenotypic variance explained by the QTLs ranged from 30.0 to 34.0%. Candidate genes annotation within QTLs suggested the role of transcription factors and genes involved in osmotic potential regulation through catalytic/metabolic pathways in drought tolerance mechanism contributing to yield.
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Affiliation(s)
- Julio Solis
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States.,Instituto de Biotecnología, Universidad Nacional Agraria La Molina, Lima, Peru
| | - Andres Gutierrez
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Venkata Mangu
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States.,Department of Biochemistry, University of Pennsylvania, Philadelphia, PA, United States
| | - Eduardo Sanchez
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States.,Center for Biotechnology Investigation, Escuela Superior Politecnica del Litoral, Guayaquil, Ecuador
| | - Renesh Bedre
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States.,Texas A&M AgriLife Research Station, Weslaco, TX, United States
| | - Steve Linscombe
- Rice Research Station, Louisiana State University Agricultural Center, Crowley, LA, United States
| | - Niranjan Baisakh
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
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514
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Voss-Fels KP, Robinson H, Mudge SR, Richard C, Newman S, Wittkop B, Stahl A, Friedt W, Frisch M, Gabur I, Miller-Cooper A, Campbell BC, Kelly A, Fox G, Christopher J, Christopher M, Chenu K, Franckowiak J, Mace ES, Borrell AK, Eagles H, Jordan DR, Botella JR, Hammer G, Godwin ID, Trevaskis B, Snowdon RJ, Hickey LT. VERNALIZATION1 Modulates Root System Architecture in Wheat and Barley. MOLECULAR PLANT 2018; 11:226-229. [PMID: 29056533 DOI: 10.1016/j.molp.2017.10.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/09/2017] [Accepted: 10/11/2017] [Indexed: 05/18/2023]
Affiliation(s)
- Kai P Voss-Fels
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Hannah Robinson
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Stephen R Mudge
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Cecile Richard
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Saul Newman
- CSIRO, Agriculture, Canberra, ACT 2601, Australia
| | - Benjamin Wittkop
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Andreas Stahl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Wolfgang Friedt
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Matthias Frisch
- Department of Biometry and Population Genetics, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Iulian Gabur
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Anika Miller-Cooper
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Bradley C Campbell
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Alison Kelly
- Department of Agriculture and Fisheries, Leslie Research Facility, Toowoomba, QLD 4350, Australia
| | - Glen Fox
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Toowoomba, QLD 4350, Australia
| | - Jack Christopher
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Toowoomba, QLD 4350, Australia
| | - Mandy Christopher
- Department of Agriculture and Fisheries, Leslie Research Facility, Toowoomba, QLD 4350, Australia
| | - Karine Chenu
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Toowoomba, QLD 4350, Australia
| | - Jerome Franckowiak
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN, USA
| | - Emma S Mace
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD 4370, Australia
| | - Andrew K Borrell
- Queensland Alliance for Agriculture and Food Innovation, Hermitage Research Facility, The University of Queensland, Warwick, QLD 4370, Australia
| | | | - David R Jordan
- Queensland Alliance for Agriculture and Food Innovation, Hermitage Research Facility, The University of Queensland, Warwick, QLD 4370, Australia
| | - José R Botella
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Graeme Hammer
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Ian D Godwin
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia.
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515
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Wang Y, Zhang T, Wang R, Zhao Y. Recent advances in auxin research in rice and their implications for crop improvement. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:255-263. [PMID: 28992208 DOI: 10.1093/jxb/erx228] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/08/2017] [Indexed: 05/18/2023]
Abstract
Auxin is essential for various aspects of plant development, and modulation of auxin pathways has great potential for crop improvement. Although the current understanding of auxin biology including auxin biosynthesis, transport, and signaling mainly originated from studies in Arabidopsis, several key auxin genes were first discovered in rice, indicating that it is useful to employ several plant systems for auxin research. In this review, we summarize the recent advances in auxin biology in rice, highlight the main contributions of rice research to auxin biology, and discuss the potential for crop improvement through modulating auxin pathways.
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Affiliation(s)
- Yidong Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, China
| | - Tao Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, China
| | - Rongchen Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, China
| | - Yunde Zhao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, China
- Section of Cell and Developmental Biology, University of California San Diego, USA
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516
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Chandran AKN, Bhatnagar N, Yoo YH, Moon S, Park SA, Hong WJ, Kim BG, An G, Jung KH. Meta-expression analysis of unannotated genes in rice and approaches for network construction to suggest the probable roles. PLANT MOLECULAR BIOLOGY 2018; 96:17-34. [PMID: 29086189 DOI: 10.1007/s11103-017-0675-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 10/22/2017] [Indexed: 06/07/2023]
Abstract
This work suggests 2020 potential candidates in rice for the functional annotation of unannotated genes using meta-analysis of anatomical samples derived from microarray and RNA-seq technologies and this information will be useful to identify novel morphological agronomic traits. Although the genome of rice (Oryza sativa) has been sequenced, 14,365 genes are considered unannotated because they lack putative annotation information. According to the Rice Genome Annotation Project Database ( http://rice.plantbiology.msu.edu/ ), the proportion of functionally characterized unannotated genes (0.35%) is quite limited when compared with the approximately 3.9% of annotated genes with assigned putative functions. Researchers require additional information to help them investigate the molecular mechanisms associated with those unannotated genes. To determine which of them might regulate morphological or physiological traits in the rice genome, we conducted a meta-analysis of expression data that covered a wide range of tissue/organ samples. Overall, 2020 genes showed cultivar-, tissue-, or organ-preferential patterns of expression. Representative candidates from featured groups were validated by RT-PCR, and the GUS reporter system was used to validate the expression of genes that were clustered according to their leaf or root preference. Taking a molecular and genetics approach, we examined meta-expression data and found that 127 genes were differentially expressed between japonica and indica rice cultivars. This is potentially significant for future agronomic applications. We also used a T-DNA insertional mutant and performed a co-expression network analysis of Sword shape dwarf1 (SSD1), a gene that regulates cell division. This network was refined via RT-PCR analysis. Our results suggested that SSD1 represses the expression of four genes related to the processes of DNA replication or cell division and provides insight into possible molecular mechanisms. Together, these strategies present a valuable tool for in-depth characterization of currently unannotated genes.
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Affiliation(s)
- Anil Kumar Nalini Chandran
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Nikita Bhatnagar
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
- Molecular Breeding Division, National Academy of Agricultural Science, RDA, Jeonju, 54875, Republic of Korea
| | - Yo-Han Yoo
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Sunok Moon
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Sun-Ah Park
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Woo-Jong Hong
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Beom-Gi Kim
- Molecular Breeding Division, National Academy of Agricultural Science, RDA, Jeonju, 54875, Republic of Korea
| | - Gynheung An
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea.
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517
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Li P, Zhang Y, Yin S, Zhu P, Pan T, Xu Y, Wang J, Hao D, Fang H, Xu C, Yang Z. QTL-By-Environment Interaction in the Response of Maize Root and Shoot Traits to Different Water Regimes. FRONTIERS IN PLANT SCIENCE 2018; 9:229. [PMID: 29527220 PMCID: PMC5829059 DOI: 10.3389/fpls.2018.00229] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 02/08/2018] [Indexed: 05/19/2023]
Abstract
Drought is a major abiotic stress factor limiting maize production, and elucidating the genetic control of root system architecture and plasticity to water-deficit stress is a crucial problem to improve drought adaptability. In this study, 13 root and shoot traits and genetic plasticity were evaluated in a recombinant inbred line (RIL) population under well-watered (WW) and water stress (WS) conditions. Significant phenotypic variation was observed for all observed traits both under WW and WS conditions. Most of the measured traits showed significant genotype-environment interaction (GEI) in both environments. Strong correlations were observed among traits in the same class. Multi-environment (ME) and multi-trait (MT) QTL analyses were conducted for all observed traits. A total of 48 QTLs were identified by ME, including 15 QTLs associated with 9 traits showing significant QTL-by-Environment interactions (QEI). QTLs associated with crown root angle (CRA2) and crown root length (CRL1) were identified as having antagonistic pleiotropic effects, while 13 other QTLs showed signs of conditional neutrality (CN), including 9 and 4 QTLs detected under WW and WS conditions, respectively. MT analysis identified 14 pleiotropic QTLs for 13 traits, SNP20 (1@79.2 cM) was associated with the length of crown root (CR), primary root (PR), and seminal root (SR) and might contribute to increases in root length under WS condition. Taken together, these findings contribute to our understanding of the phenotypic and genotypic patterns of root plasticity in response to water deficiency, which will be useful to improve drought tolerance in maize.
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Affiliation(s)
- Pengcheng Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Yingying Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Shuangyi Yin
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Pengfei Zhu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Ting Pan
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Yang Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Jieyu Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Derong Hao
- Nantong Key Laboratory for Exploitation of Crop Genetic Resources and Molecular Breeding, Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, China
| | - Huimin Fang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Chenwu Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
- *Correspondence: Chenwu Xu
| | - Zefeng Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
- Zefeng Yang
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518
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Huang L, Wang Y, Wang W, Zhao X, Qin Q, Sun F, Hu F, Zhao Y, Li Z, Fu B, Li Z. Characterization of Transcription Factor Gene OsDRAP1 Conferring Drought Tolerance in Rice. FRONTIERS IN PLANT SCIENCE 2018; 9:94. [PMID: 29449862 PMCID: PMC5799227 DOI: 10.3389/fpls.2018.00094] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 01/17/2018] [Indexed: 05/21/2023]
Abstract
HIGHLIGHTS Overexpressing and RNA interfering OsDRAP1 transgenic rice plants exhibited significantly improved and reduced drought tolerance, but accompanied with negative effects on development and yield. The dehydration responsive element binding (DREBs) genes are important transcription factors which play a crucial role in plant abiotic stress tolerances. In this study, we functionally characterized a DREB2-like gene, OsDRAP1 conferring drought tolerance (DT) in rice. OsDRAP1, containing many cis-elements in its promoter region, was expressed in all organs (mainly expressed in vascular tissues) of rice, and induced by a variety of environmental stresses and plant hormones. Overexpressing OsDRAP1 transgenic plants exhibited significantly improved DT; while OsDRAP1 RNA interfering plants exhibited significantly reduced DT which also accompanied with significant negative effects on development and yield. Overexpression of OsDRAP1 has a positive impact on maintaining water balance, redox homeostasis and vascular development in transgenic rice plants under drought stress. OsDRAP1 interacted with many genes/proteins and could activate many downstream DT related genes, including important transcription factors such as OsCBSX3 to response drought stress, indicating the OsDRAP1-mediated pathways for DT involve complex genes networks. All these results provide a basis for further complete understanding of the OsDRAP1 mediated gene networks and their related phenotypic effects.
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Affiliation(s)
- Liyu Huang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- School of Agriculture, Yunnan University, Yunnan, China
| | - Yinxiao Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wensheng Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiuqin Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiao Qin
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fan Sun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fengyi Hu
- School of Agriculture, Yunnan University, Yunnan, China
| | - Yan Zhao
- Key Lab of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Zichao Li
- Key Lab of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Binying Fu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Shenzhen Institute for Innovative Breeding, Chinese Academy of Agricultural Sciences, Shenzhen, China
- *Correspondence: Binying Fu
| | - Zhikang Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Shenzhen Institute for Innovative Breeding, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Zhikang Li
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519
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Moon S, Chandran AKN, Gho YS, Park SA, Kim SR, Yoo YH, Jung KH. Integrated omics analysis of root-preferred genes across diverse rice varieties including Japonica and indica cultivars. JOURNAL OF PLANT PHYSIOLOGY 2018; 220:11-23. [PMID: 29132026 DOI: 10.1016/j.jplph.2017.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 10/02/2017] [Accepted: 10/16/2017] [Indexed: 06/07/2023]
Abstract
Plant root systems play essential roles in developmental processes, such as the absorption of water and inorganic nutrients, and structural support. Gene expression is affected by growth conditions and the genetic background of plants. To identify highly conserved root-preferred genes in rice across diverse growth conditions and varieties, we used two independent meta-anatomical expression profiles based on a large collection of Affymetrix and Agilent 44K microarray data sets available for public use. We then identified 684 loci with root-preferred expression, which were validated with in silico analysis using both meta-expression profiles. The expression patterns of four candidate genes were confirmed in vivo by monitoring expression of β-glucuronidase under control of the candidate-gene promoters, providing new tools to manipulate agronomic traits associated with roots. We also utilized real-time PCR to examine the root-preferential expression of 14 genes across four rice varieties, including japonica and indica cultivars. Using a database of rice genes with known functions, we identified the reported functions of 39 out of the 684 candidate genes. Sixteen genes are directly involved in root development, while the remaining are involved in processes indirectly related to root development (i.e., soil-stress tolerance or growth retardation). This indicates the importance of our candidate genes for studies on root development and function. Gene ontology enrichment analysis in the 'biological processes' category revealed that root-preferred genes in rice are closely associated with nutrient transport-related genes, indicating that the primary role of roots is the uptake of nutrients from soil. In addition, predicted protein-protein interaction analysis suggested a molecular network for root development composed of 215 interactions associated with 44 root-preferred or root development-related genes. Taken together, our data provide an important foundation for future research on root development in rice.
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Affiliation(s)
- Sunok Moon
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | | | - Yun-Shil Gho
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Sun-A Park
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Sung-Ryul Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Yo-Han Yoo
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea.
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520
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Ayalew H, Liu H, Börner A, Kobiljski B, Liu C, Yan G. Genome-Wide Association Mapping of Major Root Length QTLs Under PEG Induced Water Stress in Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:1759. [PMID: 30555498 PMCID: PMC6281995 DOI: 10.3389/fpls.2018.01759] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/12/2018] [Indexed: 05/18/2023]
Abstract
Roots are vital plant organs that determine adaptation to various soil conditions. The present study evaluated a core winter wheat collection for rooting depth under PEG induced early stage water stress and non-stress growing conditions. Analysis of phenotypic data indicated highly significant (p < 0.01) variation among genotypes. Broad sense heritability of 59 and 73% with corresponding genetic gains of 7.6 and 9.7 (5% selection intensity) were found under non-stress and stress conditions, respectively. The test genotypes were grouped in to three distinct clusters using unweighted pair group method with arithmetic mean (UPGMA) clustering based on maximum Euclidian distance. The first three principal components gave optimum mixed linear model for genome wide association study (GWAS). Linkage disequilibrium (LD) analysis showed significant LD (p < 0.05) amongst 15% of total marker pairs (25,125). Nearly 16% of the significant LDs were among inter chromosomal marker pairs. GWAS revealed five significant root length QTLs spread across four chromosomes. None of the identified QTLs were common between the two growing conditions. Stress specific QTLs, combined explaining 31% of phenotypic variation were located on chromosomes 2B (wPt6278) and 3B (wPt1159). Similarly, two of the three QTLs (wPt0021 and wPt8890) identified under the non-stress condition were found on chromosomes 3B and 5B, respectively. The B genome showed significant importance in controlling root growth both under stress and non-stress conditions. The identified markers can potentially be validated and used for marker assisted selection.
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Affiliation(s)
- Habtamu Ayalew
- School of Agriculture and Environment, Faculty of Science, The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
- Noble Research Institute LLC, Ardmore, OK, United States
| | - Hui Liu
- School of Agriculture and Environment, Faculty of Science, The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Andreas Börner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | | - Chunji Liu
- CSIRO Agriculture Flagship, Townsville, QLD, Australia
| | - Guijun Yan
- School of Agriculture and Environment, Faculty of Science, The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
- *Correspondence: Guijun Yan,
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Bettembourg M, Dal-Soglio M, Bureau C, Vernet A, Dardoux A, Portefaix M, Bes M, Meynard D, Mieulet D, Cayrol B, Perin C, Courtois B, Ma JF, Dievart A. Root cone angle is enlarged in docs1 LRR-RLK mutants in rice. RICE (NEW YORK, N.Y.) 2017; 10:50. [PMID: 29247303 PMCID: PMC5732118 DOI: 10.1186/s12284-017-0190-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/30/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND The DEFECTIVE IN OUTER CELL LAYER SPECIFICATION 1 (DOCS1) gene belongs to the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) subfamily. It has been discovered few years ago in Oryza sativa (rice) in a screen to isolate mutants with defects in sensitivity to aluminum. The c68 (docs1-1) mutant possessed a nonsense mutation in the C-terminal part of the DOCS1 kinase domain. FINDINGS We have generated a new loss-of-function mutation in the DOCS1 gene (docs1-2) using the CRISPR-Cas9 technology. This new loss-of-function mutant and docs1-1 present similar phenotypes suggesting the original docs1-1 was a null allele. Besides the aluminum sensitivity phenotype, both docs1 mutants shared also several root phenotypes described previously: less root hairs and mixed identities of the outer cell layers. Moreover, our new results suggest that DOCS1 could also play a role in root cap development. We hypothesized these docs1 root phenotypes may affect gravity responses. As expected, in seedlings, the early gravitropic response was delayed. Furthermore, at adult stage, the root gravitropic set angle of docs1 mutants was also affected since docs1 mutant plants displayed larger root cone angles. CONCLUSIONS All these observations add new insights into the DOCS1 gene function in gravitropic responses at several stages of plant development.
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Affiliation(s)
- M. Bettembourg
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - M. Dal-Soglio
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - C. Bureau
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - A. Vernet
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - A. Dardoux
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - M. Portefaix
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - M. Bes
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - D. Meynard
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - D. Mieulet
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - B. Cayrol
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - C. Perin
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - B. Courtois
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - J. F. Ma
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, 710-0046 Japan
| | - A. Dievart
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- Present address: Shanghai Jiao Tong University (SJTU), School of Life Sciences and Biotechnology, Shanghai, 200240 China
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Kulkarni M, Soolanayakanahally R, Ogawa S, Uga Y, Selvaraj MG, Kagale S. Drought Response in Wheat: Key Genes and Regulatory Mechanisms Controlling Root System Architecture and Transpiration Efficiency. Front Chem 2017; 5:106. [PMID: 29259968 PMCID: PMC5723305 DOI: 10.3389/fchem.2017.00106] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/07/2017] [Indexed: 12/24/2022] Open
Abstract
Abiotic stresses such as, drought, heat, salinity, and flooding threaten global food security. Crop genetic improvement with increased resilience to abiotic stresses is a critical component of crop breeding strategies. Wheat is an important cereal crop and a staple food source globally. Enhanced drought tolerance in wheat is critical for sustainable food production and global food security. Recent advances in drought tolerance research have uncovered many key genes and transcription regulators governing morpho-physiological traits. Genes controlling root architecture and stomatal development play an important role in soil moisture extraction and its retention, and therefore have been targets of molecular breeding strategies for improving drought tolerance. In this systematic review, we have summarized evidence of beneficial contributions of root and stomatal traits to plant adaptation to drought stress. Specifically, we discuss a few key genes such as, DRO1 in rice and ERECTA in Arabidopsis and rice that were identified to be the enhancers of drought tolerance via regulation of root traits and transpiration efficiency. Additionally, we highlight several transcription factor families, such as, ERF (ethylene response factors), DREB (dehydration responsive element binding), ZFP (zinc finger proteins), WRKY, and MYB that were identified to be both positive and negative regulators of drought responses in wheat, rice, maize, and/or Arabidopsis. The overall aim of this review is to provide an overview of candidate genes that have been identified as regulators of drought response in plants. The lack of a reference genome sequence for wheat and non-transgenic approaches for manipulation of gene functions in wheat in the past had impeded high-resolution interrogation of functional elements, including genes and QTLs, and their application in cultivar improvement. The recent developments in wheat genomics and reverse genetics, including the availability of a gold-standard reference genome sequence and advent of genome editing technologies, are expected to aid in deciphering of the functional roles of genes and regulatory networks underlying adaptive phenological traits, and utilizing the outcomes of such studies in developing drought tolerant cultivars.
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Affiliation(s)
- Manoj Kulkarni
- Canadian Wheat Improvement Flagship Program, National Research Council Canada (NRC-CNRC), Saskatoon, SK, Canada
| | - Raju Soolanayakanahally
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
| | - Satoshi Ogawa
- Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yusaku Uga
- Institute of Crop Science (NICS), National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Michael G. Selvaraj
- Agrobioversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Sateesh Kagale
- Canadian Wheat Improvement Flagship Program, National Research Council Canada (NRC-CNRC), Saskatoon, SK, Canada
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524
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Eapen D, Martínez-Guadarrama J, Hernández-Bruno O, Flores L, Nieto-Sotelo J, Cassab GI. Synergy between root hydrotropic response and root biomass in maize (Zea mays L.) enhances drought avoidance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 265:87-99. [PMID: 29223345 DOI: 10.1016/j.plantsci.2017.09.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 09/19/2017] [Accepted: 09/20/2017] [Indexed: 06/07/2023]
Abstract
Roots of higher plants change their growth direction in response to moisture, avoiding drought and gaining maximum advantage for development. This response is termed hydrotropism. There have been few studies of root hydrotropism in grasses, particularly in maize. Our goal was to test whether an enhanced hydrotropic response of maize roots correlates with a better adaptation to drought and partial/lateral irrigation in field studies. We developed a laboratory bioassay for testing hydrotropic response in primary roots of 47 maize elite DTMA (Drought Tolerant Maize for Africa) hybrids. After phenotyping these hybrids in the laboratory, selected lines were tested in the field. Three robust and three weak hybrids were evaluated employing three irrigation procedures: normal irrigation, partial lateral irrigation and drought. Hybrids with a robust hydrotropic response showed growth and developmental patterns, under drought and partial lateral irrigation, that differed from weak hydrotropic responders. A correlation between root crown biomass and grain yield in hybrids with robust hydrotropic response was detected. Hybrids with robust hydrotropic response showed earlier female flowering whereas several root system traits, such as projected root area, median width, maximum width, skeleton width, skeleton nodes, average tip diameter, rooting depth skeleton, thinner aboveground crown roots, as well as stem diameter, were considerably higher than in weak hydrotropic responders in the three irrigation procedures utilized. These results demonstrate the benefit of intensive phenotyping of hydrotropism in primary roots since maize plants that display a robust hydrotropic response grew better under drought and partial lateral irrigation, indicating that a selection for robust hydrotropism might be a promising breeding strategy to improve drought avoidance in maize.
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Affiliation(s)
- Delfeena Eapen
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México,Av. Universidad 2001, Cuernavaca, Mor. 62210, Mexico.
| | - Jesús Martínez-Guadarrama
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México,Av. Universidad 2001, Cuernavaca, Mor. 62210, Mexico
| | - Oralia Hernández-Bruno
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México,Av. Universidad 2001, Cuernavaca, Mor. 62210, Mexico
| | - Leonardo Flores
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México,Av. Universidad 2001, Cuernavaca, Mor. 62210, Mexico
| | - Jorge Nieto-Sotelo
- Laboratorio de Fisiología Molecular, Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Circuito Zona Deportiva s/n, Ciudad Universitaria, Ciudad de Mexico, 04510, Mexico
| | - Gladys I Cassab
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México,Av. Universidad 2001, Cuernavaca, Mor. 62210, Mexico.
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525
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Aguilar E, Cutrona C, Del Toro FJ, Vallarino JG, Osorio S, Pérez-Bueno ML, Barón M, Chung BN, Canto T, Tenllado F. Virulence determines beneficial trade-offs in the response of virus-infected plants to drought via induction of salicylic acid. PLANT, CELL & ENVIRONMENT 2017; 40:2909-2930. [PMID: 28718885 DOI: 10.1111/pce.13028] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 06/28/2017] [Accepted: 07/02/2017] [Indexed: 05/21/2023]
Abstract
It has been hypothesized that plants can get beneficial trade-offs from viral infections when grown under drought conditions. However, experimental support for a positive correlation between virus-induced drought tolerance and increased host fitness is scarce. We investigated whether increased virulence exhibited by the synergistic interaction involving Potato virus X (PVX) and Plum pox virus (PPV) improves tolerance to drought and host fitness in Nicotiana benthamiana and Arabidopsis thaliana. Infection by the pair PPV/PVX and by PPV expressing the virulence protein P25 of PVX conferred an enhanced drought-tolerant phenotype compared with single infections with either PPV or PVX. Decreased transpiration rates in virus-infected plants were correlated with drought tolerance in N. benthamiana but not in Arabidopsis. Metabolite and hormonal profiles of Arabidopsis plants infected with the different viruses showed a range of changes that positively correlated with a greater impact on drought tolerance. Virus infection enhanced drought tolerance in both species by increasing salicylic acid accumulation in an abscisic acid-independent manner. Viable offspring derived from Arabidopsis plants infected with PPV increased relative to non-infected plants, when exposed to drought. By contrast, the detrimental effect caused by the more virulent viruses overcame potential benefits associated with increased drought tolerance on host fitness.
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Affiliation(s)
- Emmanuel Aguilar
- Departamento de Biología Medioambiental, Centro de Investigaciones Biológicas, CSIC, Madrid, 28040, Spain
| | - Carmen Cutrona
- Departamento de Biología Medioambiental, Centro de Investigaciones Biológicas, CSIC, Madrid, 28040, Spain
| | - Francisco J Del Toro
- Departamento de Biología Medioambiental, Centro de Investigaciones Biológicas, CSIC, Madrid, 28040, Spain
| | - José G Vallarino
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga-CSIC, Málaga, 2907, Spain
| | - Sonia Osorio
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga-CSIC, Málaga, 2907, Spain
| | - María Luisa Pérez-Bueno
- Departamento de Bioquímica, Biología Celular y Molecular de Plantas, Estación Experimental del Zaidín, CSIC, Granada, 18008, Spain
| | - Matilde Barón
- Departamento de Bioquímica, Biología Celular y Molecular de Plantas, Estación Experimental del Zaidín, CSIC, Granada, 18008, Spain
| | - Bong-Nam Chung
- National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Tomás Canto
- Departamento de Biología Medioambiental, Centro de Investigaciones Biológicas, CSIC, Madrid, 28040, Spain
| | - Francisco Tenllado
- Departamento de Biología Medioambiental, Centro de Investigaciones Biológicas, CSIC, Madrid, 28040, Spain
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526
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Yu G, Li J, Sun X, Liu Y, Wang X, Zhang H, Pan H. Exploration for the Salinity Tolerance-Related Genes from Xero-Halophyte Atriplex canescens Exploiting Yeast Functional Screening System. Int J Mol Sci 2017; 18:ijms18112444. [PMID: 29149055 PMCID: PMC5713411 DOI: 10.3390/ijms18112444] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/13/2017] [Accepted: 11/15/2017] [Indexed: 12/22/2022] Open
Abstract
Plant productivity is limited by salinity stress, both in natural and agricultural systems. Identification of salt stress-related genes from halophyte can provide insights into mechanisms of salt stress tolerance in plants. Atriplex canescens is a xero-halophyte that exhibits optimum growth in the presence of 400 mM NaCl. A cDNA library derived from highly salt-treated A. canescens plants was constructed based on a yeast expression system. A total of 53 transgenic yeast clones expressing enhanced salt tolerance were selected from 10⁵ transformants. Their plasmids were sequenced and the gene characteristics were annotated using a BLASTX search. Retransformation of yeast cells with the selected plasmids conferred salt tolerance to the resulting transformants. The expression patterns of 28 of these stress-related genes were further investigated in A. canescens leaves by quantitative reverse transcription-PCR. In this study, we provided a rapid and robust assay system for large-scale screening of genes for varied abiotic stress tolerance with high efficiency in A. canescens.
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Affiliation(s)
- Gang Yu
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Jingtao Li
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Xinhua Sun
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Yanzhi Liu
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Xueliang Wang
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Hao Zhang
- College of Resource and Environment, Jilin Agricultural University, Changchun 130062, China.
| | - Hongyu Pan
- College of Plant Sciences, Jilin University, Changchun 130062, China.
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527
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Dixit S, Singh A, Sandhu N, Bhandari A, Vikram P, Kumar A. Combining drought and submergence tolerance in rice: marker-assisted breeding and QTL combination effects. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2017; 37:143. [PMID: 29151804 PMCID: PMC5670188 DOI: 10.1007/s11032-017-0737-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 10/09/2017] [Indexed: 05/21/2023]
Abstract
TDK1 is a popular rice variety from the Lao PDR. Originally developed for irrigated conditions, this variety suffers a high decline in yield under drought conditions. Studies have identified three quantitative trait loci (QTLs) for grain yield under drought conditions, qDTY3.1 , qDTY6.1 , and qDTY6.2 , that show a high effect in the background of this variety. We report here the pyramiding of these three QTLs with SUB1 that provides 2-3 weeks of tolerance to complete submergence, with the aim to develop drought- and submergence-tolerant near-isogenic lines (NILs) of TDK1. We used a tandem approach that combined marker-assisted backcross breeding with phenotypic selection to develop NILs with high yield under drought stress and non-stress conditions and preferred grain quality. The effect of different QTL combinations on yield and yield-related traits under drought stress and non-stress conditions is also reported. Our results show qDTY3.1 to be the largest and most consistent QTL affecting yield under drought conditions, followed by qDTY6.1 and qDTY6.2 , respectively. QTL class analysis also showed that lines with a combination of qDTY3.1 and qDTY6.1 consistently showed a higher tolerance to drought than those in which one of these QTLs was missing. In countries such as Lao PDR, where large areas under rice cultivation suffer vegetative-stage submergence and reproductive-stage drought, these lines could ensure yield stability. These lines can also serve as valuable genetic material to be used for further breeding of high-yielding, drought- and submergence-tolerant varieties in local breeding programs.
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Affiliation(s)
- Shalabh Dixit
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Anshuman Singh
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- Rani Lakshmi Bai Central Agriculture University, Jhansi, India
| | - Nitika Sandhu
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Aditi Bhandari
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Prashant Vikram
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera México-Veracruz, El Batán, 56237 Texcoco, CP Mexico
| | - Arvind Kumar
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
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Bettembourg M, Dardou A, Audebert A, Thomas E, Frouin J, Guiderdoni E, Ahmadi N, Perin C, Dievart A, Courtois B. Genome-wide association mapping for root cone angle in rice. RICE (NEW YORK, N.Y.) 2017; 10:45. [PMID: 28971382 PMCID: PMC5624858 DOI: 10.1186/s12284-017-0184-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/19/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND Plant root systems play a major role in anchoring and in water and nutrient uptake from the soil. The root cone angle is an important parameter of the root system architecture because, combined with root depth, it helps to determine the volume of soil explored by the plant. Two genes, DRO1 and SOR1, and several QTLs for root cone angle have been discovered in the last 5 years. RESULTS To find other QTLs linked to root cone angle, a genome-wide association mapping study was conducted on two panels of 162 indica and 169 japonica rice accessions genotyped with two sets of SNP markers (genotyping-by-sequencing set with approximately 16,000 markers and high-density-rice-array set with approximately 300,000 markers). The root cone angle of all accessions was measured using a screen protractor on images taken after 1 month of plant growth in the Rhizoscope phenotyping system. The distribution of the root cone angle in the indica panel was Gaussian, but several accessions of the japonica panel (all the bulus from Indonesia and three temperate japonicas from Nepal or India) appeared as outliers with a very wide root cone angle. The data were submitted to association mapping using a mixed model with control of structure and kinship. A total of 15 QTLs for the indica panel and 40 QTLs for the japonica panel were detected. Genes underlying these QTLs (+/-50 kb from the significant markers) were analyzed. We focused our analysis on auxin-related genes, kinases, and genes involved in root developmental processes and identified 8 particularly interesting genes. CONCLUSIONS The present study identifies new sources of wide root cone angle in rice, proposes ways to bypass some drawbacks of association mapping to further understand the genetics of the trait and identifies candidate genes deserving further investigation.
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Affiliation(s)
| | | | - Alain Audebert
- Cirad, UMR AGAP, F34398 Montpellier Cedex 5, France
- Cirad / ISRA-Ceraas, BP 3320 Thies, Senegal
| | | | | | | | | | | | - Anne Dievart
- Cirad, UMR AGAP, F34398 Montpellier Cedex 5, France
- Shanghai Jiao Tong University (SJTU), School of Life Sciences and Biotechnology, Shanghai, 200240 China
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Jung H, Chung PJ, Park S, Redillas MCFR, Kim YS, Suh J, Kim J. Overexpression of OsERF48 causes regulation of OsCML16, a calmodulin-like protein gene that enhances root growth and drought tolerance. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1295-1308. [PMID: 28244201 PMCID: PMC5595718 DOI: 10.1111/pbi.12716] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 02/07/2017] [Accepted: 02/19/2017] [Indexed: 05/19/2023]
Abstract
The AP2/ERF family is a plant-specific transcription factor family whose members have been associated with various developmental processes and stress tolerance. Here, we functionally characterized the drought-inducible OsERF48, a group Ib member of the rice ERF family with four conserved motifs, CMI-1, -2, -3 and -4. A transactivation assay in yeast revealed that the C-terminal CMI-1 motif was essential for OsERF48 transcriptional activity. When OsERF48 was overexpressed in an either a root-specific (ROXOsERF48 ) or whole-body (OXOsERF48 ) manner, transgenic plants showed a longer and denser root phenotype compared to the nontransgenic (NT) controls. When plants were grown on a 40% polyethylene glycol-infused medium under in vitro drought conditions, ROXOsERF48 plants showed a more vigorous root growth than OXOsERF48 and NT plants. In addition, the ROXOsERF48 plants exhibited higher grain yield than OXOsERF48 and NT plants under field-drought conditions. We constructed a putative OsERF48 regulatory network by cross-referencing ROXOsERF48 root-specific RNA-seq data with a co-expression network database, from which we inferred the involvement of 20 drought-related genes in OsERF48-mediated responses. These included genes annotated as being involved in stress signalling, carbohydrate metabolism, cell-wall proteins and drought responses. They included, OsCML16, a key gene in calcium signalling during abiotic stress, which was shown to be a direct target of OsERF48 by chromatin immunoprecipitation-qPCR analysis and a transient protoplast expression assay. Our results demonstrated that OsERF48 regulates OsCML16, a calmodulin-like protein gene that enhances root growth and drought tolerance.
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Affiliation(s)
- Harin Jung
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
- Center for Nutraceutical and Pharmaceutical MaterialsDivision of Bioscience and BioinformaticsMyongji UniversityYonginGyeonggiKorea
| | - Pil Joong Chung
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Su‐Hyun Park
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
- Present address:
Laboratory of Plant Molecular BiologyRockefeller UniversityNew YorkNYUSA
| | - Mark Christian Felipe Reveche Redillas
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Youn Shic Kim
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Joo‐Won Suh
- Center for Nutraceutical and Pharmaceutical MaterialsDivision of Bioscience and BioinformaticsMyongji UniversityYonginGyeonggiKorea
| | - Ju‐Kon Kim
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
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Gong X, Shi S, Dou F, Song Y, Ma F. Exogenous Melatonin Alleviates Alkaline Stress in Malus hupehensis Rehd. by Regulating the Biosynthesis of Polyamines. Molecules 2017; 22:molecules22091542. [PMID: 28902159 PMCID: PMC6151414 DOI: 10.3390/molecules22091542] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 09/07/2017] [Accepted: 09/11/2017] [Indexed: 12/25/2022] Open
Abstract
Since melatonin was identified in plants decades ago, much attention has been devoted to discovering its role in plant science. There is still a great deal to learn about the functional importance of melatonin, as well as its functional mode. In this paper, we examine the role of melatonin treatment in the response of Malus hupehensis Rehd. to alkaline conditions. Stressed seedlings showed chlorosis and suppressed growth. However, this phenotype was ameliorated when 5 µM melatonin was added to the irrigation solution. This supplementation was also associated with a reduction in cell membrane damage and maintenance of a normal root system architecture. Fewer reactive oxygen species (ROS) were accumulated due to the enhanced scavenging activity of antioxidant enzymes superoxide dismutase, peroxidase, and catalase. In addition, alkaline-stressed seedlings that received the melatonin supplement accumulated more polyamines compared with untreated seedlings. Transcript levels of six genes involved in polyamine synthesis, including SAMDC1, -3, and -4, and SPDS1, -3, and -5, -6, were upregulated in response to melatonin application. All of these results demonstrate that melatonin has a positive function in plant tolerance to alkaline stress because it regulates enzyme activity and the biosynthesis of polyamines.
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Affiliation(s)
- Xiaoqing Gong
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, Shaanxi, China.
| | - Shuting Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, Shaanxi, China.
| | - Fangfang Dou
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, Shaanxi, China.
| | - Yi Song
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, Shaanxi, China.
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, Shaanxi, China.
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531
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Kang J, Li J, Gao S, Tian C, Zha X. Overexpression of the leucine-rich receptor-like kinase gene LRK2 increases drought tolerance and tiller number in rice. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1175-1185. [PMID: 28182328 PMCID: PMC5552483 DOI: 10.1111/pbi.12707] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 01/29/2017] [Accepted: 01/30/2017] [Indexed: 05/18/2023]
Abstract
Drought represents a key limiting factor of global crop distribution. Receptor-like kinases play major roles in plant development and defence responses against stresses such as drought. In this study, LRK2, which encodes a leucine-rich receptor-like kinase, was cloned and characterized and found to be localized on the plasma membrane in rice. Promoter-GUS analysis revealed strong expression in tiller buds, roots, nodes and anthers. Transgenic plants overexpressing LRK2 exhibited enhanced tolerance to drought stress due to an increased number of lateral roots compared with the wild type at the vegetative stage. Moreover, ectopic expression of LRK2 seedlings resulted in increased tiller development. Yeast two-hybrid screening and bimolecular fluorescence complementation (BiFC) indicated a possible interaction between LRK2 and elongation factor 1 alpha (OsEF1A) in vitro. These results suggest that LRK2 functions as a positive regulator of the drought stress response and tiller development via increased branch development in rice. These findings will aid our understanding of branch regulation in other grasses and support improvements in rice genetics.
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Affiliation(s)
- Junfang Kang
- College of Chemistry and Life SciencesZhejiang Normal UniversityJinhuaChina
| | - Jianmin Li
- College of Chemistry and Life SciencesZhejiang Normal UniversityJinhuaChina
| | - Shuang Gao
- College of Chemistry and Life SciencesZhejiang Normal UniversityJinhuaChina
| | - Chao Tian
- College of Chemistry and Life SciencesZhejiang Normal UniversityJinhuaChina
| | - Xiaojun Zha
- College of Chemistry and Life SciencesZhejiang Normal UniversityJinhuaChina
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532
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533
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Brophy JAN, LaRue T, Dinneny JR. Understanding and engineering plant form. Semin Cell Dev Biol 2017; 79:68-77. [PMID: 28864344 DOI: 10.1016/j.semcdb.2017.08.051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/25/2017] [Accepted: 08/28/2017] [Indexed: 11/18/2022]
Abstract
A plant's form is an important determinant of its fitness and economic value. Here, we review strategies for producing plants with altered forms. Historically, the process of changing a plant's form has been slow in agriculture, requiring iterative rounds of growth and selection. We discuss modern techniques for identifying genes involved in the development of plant form and tools that will be needed to effectively design and engineer plants with altered forms. Synthetic genetic circuits are highlighted for their potential to generate novel plant forms. We emphasize understanding development as a prerequisite to engineering and discuss the potential role of computer models in translating knowledge about single genes or pathways into a more comprehensive understanding of development.
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Affiliation(s)
- Jennifer A N Brophy
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA
| | - Therese LaRue
- Stanford University, Department of Biology, Stanford, CA 94305, USA
| | - José R Dinneny
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA.
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534
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The activation of OsEIL1 on YUC8 transcription and auxin biosynthesis is required for ethylene-inhibited root elongation in rice early seedling development. PLoS Genet 2017; 13:e1006955. [PMID: 28829777 PMCID: PMC5581195 DOI: 10.1371/journal.pgen.1006955] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 09/01/2017] [Accepted: 08/04/2017] [Indexed: 11/21/2022] Open
Abstract
Rice is an important monocotyledonous crop worldwide; it differs from the dicotyledonous plant Arabidopsis in many aspects. In Arabidopsis, ethylene and auxin act synergistically to regulate root growth and development. However, their interaction in rice is still unclear. Here, we report that the transcriptional activation of OsEIL1 on the expression of YUC8/REIN7 and indole-3-pyruvic acid (IPA)-dependent auxin biosynthesis is required for ethylene-inhibited root elongation. Using an inhibitor of YUC activity, which regulates auxin biosynthesis via the conversion of IPA to indole-3-acetic acid (IAA), we showed that ethylene-inhibited primary root elongation is dependent on YUC-based auxin biosynthesis. By screening phenotypes of seedling primary root from mutagenesis libraries following ethylene treatment, we identified a rice ethylene-insensitive mutant, rein7-1, in which YUC8/REIN7 is truncated at its C-terminus. Mutation in YUC8/REIN7 reduced auxin biosynthesis in rice, while YUC8/REIN7 overexpression enhanced ethylene sensitivity in the roots. Moreover, YUC8/REIN7 catalyzed the conversion of IPA to IAA, truncated version at C-terminal end of the YUC8/REIN7 resulted in significant reduction of enzymatic activity, indicating that YUC8/REIN7 is required for IPA-dependent auxin biosynthesis and ethylene-inhibited root elongation in rice early seedlings. Further investigations indicated that ethylene induced YUC8/REIN7 expression and promoted auxin accumulation in roots. Addition of low concentrations of IAA rescued the ethylene response in the rein7-1, strongly demonstrating that ethylene-inhibited root elongation depends on IPA-dependent auxin biosynthesis. Genetic studies revealed that YUC8/REIN7-mediated auxin biosynthesis functioned downstream of OsEIL1, which directly activated the expression of YUC8/REIN7. Thus, our findings reveal a model of interaction between ethylene and auxin in rice seedling primary root elongation, enhancing our understanding of ethylene signaling in rice. Rice is an important crop worldwide and is grown in water-saturated environments during its life cycle. This unique feature confers that rice might have different aspects from Arabidopsis in ethylene signaling. Although the crosstalk between ethylene and auxin is well understood in Arabidopsis, however, the interaction in rice is largely unclear. Here, we show that YUC8/REIN7, a member of the YUC gene family, catalyzing the conversion of IPA to IAA in auxin biosynthesis, is transcriptionally modulated by ethylene signaling component OsEIL1, and mainly participates in auxin biosynthesis and ethylene-inhibited root growth. We first identified that ethylene-inhibited root elongation is suppressed by the inhibitor of YUC activity, and YUC8/REIN7 is required for IPA-dependent auxin biosynthesis, indicating that YUC8/REIN7 is involved in ethylene-inhibited root elongation in rice early seedlings. Moreover, ethylene induced YUC8/REIN7 transcription and promoted auxin accumulation in roots. Addition of low concentrations of IAA rescued the ethylene response in the rein7-1, demonstrating that ethylene stimulates auxin biosynthesis dependent on YUC8/REIN7 function. Further evidence revealed that OsEIL1 transcriptionally activates the expression of YUC8/REIN7, and YUC8/REIN7-mediated auxin biosynthesis genetically acts downstream of OsEIL1. Our data in the present report identified an interaction between ethylene and auxin in rice seedling primary root elongation, increasing our understanding of ethylene signaling in rice root growth.
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535
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Kumar J, Gupta DS, Gupta S, Dubey S, Gupta P, Kumar S. Quantitative trait loci from identification to exploitation for crop improvement. PLANT CELL REPORTS 2017; 36:1187-1213. [PMID: 28352970 DOI: 10.1007/s00299-017-2127-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/09/2017] [Indexed: 05/24/2023]
Abstract
Advancement in the field of genetics and genomics after the discovery of Mendel's laws of inheritance has led to map the genes controlling qualitative and quantitative traits in crop plant species. Mapping of genomic regions controlling the variation of quantitatively inherited traits has become routine after the advent of different types of molecular markers. Recently, the next generation sequencing methods have accelerated the research on QTL analysis. These efforts have led to the identification of more closely linked molecular markers with gene/QTLs and also identified markers even within gene/QTL controlling the trait of interest. Efforts have also been made towards cloning gene/QTLs or identification of potential candidate genes responsible for a trait. Further new concepts like crop QTLome and QTL prioritization have accelerated precise application of QTLs for genetic improvement of complex traits. In the past years, efforts have also been made in exploitation of a number of QTL for improving grain yield or other agronomic traits in various crops through markers assisted selection leading to cultivation of these improved varieties at farmers' field. In present article, we reviewed QTLs from their identification to exploitation in plant breeding programs and also reviewed that how improved cultivars developed through introgression of QTLs have improved the yield productivity in many crops.
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Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India.
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sunanda Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sonali Dubey
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Priyanka Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat-Institutes, B.P. 6299, Rabat, Morocco
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536
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Lou Q, Chen L, Mei H, Xu K, Wei H, Feng F, Li T, Pang X, Shi C, Luo L, Zhong Y. Root Transcriptomic Analysis Revealing the Importance of Energy Metabolism to the Development of Deep Roots in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1314. [PMID: 28798764 PMCID: PMC5526896 DOI: 10.3389/fpls.2017.01314] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/12/2017] [Indexed: 05/19/2023]
Abstract
Drought is the most serious abiotic stress limiting rice production, and deep root is the key contributor to drought avoidance. However, the genetic mechanism regulating the development of deep roots is largely unknown. In this study, the transcriptomes of 74 root samples from 37 rice varieties, representing the extreme genotypes of shallow or deep rooting, were surveyed by RNA-seq. The 13,242 differentially expressed genes (DEGs) between deep rooting and shallow rooting varieties (H vs. L) were enriched in the pathway of genetic information processing and metabolism, while the 1,052 DEGs between the deep roots and shallow roots from each of the plants (D vs. S) were significantly enriched in metabolic pathways especially energy metabolism. Ten quantitative trait transcripts (QTTs) were identified and some were involved in energy metabolism. Forty-nine candidate DEGs were confirmed by qRT-PCR and microarray. Through weighted gene co-expression network analysis (WGCNA), we found 18 hub genes. Surprisingly, all these hub genes expressed higher in deep roots than in shallow roots, furthermore half of them functioned in energy metabolism. We also estimated that the ATP production in the deep roots was faster than shallow roots. Our results provided a lot of reliable candidate genes to improve deep rooting, and firstly highlight the importance of energy metabolism to the development of deep roots.
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Affiliation(s)
- Qiaojun Lou
- Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan UniversityShanghai, China
- Shanghai Agrobiological Gene CenterShanghai, China
| | - Liang Chen
- Shanghai Agrobiological Gene CenterShanghai, China
| | - Hanwei Mei
- Shanghai Agrobiological Gene CenterShanghai, China
| | - Kai Xu
- Shanghai Agrobiological Gene CenterShanghai, China
| | - Haibin Wei
- Shanghai Agrobiological Gene CenterShanghai, China
| | - Fangjun Feng
- Shanghai Agrobiological Gene CenterShanghai, China
| | - Tiemei Li
- Shanghai Agrobiological Gene CenterShanghai, China
| | | | - Caiping Shi
- Shanghai Majorbio Bio-Pharm Technology Co., Ltd.Shanghai, China
| | - Lijun Luo
- Shanghai Agrobiological Gene CenterShanghai, China
| | - Yang Zhong
- Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan UniversityShanghai, China
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537
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Li X, Guo Z, Lv Y, Cen X, Ding X, Wu H, Li X, Huang J, Xiong L. Genetic control of the root system in rice under normal and drought stress conditions by genome-wide association study. PLoS Genet 2017; 13:e1006889. [PMID: 28686596 PMCID: PMC5521850 DOI: 10.1371/journal.pgen.1006889] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/21/2017] [Accepted: 06/22/2017] [Indexed: 12/13/2022] Open
Abstract
A variety of adverse conditions including drought stress severely affect rice production. Root system plays a critical role in drought avoidance, which is one of the major mechanisms of drought resistance. In this study, we adopted genome-wide association study (GWAS) to dissect the genetic basis controlling various root traits by using a natural population consisting of 529 representative rice accessions. A total of 413 suggestive associations, containing 143 significant associations, were identified for 21 root traits, such as maximum root length, root volume, and root dry weight under normal and drought stress conditions at the maturation stage. More than 80 percent of the suggestive loci were located in the region of reported QTLs for root traits, while about 20 percent of suggestive loci were novel loci detected in this study. Besides, 11 reported root-related genes, including DRO1, WOX11, and OsPID, were found to co-locate with the association loci. We further proved that the association results can facilitate the efficient identification of causal genes for root traits by the two case studies of Nal1 and OsJAZ1. These loci and their candidate causal genes provide an important basis for the genetic improvement of root traits and drought resistance.
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Affiliation(s)
- Xiaokai Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Zilong Guo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Yan Lv
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Xiang Cen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Xipeng Ding
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Hua Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Jianping Huang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
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538
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Chen HC, Hsieh-Feng V, Liao PC, Cheng WH, Liu LY, Yang YW, Lai MH, Chang MC. The function of OsbHLH068 is partially redundant with its homolog, AtbHLH112, in the regulation of the salt stress response but has opposite functions to control flowering in Arabidopsis. PLANT MOLECULAR BIOLOGY 2017; 94:531-548. [PMID: 28631168 PMCID: PMC5504132 DOI: 10.1007/s11103-017-0624-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 06/12/2017] [Indexed: 05/20/2023]
Abstract
KEY MESSAGE The homologous genes OsbHLH068 and AtbHLH112 have partially redundant functions in the regulation of the salt stress response but opposite functions to control flowering in Arabidopsis. The transcription factor (TF) basic/Helix-Loop-Helix (bHLH) is important for plant growth, development, and stress responses. OsbHLH068, which is a homologous gene of AtbHLH112 that is up-regulated under drought and salt stresses, as indicated by previous microarray data analysis. However, the intrinsic function of OsbHLH068 remains unknown. In the present study, we characterized the function and compared the role of OsbHLH068 with that of its homolog, AtbHLH112. Histochemical GUS staining indicated that OsbHLH068 and AtbHLH112 share a similar expression pattern in transgenic Arabidopsis during the juvenile-to-adult phase transition. Heterologous overexpression of OsbHLH068 in Arabidopsis delays seed germination, decreases salt-induced H2O2 accumulation, and promotes root elongation, whereas AtbHLH112 knock-out mutant displays an opposite phenotype. Both OsbHLH068-overexpressing transgenic Arabidopsis seedlings and the Atbhlh112 mutant display a late-flowering phenotype. Moreover, the expression of OsbHLH068-GFP driven by an AtbHLH112 promoter can compensate for the germination deficiency in the Atbhlh112 mutant, but the delayed-flowering phenotype tends to be more severe. Further analysis by microarray and qPCR indicated that the expression of FT is down-regulated in both OsbHLH068-overexpressing Arabidopsis plants and Atbhlh112 mutant plants, whereas SOC1 but not FT is highly expressed in AtbHLH112-overexpressing Arabidopsis plants. A comparative transcriptomic analysis also showed that several stress-responsive genes, such as AtERF15 and AtPUB23, were affected in both OsbHLH068- and AtbHLH112-overexpressing transgenic Arabidopsis plants. Thus, we propose that OsbHLH068 and AtbHLH112 share partially redundant functions in the regulation of abiotic stress responses but have opposite functions to control flowering in Arabidopsis, presumably due to the evolutionary functional divergence of homolog-encoded proteins.
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Affiliation(s)
- Hung-Chi Chen
- Department of Agronomy, National Taiwan University, Taipei, Taiwan, ROC
| | - Vicki Hsieh-Feng
- Department of Agronomy, National Taiwan University, Taipei, Taiwan, ROC
| | - Pei-Chun Liao
- Department of Agronomy, National Taiwan University, Taipei, Taiwan, ROC
| | - Wan-Hsing Cheng
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Li-Yu Liu
- Department of Agronomy, National Taiwan University, Taipei, Taiwan, ROC
| | - Yun-Wei Yang
- Department of Agronomy, National Taiwan University, Taipei, Taiwan, ROC
| | - Ming-Hsin Lai
- Crop Science Division, Taiwan Agricultural Research Institute, Taichung, Taiwan, ROC
| | - Men-Chi Chang
- Department of Agronomy, National Taiwan University, Taipei, Taiwan, ROC.
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539
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Lopez JR, Erickson JE, Munoz P, Saballos A, Felderhoff TJ, Vermerris W. QTLs Associated with Crown Root Angle, Stomatal Conductance, and Maturity in Sorghum. THE PLANT GENOME 2017; 10. [PMID: 28724080 DOI: 10.3835/plantgenome2016.04.0038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Three factors that directly affect the water inputs in cropping systems are root architecture, length of the growing season, and stomatal conductance to water vapor (). Deeper-rooted cultivars will perform better under water-limited conditions because they can access water stored deeper in the soil profile. Reduced limits transpiration rate () and thus throughout the vegetative phase conserves water that may be used during grain filling in water-limited environments. Additionally, growing early-maturing varieties in regions that rely on soil-stored water is a key water management strategy. To further our understanding of the genetic basis underlying root depth, growing season length, and we conducted a quantitative trait locus (QTL) study. A QTL for crown root angle (a proxy for root depth) new to sorghum was identified in chromosome 3. For , a QTL in chromosome seven was identified. In a follow-up field study it was determined that the QTL for was associated with reduced but not with net carbon assimilation rate () or shoot biomass. No differences in guard-cell length or stomatal density were observed among the lines, leading to the conclusion that the observed differences in must be explained by partial stomatal closure. The well-studied maturity gene was identified in the QTL for maturity. The transgressive segregation of the population was explained by the possible interaction of with other loci. Finally, the most probable position of the genes underlying the QTLs and candidate genes were proposed.
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540
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Wang H, Qin F. Genome-Wide Association Study Reveals Natural Variations Contributing to Drought Resistance in Crops. FRONTIERS IN PLANT SCIENCE 2017; 8:1110. [PMID: 28713401 PMCID: PMC5491614 DOI: 10.3389/fpls.2017.01110] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 06/08/2017] [Indexed: 05/18/2023]
Abstract
Crops are often cultivated in regions where they will face environmental adversities; resulting in substantial yield loss which can ultimately lead to food and societal problems. Thus, significant efforts have been made to breed stress tolerant cultivars in an attempt to minimize these problems and to produce more stability with respect to crop yields across broad geographies. Since stress tolerance is a complex and multi-genic trait, advancements with classical breeding approaches have been challenging. On the other hand, molecular breeding, which is based on transgenics, marker-assisted selection and genome editing technologies; holds great promise to enable farmers to better cope with these challenges. However, identification of the key genetic components underlying the trait is critical and will serve as the foundation for future crop genetic improvement. Recently, genome-wide association studies have made significant contributions to facilitate the discovery of natural variation contributing to stress tolerance in crops. From these studies, the identified loci can serve as targets for genomic selection or editing to enable the molecular design of new cultivars. Here, we summarize research progress on this issue and focus on the genetic basis of drought tolerance as revealed by genome-wide association studies and quantitative trait loci mapping. Although many favorable loci have been identified, elucidation of their molecular mechanisms contributing to increased stress tolerance still remains a challenge. Thus, continuous efforts are still required to functionally dissect this complex trait through comprehensive approaches, such as system biological studies. It is expected that proper application of the acquired knowledge will enable the development of stress tolerant cultivars; allowing agricultural production to become more sustainable under dynamic environmental conditions.
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Affiliation(s)
- Hongwei Wang
- Agricultural College, Yangtze UniversityJingzhou, China
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze UniversityJingzhou, China
| | - Feng Qin
- College of Biological Sciences, China Agricultural UniversityBeijing, China
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Fahad S, Bajwa AA, Nazir U, Anjum SA, Farooq A, Zohaib A, Sadia S, Nasim W, Adkins S, Saud S, Ihsan MZ, Alharby H, Wu C, Wang D, Huang J. Crop Production under Drought and Heat Stress: Plant Responses and Management Options. FRONTIERS IN PLANT SCIENCE 2017; 8:1147. [PMID: 28706531 PMCID: PMC5489704 DOI: 10.3389/fpls.2017.01147] [Citation(s) in RCA: 727] [Impact Index Per Article: 103.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/15/2017] [Indexed: 05/18/2023]
Abstract
Abiotic stresses are one of the major constraints to crop production and food security worldwide. The situation has aggravated due to the drastic and rapid changes in global climate. Heat and drought are undoubtedly the two most important stresses having huge impact on growth and productivity of the crops. It is very important to understand the physiological, biochemical, and ecological interventions related to these stresses for better management. A wide range of plant responses to these stresses could be generalized into morphological, physiological, and biochemical responses. Interestingly, this review provides a detailed account of plant responses to heat and drought stresses with special focus on highlighting the commonalities and differences. Crop growth and yields are negatively affected by sub-optimal water supply and abnormal temperatures due to physical damages, physiological disruptions, and biochemical changes. Both these stresses have multi-lateral impacts and therefore, complex in mechanistic action. A better understanding of plant responses to these stresses has pragmatic implication for remedies and management. A comprehensive account of conventional as well as modern approaches to deal with heat and drought stresses have also been presented here. A side-by-side critical discussion on salient responses and management strategies for these two important abiotic stresses provides a unique insight into the phenomena. A holistic approach taking into account the different management options to deal with heat and drought stress simultaneously could be a win-win approach in future.
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Affiliation(s)
- Shah Fahad
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Ecophysiology and Farming System, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Ali A. Bajwa
- School of Agriculture and Food Sciences, The University of Queensland, GattonQLD, Australia
| | - Usman Nazir
- Department of Agronomy, University of AgricultureFaisalabad, Pakistan
| | - Shakeel A. Anjum
- Department of Agronomy, University of AgricultureFaisalabad, Pakistan
| | - Ayesha Farooq
- Department of Agronomy, University of AgricultureFaisalabad, Pakistan
| | - Ali Zohaib
- Department of Agronomy, University of AgricultureFaisalabad, Pakistan
| | - Sehrish Sadia
- College of Life Sciences, Beijing Normal UniversityBeijing, China
| | - Wajid Nasim
- Department of Environmental Sciences, COMSATS Institute of Information TechnologyVehari, Pakistan
| | - Steve Adkins
- School of Agriculture and Food Sciences, The University of Queensland, GattonQLD, Australia
| | - Shah Saud
- College of Horticulture, Northeast Agricultural University HarbinHarbin, China
- Royal Wellington Golf ClubUpper Hutt, New Zealand
| | - Muhammad Z. Ihsan
- Cholistan Institute of Desert Studied, The Islamia University of BahawalpurBahawalpur, Pakistan
- Department of Agronomy, The Islamia University of BahawalpurBahawalpur, Pakistan
| | - Hesham Alharby
- Department of Biological Sciences, Faculty of Science, King Abdulaziz UniversityJeddah, Saudi Arabia
| | - Chao Wu
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Ecophysiology and Farming System, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Depeng Wang
- College of Life Science, Linyi UniversityLinyi, China
| | - Jianliang Huang
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Ecophysiology and Farming System, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze UniversityWuhan, China
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542
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Ghneim-Herrera T, Selvaraj MG, Meynard D, Fabre D, Peña A, Ben Romdhane W, Ben Saad R, Ogawa S, Rebolledo MC, Ishitani M, Tohme J, Al-Doss A, Guiderdoni E, Hassairi A. Expression of the Aeluropus littoralis AlSAP Gene Enhances Rice Yield under Field Drought at the Reproductive Stage. FRONTIERS IN PLANT SCIENCE 2017; 8:994. [PMID: 28659945 PMCID: PMC5466986 DOI: 10.3389/fpls.2017.00994] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/26/2017] [Indexed: 05/03/2023]
Abstract
We evaluated the yields of Oryza sativa L. 'Nipponbare' rice lines expressing a gene encoding an A20/AN1 domain stress-associated protein, AlSAP, from the halophyte grass Aeluropus littoralis under the control of different promoters. Three independent field trials were conducted, with drought imposed at the reproductive stage. In all trials, the two transgenic lines, RN5 and RN6, consistently out-performed non-transgenic (NT) and wild-type (WT) controls, providing 50-90% increases in grain yield (GY). Enhancement of tillering and panicle fertility contributed to this improved GY under drought. In contrast with physiological records collected during previous greenhouse dry-down experiments, where drought was imposed at the early tillering stage, we did not observe significant differences in photosynthetic parameters, leaf water potential, or accumulation of antioxidants in flag leaves of AlSAP-lines subjected to drought at flowering. However, AlSAP expression alleviated leaf rolling and leaf drying induced by drought, resulting in increased accumulation of green biomass. Therefore, the observed enhanced performance of the AlSAP-lines subjected to drought at the reproductive stage can be tentatively ascribed to a primed status of the transgenic plants, resulting from a higher accumulation of biomass during vegetative growth, allowing reserve remobilization and maintenance of productive tillering and grain filling. Under irrigated conditions, the overall performance of AlSAP-lines was comparable with, or even significantly better than, the NT and WT controls. Thus, AlSAP expression inflicted no penalty on rice yields under optimal growth conditions. Our results support the use of AlSAP transgenics to reduce rice GY losses under drought conditions.
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Affiliation(s)
| | | | - Donaldo Meynard
- UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, Centre de Coopération Internationale en Recherche Agronomique pour le DéveloppementMontpellier, France
| | - Denis Fabre
- UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, Centre de Coopération Internationale en Recherche Agronomique pour le DéveloppementMontpellier, France
| | - Alexandra Peña
- Departamento de Ciencias Biológicas, Universidad IcesiCali, Colombia
| | - Walid Ben Romdhane
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud UniversityRiyadh, Saudi Arabia
| | - Rania Ben Saad
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of SfaxSfax, Tunisia
| | - Satoshi Ogawa
- International Center for Tropical AgricultureCali, Colombia
- Graduate School of Agricultural and Life Science, Department of Global Agricultural Science, The University of TokyoTokyo, Japan
| | | | | | - Joe Tohme
- International Center for Tropical AgricultureCali, Colombia
| | - Abdullah Al-Doss
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud UniversityRiyadh, Saudi Arabia
| | - Emmanuel Guiderdoni
- UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, Centre de Coopération Internationale en Recherche Agronomique pour le DéveloppementMontpellier, France
| | - Afif Hassairi
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud UniversityRiyadh, Saudi Arabia
- Centre of Biotechnology of SfaxSfax, Tunisia
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Bucksch A, Atta-Boateng A, Azihou AF, Battogtokh D, Baumgartner A, Binder BM, Braybrook SA, Chang C, Coneva V, DeWitt TJ, Fletcher AG, Gehan MA, Diaz-Martinez DH, Hong L, Iyer-Pascuzzi AS, Klein LL, Leiboff S, Li M, Lynch JP, Maizel A, Maloof JN, Markelz RJC, Martinez CC, Miller LA, Mio W, Palubicki W, Poorter H, Pradal C, Price CA, Puttonen E, Reese JB, Rellán-Álvarez R, Spalding EP, Sparks EE, Topp CN, Williams JH, Chitwood DH. Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences. FRONTIERS IN PLANT SCIENCE 2017; 8:900. [PMID: 28659934 PMCID: PMC5465304 DOI: 10.3389/fpls.2017.00900] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 05/12/2017] [Indexed: 05/21/2023]
Abstract
The geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fascinated plant biologists and mathematicians alike. As such, plant morphology is inherently mathematical in that it describes plant form and architecture with geometrical and topological techniques. Gaining an understanding of how to modify plant morphology, through molecular biology and breeding, aided by a mathematical perspective, is critical to improving agriculture, and the monitoring of ecosystems is vital to modeling a future with fewer natural resources. In this white paper, we begin with an overview in quantifying the form of plants and mathematical models of patterning in plants. We then explore the fundamental challenges that remain unanswered concerning plant morphology, from the barriers preventing the prediction of phenotype from genotype to modeling the movement of leaves in air streams. We end with a discussion concerning the education of plant morphology synthesizing biological and mathematical approaches and ways to facilitate research advances through outreach, cross-disciplinary training, and open science. Unleashing the potential of geometric and topological approaches in the plant sciences promises to transform our understanding of both plants and mathematics.
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Affiliation(s)
- Alexander Bucksch
- Department of Plant Biology, University of Georgia, AthensGA, United States
- Warnell School of Forestry and Natural Resources, University of Georgia, AthensGA, United States
- Institute of Bioinformatics, University of Georgia, AthensGA, United States
| | | | - Akomian F. Azihou
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-CalaviCotonou, Benin
| | - Dorjsuren Battogtokh
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, BlacksburgVA, United States
| | - Aly Baumgartner
- Department of Geosciences, Baylor University, WacoTX, United States
| | - Brad M. Binder
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, KnoxvilleTN, United States
| | | | - Cynthia Chang
- Division of Biology, University of Washington, BothellWA, United States
| | - Viktoirya Coneva
- Donald Danforth Plant Science Center, St. LouisMO, United States
| | - Thomas J. DeWitt
- Department of Wildlife and Fisheries Sciences–Department of Plant Pathology and Microbiology, Texas A&M University, College StationTX, United States
| | - Alexander G. Fletcher
- School of Mathematics and Statistics and Bateson Centre, University of SheffieldSheffield, United Kingdom
| | - Malia A. Gehan
- Donald Danforth Plant Science Center, St. LouisMO, United States
| | | | - Lilan Hong
- Weill Institute for Cell and Molecular Biology and Section of Plant Biology, School of Integrative Plant Sciences, Cornell University, IthacaNY, United States
| | - Anjali S. Iyer-Pascuzzi
- Department of Botany and Plant Pathology, Purdue University, West LafayetteIN, United States
| | - Laura L. Klein
- Department of Biology, Saint Louis University, St. LouisMO, United States
| | - Samuel Leiboff
- School of Integrative Plant Science, Cornell University, IthacaNY, United States
| | - Mao Li
- Department of Mathematics, Florida State University, TallahasseeFL, United States
| | - Jonathan P. Lynch
- Department of Plant Science, The Pennsylvania State University, University ParkPA, United States
| | - Alexis Maizel
- Center for Organismal Studies, Heidelberg UniversityHeidelberg, Germany
| | - Julin N. Maloof
- Department of Plant Biology, University of California, Davis, DavisCA, United States
| | - R. J. Cody Markelz
- Department of Plant Biology, University of California, Davis, DavisCA, United States
| | - Ciera C. Martinez
- Department of Molecular and Cell Biology, University of California, Berkeley, BerkeleyCA, United States
| | - Laura A. Miller
- Program in Bioinformatics and Computational Biology, The University of North Carolina, Chapel HillNC, United States
| | - Washington Mio
- Department of Mathematics, Florida State University, TallahasseeFL, United States
| | - Wojtek Palubicki
- The Sainsbury Laboratory, University of CambridgeCambridge, United Kingdom
| | - Hendrik Poorter
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, JülichGermany
| | | | - Charles A. Price
- National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, KnoxvilleTN, United States
| | - Eetu Puttonen
- Department of Remote Sensing and Photogrammetry, Finnish Geospatial Research Institute, National Land Survey of FinlandMasala, Finland
- Centre of Excellence in Laser Scanning Research, National Land Survey of FinlandMasala, Finland
| | - John B. Reese
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, KnoxvilleTN, United States
| | - Rubén Rellán-Álvarez
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV)Irapuato, Mexico
| | - Edgar P. Spalding
- Department of Botany, University of Wisconsin–Madison, MadisonWI, United States
| | - Erin E. Sparks
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, NewarkDE, United States
| | | | - Joseph H. Williams
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, KnoxvilleTN, United States
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544
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Lee D, Chung PJ, Jeong JS, Jang G, Bang SW, Jung H, Kim YS, Ha S, Choi YD, Kim J. The rice OsNAC6 transcription factor orchestrates multiple molecular mechanisms involving root structural adaptions and nicotianamine biosynthesis for drought tolerance. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:754-764. [PMID: 27892643 PMCID: PMC5425393 DOI: 10.1111/pbi.12673] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 11/16/2016] [Accepted: 11/23/2016] [Indexed: 05/02/2023]
Abstract
Drought has a serious impact on agriculture worldwide. A plant's ability to adapt to rhizosphere drought stress requires reprogramming of root growth and development. Although physiological studies have documented the root adaption for tolerance to the drought stress, underlying molecular mechanisms is still incomplete, which is essential for crop engineering. Here, we identified OsNAC6-mediated root structural adaptations, including increased root number and root diameter, which enhanced drought tolerance. Multiyear drought field tests demonstrated that the grain yield of OsNAC6 root-specific overexpressing transgenic rice lines was less affected by drought stress than were nontransgenic controls. Genome-wide analyses of loss- and gain-of-function mutants revealed that OsNAC6 up-regulates the expression of direct target genes involved in membrane modification, nicotianamine (NA) biosynthesis, glutathione relocation, 3'-phophoadenosine 5'-phosphosulphate accumulation and glycosylation, which represent multiple drought tolerance pathways. Moreover, overexpression of NICOTIANAMINE SYNTHASE genes, direct targets of OsNAC6, promoted the accumulation of the metal chelator NA and, consequently, drought tolerance. Collectively, OsNAC6 orchestrates novel molecular drought tolerance mechanisms and has potential for the biotechnological development of high-yielding crops under water-limiting conditions.
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Affiliation(s)
- Dong‐Keun Lee
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Pil Joong Chung
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Jin Seo Jeong
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Geupil Jang
- Department of Agricultural BiotechnologySeoul National UniversitySeoulKorea
| | - Seung Woon Bang
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Harin Jung
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Youn Shic Kim
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Sun‐Hwa Ha
- Department of Genetic Engineering and Graduate School of BiotechnologyKyung Hee UniversityYonginKorea
| | - Yang Do Choi
- Department of Agricultural BiotechnologySeoul National UniversitySeoulKorea
| | - Ju‐Kon Kim
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
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545
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Tomita A, Sato T, Uga Y, Obara M, Fukuta Y. Genetic variation of root angle distribution in rice ( Oryza sativa L.) seedlings. BREEDING SCIENCE 2017; 67:181-190. [PMID: 28744171 PMCID: PMC5515312 DOI: 10.1270/jsbbs.16185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 12/29/2016] [Indexed: 05/19/2023]
Abstract
We developed a new method of using seedling trays to evaluate root angle distribution in rice (Oryza sativa. L), and found a wide genetic variation among cultivars. The seedling tray method can be used to evaluate in detail the growth angles of rice crown roots at the seedling stage by allocating nine scores (10° to 90°). Unlike basket methods, it can handle large plant populations over a short growth period (only 14 days). By using the method, we characterized the root angle distributions of 97 accessions into two cluster groups: A and B. The numbers of accessions in group A were limited, and these were categorized as shallow rooting types including soil-surface root. Group B included from shallow to deep rooting types; both included Indica and Japonica Group cultivars, lowland and upland cultivars, and landraces and improved types. No relationship between variation in root vertical angle and total root number was found. The variation in root angle distribution was not related to differentiation between the Japonica and Indica Groups, among ecosystems used for rice cultivation, or among degrees of genetic improvement. The new evaluation method and associated information on genetic variation of rice accessions will be useful in root architecture breeding of rice.
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Affiliation(s)
- Asami Tomita
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Tadashi Sato
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 981-8555, Japan
| | - Yusaku Uga
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
| | - Mitsuhiro Obara
- Biological Resources Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki 305-8686, Japan
| | - Yoshimichi Fukuta
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences, Ishigaki, Okinawa 907-0002, Japan
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546
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Xu Y, Li P, Zou C, Lu Y, Xie C, Zhang X, Prasanna BM, Olsen MS. Enhancing genetic gain in the era of molecular breeding. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2641-2666. [PMID: 28830098 DOI: 10.1093/jxb/erx135] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 04/03/2017] [Indexed: 05/20/2023]
Abstract
As one of the important concepts in conventional quantitative genetics and breeding, genetic gain can be defined as the amount of increase in performance that is achieved annually through artificial selection. To develop pro ducts that meet the increasing demand of mankind, especially for food and feed, in addition to various industrial uses, breeders are challenged to enhance the potential of genetic gain continuously, at ever higher rates, while they close the gaps that remain between the yield potential in breeders' demonstration trials and the actual yield in farmers' fields. Factors affecting genetic gain include genetic variation available in breeding materials, heritability for traits of interest, selection intensity, and the time required to complete a breeding cycle. Genetic gain can be improved through enhancing the potential and closing the gaps, which has been evolving and complemented with modern breeding techniques and platforms, mainly driven by molecular and genomic tools, combined with improved agronomic practice. Several key strategies are reviewed in this article. Favorable genetic variation can be unlocked and created through molecular and genomic approaches including mutation, gene mapping and discovery, and transgene and genome editing. Estimation of heritability can be improved by refining field experiments through well-controlled and precisely assayed environmental factors or envirotyping, particularly for understanding and controlling spatial heterogeneity at the field level. Selection intensity can be significantly heightened through improvements in the scale and precision of genotyping and phenotyping. The breeding cycle time can be shortened by accelerating breeding procedures through integrated breeding approaches such as marker-assisted selection and doubled haploid development. All the strategies can be integrated with other widely used conventional approaches in breeding programs to enhance genetic gain. More transdisciplinary approaches, team breeding, will be required to address the challenge of maintaining a plentiful and safe food supply for future generations. New opportunities for enhancing genetic gain, a high efficiency breeding pipeline, and broad-sense genetic gain are also discussed prospectively.
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Affiliation(s)
- Yunbi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, CP 56130, México
| | - Ping Li
- Nantong Xinhe Bio-Technology, Nantong 226019, PR China
| | - Cheng Zou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Chuanxiao Xie
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xuecai Zhang
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, CP 56130, México
| | - Boddupalli M Prasanna
- CIMMYT (International Maize and Wheat Improvement Center), ICRAF campus, United Nations Avenue, Nairobi, Kenya
| | - Michael S Olsen
- CIMMYT (International Maize and Wheat Improvement Center), ICRAF campus, United Nations Avenue, Nairobi, Kenya
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548
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Ponce G, Corkidi G, Eapen D, Lledías F, Cárdenas L, Cassab G. Root hydrotropism and thigmotropism in Arabidopsis thaliana are differentially controlled by redox status. PLANT SIGNALING & BEHAVIOR 2017; 12:e1305536. [PMID: 28318377 PMCID: PMC5437835 DOI: 10.1080/15592324.2017.1305536] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 05/26/2023]
Abstract
Factors that affect the direction of root growth in response to environmental signals influence crop productivity. We analyzed the root tropic responses of thioredoxin (trxs), thigmotropic (wav2-1), and hydrotropic (ahr1 and nhr1) Arabidopsis thaliana mutants treated with low concentrations of paraquat (PQ), which induces mild oxidative stress, and established a new method for evaluating root waviness (root bending effort, RBE). This method estimates root bending by measuring and summing local curvature over the whole length of the root, regardless of the asymmetry of the wavy pattern under thigmostimulation. In roots of the wav2-1 mutant, but not in those of the trxs and ahr1 mutants, RBE was significantly inhibited under mild oxidative stress. Thigmotropic stimulation of wav2-1 mutant roots, with or without PQ treatment, showed high levels of reactive oxygen species fluorescence, in contrast to roots of the ahr1 mutant. Furthermore, PQ inhibited root growth in all genotypes tested, except in the wav2-1 mutant. In a hydrotropism assay of the trxs and wav2-1 mutants, root growth behavior was similar to the wild type with and without PQ, while the root growth of ahr1 and nhr1 mutants was diminished with PQ. These results indicate that hydrotropic and thigmotropic mutants respond differently to exogenous PQ, depending on the tropic stimulus perceived. Therefore, the mechanisms underlying hydrotropism and thigmotropism may differ.
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Affiliation(s)
- Georgina Ponce
- Departamento de Biología Molecular de Plantas, Col. Chamilpa, Cuernavaca, Mor., México
| | - Gabriel Corkidi
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Col. Chamilpa, Cuernavaca, Mor., México
| | - Delfeena Eapen
- Departamento de Biología Molecular de Plantas, Col. Chamilpa, Cuernavaca, Mor., México
| | - Fernando Lledías
- Departamento de Biología Molecular de Plantas, Col. Chamilpa, Cuernavaca, Mor., México
| | - Luis Cárdenas
- Departamento de Biología Molecular de Plantas, Col. Chamilpa, Cuernavaca, Mor., México
| | - Gladys Cassab
- Departamento de Biología Molecular de Plantas, Col. Chamilpa, Cuernavaca, Mor., México
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549
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Fudge J, Mangel N, Gruissem W, Vanderschuren H, Fitzpatrick TB. Rationalising vitamin B6 biofortification in crop plants. Curr Opin Biotechnol 2017; 44:130-137. [DOI: 10.1016/j.copbio.2016.12.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/17/2016] [Accepted: 12/19/2016] [Indexed: 12/31/2022]
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550
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Urano K, Maruyama K, Jikumaru Y, Kamiya Y, Yamaguchi-Shinozaki K, Shinozaki K. Analysis of plant hormone profiles in response to moderate dehydration stress. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:17-36. [PMID: 27995695 DOI: 10.1111/tpj.13460] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 12/14/2016] [Accepted: 12/14/2016] [Indexed: 05/19/2023]
Abstract
Plant responses to dehydration stress are mediated by highly complex molecular systems involving hormone signaling and metabolism, particularly the major stress hormone abscisic acid (ABA) and ABA-dependent gene expression. To understand the roles of plant hormones and their interactions during dehydration, we analyzed the plant hormone profiles with respect to dehydration responses in Arabidopsis thaliana wild-type (WT) plants and ABA biosynthesis mutants (nced3-2). We developed a procedure for moderate dehydration stress, and then investigated temporal changes in the profiles of ABA, jasmonic acid isoleucine (JA-Ile), salicylic acid (SA), cytokinin (trans-zeatin, tZ), auxin (indole-acetic acid, IAA), and gibberellin (GA4 ), along with temporal changes in the expression of key genes involved in hormone biosynthesis. ABA levels increased in a bi-phasic pattern (at the early and late phases) in response to moderate dehydration stress. JA-Ile levels increased slightly in WT plants and strongly increased in nced3-2 mutant plants at 72 h after the onset of dehydration. The expression profiles of dehydration-inducible genes displayed temporal responses in an ABA-dependent manner. The early phase of ABA accumulation correlated with the expression of touch-inducible genes and was independent of factors involved in the major ABA regulatory pathway, including the ABA-responsive element-binding (AREB/ABF) transcription factor. JA-Ile, SA, and tZ were negatively regulated during the late dehydration response phase. Transcriptome analysis revealed important roles for hormone-related genes in metabolism and signaling during dehydration-induced plant responses.
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Affiliation(s)
- Kaoru Urano
- RIKEN Center for Sustainable Resource Science (CSRS), 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Kyonoshin Maruyama
- Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - Yusuke Jikumaru
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Yuji Kamiya
- RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | | | - Kazuo Shinozaki
- RIKEN Center for Sustainable Resource Science (CSRS), 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
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