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Jamil S, Ahmad S, Shahzad R, Umer N, Kanwal S, Rehman HM, Rana IA, Atif RM. Leveraging Multiomics Insights and Exploiting Wild Relatives' Potential for Drought and Heat Tolerance in Maize. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:16048-16075. [PMID: 38980762 DOI: 10.1021/acs.jafc.4c01375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Climate change, particularly drought and heat stress, may slash agricultural productivity by 25.7% by 2080, with maize being the hardest hit. Therefore, unraveling the molecular nature of plant responses to these stressors is vital for the development of climate-smart maize. This manuscript's primary objective was to examine how maize plants respond to these stresses, both individually and in combination. Additionally, the paper delved into harnessing the potential of maize wild relatives as a valuable genetic resource and leveraging AI-based technologies to boost maize resilience. The role of multiomics approaches particularly genomics and transcriptomics in dissecting the genetic basis of stress tolerance was also highlighted. The way forward was proposed to utilize a bunch of information obtained through omics technologies by an interdisciplinary state-of-the-art forward-looking big-data, cyberagriculture system, and AI-based approach to orchestrate the development of climate resilient maize genotypes.
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Affiliation(s)
- Shakra Jamil
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan
| | - Shakeel Ahmad
- Seed Centre and Plant Genetic Resources Bank Ministry of Environment, Water and Agriculture, Riyadh 14712, Saudi Arabia
| | - Rahil Shahzad
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan
| | - Noroza Umer
- Dr. Ikram ul Haq - Institute of Industrial Biotechnology, Government College University, Lahore 54590, Pakistan
| | - Shamsa Kanwal
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan
| | - Hafiz Mamoon Rehman
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38000, Pakistan
| | - Iqrar Ahmad Rana
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad 38000, Pakistan
| | - Rana Muhammad Atif
- Department of Plant Sciences, University of California Davis, California 95616, United States
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan
- Precision Agriculture and Analytics Lab, Centre for Advanced Studies in Agriculture and Food Security, National Centre in Big Data and Cloud Computing, University of Agriculture, Faisalabad 38000, Pakistan
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McLaughlin CM, Li M, Perryman M, Heymans A, Schneider H, Lasky JR, Sawers RJH. Evidence that variation in root anatomy contributes to local adaptation in Mexican native maize. Evol Appl 2024; 17:e13673. [PMID: 38468714 PMCID: PMC10925829 DOI: 10.1111/eva.13673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/07/2024] [Accepted: 02/22/2024] [Indexed: 03/13/2024] Open
Abstract
Mexican native maize (Zea mays ssp. mays) is adapted to a wide range of climatic and edaphic conditions. Here, we focus specifically on the potential role of root anatomical variation in this adaptation. Given the investment required to characterize root anatomy, we present a machine-learning approach using environmental descriptors to project trait variation from a relatively small training panel onto a larger panel of genotyped and georeferenced Mexican maize accessions. The resulting models defined potential biologically relevant clines across a complex environment that we used subsequently for genotype-environment association. We found evidence of systematic variation in maize root anatomy across Mexico, notably a prevalence of trait combinations favoring a reduction in axial hydraulic conductance in varieties sourced from cooler, drier highland areas. We discuss our results in the context of previously described water-banking strategies and present candidate genes that are associated with both root anatomical and environmental variation. Our strategy is a refinement of standard environmental genome-wide association analysis that is applicable whenever a training set of georeferenced phenotypic data is available.
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Affiliation(s)
- Chloee M. McLaughlin
- Intercollege Graduate Degree Program in Plant BiologyThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Meng Li
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Melanie Perryman
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Adrien Heymans
- Umeå Plant Science Centre, Department of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeåSweden
- Earth and Life InstituteUC LouvainLouvain‐la‐NeuveBelgium
| | - Hannah Schneider
- Department of Physiology and Cell BiologyLeibniz Institute for Plant Genetics and Crop Plant Research (IPK)SeelandGermany
| | - Jesse R. Lasky
- Department of BiologyThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Ruairidh J. H. Sawers
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
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Schmitt KFM, do Amaral Junior AT, Kamphorst SH, Pinto VB, de Lima VJ, de Oliveira UA, Viana FN, Leite JT, Gomes LP, Silva JGDS, Lamêgo DL, Bernado WDP, de Souza GAR, de Almeida FA, de Souza Filho GA, Silveira V, Campostrini E. Decoding the effects of drought stress on popcorn (Zea mays var. everta) flowering combining proteomics and physiological analysis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108444. [PMID: 38382344 DOI: 10.1016/j.plaphy.2024.108444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 02/05/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024]
Abstract
Under conditions of soil water limitation and adequate irrigation, we conducted an investigation into the growth dynamics, gas exchange performance, and proteomic profiles of two inbred popcorn lines-L71, characterized as drought-tolerant, and L61, identified as drought-sensitive. Our goal was to uncover the mechanisms associated with tolerance to soil water limitation during the flowering. The plants were cultivated until grain filling in a substrate composed of perlite and peat within 150cm long lysimeter, subjected to two water conditions (WC): i) irrigated (WW) at lysimeter capacity (LC - 100%), and ii) water-stressed (WS). Under WS conditions, the plants gradually reached 45% of LC and were maintained at this level for 10 days. Irrespective of the WC, L71 exhibited the highest values of dry biomass in both shoot and root systems, signifying its status as the most robust genotype. The imposed water limitation led to early senescence, chlorophyll degradation, and increased anthocyanin levels, with a more pronounced impact observed in L61. Traits related to gas exchange manifested differences between the lines only under WS conditions. A total of 1838 proteins were identified, with 169 differentially accumulated proteins (DAPs) in the tolerant line and 386 DAPs in the sensitive line. Notably, differences in energy metabolism, photosynthesis, oxidative stress response, and protein synthesis pathways were identified as the key distinctions between L71 and L61. Consequently, our findings offer valuable insights into the alterations in proteomic profiles associated with the adaptation to soil water limitation in popcorn.
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Affiliation(s)
- Katia Fabiane Medeiros Schmitt
- Laboratório de Melhoramento Vegetal, Centro de Ciência e Tecnologia Agronômica, Universidade Estadual do Norte Fluminense, Av. Prof. Alberto Lamego 2000, Campos dos Goytacazes, 28013-602, Brazil.
| | - Antônio Teixeira do Amaral Junior
- Laboratório de Melhoramento Vegetal, Centro de Ciência e Tecnologia Agronômica, Universidade Estadual do Norte Fluminense, Av. Prof. Alberto Lamego 2000, Campos dos Goytacazes, 28013-602, Brazil.
| | - Samuel Henrique Kamphorst
- Instituto Latino-Americano de Ciências da Vida e da Natureza. Universidade Federal da Integração Latino-Americana.
| | - Vitor Batista Pinto
- Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia (CBB). Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, 28013-602, Brazil.
| | - Valter Jário de Lima
- Laboratório de Melhoramento Vegetal, Centro de Ciência e Tecnologia Agronômica, Universidade Estadual do Norte Fluminense, Av. Prof. Alberto Lamego 2000, Campos dos Goytacazes, 28013-602, Brazil.
| | - Uéliton Alves de Oliveira
- Laboratório de Melhoramento Vegetal, Centro de Ciência e Tecnologia Agronômica, Universidade Estadual do Norte Fluminense, Av. Prof. Alberto Lamego 2000, Campos dos Goytacazes, 28013-602, Brazil.
| | - Flávia Nicácio Viana
- Laboratório de Melhoramento Vegetal, Centro de Ciência e Tecnologia Agronômica, Universidade Estadual do Norte Fluminense, Av. Prof. Alberto Lamego 2000, Campos dos Goytacazes, 28013-602, Brazil.
| | - Jhean Torres Leite
- Pesquisador em Ciências agronômicas GDM Seeds, Porto Nacional, TO, 77500-000, Brazil.
| | - Leticia Peixoto Gomes
- Laboratório de Melhoramento Vegetal, Centro de Ciência e Tecnologia Agronômica, Universidade Estadual do Norte Fluminense, Av. Prof. Alberto Lamego 2000, Campos dos Goytacazes, 28013-602, Brazil.
| | - José Gabriel de Souza Silva
- Laboratório de Melhoramento Vegetal, Centro de Ciência e Tecnologia Agronômica, Universidade Estadual do Norte Fluminense, Av. Prof. Alberto Lamego 2000, Campos dos Goytacazes, 28013-602, Brazil.
| | - Danielle Leal Lamêgo
- Laboratório de Melhoramento Vegetal, Centro de Ciência e Tecnologia Agronômica, Universidade Estadual do Norte Fluminense, Av. Prof. Alberto Lamego 2000, Campos dos Goytacazes, 28013-602, Brazil.
| | - Wallace de Paula Bernado
- Laboratório de Melhoramento Vegetal, Centro de Ciência e Tecnologia Agronômica, Universidade Estadual do Norte Fluminense, Av. Prof. Alberto Lamego 2000, Campos dos Goytacazes, 28013-602, Brazil.
| | - Guilherme Augusto Rodrigues de Souza
- Laboratório de Melhoramento Vegetal, Centro de Ciência e Tecnologia Agronômica, Universidade Estadual do Norte Fluminense, Av. Prof. Alberto Lamego 2000, Campos dos Goytacazes, 28013-602, Brazil.
| | - Felipe Astolpho de Almeida
- Laboratório de Química e Função de Proteínas e Peptídes, CBB. Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, 28013-602, Brazil.
| | - Gonçalo Apolinário de Souza Filho
- Laboratório de Biotecnologia, CBB. Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, 28013-602, Brazil.
| | - Vanildo Silveira
- Laboratório de Biotecnologia, CBB. Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, 28013-602, Brazil.
| | - Eliemar Campostrini
- Laboratório de Melhoramento Vegetal, Centro de Ciência e Tecnologia Agronômica, Universidade Estadual do Norte Fluminense, Av. Prof. Alberto Lamego 2000, Campos dos Goytacazes, 28013-602, Brazil.
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Molla MSH, Kumdee O, Wongkaew A, Khongchiu P, Worathongchai N, Alam MR, Mahmud AA, Nakasathien S. Potentiality of Sustainable Maize Production under Rainfed Conditions in the Tropics by Triggering Agro-Physio-Biochemical Traits Ascertained from a Greenhouse. PLANTS (BASEL, SWITZERLAND) 2023; 12:4192. [PMID: 38140518 PMCID: PMC10748014 DOI: 10.3390/plants12244192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023]
Abstract
A major portion of maize is produced under rainfed conditions in the tropics with relatively poor yield because of the unpredictable and irregular distribution of seasonal rainfall, as well as a decline in pre-rainy season rainfall due to climate change, so identification of sustainable production options is utmost needed. Thus, the present studies were conducted in a greenhouse (GH) to ascertain the water stress-tolerant traits of maize and at the field level in the tropical environment of Thailand to see the stimulating possibility of the ascertained traits in a locally popular cultivar using ethephon. Depending on tolerance level, three maize genotypes (Suwan 2301 > Suwan 4452 > S 7328) were tested under different water conditions-well-watered, short-term, and long-term water stress-in the GH. At the field level, the locally popular maize cultivar Suwan 5819 was examined with six ethephon levels (doses in g a.i. ha-1 of ethephon, i.e., T1, 281 at V6 stage; T2, 281 at V6 + 281 at V10 stage; T3, 281 at V10 stage; T4, 562 at V6 stage; T5, 562 at V6 + 562 at V10 stage; T6, 562 at V10 stage) against no ethephon application (T0) under rainfed conditions. Maize suffered from the scarcity of sufficient rainfall during 26-39 days after planting (DAP) and 43-63 DAP in the field. The yield index (YI) was identified from biplot analysis as one of the suitable standards for drought tolerance checks for maize at GH as well as at field level in the tropics. The YI value of observed agro-physio-biochemical traits of maize in GH showed that relative water content (RWC, 1.23), stem base diameter (SBD, 1.21), total soluble sugar (TSS, 1.15), proline (Pr, 1.13), aboveground plant biomass (APB, 1.13), root weight (RW, 1.13), relative growth rate (RGR, 1.15), specific leaf weight (SLW, 1.12), and net assimilation rate (NAR, 1.08) were the most desirable. Efforts were made to stimulate these traits under water stress at the field level. Ethephon application as T1 helped to gain higher kernel yield (KY) (5.26 t ha-1) with the support of higher RWC (90.38%), proline (24.79 µmol g-1 FW), TSS (1629 mg g-1 FW), SBD (24.49 mm), APB (271.34 g plant-1), SLW (51.71 g m-2), RGR (25.26 mg plant-1 day-1), and NAR (0.91 mg cm-2 day-1) compared to others, especially no ethephon application. Furthermore, the attributes SLW, SBD, Pr, heat utilization efficiency (HUE), 100-kernel weight, TSS, electrolyte leakage, and lodging percentage showed a substantial direct effect and significant correlation with KY. Aside from higher KY, ethephon application as T1 tactics resulted in higher values of energy efficiency (1.66), HUE (2.99 kg ha-1 °C days-1), gross margin (682.02 USD ha-1), MBCR (3.32), and C absorption (6.19 t C ha-1), indicating that this practice may be a good option for maize sustainable production under rainfed conditions.
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Affiliation(s)
- Md. Samim Hossain Molla
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand; (A.W.)
- On-Farm Research Division, Bangladesh Agricultural Research Institute, Gazipur 1701, Bangladesh; (M.R.A.); (A.-A.M.)
| | - Orawan Kumdee
- Agricultural Research and Technology Transfer Center, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand;
| | - Arunee Wongkaew
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand; (A.W.)
| | - Phanuphong Khongchiu
- Expert Center of Innovative Agriculture, Thailand Institute of Scientific and Technological Research, Pathum Thani 12120, Thailand;
| | - Nattaporn Worathongchai
- National Corn and Sorghum Research Center, Faculty of Agriculture, Kasetsart University, Nakhon Ratchasima 30320, Thailand;
| | - Md. Robiul Alam
- On-Farm Research Division, Bangladesh Agricultural Research Institute, Gazipur 1701, Bangladesh; (M.R.A.); (A.-A.M.)
| | - Abdullah-Al Mahmud
- On-Farm Research Division, Bangladesh Agricultural Research Institute, Gazipur 1701, Bangladesh; (M.R.A.); (A.-A.M.)
| | - Sutkhet Nakasathien
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand; (A.W.)
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Dwiningsih Y, Thomas J, Kumar A, Gupta C, Gill N, Ruiz C, Alkahtani J, Baisakh N, Pereira A. QTLs and Candidate Loci Associated with Drought Tolerance Traits of Kaybonnet x ZHE733 Recombinant Inbred Lines Rice Population. Int J Mol Sci 2023; 24:15167. [PMID: 37894848 PMCID: PMC10606886 DOI: 10.3390/ijms242015167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/02/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Rice is the most important staple crop for the sustenance of the world's population, and drought is a major factor limiting rice production. Quantitative trait locus (QTL) analysis of drought-resistance-related traits was conducted on a recombinant inbred line (RIL) population derived from the self-fed progeny of a cross between the drought-resistant tropical japonica U.S. adapted cultivar Kaybonnet and the drought-sensitive indica cultivar ZHE733. K/Z RIL population of 198 lines was screened in the field at Fayetteville (AR) for three consecutive years under controlled drought stress (DS) and well-watered (WW) treatment during the reproductive stage. The effects of DS were quantified by measuring morphological traits, grain yield components, and root architectural traits. A QTL analysis using a set of 4133 single nucleotide polymorphism (SNP) markers and the QTL IciMapping identified 41 QTLs and 184 candidate genes for drought-related traits within the DR-QTL regions. RT-qPCR in parental lines was used to confirm the putative candidate genes. The comparison between the drought-resistant parent (Kaybonnet) and the drought-sensitive parent (ZHE733) under DS conditions revealed that the gene expression of 15 candidate DR genes with known annotations and two candidate DR genes with unknown annotations within the DR-QTL regions was up-regulated in the drought-resistant parent (Kaybonnet). The outcomes of this research provide essential information that can be utilized in developing drought-resistant rice cultivars that have higher productivity when DS conditions are prevalent.
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Affiliation(s)
- Yheni Dwiningsih
- Department of Crop, Soil, and Environmental Sciences, Faculty of Agriculture Food and Life Sciences, University of Arkansas System Division of Agriculture, Fayetteville, AR 72701, USA; (Y.D.); (J.T.); (A.K.); (C.R.); (J.A.)
| | - Julie Thomas
- Department of Crop, Soil, and Environmental Sciences, Faculty of Agriculture Food and Life Sciences, University of Arkansas System Division of Agriculture, Fayetteville, AR 72701, USA; (Y.D.); (J.T.); (A.K.); (C.R.); (J.A.)
| | - Anuj Kumar
- Department of Crop, Soil, and Environmental Sciences, Faculty of Agriculture Food and Life Sciences, University of Arkansas System Division of Agriculture, Fayetteville, AR 72701, USA; (Y.D.); (J.T.); (A.K.); (C.R.); (J.A.)
| | - Chirag Gupta
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA;
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Navdeep Gill
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL 33314, USA;
| | - Charles Ruiz
- Department of Crop, Soil, and Environmental Sciences, Faculty of Agriculture Food and Life Sciences, University of Arkansas System Division of Agriculture, Fayetteville, AR 72701, USA; (Y.D.); (J.T.); (A.K.); (C.R.); (J.A.)
| | - Jawaher Alkahtani
- Department of Crop, Soil, and Environmental Sciences, Faculty of Agriculture Food and Life Sciences, University of Arkansas System Division of Agriculture, Fayetteville, AR 72701, USA; (Y.D.); (J.T.); (A.K.); (C.R.); (J.A.)
| | - Niranjan Baisakh
- Department of School of Plant, Environmental and Soil Sciences, Louisiana State University, Baton Rouge, LA 70803, USA;
| | - Andy Pereira
- Department of Crop, Soil, and Environmental Sciences, Faculty of Agriculture Food and Life Sciences, University of Arkansas System Division of Agriculture, Fayetteville, AR 72701, USA; (Y.D.); (J.T.); (A.K.); (C.R.); (J.A.)
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Wang Y, Zhou Y, Ye J, Jin C, Hu Y. Continuous Cropping Inhibits Photosynthesis of Polygonatum odoratum. PLANTS (BASEL, SWITZERLAND) 2023; 12:3374. [PMID: 37836114 PMCID: PMC10574191 DOI: 10.3390/plants12193374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/17/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023]
Abstract
Polygonatum odoratum (Mill.) Druce possesses widespread medicinal properties; however, the continuous cropping (CC) often leads to a severe consecutive monoculture problem (CMP), ultimately causing a decline in yield and quality. Photosynthesis is the fundamental process for plant growth development. Improving photosynthesis is one of the most promising approaches to increase plant yields. To better understand how P. odoratum leaves undergo photosynthesis in response to CC, this study analyzed the physiochemical indexes and RNA-seq. The physiochemical indexes, such as the content of chlorophyll (chlorophyll a, b, and total chlorophyll), light response curves (LRCs), and photosynthetic parameters (Fv/Fm, Fv/F0, Fm/F0, Piabs, ABS/RC, TRo/RC, ETo/RC, and DIo/RC) were all changed in P. odoratum under the CC system. Furthermore, 13,798 genes that exhibited differential expression genes (DEGs) were identified in the P. odoratum leaves of CC and first cropping (FC) plants. Among them, 7932 unigenes were upregulated, while 5860 unigenes were downregulated. Here, the DEGs encoding proteins associated with photosynthesis and carbon assimilation showed a significant decrease in expression under the CC system, such as the PSII protein complex, PSI protein complex, Cytochorome b6/f complex, the photosynthetic electron transport chain, light-harvesting chlorophyll protein complex, and Calvin cycle, etc., -related gene. This study demonstrates that CC can suppress photosynthesis and carbon mechanism in P. odoratum, pinpointing potential ways to enhance photosynthetic efficiency in the CC of plants.
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Affiliation(s)
- Yan Wang
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China; (Y.W.); (Y.Z.); (J.Y.)
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, National Center of Technology Innovation for Saline-Alkali Tolerant Rice, College of Biology, Hunan University, Changsha 410082, China
| | - Yunyun Zhou
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China; (Y.W.); (Y.Z.); (J.Y.)
- Biodiversity Institute, Hunan Academy of Forestry, Changsha 410018, China
| | - Jing Ye
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China; (Y.W.); (Y.Z.); (J.Y.)
| | - Chenzhong Jin
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China; (Y.W.); (Y.Z.); (J.Y.)
| | - Yihong Hu
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China; (Y.W.); (Y.Z.); (J.Y.)
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Sakurai K, Toda Y, Hamazaki K, Ohmori Y, Yamasaki Y, Takahashi H, Takanashi H, Tsuda M, Tsujimoto H, Kaga A, Nakazono M, Fujiwara T, Iwata H. Random regression for modeling soybean plant response to irrigation changes using time-series multispectral data. FRONTIERS IN PLANT SCIENCE 2023; 14:1201806. [PMID: 37476172 PMCID: PMC10354427 DOI: 10.3389/fpls.2023.1201806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/15/2023] [Indexed: 07/22/2023]
Abstract
Plant response to drought is an important yield-related trait under abiotic stress, but the method for measuring and modeling plant responses in a time series has not been fully established. The objective of this study was to develop a method to measure and model plant response to irrigation changes using time-series multispectral (MS) data. We evaluated 178 soybean (Glycine max (L.) Merr.) accessions under three irrigation treatments at the Arid Land Research Center, Tottori University, Japan in 2019, 2020 and 2021. The irrigation treatments included W5: watering for 5 d followed by no watering 5 d, W10: watering for 10 d followed by no watering 10 d, D10: no watering for 10 d followed by watering 10 d, and D: no watering. To capture the plant responses to irrigation changes, time-series MS data were collected by unmanned aerial vehicle during the irrigation/non-irrigation switch of each irrigation treatment. We built a random regression model (RRM) for each of combination of treatment by year using the time-series MS data. To test the accuracy of the information captured by RRM, we evaluated the coefficient of variation (CV) of fresh shoot weight of all accessions under a total of nine different drought conditions as an indicator of plant's stability under drought stresses. We built a genomic prediction model (MT RRM model ) using the genetic random regression coefficients of RRM as secondary traits and evaluated the accuracy of each model for predicting CV. In 2020 and 2021,the mean prediction accuracies of MT RRM models built in the changing irrigation treatments (r = 0.44 and 0.49, respectively) were higher than that in the continuous drought treatment (r = 0.34 and 0.44, respectively) in the same year. When the CV was predicted using the MT RRM model across 2020 and 2021 in the changing irrigation treatment, the mean prediction accuracy (r = 0.46) was 42% higher than that of the simple genomic prediction model (r =0.32). The results suggest that this RRM method using the time-series MS data can effectively capture the genetic variation of plant response to drought.
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Affiliation(s)
- Kengo Sakurai
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Yusuke Toda
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Kosuke Hamazaki
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Yoshihiro Ohmori
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Yuji Yamasaki
- Arid Land Research Center, Tottori University, Tottori, Japan
| | - Hirokazu Takahashi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hideki Takanashi
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Mai Tsuda
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Japan
| | | | - Akito Kaga
- Soybean and Field Crop Applied Genomics Research Unit, Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Mikio Nakazono
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Toru Fujiwara
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Hiroyoshi Iwata
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
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Teshome DT, Zharare GE, Ployet R, Naidoo S. Transcriptional reprogramming during recovery from drought stress in Eucalyptus grandis. TREE PHYSIOLOGY 2023; 43:979-994. [PMID: 36851855 DOI: 10.1093/treephys/tpad022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 02/23/2023] [Indexed: 06/11/2023]
Abstract
The importance of drought as a constraint to agriculture and forestry is increasing with climate change. Genetic improvement of plants' resilience is one of the mitigation strategies to curb this threat. Although recovery from drought stress is important to long-term drought adaptation and has been considered as an indicator of dehydration tolerance in annual crops, this has not been well explored in forest trees. Thus, we aimed to investigate the physiological and transcriptional changes during drought stress and rewatering in Eucalyptus grandis W. Hill ex Maiden. We set up a greenhouse experiment where we imposed drought stress on 2-year-old seedlings and rewatered the recovery group after 17 days of drought. Our measurement of leaf stomatal conductance (gs) showed that, while gs was reduced by drought stress, it fully recovered after 5 days of rewatering. The RNA-seq analysis from stem samples revealed that genes related to known stress responses such as phytohormone and reactive oxygen species signaling were upregulated, while genes involved in metabolism and growth were downregulated due to drought stress. We observed reprogramming of signal transduction pathways and metabolic processes at 1 day of rewatering, indicating a quick response to rewatering. Our results suggest that recovery from drought stress may entail alterations in the jasmonic acid, salicylic acid, ethylene and brassinosteroid signaling pathways. Using co-expression network analysis, we identified hub genes, including the putative orthologs of ABI1, ABF2, ABF3, HAI2, BAM1, GolS2 and SIP1 during drought and CAT2, G6PD1, ADG1 and FD-1 during recovery. Taken together, by highlighting the molecular processes and identifying key genes, this study gives an overview of the mechanisms underlying the response of E. grandis to drought stress and recovery that trees may face repeatedly throughout their long life cycle. This provides a useful reference to the identification and further investigation of signaling pathways and target genes for future tree improvement.
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Affiliation(s)
- Demissew Tesfaye Teshome
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Lynwood Road, Pretoria 0028, South Africa
| | - Godfrey Elijah Zharare
- Department of Agriculture, University of Zululand, 1 Main Road Vulindlela, KwaDlangezwa, 3886, South Africa
| | - Raphael Ployet
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831, USA
| | - Sanushka Naidoo
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Lynwood Road, Pretoria 0028, South Africa
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9
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Dash PK, Rai R, Pradhan SK, Shivaraj SM, Deshmukh R, Sreevathsa R, Singh NK. Drought and Oxidative Stress in Flax ( Linum usitatissimum L.) Entails Harnessing Non-Canonical Reference Gene for Precise Quantification of qRT-PCR Gene Expression. Antioxidants (Basel) 2023; 12:antiox12040950. [PMID: 37107326 PMCID: PMC10136167 DOI: 10.3390/antiox12040950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Flax (Linum usitatissimum L.) is a self-pollinating, annual, diploid crop grown for multi-utility purposes for its quality oil, shining bast fiber, and industrial solvent. Being a cool (Rabi) season crop, it is affected by unprecedented climatic changes such as high temperature, drought, and associated oxidative stress that, globally, impede its growth, production, and productivity. To precisely assess the imperative changes that are inflicted by drought and associated oxidative stress, gene expression profiling of predominant drought-responsive genes (AREB, DREB/CBF, and ARR) was carried out by qRT-PCR. Nevertheless, for normalization/quantification of data obtained from qRT-PCR results, a stable reference gene is mandatory. Here, we evaluated a panel of four reference genes (Actin, EF1a, ETIF5A, and UBQ) and assessed their suitability as stable reference genes for the normalization of gene expression data obtained during drought-induced oxidative stress in flax. Taking together, from the canonical expression of the proposed reference genes in three different genotypes, we report that EF1a as a stand-alone and EF1a and ETIF5A in tandem are suitable reference genes to be used for the real-time visualization of cellular impact of drought and oxidative stress on flax.
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Affiliation(s)
- Prasanta K Dash
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Rhitu Rai
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Sharat Kumar Pradhan
- ICAR-National Rice Research Institute, Cuttack 753006, India
- Indian Council of Agricultural Research, Krishi Bhawan, New Delhi 110012, India
| | | | - Rupesh Deshmukh
- Department of Biotechnology, Central University of Haryana, Mahendragarh 123031, India
| | - Rohini Sreevathsa
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Nagendra K Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
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10
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Wang J, Sun Z, Wang X, Tang Y, Li X, Ren C, Ren J, Wang X, Jiang C, Zhong C, Zhao S, Zhang H, Liu X, Kang S, Zhao X, Yu H. Transcriptome-based analysis of key pathways relating to yield formation stage of foxtail millet under different drought stress conditions. FRONTIERS IN PLANT SCIENCE 2023; 13:1110910. [PMID: 36816479 PMCID: PMC9937063 DOI: 10.3389/fpls.2022.1110910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Although foxtail millet, as small Panicoid crop, is of drought resilient, drought stress has a significant effect on panicle of foxtail millet at the yield formation stage. In this study, the changes of panicle morphology, photosynthesis, antioxidant protective enzyme system, reactive oxygen species (ROS) system, and osmotic regulatory substance and RNA-seq of functional leaves under light drought stress (LD), heavy drought stress (HD), light drought control (LDCK) and heavy drought control (HDCK) were studied to get a snap-shot of specific panicle morphological changes, physiological responses and related molecular mechanisms. The results showed that the length and weight of panicle had decreased, but with increased empty abortive rate, and then yield dropped off 14.9% and 36.9%, respectively. The photosynthesis of millet was significantly decreased, like net photosynthesis rate, stomatal conductance and transpiration rate, especially under HD treatment with reluctant recovery from rehydration. Under LD and HD treatment, the peroxidase (POD) was increased by 34% and 14% and the same as H2O2 by 34.7% and 17.2% compared with LDCK and HDCK. The ability to produce and inhibit O2- free radicals under LD treatment was higher than HD. The content of soluble sugar was higher under LD treatment but the proline was higher under HD treatment. Through RNA-seq analysis, there were 2,393 and 3,078 different genes expressed under LD and HD treatment. According to the correlation analysis between weighted gene coexpression network analysis (WGCNA) and physiological traits, the co-expression network of several modules with high correlation was constructed, and some hub genes of millet in response to drought stress were found. The expression changes relating to carbon fixation, sucrose and starch synthesis, lignin synthesis, gibberellin synthesis, and proline synthesis of millet were specifically analyzed. These findings provide a full perspective on how drought affects the yield formation of foxtail millet by constructing one work model thereby providing theoretical foundation for hub genes exploration and drought resistance breeding of foxtail millet.
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11
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Ahmed AAM, Dawood MFA, Elfarash A, Mohamed EA, Hussein MY, Börner A, Sallam A. Genetic and morpho-physiological analyses of the tolerance and recovery mechanisms in seedling stage spring wheat under drought stress. Front Genet 2022; 13:1010272. [PMID: 36303538 PMCID: PMC9593057 DOI: 10.3389/fgene.2022.1010272] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Drought is one of the complex abiotic stresses that affect the growth and production of wheat in arid and semiarid countries. In this study, a set of 172 diverse spring wheat genotypes from 20 different countries were assessed under drought stress at the seedling stage. Besides seedling length, two types of traits were recorded, namely: tolerance traits (days to wilting, leaf wilting, and the sum of leaf wilting), and recovery traits (days to regrowth, regrowth biomass, and drought survival rate). In addition, tolerance index, recovery index, and drought tolerance index (DTI) were estimated to select the most drought tolerant genotypes. Moreover, leaf protein content (P), amino acid (AM), proline content (PRO), glucose (G), fructose (F), and total soluble carbohydrates (TSC) were measured under control and drought conditions to study the changes in each physiological trait due to drought stress. All genotypes showed a high significant genetic variation in all the physio-morphological traits scored under drought stress. High phenotypic and genotypic correlations were found among all seedling morphological traits. Among the studied indices, the drought tolerance index (DTI) had the highest phenotypic and genotypic correlations with all tolerance and recovery traits. The broad-sense heritability (H2) estimates were high for morphological traits (83.85–92.27), while the physiological traits ranged from 96.41 to 98.68 under the control conditions and from 97.13 to 99.99 under drought stress. The averages of the physiological traits (proteins, amino acids, proline, glucose, fructose, and total soluble carbohydrates) denoted under drought stress were higher than those recorded under well-watered conditions except for proteins. In this regard, amino acids, glucose, and total soluble carbohydrates had a significant correlation with all morphological traits. The selection for drought tolerance revealed 10 tolerant genotypes from different countries (8 genotypes from Egypt, one from Morocco, and one from the United States). These selected genotypes were screened for the presence of nine specific TaDREB1 alleles. Six primers were polymorphic among the selected genotypes. Genetic diversity among the selected genotypes was investigated using 21,450 SNP markers. The results of the study shed light on the different mechanisms for drought tolerance that wheat plants use to tolerate and survive under drought stress. The genetic analysis performed in this study suggested the most suitable genotypes for selective breeding at the seedling stage under water deficit.
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Affiliation(s)
- Asmaa A. M. Ahmed
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Mona F. A. Dawood
- Department of Botany and Microbiology, Faculty of Science, Assiut University, Assiut, Egypt
| | - Ameer Elfarash
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Elsayed A. Mohamed
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Mohamed Y. Hussein
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Andreas Börner
- Resources Genetics and Reproduction, Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Ahmed Sallam
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, Egypt
- Resources Genetics and Reproduction, Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- *Correspondence: Ahmed Sallam, ,
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12
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Sancho R, Catalán P, Contreras‐Moreira B, Juenger TE, Des Marais DL. Patterns of pan-genome occupancy and gene coexpression under water-deficit in Brachypodium distachyon. Mol Ecol 2022; 31:5285-5306. [PMID: 35976181 PMCID: PMC9804473 DOI: 10.1111/mec.16661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/29/2022] [Accepted: 08/11/2022] [Indexed: 01/05/2023]
Abstract
Natural populations are characterized by abundant genetic diversity driven by a range of different types of mutation. The tractability of sequencing complete genomes has allowed new insights into the variable composition of genomes, summarized as a species pan-genome. These analyses demonstrate that many genes are absent from the first reference genomes, whose analysis dominated the initial years of the genomic era. Our field now turns towards understanding the functional consequence of these highly variable genomes. Here, we analysed weighted gene coexpression networks from leaf transcriptome data for drought response in the purple false brome Brachypodium distachyon and the differential expression of genes putatively involved in adaptation to this stressor. We specifically asked whether genes with variable "occupancy" in the pan-genome - genes which are either present in all studied genotypes or missing in some genotypes - show different distributions among coexpression modules. Coexpression analysis united genes expressed in drought-stressed plants into nine modules covering 72 hub genes (87 hub isoforms), and genes expressed under controlled water conditions into 13 modules, covering 190 hub genes (251 hub isoforms). We find that low occupancy pan-genes are under-represented among several modules, while other modules are over-enriched for low-occupancy pan-genes. We also provide new insight into the regulation of drought response in B. distachyon, specifically identifying one module with an apparent role in primary metabolism that is strongly responsive to drought. Our work shows the power of integrating pan-genomic analysis with transcriptomic data using factorial experiments to understand the functional genomics of environmental response.
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Affiliation(s)
- Rubén Sancho
- Department of Agricultural and Environmental Sciences, High Polytechnic School of HuescaUniversity of ZaragozaHuescaSpain,Unidad Associada al CSIC, Grupo de BioquímicaGrupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR)ZaragozaSpain
| | - Pilar Catalán
- Department of Agricultural and Environmental Sciences, High Polytechnic School of HuescaUniversity of ZaragozaHuescaSpain,Unidad Associada al CSIC, Grupo de BioquímicaGrupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR)ZaragozaSpain
| | - Bruno Contreras‐Moreira
- Unidad Associada al CSIC, Grupo de BioquímicaGrupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR)ZaragozaSpain,Estación Experimental de Aula Dei‐Consejo Superior de Investigaciones CientíficasZaragozaSpain,Fundación ARAIDZaragozaSpain
| | - Thomas E. Juenger
- Department of Integrative BiologyThe University of Texas at AustinAustinTexasUSA
| | - David L. Des Marais
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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13
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Zhang J, An H, Zhang X, Xu F, Zhou B. Transcriptomic Analysis Reveals Potential Gene Regulatory Networks Under Cold Stress of Loquat ( Eriobotrya japonica Lindl.). FRONTIERS IN PLANT SCIENCE 2022; 13:944269. [PMID: 35937353 PMCID: PMC9354853 DOI: 10.3389/fpls.2022.944269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/17/2022] [Indexed: 05/02/2023]
Abstract
Loquat (Eriobotrya japonica Lindl. ) is one of the most economically important evergreen fruit crops in China, while it often suffered the injury of cold stress in winter and earlier spring, and the annual yield loss of loquat fruits caused by cold or freezing stress was immeasurable. However, knowledge about the physiological response and molecular mechanism under cold stress is still limited. To investigate the potential regulation mechanism pre- and post-cold stress in loquat and the changes in physiological indicators, a comparative transcriptome analysis was performed against a cold-resistant cv. "Huoju" and a cold-sensitive cv. "Ninghaibai". The results of physiological indicators related to cold resistance indicated that rachis was most sensitive to cold stress and was considered as the representative organ to directly evaluate cold resistance of loquat based on subordinate function analysis. Here, we compared the transcriptome profiles of rachis pre- and under cold stress in "Huoju" and "Ninghaibai". A total of 4,347 and 3,513 differentially expressed genes (DEGs) were detected in "Ninghaibai" and "Huoju", among which 223 and 166 were newly identified genes, respectively, most of them were functionally enriched in plant hormone signal transduction (Huoju: 142; Ninghaibai: 200), and there were higher plant hormone content and related DEG expression levels in "Huoju" than that of "Ninghaibai". Moreover, a total of 3,309 differentially expressed transcription factors (DETFs) were identified, and some DEGs and DETFs were screened to be subjected to co-expression network analysis based on the gene expression profile data. Some candidate DEGs, including UDP-glycosyltransferase (UGT), glycosyltransferase (GT), sugar phosphate/phosphate translocator (SPT), sugar transport protein (STP), proline-rich receptor-like protein kinase (PERK), and peroxidise (POD), were significantly affected by cold stress, and the expression level of these genes obtained from real-time quantitative RT-PCR was consistent with the pattern of transcriptome profile, which suggested that these genes might play the vital roles in cold resistance of loquat. Our results provide an invaluable resource for the identification of specific genes and TFs and help to clarify gene transcription during the cold stress response of loquat.
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Affiliation(s)
- Jiaying Zhang
- Forestry and Pomology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Haishan An
- Forestry and Pomology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Xueying Zhang
- Forestry and Pomology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Fangjie Xu
- Forestry and Pomology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Boqiang Zhou
- Forestry and Pomology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
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14
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Pipatsitee P, Theerawitaya C, Tiasarum R, Samphumphuang T, Singh HP, Datta A, Cha-Um S. Physio-morphological traits and osmoregulation strategies of hybrid maize (Zea mays) at the seedling stage in response to water-deficit stress. PROTOPLASMA 2022; 259:869-883. [PMID: 34581924 DOI: 10.1007/s00709-021-01707-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 09/16/2021] [Indexed: 05/27/2023]
Abstract
Drought has been identified as a major factor restricting maize productivity worldwide, especially in the rainfed areas. The objective of the present study was to investigate the physiological adaptation strategies and sugar-related gene expression levels in three maize (Zea mays L.) genotypes with different drought tolerance abilities (Suwan4452, drought tolerant as a positive check; S7328, drought susceptible as a negative check; Pac339, drought susceptible) at the seedling stage. Ten-day old seedlings of maize genotypes were subjected to (i) well-watered (WW) or control and (ii) water-deficit (WD) conditions. Leaf osmotic potential of cv. S7328 under WD was significantly decreased by 1.35-1.45 folds compared with cv. Pac339 under WW, whereas it was retained in cv. Suwan4452, which utilized total soluble sugars as the major osmolytes for maintaining leaf greenness, Fv/Fm, ΦPSII, and stomatal function (Pn, net photosynthetic rate; gs, stomatal conductance; and E, transpiration rate). Interestingly, sucrose degradation (65% over the control) in cv. Pac339 under WD was evident in relation to the downregulation of the ZmSPS1 level, whereas glucose enrichment (1.65 folds over the control) was observed in relation to the upregulation of ZmSPS1 and ZmSUS1. Moreover, CWSI (crop water stress index), calculated from leaf temperature of stressed plants, was negatively correlated with E, gs, and Pn. Overall, growth characteristics, aboveground and belowground parts, in the drought-susceptible cv. Pac339 and cv. S7328, were significantly decreased (> 25% over the control), whereas these parameters in the drought-tolerant cv. Suwan4452 were unaffected. The study validates the use of leaf temperature, CWSI, Pn, gs, and E as sensitive parameters and overall growth characters as effective indices for drought tolerance screening in maize genotypes at the seedling stage. However, further experiments are required to validate the results observed in this study under field conditions.
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Affiliation(s)
- Piyanan Pipatsitee
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Cattarin Theerawitaya
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Rujira Tiasarum
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Thapanee Samphumphuang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Harminder Pal Singh
- Department of Environment Studies, Faculty of Science, Panjab University, Chandigarh, 160014, India
| | - Avishek Datta
- Agricultural Systems and Engineering, Department of Food, Agriculture and Bioresources, School of Environment, Resources and Development, Asian Institute of Technology, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Suriyan Cha-Um
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand.
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15
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Freeg HA, Attia KA, Casson S, Fiaz S, Ramadan EA, Banna AE, Zoulias N, Aboshosha A, Alamery S. Physio-biochemical responses and expressional profiling analysis of drought tolerant genes in new promising rice genotype. PLoS One 2022; 17:e0266087. [PMID: 35349595 PMCID: PMC8963560 DOI: 10.1371/journal.pone.0266087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/13/2022] [Indexed: 11/18/2022] Open
Abstract
Rice cultivation in Egypt is limited by the scarcity of water resources. The main strategy of rice breeders to overcome this problem is to develop new high-yielding varieties that are tolerant to drought stress. In this study, an drought-tolerant (IR60080-46A) variety was crossed with commercial Egyptian varieties using the back-cross method and marker-assisted selection (MAS) approach. The advanced lines of these crosses were selected under drought stress conditions. The best-performing candidate line, RBL-112, and its parental genotypes, were evaluated under drought stress and control conditions. The RBL-112 line showed superior its root system, which in turn produced higher grain yield under drought-stress conditions than its parental and check genotypes. Furthermore, physiological and biochemical studies showed that the RBL-112 line maintained higher relative water content (RWC), maximum quantum efficiency of photosystem II (Fv/Fm) values, proline content, superoxide dismutase (SOD) activity, and lower malondialdehyde (MDA) content compared to its parents and the check. The functional expression profiles of 22 drought tolerance-related genes were studied, out of which the genes OsAHL1, OsLEA3, OsCATA, OsP5CS, OsSNAC1, Os1g64660, OsRab21, OsAPX2, OsDREB2A, OsSKIPa, and OsLG3 were strongly induced in the newly developed RBL-112 line under drought-stress conditions. It could be concluded that the new line has a higher capacity to modulate physiological activities and expression levels of several drought-induced genes to withstand drought stress with high yielding ability. This finding suggests that the RBL-112 line presents a promising new addition to enable sustainable rice cultivation under water-limited conditions, and confirms the efficiency of the approach implemented in the current study.
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Affiliation(s)
- Haytham A. Freeg
- Department of Molecular Biology and Biotechnology, College of Science, Sheffield University, Sheffield, TN, United Kingdom
- Rice Biotechnology Lab., Rice Research & Training Center (RRTC), Field Crops Research Institute, ARC, Sakhah, Egypt
- Department of Genetics, College of Agriculture, Kafr-El-Sheikh University, Kafr El Sheikh, Egypt
| | - Kotb A. Attia
- Rice Biotechnology Lab., Rice Research & Training Center (RRTC), Field Crops Research Institute, ARC, Sakhah, Egypt
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
- * E-mail: (KAA); (SF)
| | - Stuart Casson
- Department of Molecular Biology and Biotechnology, College of Science, Sheffield University, Sheffield, TN, United Kingdom
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
- * E-mail: (KAA); (SF)
| | - Ebrahim A. Ramadan
- Rice Biotechnology Lab., Rice Research & Training Center (RRTC), Field Crops Research Institute, ARC, Sakhah, Egypt
| | - Antar El- Banna
- Department of Genetics, College of Agriculture, Kafr-El-Sheikh University, Kafr El Sheikh, Egypt
| | - Nicholas Zoulias
- Department of Molecular Biology and Biotechnology, College of Science, Sheffield University, Sheffield, TN, United Kingdom
| | - Ali Aboshosha
- Department of Genetics, College of Agriculture, Kafr-El-Sheikh University, Kafr El Sheikh, Egypt
| | - Salman Alamery
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
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Janzen GM, Aguilar‐Rangel MR, Cíntora‐Martínez C, Blöcher‐Juárez KA, González‐Segovia E, Studer AJ, Runcie DE, Flint‐Garcia SA, Rellán‐Álvarez R, Sawers RJH, Hufford MB. Demonstration of local adaptation in maize landraces by reciprocal transplantation. Evol Appl 2022; 15:817-837. [PMID: 35603032 PMCID: PMC9108319 DOI: 10.1111/eva.13372] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 01/24/2022] [Accepted: 01/31/2022] [Indexed: 11/28/2022] Open
Abstract
Populations are locally adapted when they exhibit higher fitness than foreign populations in their native habitat. Maize landrace adaptations to highland and lowland conditions are of interest to researchers and breeders. To determine the prevalence and strength of local adaptation in maize landraces, we performed a reciprocal transplant experiment across an elevational gradient in Mexico. We grew 120 landraces, grouped into four populations (Mexican Highland, Mexican Lowland, South American Highland, South American Lowland), in Mexican highland and lowland common gardens and collected phenotypes relevant to fitness and known highland‐adaptive traits such as anthocyanin pigmentation and macrohair density. 67k DArTseq markers were generated from field specimens to allow comparisons between phenotypic patterns and population genetic structure. We found phenotypic patterns consistent with local adaptation, though these patterns differ between the Mexican and South American populations. Quantitative trait differentiation (QST) was greater than neutral allele frequency differentiation (FST) for many traits, signaling directional selection between pairs of populations. All populations exhibited higher fitness metric values when grown at their native elevation, and Mexican landraces had higher fitness than South American landraces when grown in these Mexican sites. As environmental distance between landraces’ native collection sites and common garden sites increased, fitness values dropped, suggesting landraces are adapted to environmental conditions at their natal sites. Correlations between fitness and anthocyanin pigmentation and macrohair traits were stronger in the highland site than the lowland site, supporting their status as highland‐adaptive. These results give substance to the long‐held presumption of local adaptation of New World maize landraces to elevation and other environmental variables across North and South America.
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Affiliation(s)
- Garrett M. Janzen
- Department of Ecology, Evolution, and Organismal Biology Iowa State University Ames Iowa USA 50011
- Department of Plant Biology University of Georgia Athens Georgia USA 30602
| | | | | | | | - Eric González‐Segovia
- Langebio, Cinvestav, Km 9.6 Libramiento Norte Carretera Len Irapuato, Guanajuato Mexico 36821
| | - Anthony J. Studer
- Department of Crop Sciences University of Illinois Urbana‐Champaign 1201 West Gregory Drive Urbana Illinois USA 61801
| | - Daniel E. Runcie
- Department of Plant Sciences University of California‐Davis 278 Robbins Berkeley California USA 95616
| | - Sherry A. Flint‐Garcia
- Agricultural Research Service United States Department of Agriculture Columbia Missouri 65211 USA
- University of Missouri 301 Curtis Hall Columbia Missouri USA 65211
| | - Rubén Rellán‐Álvarez
- Langebio, Cinvestav, Km 9.6 Libramiento Norte Carretera Len Irapuato, Guanajuato Mexico 36821
- Present address: Molecular and Structural Biochemistry North Carolina State University 128 Polk Hall Raleigh North Carolina USA 27695‐7622
| | - Ruairidh J. H. Sawers
- Langebio, Cinvestav, Km 9.6 Libramiento Norte Carretera Len Irapuato, Guanajuato Mexico 36821
- Department of Plant Science Pennsylvania State University University Park Pennsylvania USA 16802
| | - Matthew B. Hufford
- Department of Ecology, Evolution, and Organismal Biology Iowa State University Ames Iowa USA 50011
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17
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Kim KH, Kim JY. Understanding Wheat Starch Metabolism in Properties, Environmental Stress Condition, and Molecular Approaches for Value-Added Utilization. PLANTS 2021; 10:plants10112282. [PMID: 34834645 PMCID: PMC8624758 DOI: 10.3390/plants10112282] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 10/21/2021] [Accepted: 10/21/2021] [Indexed: 01/19/2023]
Abstract
Wheat starch is one of the most important components in wheat grain and is extensively used as the main source in bread, noodles, and cookies. The wheat endosperm is composed of about 70% starch, so differences in the quality and quantity of starch affect the flour processing characteristics. Investigations on starch composition, structure, morphology, molecular markers, and transformations are providing new and efficient techniques that can improve the quality of bread wheat. Additionally, wheat starch composition and quality are varied due to genetics and environmental factors. Starch is more sensitive to heat and drought stress compared to storage proteins. These stresses also have a great influence on the grain filling period and anthesis, and, consequently, a negative effect on starch synthesis. Sucrose metabolizing and starch synthesis enzymes are suppressed under heat and drought stress during the grain filling period. Therefore, it is important to illustrate starch and sucrose mechanisms during plant responses in the grain filling period. In recent years, most of these quality traits have been investigated through genetic modification studies. This is an attractive approach to improve functional properties in wheat starch. The new information collected from hybrid and transgenic plants is expected to help develop novel starch for understanding wheat starch biosynthesis and commercial use. Wheat transformation research using plant genetic engineering technology is the main purpose of continuously controlling and analyzing the properties of wheat starch. The aim of this paper is to review the structure, biosynthesis mechanism, quality, and response to heat and drought stress of wheat starch. Additionally, molecular markers and transformation studies are reviewed to elucidate starch quality in wheat.
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Affiliation(s)
- Kyung-Hee Kim
- Department of Life Science, Dongguk University-Seoul, Seoul 04620, Korea;
| | - Jae-Yoon Kim
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, Korea
- Correspondence: ; Tel.: +82-41-330-1203
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18
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Cao L, Lu X, Wang G, Zhang P, Fu J, Wang Z, Wei L, Wang T. Transcriptional regulatory networks in response to drought stress and rewatering in maize (Zea mays L.). Mol Genet Genomics 2021; 296:1203-1219. [PMID: 34601650 DOI: 10.1007/s00438-021-01820-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/31/2021] [Indexed: 11/26/2022]
Abstract
Drought severely affects the growth and development of maize, but there is a certain degree of compensation effect after rewatering. This study intends to elaborate the response mechanism of maize at the physiological and molecular level as well as excavating potential genes with strong drought resistance and recovery ability. Physiological indexes analysis demonstrated that stomata conductance, transpiration rate, photosynthesis rate, antioxidant enzymes, and proline levels in maize were significantly altered in response to drought for 60 and 96 h and rewatering for 3 days. At 60 h, 96 h, and R3d, we detected 3095, 1941, and 5966 differentially expressed genes (DEGs) and 221, 226, and 215 differentially expressed miRNAs. Weighted correlation network analysis (WGCNA) showed that DEGs responded to maize drought and rewatering through participating in photosynthesis, proline metabolism, ABA signaling, and oxidative stress. Joint analysis of DEGs, miRNA, and target genes showed that zma-miR529, miR5072, zma-miR167e, zma-miR167f, zma-miR167j, miR397, and miR6214 were involved to regulate SBPs, MYBs, ARFs, laccases, and antioxidant enzymes, respectively. Hundreds of differentially expressed DNA methylation-related 24-nt siRNA clusters overlap with DEGs, indicating that DNA methylation is involved in responses under drought stress. These results provide new insights into the molecular mechanisms of drought tolerance, and may identify new targets for breeding drought-tolerant maize lines.
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Affiliation(s)
- Liru Cao
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Xiaomin Lu
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Guorui Wang
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Pengyu Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jiaxu Fu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhenhua Wang
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
| | - Li Wei
- National Engineering Research Centre for Wheat, Zhengzhou, 450002, China.
| | - Tongchao Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
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19
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Ma Q, Xu X, Wang W, Zhao L, Ma D, Xie Y. Comparative analysis of alfalfa (Medicago sativa L.) seedling transcriptomes reveals genotype-specific drought tolerance mechanisms. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:203-214. [PMID: 34118683 DOI: 10.1016/j.plaphy.2021.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
Drought is one of the main abiotic factors that affect alfalfa yield. The identification of genes that control this complex trait can provide important insights for alfalfa breeding. However, little is known about how alfalfa responds and adapts to drought stress, particularly in cultivars of differing drought tolerance. In this study, the drought-tolerant cultivar Dryland 'DT' and the drought-sensitive cultivar WL343HQ 'DS' were used to characterize leaf and root physiological responses and transcriptional changes in response to water deficit. Under drought stress, Dryland roots (DTR) showed more differentially expressed genes than WL343HQ roots (DSR), whereas WL343HQ leaves (DSL) showed more differentially expressed genes than Dryland leaves (DTL). Many of these genes were involved in stress-related pathways, carbohydrate metabolism, and lignin and wax biosynthesis, which may have improved the drought tolerance of alfalfa. We also observed that several genes related to ABA metabolism, root elongation, peroxidase activity, cell membrane stability, ubiquitination, and genetic processing responded to drought stress in alfalfa. We highlighted several candidate genes, including sucrose synthase, xylan 1,4-beta-xylosidase, primary-amine oxidase, and alcohol-forming fatty acyl-CoA reductase, for future studies on drought stress resistance in alfalfa and other plant species. In summary, our results reveal the unique drought adaptation and resistance characteristics of two alfalfa genotypes. These findings, which may be valuable for drought resistance breeding, warrant further gene functional analysis to augment currently available information and to clarify the drought stress regulatory mechanisms of alfalfa and other plants.
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Affiliation(s)
- Qiaoli Ma
- Agricultural College, Ningxia University, Yinchuan, 750021, China.
| | - Xing Xu
- Agricultural College, Ningxia University, Yinchuan, 750021, China.
| | - Wenjing Wang
- Key Laboratory for Restoration and Reconstruction of Degraded Ecosystem in Northwest China of Ministry of Education, Ningxia University, Yinchuan, 750021, China.
| | - Lijuan Zhao
- Key Laboratory for Restoration and Reconstruction of Degraded Ecosystem in Northwest China of Ministry of Education, Ningxia University, Yinchuan, 750021, China.
| | - Dongmei Ma
- Key Laboratory for Restoration and Reconstruction of Degraded Ecosystem in Northwest China of Ministry of Education, Ningxia University, Yinchuan, 750021, China.
| | - Yingzhong Xie
- Agricultural College, Ningxia University, Yinchuan, 750021, China.
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20
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Choe E, Ko Y, Williams MM. Transcriptional analysis of sweet corn hybrids in response to crowding stress. PLoS One 2021; 16:e0253190. [PMID: 34138910 PMCID: PMC8211227 DOI: 10.1371/journal.pone.0253190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/31/2021] [Indexed: 11/18/2022] Open
Abstract
Crop tolerance to crowding stress, specifically plant population density, is an important target to improve productivity in processing sweet corn. Due to limited knowledge of biological mechanisms involved in crowding stress in sweet corn, a study was conducted to 1) investigate phenotypic and transcriptional response of sweet corn hybrids under different plant densties, 2) compare the crowding stress response mechanisms between hybrids and 3) identify candidate biological mechanisms involved in crowding stress response. Yield per hectare of a tolerant hybrid (DMC21-84) increased with plant density. Yield per hectare of a sensitive hybrid (GSS2259P) declined with plant density. Transcriptional analysis found 694, 537, 359 and 483 crowding stress differentially expressed genes (DEGs) for GSS2259P at the Fruit Farm and Vegetable Farm and for DMC21-84 at the Fruit Farm and Vegetable Farm, respectively. Strong transcriptional change due to hybrid was observed. Functional analyses of DEGs involved in crowding stress also revealed that protein folding and photosynthetic processes were common response mechanisms for both hybrids. However, DEGs related to starch biosynthetic, carbohydrate metabolism, and ABA related processes were significant only for DMC21-84, suggesting the genes have closer relationship to plant productivity under stress than other processes. These results collectively provide initial insight into potential crowding stress response mechanisms in sweet corn.
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Affiliation(s)
- Eunsoo Choe
- Global Change and Photosynthesis Research Unit, USDA-ARS, Urbana, Illinois, United States of America
| | - Younhee Ko
- Division of Biomedical Engineering, Hankuk University of Foreign Studies, Kyoungki-do, South Korea
| | - Martin M. Williams
- Global Change and Photosynthesis Research Unit, USDA-ARS, Urbana, Illinois, United States of America
- * E-mail:
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21
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Guo Q, Li X, Niu L, Jameson PE, Zhou W. Transcription-associated metabolomic adjustments in maize occur during combined drought and cold stress. PLANT PHYSIOLOGY 2021; 186:677-695. [PMID: 33582802 PMCID: PMC8154062 DOI: 10.1093/plphys/kiab050] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/15/2021] [Indexed: 05/25/2023]
Abstract
Although simultaneous drought and cold stress occurs, especially in northwestern and eastern regions of China, and is an important factor limiting agricultural productivity, there are few studies focusing on plant responses to a combination of drought and cold stress. Here, by partially overlapping drought and cold stresses, we characterized the acclimation of maize (Zea mays B73) to these two stresses using physiological measurements, as well as comparative transcriptomics combined with metabolomics and hormonal analyses during the stress treatments and recovery stages. The combined drought and cold stress and drought stress alone were accompanied by a decline in photosynthetic capacity and enhanced transcriptional response, and subsequent recovery of these following removal from stress, whereas cold stress alone was accompanied by irreversible damage to photosynthetic capacity and chloroplast structure. The stress combination induced transcription-associated metabolomic alterations, in which raffinose, trehalose-6-phosphate, and proline accumulated, and monosaccharide abundance increased. Concomitantly, the increased abscisic acid (ABA) content and upregulated ABA signaling pathway may have provided the transcriptional regulation for the metabolic changes. In a parallel experiment, ABA treatments prior to exposure of the plants to cold stress primed the plants to survive the cold stress, thus confirming a key role for the endogenous ABA activated by the drought pretreatment in acclimation of the plants to cold. We present a model showing that the plant response to the combined stress is multi-faceted and reveal an ABA-dependent maize acclimation mechanism to the stress combination.
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Affiliation(s)
- Qianqian Guo
- China Grassland Research Center, School of Grassland Science, Beijing Forestry University, Beijing 100083, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xia Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Li Niu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Paula E Jameson
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Wenbin Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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22
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Modulation of photosynthesis and other proteins during water-stress. Mol Biol Rep 2021; 48:3681-3693. [PMID: 33856605 DOI: 10.1007/s11033-021-06329-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/31/2021] [Indexed: 10/25/2022]
Abstract
Protein changes under drought or water stress conditions have been widely investigated. These investigations have given us enormous understanding of how drought is manifested in plants and how plants respond and adopt to such conditions. Chlorophyll fluoroescence, gas exchange, OMICS, biochemical and molecular analyses have shed light on regulation of physiology and photosynthesis of plants under drought. Use of proteomics has greatly increased the repertoire of drought-associated proteins which nevertheless, need to be investigated for their mechanistic and functional roles. Roles of such proteins have been succinctly discussed in various review articles, however more information on their functional role in countering drought is needed. In this review, recent developments in the field, alterations in the abundance of plant proteins in response to drought, monitored through numerous proteomic and immuno-blot analyses, and how these could affect plants growth and development, are discussed.
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23
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Wang W, Wang L, Wang L, Tan M, Ogutu CO, Yin Z, Zhou J, Wang J, Wang L, Yan X. Transcriptome analysis and molecular mechanism of linseed (Linum usitatissimum L.) drought tolerance under repeated drought using single-molecule long-read sequencing. BMC Genomics 2021; 22:109. [PMID: 33563217 PMCID: PMC7871411 DOI: 10.1186/s12864-021-07416-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 01/29/2021] [Indexed: 12/13/2022] Open
Abstract
Background Oil flax (linseed, Linum usitatissimum L.) is one of the most important oil crops., However, the increases in drought resulting from climate change have dramatically reduces linseed yield and quality, but very little is known about how linseed coordinates the expression of drought resistance gene in response to different level of drought stress (DS) on the genome-wide level. Results To explore the linseed transcriptional response of DS and repeated drought (RD) stress, we determined the drought tolerance of different linseed varieties. Then we performed full-length transcriptome sequencing of drought-resistant variety (Z141) and drought-sensitive variety (NY-17) under DS and RD stress at the seedling stage using single-molecule real-time sequencing and RNA-sequencing. Gene Ontology (GO) and reduce and visualize GO (REVIGO) enrichment analysis showed that upregulated genes of Z141 were enriched in more functional pathways related to plant drought tolerance than those of NY-17 were under DS. In addition, 4436 linseed transcription factors were identified, and 1190 were responsive to stress treatments. Moreover, protein-protein interaction (PPI) network analysis showed that the proline biosynthesis pathway interacts with stress response genes through RAD50 (DNA repair protein 50) interacting protein 1 (RIN-1). Finally, proline biosynthesis and DNA repair structural gene expression patterns were verified by RT- PCR. Conclusions The drought tolerance of Z141 may be related to its upregulation of drought tolerance genes under DS. Proline may play an important role in linseed drought tolerance by maintaining cell osmotic and protecting DNA from ROS damage. In summary, this study provides a new perspective to understand the drought adaptability of linseed. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07416-5.
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Affiliation(s)
- Wei Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China
| | - Lei Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China
| | - Ling Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China
| | - Meilian Tan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China
| | - Collins O Ogutu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specicalty Agriculature, Wuhan Botanical Garden, The Innovative Academy of Science Design, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Ziyan Yin
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China
| | - Jian Zhou
- Wuhan Igenebook Biotechnology Co.,Ltd, Wuhan, 430075, China
| | - Jiaomei Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China
| | - Lijun Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China
| | - Xingchu Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China.
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24
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Della Lucia MC, Baghdadi A, Mangione F, Borella M, Zegada-Lizarazu W, Ravi S, Deb S, Broccanello C, Concheri G, Monti A, Stevanato P, Nardi S. Transcriptional and Physiological Analyses to Assess the Effects of a Novel Biostimulant in Tomato. FRONTIERS IN PLANT SCIENCE 2021; 12:781993. [PMID: 35087552 PMCID: PMC8787302 DOI: 10.3389/fpls.2021.781993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/07/2021] [Indexed: 05/08/2023]
Abstract
This work aimed to study the effects in tomato (Solanum lycopersicum L.) of foliar applications of a novel calcium-based biostimulant (SOB01) using an omics approach involving transcriptomics and physiological profiling. A calcium-chloride fertilizer (SOB02) was used as a product reference standard. Plants were grown under well-watered (WW) and water stress (WS) conditions in a growth chamber. We firstly compared the transcriptome profile of treated and untreated tomato plants using the software RStudio. Totally, 968 and 1,657 differentially expressed genes (DEGs) (adj-p-value < 0.1 and |log2(fold change)| ≥ 1) were identified after SOB01 and SOB02 leaf treatments, respectively. Expression patterns of 9 DEGs involved in nutrient metabolism and osmotic stress tolerance were validated by real-time quantitative reverse transcription PCR (RT-qPCR) analysis. Principal component analysis (PCA) on RT-qPCR results highlighted that the gene expression profiles after SOB01 treatment in different water regimes were clustering together, suggesting that the expression pattern of the analyzed genes in well water and water stress plants was similar in the presence of SOB01 treatment. Physiological analyses demonstrated that the biostimulant application increased the photosynthetic rate and the chlorophyll content under water deficiency compared to the standard fertilizer and led to a higher yield in terms of fruit dry matter and a reduction in the number of cracked fruits. In conclusion, transcriptome and physiological profiling provided comprehensive information on the biostimulant effects highlighting that SOB01 applications improved the ability of the tomato plants to mitigate the negative effects of water stress.
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Affiliation(s)
- Maria Cristina Della Lucia
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Padua, Italy
| | - Ali Baghdadi
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Francesca Mangione
- Sipcam Italia S.p.A. Belonging Together With Sofbey SA to the Sipcam Oxon S.p.A. Group, Pero, Italy
| | - Matteo Borella
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Padua, Italy
| | | | - Samathmika Ravi
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Padua, Italy
| | - Saptarathi Deb
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Padua, Italy
| | - Chiara Broccanello
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Padua, Italy
| | - Giuseppe Concheri
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Padua, Italy
| | - Andrea Monti
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Piergiorgio Stevanato
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Padua, Italy
- *Correspondence: Piergiorgio Stevanato,
| | - Serenella Nardi
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Padua, Italy
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Ghouili E, Sassi K, Jebara M, Hidri Y, Ouertani RN, Muhovski Y, Jebara SH, El Ayed M, Abdelkarim S, Chaieb O, Jallouli S, Kalleli F, M’hamdi M, Souissi F, Abid G. Physiological responses and expression of sugar associated genes in faba bean ( Vicia faba L.) exposed to osmotic stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:135-150. [PMID: 33627968 PMCID: PMC7873190 DOI: 10.1007/s12298-021-00935-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 12/22/2020] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
Faba bean (Vicia faba L.) is the major food legume crop in Tunisia. However, its growth and yield is strongly affected by water-limited environments. In this study, osmotic stress exhibited a negative effect on Bachar and Badii cultivar. Nevertheless, the deteriorating effects of osmotic stress were relatively low on studied parameters of Bachar due to its better efficiency to reduce oxidative damage by increasing enzymatic activities such as catalase (CAT), superoxide dismutase (SOD) and ascorbate peroxidase (APX), accumulation of total chlorophyll (Chlt), soluble sugars and leaf relative water content (RWC). GC-MS analysis determined a total of 11 soluble carbohydrates induced by osmotic stress and differentially accumulated in the both cultivars. Bachar showed elevated levels of mannose, glucose, galactose, ribose, rhamnose and myo-inositol which might help to maintain osmotic adjustment, membranes and proteins protection from the damaging effect of reactive oxygen species. Sugar metabolism related genes (VfNINV3, VfPHS2, VfFRK4, VfHXK1, VfGPI1, VfSTP1.1, VfpGlcT1.1, VfSTP5.1, VfpGlcT1.2, VfSWEET2.1, VfVINV2, VfSUS1, VfPGM1, VfSUT1.1, VfGPT1, VfSPS1, VfSPP1, VfPHS1, VfSUT4.1 and VfTMT1.1) were differentially expressed in both cultivars demonstrating their important roles in sugar accumulation. Most of these genes were upregulated in the leaves of Bachar under moderate and severe stress, which could lead to increase glycolysis and tricarboxylic acid cycle in order to accelerate energy production, necessary to increase osmotic regulation and consequently enhancing the osmotic stress tolerance in that cultivar. Overall, sugars accumulation ability can be used as a useful indicator for the osmotic stress tolerant potential in faba bean breeding programs. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at (10.1007/s12298-021-00935-1).
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Affiliation(s)
- Emna Ghouili
- Laboratory of Legumes, Centre of Biotechnology of Borj Cedria, BP 901, 2050 Hammam-Lif, Tunisia
| | - Khaled Sassi
- Laboratory of Agronomy, National Agronomy Institute of Tunisia (INAT), University of Carthage, Avenue Charles Nicolle, BP 43, 1082 Tunis-Mahrajène, Tunisia
| | - Moez Jebara
- Laboratory of Legumes, Centre of Biotechnology of Borj Cedria, BP 901, 2050 Hammam-Lif, Tunisia
| | - Yassine Hidri
- Laboratory of Integrated Olive Production, Olive Tree Institute, BP 208, 1082 Tunis-Mahrajène, Tunisia
| | - Rim Nefissi Ouertani
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj Cedria, BP 901, 2050 Hammam-Lif, Tunisia
| | - Yordan Muhovski
- Department of Life Sciences, Walloon Agricultural Research Centre, Chaussée de Charleroi, BP 234, 5030 Gembloux, Belgium
| | - Salwa Harzalli Jebara
- Laboratory of Legumes, Centre of Biotechnology of Borj Cedria, BP 901, 2050 Hammam-Lif, Tunisia
| | - Mohamed El Ayed
- Laboratory of Bioactive Substances, Centre of Biotechnology of Borj Cedria, BP 901, 2050 Hammam-Lif, Tunisia
| | - Souhir Abdelkarim
- Laboratory of Legumes, Centre of Biotechnology of Borj Cedria, BP 901, 2050 Hammam-Lif, Tunisia
| | - Oumaima Chaieb
- Laboratory of Legumes, Centre of Biotechnology of Borj Cedria, BP 901, 2050 Hammam-Lif, Tunisia
| | - Selim Jallouli
- Laboratory of Bioactive Substances, Centre of Biotechnology of Borj Cedria, BP 901, 2050 Hammam-Lif, Tunisia
| | - Fatma Kalleli
- Department of Horticultural Sciences and Vegetable Crops, High Institute of Agronomy of Chott Mariem, University of Sousse, 4042 Sousse, Tunisia
| | - Mahmoud M’hamdi
- Department of Horticultural Sciences and Vegetable Crops, High Institute of Agronomy of Chott Mariem, University of Sousse, 4042 Sousse, Tunisia
| | - Fatma Souissi
- Laboratory of Legumes, Centre of Biotechnology of Borj Cedria, BP 901, 2050 Hammam-Lif, Tunisia
| | - Ghassen Abid
- Laboratory of Legumes, Centre of Biotechnology of Borj Cedria, BP 901, 2050 Hammam-Lif, Tunisia
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26
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Diniz AL, da Silva DIR, Lembke CG, Costa MDBL, ten-Caten F, Li F, Vilela RD, Menossi M, Ware D, Endres L, Souza GM. Amino Acid and Carbohydrate Metabolism Are Coordinated to Maintain Energetic Balance during Drought in Sugarcane. Int J Mol Sci 2020; 21:ijms21239124. [PMID: 33266228 PMCID: PMC7729667 DOI: 10.3390/ijms21239124] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 01/10/2023] Open
Abstract
The ability to expand crop plantations without irrigation is a major goal to increase agriculture sustainability. To achieve this end, we need to understand the mechanisms that govern plant growth responses under drought conditions. In this study, we combined physiological, transcriptomic, and genomic data to provide a comprehensive picture of drought and recovery responses in the leaves and roots of sugarcane. Transcriptomic profiling using oligoarrays and RNA-seq identified 2898 (out of 21,902) and 46,062 (out of 373,869) transcripts as differentially expressed, respectively. Co-expression analysis revealed modules enriched in photosynthesis, small molecule metabolism, alpha-amino acid metabolism, trehalose biosynthesis, serine family amino acid metabolism, and carbohydrate transport. Together, our findings reveal that carbohydrate metabolism is coordinated with the degradation of amino acids to provide carbon skeletons to the tricarboxylic acid cycle. This coordination may help to maintain energetic balance during drought stress adaptation, facilitating recovery after the stress is alleviated. Our results shed light on candidate regulatory elements and pave the way to biotechnology strategies towards the development of drought-tolerant sugarcane plants.
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Affiliation(s)
- Augusto Lima Diniz
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil; (A.L.D.); (D.I.R.d.S.); (C.G.L.); (M.D.-B.L.C.); (F.t.-C.)
| | - Danielle Izilda Rodrigues da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil; (A.L.D.); (D.I.R.d.S.); (C.G.L.); (M.D.-B.L.C.); (F.t.-C.)
- Center for Applied Plant Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA
- Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, SP 13418-900, Brazil
| | - Carolina Gimiliani Lembke
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil; (A.L.D.); (D.I.R.d.S.); (C.G.L.); (M.D.-B.L.C.); (F.t.-C.)
| | - Maximiller Dal-Bianco Lamas Costa
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil; (A.L.D.); (D.I.R.d.S.); (C.G.L.); (M.D.-B.L.C.); (F.t.-C.)
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Felipe ten-Caten
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil; (A.L.D.); (D.I.R.d.S.); (C.G.L.); (M.D.-B.L.C.); (F.t.-C.)
| | - Forrest Li
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; (F.L.); (D.W.)
| | - Romel Duarte Vilela
- Centro de Ciências Agrárias, Universidade Federal de Alagoas, Rio Largo, AL 57100-000, Brazil; (R.D.V.); (L.E.)
| | - Marcelo Menossi
- Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP 13083-862, Brazil;
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; (F.L.); (D.W.)
- USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Lauricio Endres
- Centro de Ciências Agrárias, Universidade Federal de Alagoas, Rio Largo, AL 57100-000, Brazil; (R.D.V.); (L.E.)
| | - Glaucia Mendes Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil; (A.L.D.); (D.I.R.d.S.); (C.G.L.); (M.D.-B.L.C.); (F.t.-C.)
- Correspondence:
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Qiu F, Bachle S, Estes R, Duvall MR, Nippert JB, Ungerer MC. Transcriptional responses to water stress and recovery in a drought-tolerant fescue wild grass ( Festuca ovina; Poaceae). Genome 2020; 64:15-27. [PMID: 33002373 DOI: 10.1139/gen-2020-0055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Water stress associated with drought-like conditions is a major factor limiting plant growth and impacts productivity of natural plant communities and agricultural crops. Molecular responses of plants to water stress have been studied most extensively in model species and crops, few of which have evolved natural drought tolerance. In the current study, we examined physiological and transcriptomic responses at multiple timepoints during increasing water stress and following initial recovery from stress in a drought-tolerant C3 species, Festuca ovina. Results demonstrated non-linear transcriptomic changes during increasing stress, but largely linear declines in physiological measurements during this same period. Transcription factors represented approximately 12.7% of all differentially expressed genes. In total, 117 F. ovina homologs of previously identified and molecularly characterized drought-responsive plant genes were identified. This information will be valuable for further investigations of the molecular mechanisms involved in drought tolerance in C3 plants.
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Affiliation(s)
- Fan Qiu
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Seton Bachle
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Ryan Estes
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Melvin R Duvall
- Department of Biological Sciences and Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL, USA
| | - Jesse B Nippert
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Mark C Ungerer
- Division of Biology, Kansas State University, Manhattan, KS, USA
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Khan R, Zhou P, Ma X, Zhou L, Wu Y, Ullah Z, Wang S. Transcriptome Profiling, Biochemical and Physiological Analyses Provide New Insights towards Drought Tolerance in Nicotiana tabacum L. Genes (Basel) 2019; 10:E1041. [PMID: 31847498 PMCID: PMC6947287 DOI: 10.3390/genes10121041] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 02/06/2023] Open
Abstract
Drought stress is one of the main factors limiting crop production, which provokes a number of changes in plants at physiological, anatomical, biochemical and molecular level. To unravel the various mechanisms underpinning tobacco (Nicotiana tabacum L.) drought stress tolerance, we conducted a comprehensive physiological, anatomical, biochemical and transcriptome analyses of three tobacco cultivars (i.e., HongHuaDaJinYuan (H), NC55 (N) and Yun Yan-100 (Y)) seedlings that had been exposed to drought stress. As a result, H maintained higher growth in term of less reduction in plant fresh weight, dry weight and chlorophyll content as compared with N and Y. Anatomical studies unveiled that drought stress had little effect on H by maintaining proper leaf anatomy while there were significant changes in the leaf anatomy of N and Y. Similarly, H among the three varieties was the least affected variety under drought stress, with more proline content accumulation and a powerful antioxidant defense system, which mitigates the negative impacts of reactive oxygen species. The transcriptomic analysis showed that the differential genes expression between HongHuaDaJinYuan, NC55 and Yun Yan-100 were enriched in the functions of plant hormone signal transduction, starch and sucrose metabolism, and arginine and proline metabolism. Compared to N and Y, the differentially expressed genes of H displayed enhanced expression in the corresponding pathways under drought stress. Together, our findings offer insights that H was more tolerant than the other two varieties, as evidenced at physiological, biochemical, anatomical and molecular level. These findings can help us to enhance our understanding of the molecular mechanisms through the networks of various metabolic pathways mediating drought stress adaptation in tobacco.
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Affiliation(s)
- Rayyan Khan
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Qingdao 266101, China; (R.K.); (L.Z.); (Y.W.); (Z.U.); (S.W.)
| | - Peilu Zhou
- College of Agronomy, Resource and Environment, Tianjin Agricultural University, Tianjin 300384, China;
| | - Xinghua Ma
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Qingdao 266101, China; (R.K.); (L.Z.); (Y.W.); (Z.U.); (S.W.)
| | - Lei Zhou
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Qingdao 266101, China; (R.K.); (L.Z.); (Y.W.); (Z.U.); (S.W.)
| | - Yuanhua Wu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Qingdao 266101, China; (R.K.); (L.Z.); (Y.W.); (Z.U.); (S.W.)
| | - Zia Ullah
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Qingdao 266101, China; (R.K.); (L.Z.); (Y.W.); (Z.U.); (S.W.)
| | - Shusheng Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Qingdao 266101, China; (R.K.); (L.Z.); (Y.W.); (Z.U.); (S.W.)
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Puglisi I, Nicolosi E, Vanella D, Lo Piero AR, Stagno F, Saitta D, Roccuzzo G, Consoli S, Baglieri A. Physiological and Biochemical Responses of Orange Trees to Different Deficit Irrigation Regimes. PLANTS (BASEL, SWITZERLAND) 2019; 8:E423. [PMID: 31627476 PMCID: PMC6843479 DOI: 10.3390/plants8100423] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 12/19/2022]
Abstract
The article presents the results of research consisting of the application of deficit irrigation (DI) criteria, combined with the adoption of micro-irrigation methods, on orange orchards (Citrus sinensis (L.) Osbeck) in Sicily (Italy) during the irrigation season of 2015. Regulated deficit irrigation (RDI, T3) and partial root-zone drying (PRD, T4) strategies were compared with full irrigation (T1) and sustained deficit irrigation (SDI, T2) treatments in terms of physiological, biochemical, and productive crop response. A geophysical survey (electrical resistivity tomography, ERT) was carried out to identify a link between the percentages of drying soil volume in T4 with leaves abscisic acid (ABA) signal. Results highlight that the orange trees physiological response to water stress conditions did not show particular differences among the different irrigation treatments, not inducing detrimental effects on crop production features. ABA levels in leaves were rather constant in all the treatments, except in T4 during late irrigation season. ERT technique identified that prolonged drying cycles during alternate PRD exposed more roots to severe soil drying, thus increasing leaf ABA accumulation.
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Affiliation(s)
- Ivana Puglisi
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), Università di Catania, Via S. Sofia 98, 95123 Catania, Italy; (I.P.); (E.N.); (A.R.L.P.); (D.S.); (S.C.); (A.B.)
| | - Elisabetta Nicolosi
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), Università di Catania, Via S. Sofia 98, 95123 Catania, Italy; (I.P.); (E.N.); (A.R.L.P.); (D.S.); (S.C.); (A.B.)
| | - Daniela Vanella
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), Università di Catania, Via S. Sofia 98, 95123 Catania, Italy; (I.P.); (E.N.); (A.R.L.P.); (D.S.); (S.C.); (A.B.)
| | - Angela Roberta Lo Piero
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), Università di Catania, Via S. Sofia 98, 95123 Catania, Italy; (I.P.); (E.N.); (A.R.L.P.); (D.S.); (S.C.); (A.B.)
| | - Fiorella Stagno
- Consiglio per la Ricerca in Agricoltura e L’analisi Dell’economia Agraria, Centro di Ricerca Olivicoltura, Frutticoltura e Agrumicoltura, via la Canapona, 1bis - 47121 Forlì, Italy; (F.S.); (G.R.)
| | - Daniela Saitta
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), Università di Catania, Via S. Sofia 98, 95123 Catania, Italy; (I.P.); (E.N.); (A.R.L.P.); (D.S.); (S.C.); (A.B.)
| | - Giancarlo Roccuzzo
- Consiglio per la Ricerca in Agricoltura e L’analisi Dell’economia Agraria, Centro di Ricerca Olivicoltura, Frutticoltura e Agrumicoltura, via la Canapona, 1bis - 47121 Forlì, Italy; (F.S.); (G.R.)
| | - Simona Consoli
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), Università di Catania, Via S. Sofia 98, 95123 Catania, Italy; (I.P.); (E.N.); (A.R.L.P.); (D.S.); (S.C.); (A.B.)
| | - Andrea Baglieri
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), Università di Catania, Via S. Sofia 98, 95123 Catania, Italy; (I.P.); (E.N.); (A.R.L.P.); (D.S.); (S.C.); (A.B.)
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Huang BL, Li X, Liu P, Ma L, Wu W, Zhang X, Li Z, Huang B. Transcriptomic analysis of Eruca vesicaria subs. sativa lines with contrasting tolerance to polyethylene glycol-simulated drought stress. BMC PLANT BIOLOGY 2019; 19:419. [PMID: 31604421 PMCID: PMC6787972 DOI: 10.1186/s12870-019-1997-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 08/29/2019] [Indexed: 05/09/2023]
Abstract
BACKGROUND Eruca vesicaria subsp. sativa is one of the Cruciferae species most tolerant to drought stress. In our previous study some extremely drought-tolerant/sensitive Eruca lines were obtained. However little is known about the mechanism for drought tolerance in Eruca. METHODS In this study two E. vesicaria subs. sativa lines with contrasting drought tolerance were treated with liquid MS/PEG solution. Total RNA was isolated from 7-day old whole seedlings and then applied to Illumina sequencing platform for high-throughput transcriptional sequencing. RESULTS KEGG pathway analysis indicated that differentially expressed genes (DEGs) involved in alpha-Linolenic acid metabolism, Tyrosine metabolism, Phenylalanine, Tyrosine and tryptophan biosynthesis, Galactose metabolism, Isoquinoline alkaloid biosynthesis, Tropane, Piperidine and pyridine alkaloid biosynthesis, Mineral absorption, were all up-regulated specifically in drought-tolerant (DT) Eruca line under drought stress, while DEGs involved in ribosome, ribosome biogenesis, Pyrimidine metabolism, RNA degradation, Glyoxylate and dicarboxylate metabolism, Aminoacyl-tRNA biosynthesis, Citrate cycle, Methane metabolism, Carbon fixation in photosynthetic organisms, were all down-regulated. 51 DEGs were found to be most significantly up-regulated (log2 ratio ≥ 8) specifically in the DT line under PEG treatment, including those for ethylene-responsive transcription factors, WRKY and bHLH transcription factors, calmodulin-binding transcription activator, cysteine-rich receptor-like protein kinase, mitogen-activated protein kinase kinase, WD repeat-containing protein, OPDA reductase, allene oxide cyclase, aquaporin, O-acyltransferase WSD1, C-5 sterol desaturase, sugar transporter ERD6-like 12, trehalose-phosphate phosphatase and galactinol synthase 4. Eight of these 51 DEGs wre enriched in 8 COG and 17 KEGG pathways. CONCLUSIONS DEGs that were found to be most significantly up-regulated specifically in the DT line under PEG treatment, up-regulation of DEGs involved in Arginine and proline metabolism, alpha-linolenic acid metabolism and down-regulation of carbon fixation and protein synthesis might be critical for the drought tolerance in Eruca. These results will be valuable for revealing mechanism of drought tolerance in Eruca and also for genetic engineering to improve drought tolerance in crops.
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Affiliation(s)
- Bang-Lian Huang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Science, Hubei University, Wuhan, 430062, China
- Jiangsu Microbe Biological & Environmental Engineering Co., Ltd, Wuxi, 214122, China
| | - Xuan Li
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Science, Hubei University, Wuhan, 430062, China
| | - Pei Liu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Science, Hubei University, Wuhan, 430062, China
| | - Lan Ma
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Science, Hubei University, Wuhan, 430062, China
| | - Wenhua Wu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Science, Hubei University, Wuhan, 430062, China
| | - Xuekun Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Zaiyun Li
- National Key Lab of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bangquan Huang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Science, Hubei University, Wuhan, 430062, China.
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Yang L, Zhao Y, Zhang Q, Cheng L, Han M, Ren Y, Yang L. Effects of drought-re-watering-drought on the photosynthesis physiology and secondary metabolite production of Bupleurum chinense DC. PLANT CELL REPORTS 2019; 38:1181-1197. [PMID: 31165250 DOI: 10.1007/s00299-019-02436-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/29/2019] [Indexed: 06/09/2023]
Abstract
Drastic changes in soil water content can activate the short-term high expression of key enzyme-encoding genes involved in secondary metabolite synthesis thereby increasing the content of secondary metabolites. Bupleurum chinense DC. is a traditional medicinal herb that is famous for its abundant saikosaponins. In the current study, the effects of drought-re-watering-drought on the photosynthesis physiology and biosynthesis of saikosaponins were investigated in 1-year-old B. chinense. The results showed that alterations in soil moisture altered the photosynthesis physiological process of B. chinense. The dry weight and fresh weight of the roots, photosynthesis capacity, chlorophyll fluorescence parameters, and SOD, POD and CAT activities were significantly reduced, and the contents of SP, soluble sugars, PRO and MDA increased. There were strong correlations between different physiological stress indices. All indices promoted and restricted each other, responded to soil moisture changes synergistically, maintained plant homeostasis and guaranteed normal biological activities. It was found that RW and RD_1 were the key stages of the water-control experiment affecting the expression of saikosaponin-related genes. At these two stages, the expression of multiple genes was affected by changes in soil moisture, with their expression levels reaching several-fold higher than those at the previous stage. We noticed that the expression of saikosaponin synthesis genes (which were rapidly upregulated at the RW and RD_1 stages) did not coincide with the rapid accumulation of saikosaponins (at the RD-2 stage), which were found to correspond to each other at the later stages of the water-control experiment. This finding indicates that there is a time lag between gene expression and the final product synthesis. Rapid changes in the external environment (RW to RD_1) have a short-term promoting effect on gene expression. This study reveals that short-term stress regulation may be an effective way to improve the quality of medicinal materials.
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Affiliation(s)
- Linlin Yang
- Cultivation Base of State Key Laboratory for Ecological Restoration and Ecosystem Management of Jilin Province, Ministry of Science and Technology, College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin, People's Republic of China
| | - Yu Zhao
- Cultivation Base of State Key Laboratory for Ecological Restoration and Ecosystem Management of Jilin Province, Ministry of Science and Technology, College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin, People's Republic of China
| | - Qi Zhang
- Cultivation Base of State Key Laboratory for Ecological Restoration and Ecosystem Management of Jilin Province, Ministry of Science and Technology, College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin, People's Republic of China
| | - Lin Cheng
- Cultivation Base of State Key Laboratory for Ecological Restoration and Ecosystem Management of Jilin Province, Ministry of Science and Technology, College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin, People's Republic of China
| | - Mei Han
- Cultivation Base of State Key Laboratory for Ecological Restoration and Ecosystem Management of Jilin Province, Ministry of Science and Technology, College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin, People's Republic of China
| | - Yueying Ren
- Cultivation Base of State Key Laboratory for Ecological Restoration and Ecosystem Management of Jilin Province, Ministry of Science and Technology, College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin, People's Republic of China.
| | - Limin Yang
- Cultivation Base of State Key Laboratory for Ecological Restoration and Ecosystem Management of Jilin Province, Ministry of Science and Technology, College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin, People's Republic of China.
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Le Pioufle O, Ganoudi M, Calonne-Salmon M, Ben Dhaou F, Declerck S. Rhizophagus irregularis MUCL 41833 Improves Phosphorus Uptake and Water Use Efficiency in Maize Plants During Recovery From Drought Stress. FRONTIERS IN PLANT SCIENCE 2019; 10:897. [PMID: 31379895 PMCID: PMC6646675 DOI: 10.3389/fpls.2019.00897] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/24/2019] [Indexed: 05/13/2023]
Abstract
Irregular precipitations are likely to affect maize production in the future. Arbuscular mycorrhizal fungi (AMF) have been reported to increase maize resistance to drought, but their role on the short-term inorganic phosphorus (Pi) uptake, leaf gas exchange parameters and water content during recovery after drought remains poorly understood. Here, we investigated these parameters in maize plants colonized or not by Rhizophagus irregularis MUCL 41833. The mycorrhizal (M) and non-mycorrhizal (NM) plants were grown for a 3-week period in a circulatory semi-hydroponic cultivation system and were submitted to well-, moderately-, or poorly-watered conditions (WW, MW, and PW, respectively), the two latter conditions corresponding to moderate and severe droughts. The plants were then watered at field capacity for 42 h with a Pi impoverished Hoagland nutrient solution and the dynamic of Pi depletion in the nutrient solution, corresponding to Pi uptake/immobilization by the maize-AMF associates, was evaluated at 0, 9, 21, and 42 h. The CO2 assimilation rate (A), stomatal conductance (gs), transpiration (E), and instantaneous water use efficiency (WUEi) were also assessed at 0 and 42 h of circulation. Plant biomass, plant water content, phosphorus concentration and content, and leaf relative water content were evaluated at harvest. During recovery, Pi uptake was significantly higher in M versus NM plants whatever the water regime (WR) applied before recovery. AMF did not affect leaf gas exchange parameters before recovery but modulated gs and E, and improved WUEi after 42 h of recovery. At harvest, no significant difference in dry biomass was found between M and NM plants but shoot fresh weight was significantly higher in M plants. This resulted in an increased shoot water content in M plants grown in the MW and PW treatments. Surprisingly, leaf relative water content was significantly lower in M plants when compared with NM plants. Finally, P content and concentration were significantly higher in roots but not in shoots of M plants. Our results suggested that AMF can play a role in drought resistance of maize plants by increasing the Pi uptake and WUEi during recovery after drought stress.
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Affiliation(s)
- Olivia Le Pioufle
- Earth and Life Institute, Applied Microbiology, Mycology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Matike Ganoudi
- Earth and Life Institute, Applied Microbiology, Mycology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
- Institut National de la Recherche Agronomique, Rabat, Morocco
| | - Maryline Calonne-Salmon
- Earth and Life Institute, Applied Microbiology, Mycology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | | | - Stéphane Declerck
- Earth and Life Institute, Applied Microbiology, Mycology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
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Neji M, Gorel A, Ojeda DI, Duminil J, Kastally C, Steppe K, Fayolle A, Hardy OJ. Comparative analysis of two sister Erythrophleum species (Leguminosae) reveal contrasting transcriptome-wide responses to early drought stress. Gene 2019; 694:50-62. [PMID: 30716444 DOI: 10.1016/j.gene.2019.01.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 12/11/2018] [Accepted: 01/22/2019] [Indexed: 02/01/2023]
Abstract
With the ongoing climate change, African rainforests are expected to experience severe drought events in the future. In Africa, the tropical genus Erythrophleum (Fabaceae) includes two forest sister timber tree species displaying contrasting geographical distributions. Erythrophleum ivorense is adapted to wet evergreen Guineo-Congolian forests, whereas E. suaveolens occurs in a wider range of climates, being found in moist dense forests but also in gallery forests under a relatively drier climate. This geographical distribution pattern suggests that the two species might cope differently to drought at the genomic level. Yet, the genetic basis of tolerance response to drought stress in both species is still uncharacterized. To bridge this gap, we performed an RNA-seq approach on seedlings from each species to monitor their transcriptional responses at different levels of drought stress (0, 2 and 6 weeks after stopping watering seedlings). Monitoring of wilting symptoms revealed that E. suaveolens displayed an earlier phenotypic response to drought stress than E. ivorense. At the transcriptomic level, results revealed 2020 (1204 down-regulated/816 up-regulated) and 1495 differentially expressed genes (DEGs) in response to drought stress from a total of 67,432 and 66,605 contigs assembled in E. ivorense and E. suaveolens, respectively. After identifying 30,374 orthologs between species, we found that only 7 of them were DEGs shared between species, while 587 and 458 were differentially expressed only in E. ivorense or E. suaveolens, respectively. GO and KEGG enrichment analysis revealed that the two species differ in terms of significantly regulated pathways as well as the number and expression profile of DEGs (Up/Down) associated with each pathway in the two stress stages. Our results suggested that the two studied species react differently to drought. E. suaveolens seems displaying a prompt response to drought at its early stage strengthened by the down-regulation of many DEGs encoding for signaling and metabolism-related pathways. A considerable up-regulation of these pathways was also found in E. ivorense at the late stage of drought, suggesting this species may be a late responder. Overall, our data may serve as basis for further understanding the genetic control of drought tolerance in tropical trees and favor the selection of crucial genes for genetically enhancing drought resistance.
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Affiliation(s)
- Mohamed Neji
- Unit of Evolutionary Biology & Ecology, Faculté des Sciences, Université Libre de Bruxelles, Av. F.D. Roosevelt, 50, CP 160/12, B-1050 Brussels, Belgium; Department of Life Sciences, Faculty of Sciences of Gabès, University of Gabès, Tunisia; Laboratory of Extremophile Plants, Centre of Biotechnology of Borj Cedria, Hammam-Lif, Tunisia.
| | - Anais Gorel
- Department Biosystem Engineering (BIOSE), Gembloux Agro-Bio Tech, University of Liege, Belgium
| | - Dario I Ojeda
- Unit of Evolutionary Biology & Ecology, Faculté des Sciences, Université Libre de Bruxelles, Av. F.D. Roosevelt, 50, CP 160/12, B-1050 Brussels, Belgium; Unit of Ecology and Genetics, Department of Biology, Oulu University, Finland; Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Jérôme Duminil
- Unit of Evolutionary Biology & Ecology, Faculté des Sciences, Université Libre de Bruxelles, Av. F.D. Roosevelt, 50, CP 160/12, B-1050 Brussels, Belgium; UMR-DIADE, Institut de Recherche pour le Développement, Univ. Montpellier, Montpellier, France
| | - Chedly Kastally
- Unit of Evolutionary Biology & Ecology, Faculté des Sciences, Université Libre de Bruxelles, Av. F.D. Roosevelt, 50, CP 160/12, B-1050 Brussels, Belgium
| | - Kathy Steppe
- Laboratory of Plant Ecology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000 Ghent, Belgium
| | - Adeline Fayolle
- Department Biosystem Engineering (BIOSE), Gembloux Agro-Bio Tech, University of Liege, Belgium
| | - Olivier J Hardy
- Unit of Evolutionary Biology & Ecology, Faculté des Sciences, Université Libre de Bruxelles, Av. F.D. Roosevelt, 50, CP 160/12, B-1050 Brussels, Belgium
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Cao Y, Xu H, Li R, Gao S, Chen N, Luo J, Jiang Y. Genetic Basis of Phenotypic Differences Between Chinese Yunling Black Goats and Nubian Goats Revealed by Allele-Specific Expression in Their F1 Hybrids. Front Genet 2019; 10:145. [PMID: 30891061 PMCID: PMC6411798 DOI: 10.3389/fgene.2019.00145] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 02/12/2019] [Indexed: 01/18/2023] Open
Abstract
Chinese Yunling black goats and African Nubian goats are divergent breeds showing significant differences in body size, milk production, and environmental adaptation. However, the genetic mechanisms underlying these phenotypic differences remain to be elucidated. In this report, we provide a detailed portrait of allele-specific expression (ASE) from 54 RNA-Seq analyses across six tissues from nine F1 hybrid offspring generated by crossing the two breeds combined with 13 genomes of the two breeds. We identified a total of 524 genes with ASE, which are involved in bone development, muscle cell differentiation, and the regulation of lipid metabolic processes. We further found that 38 genes with ASE were also under directional selection by comparing 13 genomes of the two breeds; these 38 genes play important roles in metabolism, immune responses, and the adaptation to hot and humid environments. In conclusion, our study shows that the exploration of genes with ASE in F1 hybrids provides an efficient way to understand the genetic basis underlying the phenotypic differences of two diverse goat breeds.
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Affiliation(s)
- Yanhong Cao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Guangxi Key Laboratory of Livestock Genetic Improvement, The Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Han Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ran Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shan Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jun Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Sheteiwy MS, An J, Yin M, Jia X, Guan Y, He F, Hu J. Cold plasma treatment and exogenous salicylic acid priming enhances salinity tolerance of Oryza sativa seedlings. PROTOPLASMA 2019; 256:79-99. [PMID: 29984388 DOI: 10.1007/s00709-018-1279-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 06/15/2018] [Indexed: 05/06/2023]
Abstract
The present study was designed to highlight the effects of cold plasma (10 kV) treatment and priming with 2 mM salicylic acid (SA) and their combination (10 kV of plasma + 2 mM SA) on the physiological parameters and metabolism of two cultivars of Oryza sativa, i.e., Zhu Liang You 06 (ZY) and Qian You No. 1 (QY), under salinity stress (150 mM NaCl) and normal growth condition (0 mM NaCl). Seed germination and seedling growth were enhanced by SA priming and cold plasma treatment either alone or in combination under salinity stress. Photosynthetic pigments, photosynthetic gas exchange, and chlorophyll fluorescence were improved by cold plasma treatment and SA priming under salinity stress as compared to the untreated seeds. The activities of antioxidant enzymes were significantly improved by the combination of SA priming and cold plasma treatment in both cultivars under salinity stress. There were rapid changes in the cellular content of sodium (Na+) and calcium (Ca+), where the plants grown under saline conditions accumulate more Na+ and less Ca+ contents resulting in ionic imbalances. Interestingly, cold plasma and SA treatments diminished this action by reducing Na+ accumulation and increasing K+ and Ca+ contents in the plant cell under salinity stress. The activities of enzymes involved in secondary metabolism assimilation were up-regulated with cold plasma and SA priming either alone or combination under salinity stress. An increase in reactive oxygen species (ROS) accumulation and malondialdehyde (MDA) content was also observed under salinity stress condition. On contrast, seed treated with SA and plasma alone or combined resulted in a significant decrease in ROS and MDA contents under salinity stress. Our results indicated that SA priming and cold plasma treatment either alone or combined improved plant uptake of nutrients in both cultivars under stress conditions. The ultrastructural changes were observed to be more prominent in ZY than QY cultivar. Plants without SA priming or cold plasma treatments have a big vacuole due to the movement of ions into the vacuole directly from the apoplast into the vacuole through membrane vesiculation leading to membrane destabilization. However, SA priming and cold plasma treatment alone or combined helped the plants to recover their cell turgidity under salinity stress.
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Affiliation(s)
- Mohamed S Sheteiwy
- Seed Science Center, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Department of Agronomy, Faculty of Agriculture, Mansoura University, Mansoura, 35516, Egypt
| | - Jianyu An
- Seed Science Center, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Mengqi Yin
- Seed Science Center, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xiaowen Jia
- Seed Science Center, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yajing Guan
- Seed Science Center, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Fei He
- Seed Science Center, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jin Hu
- Seed Science Center, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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Meng HL, Zhang W, Zhang GH, Wang JJ, Meng ZG, Long GQ, Yang SC. Unigene-based RNA-seq provides insights on drought stress responses in Marsdenia tenacissima. PLoS One 2018; 13:e0202848. [PMID: 30500823 PMCID: PMC6268015 DOI: 10.1371/journal.pone.0202848] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/02/2018] [Indexed: 12/28/2022] Open
Abstract
Marsdenia tenacissima is a well-known anti-cancer medicinal plant used in traditional Chinese medicine, which often grows on the karst landform and the water conservation capacity of land is very poorly and drought occurrences frequently. We found M. tenacissima has strong drought resistance because of continuousdrought16 d, the leaves of M. tenacissima were fully curly and dying. But the leaves were fully almost recovering after re-watering 24h. The activity of SOD and POD were almost doubled under drought stress. The content of osmotic regulating substance proline and soluble sugar were three times than control group. But after re-watering, these indexes were declined rapidly. Three cDNA libraries of control, drought stress, and re-watering treatments were constructed. There were 43,129,228, 47,116,844, and 42,815,454 clean reads with Q20 values of 98.06, 98.04, and 97.88respectively.SRA accession number of raw data was PRJNA498187 on NCBI. A total of 8672, 6043, and 6537 differentially expressed genes (DEGs) were identified in control vs drought stress, control vs re-watering, and drought stress vs re-watering, respectively. In addition, 1039, 1016, and 980 transcription factors (TFs) were identified, respectively. Among them, 363, 267, and 299 TFs were identified as DEGs in drought stress, re-watering, and drought stress and re-watering, respectively. These differentially expressed TFs mainly belonged to the bHLH, bZIP, C2H2, ERF, MYB, MYB-related, and NAC families. A comparative analysis found that 1174 genes were up-regulated and 2344 were down-regulated under drought stress and this pattern was the opposite to that found after re-watering. Among the up-regulated genes, 64 genes were homologous to known functional genes that directly protect plants against drought stress. Furthermore, 44 protein kinases and 38 TFs with opposite expression patterns under drought stress and re-watering were identified, which are possibly candidate regulators for drought stress resistance in M. tenacissima. Our study is the first to characterize the M. tenacissima transcriptome in response to drought stress, and will serve as a useful resource for future studies on the functions of candidate protein kinases and TFs involved in M. tenacissima drought stress resistance.
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Affiliation(s)
- Heng-Ling Meng
- The Life Science and Technology College, Honghe University, Mengzi, Yunnan, People’s Republic of China
| | - Wei Zhang
- The Life Science and Technology College, Honghe University, Mengzi, Yunnan, People’s Republic of China
| | - Guang-Hui Zhang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming,Yunnan, People’s Republic of China
| | - Jian-Jun Wang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming,Yunnan, People’s Republic of China
| | - Zhen-Gui Meng
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming,Yunnan, People’s Republic of China
| | - Guang-Qiang Long
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming,Yunnan, People’s Republic of China
- * E-mail: (GQL); (SCY)
| | - Sheng-Chao Yang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming,Yunnan, People’s Republic of China
- * E-mail: (GQL); (SCY)
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Correia B, Hancock RD, Valledor L, Pinto G. Gene expression analysis in Eucalyptus globulus exposed to drought stress in a controlled and a field environment indicates different strategies for short- and longer-term acclimation. TREE PHYSIOLOGY 2018; 38:1623-1639. [PMID: 30496539 DOI: 10.1093/treephys/tpy067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 05/18/2018] [Indexed: 06/09/2023]
Abstract
Previous knowledge suggested the involvement of specific pathways/proteins that could be identified as potential molecular indicators linked to enhanced drought tolerance in Eucalyptus globulus. Here, we looked for specific variations in key transcripts of two Eucalyptus globulus clones (AL-18 and AL-13) exposed to water deficit and rehydration with two main goals: (i) to check if and how transcripts potentially associated with stress response and protection are modulated in a controlled experiment; and (ii) to verify if the transcript response is robust in a field case study. Our results showed that the controlled experiment induced a severe acute stress that resulted in a strong realignment of gene expression resulting from an overwhelming of physiological adjustments to water limitation. A number of transcripts exhibited altered abundance after the acute water stress: reduction of RuBisCO activase and mitochondrial glycine cleavage system H protein, and increase of isoflavone reductase. Malate dehydrogenase, catalase, dehydration response element B1A and potassium channel GORK showed a different abundance pattern in each clone. The stress in the field was more moderate and chronic and the plants were able to deal with the stress primarily through physiological adjustments resulting in much smaller changes in gene expression. The transcripts of clone AL-18 showed few alterations between irrigated and non-irrigated plants throughout the experiment, while the transcript changes found in clone AL-13 highlighted the impact of early rewatering rather than growing under extended drought typical of a Mediterranean summer. Although a few concurrent responses were found, the results obtained in the field study draw a very distinct picture when compared with the controlled experiment.
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Affiliation(s)
- Barbara Correia
- Department of Biology & Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Robert D Hancock
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, UK
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, Oviedo, Spain
| | - Glória Pinto
- Department of Biology & Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
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Virlouvet L, Avenson TJ, Du Q, Zhang C, Liu N, Fromm M, Avramova Z, Russo SE. Dehydration Stress Memory: Gene Networks Linked to Physiological Responses During Repeated Stresses of Zea mays. FRONTIERS IN PLANT SCIENCE 2018; 9:1058. [PMID: 30087686 PMCID: PMC6066539 DOI: 10.3389/fpls.2018.01058] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 06/28/2018] [Indexed: 05/19/2023]
Abstract
Stress memory refers to the observation that an initial, sub-lethal stress alters plants' responses to subsequent stresses. Previous transcriptome analyses of maize seedlings exposed to a repeated dehydration stress has revealed the existence of transcriptional stress memory in Zea mays. Whether drought-related physiological responses also display memory and how transcriptional memory translates into physiological memory are fundamental questions that are still unanswered. Using a systems-biology approach we investigate whether/how transcription memory responses established in the genome-wide analysis of Z. mays correlate with 14 physiological parameters measured during a repeated exposure of maize seedlings to dehydration stress. Co-expression network analysis revealed ten gene modules correlating strongly with particular physiological processes, and one module displaying strong, yet divergent, correlations with several processes suggesting involvement of these genes in coordinated responses across networks. Two processes key to the drought response, stomatal conductance and non-photochemical quenching, displayed contrasting memory patterns that may reflect trade-offs related to metabolic costs versus benefits of cellular protection. The main contribution of this study is the demonstration of coordinated changes in transcription memory responses at the genome level and integrated physiological responses at the cellular level upon repetitive stress exposures. The results obtained by the network-based systems analysis challenge the commonly held view that short-term physiological responses to stress are primarily mediated biochemically.
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Affiliation(s)
- Laetitia Virlouvet
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | | | - Qian Du
- School of Biological Sciences, University of Nebraska, Lincoln, NE, United States
| | - Chi Zhang
- School of Biological Sciences, University of Nebraska, Lincoln, NE, United States
| | - Ning Liu
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Michael Fromm
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
| | - Zoya Avramova
- School of Biological Sciences, University of Nebraska, Lincoln, NE, United States
| | - Sabrina E. Russo
- School of Biological Sciences, University of Nebraska, Lincoln, NE, United States
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Zhang X, Lei L, Lai J, Zhao H, Song W. Effects of drought stress and water recovery on physiological responses and gene expression in maize seedlings. BMC PLANT BIOLOGY 2018; 18:68. [PMID: 29685101 PMCID: PMC5913800 DOI: 10.1186/s12870-018-1281-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 04/03/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND Drought is one of the major factors limiting global maize production. Exposure to long-term drought conditions inhibits growth and leads to yield losses. Although several drought-responsive genes have been identified and functionally analyzed, the mechanisms underlying responses to drought and water recovery treatments have not been fully elucidated. To characterize how maize seedling respond to drought stress at the transcriptional level, we analyzed physiological responses and differentially expressed genes (DEGs) in the inbred line B73 under water deficit and recovery conditions. RESULTS The data for relative leaf water content, leaf size, and photosynthesis-related parameters indicated that drought stress significantly repressed maize seedling growth. Further RNA sequencing analysis revealed that 6107 DEGs were responsive to drought stress and water recovery, with more down-regulated than up-regulated genes. Among the DEGs, the photosynthesis- and hormone-related genes were enriched in responses to drought stress and re-watering. Additionally, transcription factor genes from 37 families were differentially expressed among the three analyzed time-points. Gene ontology enrichment analyses of the DEGs indicated that 50 GO terms, including those related to photosynthesis, carbohydrate metabolism, oxidoreductase activities, nutrient metabolism and other drought-responsive pathways, were over-represented in the drought-treated seedlings. The content of gibberellin in drought treatment seedlings was decreased compared to that of control seedlings, while abscisic acid showed accumulated in the drought treated plants. The deep analysis of DEGs related to cell wall development indicated that these genes were prone to be down-regulated at drought treatment stage. CONCLUSIONS Many genes that are differentially expressed in responses to drought stress and water recovery conditions affect photosynthetic systems and hormone biosynthesis. The identified DEGs, especially those encoding transcription factors, represent potential targets for developing drought-tolerant maize lines.
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Affiliation(s)
- Xiangbo Zhang
- State Key Laboratory of Agrobiotechnology/National Maize Improvement Center of China/Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No. 2, Yuanmingyuan West Road, Haidian District, Beijing, 100193 China
| | - Lei Lei
- State Key Laboratory of Agrobiotechnology/National Maize Improvement Center of China/Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No. 2, Yuanmingyuan West Road, Haidian District, Beijing, 100193 China
| | - Jinsheng Lai
- State Key Laboratory of Agrobiotechnology/National Maize Improvement Center of China/Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No. 2, Yuanmingyuan West Road, Haidian District, Beijing, 100193 China
| | - Haiming Zhao
- State Key Laboratory of Agrobiotechnology/National Maize Improvement Center of China/Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No. 2, Yuanmingyuan West Road, Haidian District, Beijing, 100193 China
| | - Weibin Song
- State Key Laboratory of Agrobiotechnology/National Maize Improvement Center of China/Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No. 2, Yuanmingyuan West Road, Haidian District, Beijing, 100193 China
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Hoffman AM, Avolio ML, Knapp AK, Smith MD. Codominant grasses differ in gene expression under experimental climate extremes in native tallgrass prairie. PeerJ 2018; 6:e4394. [PMID: 29473008 PMCID: PMC5816582 DOI: 10.7717/peerj.4394] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 01/30/2018] [Indexed: 01/01/2023] Open
Abstract
Extremes in climate, such as heat waves and drought, are expected to become more frequent and intense with forecasted climate change. Plant species will almost certainly differ in their responses to these stressors. We experimentally imposed a heat wave and drought in the tallgrass prairie ecosystem near Manhattan, Kansas, USA to assess transcriptional responses of two ecologically important C4 grass species, Andropogon gerardii and Sorghastrum nutans. Based on previous research, we expected that S. nutans would regulate more genes, particularly those related to stress response, under high heat and drought. Across all treatments, S. nutans showed greater expression of negative regulatory and catabolism genes while A. gerardii upregulated cellular and protein metabolism. As predicted, S. nutans showed greater sensitivity to water stress, particularly with downregulation of non-coding RNAs and upregulation of water stress and catabolism genes. A. gerardii was less sensitive to drought, although A. gerardii tended to respond with upregulation in response to drought versus S. nutans which downregulated more genes under drier conditions. Surprisingly, A. gerardii only showed minimal gene expression response to increased temperature, while S. nutans showed no response. Gene functional annotation suggested that these two species may respond to stress via different mechanisms. Specifically, A. gerardii tends to maintain molecular function while S. nutans prioritizes avoidance. Sorghastrum nutans may strategize abscisic acid response and catabolism to respond rapidly to stress. These results have important implications for success of these two important grass species under a more variable and extreme climate forecast for the future.
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Affiliation(s)
- Ava M. Hoffman
- Department of Biology, Colorado State University, Fort Collins, CO, United States of America
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States of America
| | - Meghan L. Avolio
- Department of Earth & Planetary Sciences, The Johns Hopkins University, Baltimore, MD, United States of America
| | - Alan K. Knapp
- Department of Biology, Colorado State University, Fort Collins, CO, United States of America
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States of America
| | - Melinda D. Smith
- Department of Biology, Colorado State University, Fort Collins, CO, United States of America
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States of America
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Dash PK, Rai R, Mahato AK, Gaikwad K, Singh NK. Transcriptome Landscape at Different Developmental Stages of a Drought Tolerant Cultivar of Flax ( Linum usitatissimum). Front Chem 2017; 5:82. [PMID: 29170736 PMCID: PMC5684102 DOI: 10.3389/fchem.2017.00082] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/29/2017] [Indexed: 12/31/2022] Open
Affiliation(s)
- Prasanta K Dash
- National Research Centre on Plant Biotechnology, Pusa Institute, New Delhi, India
| | - Rhitu Rai
- National Research Centre on Plant Biotechnology, Pusa Institute, New Delhi, India
| | - Ajay K Mahato
- National Research Centre on Plant Biotechnology, Pusa Institute, New Delhi, India
| | - Kishor Gaikwad
- National Research Centre on Plant Biotechnology, Pusa Institute, New Delhi, India
| | - Nagendra K Singh
- National Research Centre on Plant Biotechnology, Pusa Institute, New Delhi, India
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Abstract
Landraces are key elements of agricultural biodiversity that have long been considered a source of useful traits. Their importance goes beyond subsistence agriculture and the essential need to preserve genetic diversity, because landraces are farmer-developed populations that are often adapted to environmental conditions of significance to tackle environmental concerns. It is therefore increasingly important to identify adaptive traits in crop landraces and understand their molecular basis. This knowledge is potentially useful for promoting more sustainable agricultural techniques, reducing the environmental impact of high-input cropping systems, and diminishing the vulnerability of agriculture to global climate change. In this review, we present an overview of the opportunities and limitations offered by landraces’ genomics. We discuss how rapid advances in DNA sequencing techniques, plant phenotyping, and recombinant DNA-based biotechnology encourage both the identification and the validation of the genomic signature of local adaptation in crop landraces. The integration of ‘omics’ sciences, molecular population genetics, and field studies can provide information inaccessible with earlier technological tools. Although empirical knowledge on the genetic and genomic basis of local adaptation is still fragmented, it is predicted that genomic scans for adaptation will unlock an intraspecific molecular diversity that may be different from that of modern varieties.
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Kost MA, Perales HR, Wijeratne S, Wijeratne AJ, Stockinger E, Mercer KL. Differentiated transcriptional signatures in the maize landraces of Chiapas, Mexico. BMC Genomics 2017; 18:707. [PMID: 28886704 PMCID: PMC5591509 DOI: 10.1186/s12864-017-4005-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/02/2017] [Indexed: 12/22/2022] Open
Abstract
Background Landrace farmers are the keepers of crops locally adapted to the environments where they are cultivated. Patterns of diversity across the genome can provide signals of past evolution in the face of abiotic and biotic change. Understanding this rich genetic resource is imperative especially since diversity can provide agricultural security as climate continues to shift. Results Here we employ RNA sequencing (RNA-seq) to understand the role that conditions that vary across a landscape may have played in shaping genetic diversity in the maize landraces of Chiapas, Mexico. We collected landraces from three distinct elevational zones and planted them in a midland common garden. Early season leaf tissue was collected for RNA-seq and we performed weighted gene co-expression network analysis (WGCNA). We then used association analysis between landrace co-expression module expression values and environmental parameters of landrace origin to elucidate genes and gene networks potentially shaped by environmental factors along our study gradient. Elevation of landrace origin affected the transcriptome profiles. Two co-expression modules were highly correlated with temperature parameters of landrace origin and queries into their ‘hub’ genes suggested that temperature may have led to differentiation among landraces in hormone biosynthesis/signaling and abiotic and biotic stress responses. We identified several ‘hub’ transcription factors and kinases as candidates for the regulation of these responses. Conclusions These findings indicate that natural selection may influence the transcriptomes of crop landraces along an elevational gradient in a major diversity center, and provide a foundation for exploring the genetic basis of local adaptation. While we cannot rule out the role of neutral evolutionary forces in the patterns we have identified, combining whole transcriptome sequencing technologies, established bioinformatics techniques, and common garden experimentation can powerfully elucidate structure of adaptive diversity across a varied landscape. Ultimately, gaining such understanding can facilitate the conservation and strategic utilization of crop genetic diversity in a time of climate change. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4005-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew A Kost
- Department of Horticulture and Crop Science, The Ohio State University/Ohio Agricultural Research and Development Center (OARDC), Wooster, OH, USA
| | - Hugo R Perales
- El Colegio de la Frontera Sur, Departmento de Agroecología, San Cristóbal de Las Casas, Chiapas, Mexico
| | - Saranga Wijeratne
- Molecular Cellular and Imagining Center, The Ohio State University/OARDC, Wooster, OH, USA
| | - Asela J Wijeratne
- Molecular Cellular and Imagining Center, The Ohio State University/OARDC, Wooster, OH, USA.,Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
| | - Eric Stockinger
- Department of Horticulture and Crop Science, The Ohio State University/Ohio Agricultural Research and Development Center (OARDC), Wooster, OH, USA
| | - Kristin L Mercer
- Department of Horticulture and Crop Sciences, The Ohio State University, Columbus, OH, USA.
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Aguilar-Rangel MR, Chávez Montes RA, González-Segovia E, Ross-Ibarra J, Simpson JK, Sawers RJ. Allele specific expression analysis identifies regulatory variation associated with stress-related genes in the Mexican highland maize landrace Palomero Toluqueño. PeerJ 2017; 5:e3737. [PMID: 28852597 PMCID: PMC5572453 DOI: 10.7717/peerj.3737] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/04/2017] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Gene regulatory variation has been proposed to play an important role in the adaptation of plants to environmental stress. In the central highlands of Mexico, farmer selection has generated a unique group of maize landraces adapted to the challenges of the highland niche. In this study, gene expression in Mexican highland maize and a reference maize breeding line were compared to identify evidence of regulatory variation in stress-related genes. It was hypothesised that local adaptation in Mexican highland maize would be associated with a transcriptional signature observable even under benign conditions. METHODS Allele specific expression analysis was performed using the seedling-leaf transcriptome of an F1 individual generated from the cross between the highland adapted Mexican landrace Palomero Toluqueño and the reference line B73, grown under benign conditions. Results were compared with a published dataset describing the transcriptional response of B73 seedlings to cold, heat, salt and UV treatments. RESULTS A total of 2,386 genes were identified to show allele specific expression. Of these, 277 showed an expression difference between Palomero Toluqueño and B73 alleles under benign conditions that anticipated the response of B73 cold, heat, salt and/or UV treatments, and, as such, were considered to display a prior stress response. Prior stress response candidates included genes associated with plant hormone signaling and a number of transcription factors. Construction of a gene co-expression network revealed further signaling and stress-related genes to be among the potential targets of the transcription factors candidates. DISCUSSION Prior activation of responses may represent the best strategy when stresses are severe but predictable. Expression differences observed here between Palomero Toluqueño and B73 alleles indicate the presence of cis-acting regulatory variation linked to stress-related genes in Palomero Toluqueño. Considered alongside gene annotation and population data, allele specific expression analysis of plants grown under benign conditions provides an attractive strategy to identify functional variation potentially linked to local adaptation.
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Affiliation(s)
- M. Rocío Aguilar-Rangel
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| | - Ricardo A. Chávez Montes
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
- ABACUS: Laboratorio de Matemáticas Aplicadas y Cómputo de Alto Rendimiento del Departamento de Matemáticas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ocoyoacac, Estado de México, Mexico
| | - Eric González-Segovia
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, Center for Population Biology and Genome Center, University of California, Davis, CA, United States of America
| | - June K. Simpson
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| | - Ruairidh J.H. Sawers
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
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45
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Dossa K, Li D, Wang L, Zheng X, Liu A, Yu J, Wei X, Zhou R, Fonceka D, Diouf D, Liao B, Cissé N, Zhang X. Transcriptomic, biochemical and physio-anatomical investigations shed more light on responses to drought stress in two contrasting sesame genotypes. Sci Rep 2017; 7:8755. [PMID: 28821876 PMCID: PMC5562740 DOI: 10.1038/s41598-017-09397-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 07/26/2017] [Indexed: 11/09/2022] Open
Abstract
Sesame is an important oilseed crop with a high oil quality. It is prone to drought stress in the arid and semi-arid areas where it is widely grown. This study aims to decipher the response of tolerant (DT) and sensitive (DS) genotypes to progressive drought based on transcriptome, biochemical and physio-anatomical characterizations. Results indicated that under severe stress, DT relied on a well-functioning taproot while DS displayed a disintegrated root due to collapsed cortical cells. This was attributed to a higher accumulation of osmoprotectants and strong activity of antioxidant enzymes especially peroxidases in DT. From roots, DT could supply water to the aboveground tissues to ensure photosynthetic activities and improve endurance under stress. Temporal transcriptome sequencing under drought further confirmed that DT strongly activated genes related to antioxidant activity, osmoprotection and hormonal signaling pathways including abscisic acid and Ethylene. Furthermore, DT displayed unique differentially expressed genes in root functioning as peroxidases, interleukin receptor-associated kinase, heat shock proteins, APETALA2/ethylene-responsive element-binding protein and mitogen activated protein kinase, to effectively scavenge reactive oxygen species and preserve root cell integrity. Finally, 61 candidate genes conferring higher drought tolerance in DT were discovered and may constitute useful resources for drought tolerance improvement in sesame.
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Affiliation(s)
- Komivi Dossa
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, 430062, Wuhan, Hubei, China.,Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), BP 3320 Route de Khombole, Thiès, Senegal.,Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, Code postal, 107000, Dakar, Senegal
| | - Donghua Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, 430062, Wuhan, Hubei, China
| | - Linhai Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, 430062, Wuhan, Hubei, China
| | | | - Aili Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, 430062, Wuhan, Hubei, China
| | - Jingyin Yu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, 430062, Wuhan, Hubei, China
| | - Xin Wei
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, 430062, Wuhan, Hubei, China
| | - Rong Zhou
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, 430062, Wuhan, Hubei, China
| | - Daniel Fonceka
- Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), BP 3320 Route de Khombole, Thiès, Senegal.,Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), UMR AGAP, F-34398, Montpellier, France
| | - Diaga Diouf
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, Code postal, 107000, Dakar, Senegal
| | - Boshou Liao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, 430062, Wuhan, Hubei, China
| | - Ndiaga Cissé
- Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), BP 3320 Route de Khombole, Thiès, Senegal
| | - Xiurong Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, 430062, Wuhan, Hubei, China.
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46
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Dong B, Wu B, Hong W, Li X, Li Z, Xue L, Huang Y. Transcriptome analysis of the tea oil camellia (Camellia oleifera) reveals candidate drought stress genes. PLoS One 2017; 12:e0181835. [PMID: 28759610 PMCID: PMC5536306 DOI: 10.1371/journal.pone.0181835] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 07/08/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The tea-oil camellia (Camellia oleifera) is the most important oil plant in southern China, and has a strong resistance to drought and barren soil. Understanding the molecular mechanisms of drought tolerance would greatly promote its cultivation and molecular breeding. RESULTS In total, we obtained 76,585 unigenes with an average length of 810 bp and an N50 of 1,092 bp. We mapped all the unigenes to the NCBI 'nr' (non-redundant), SwissProt, KEGG, and clusters of orthologous groups (COG) databases, where 52,531 (68.6%) unigenes were functionally annotated. According to the annotation, 46,171 (60.8%) unigenes belong to 338 KEGG pathways. We identified a series of unigenes that are related to the synthesis and regulation of abscisic acid (ABA), the activity of protective enzymes, vitamin B6 metabolism, the metabolism of osmolytes, and pathways related to the biosynthesis of secondary metabolites. After exposed to drought for 12 hours, the number of differentially-expressed genes (DEGs) between treated plants and control plants increased in the G4 cultivar, while there was no significant increase in the drought-tolerant C3 cultivar. DEGs associated with drought stress responsive pathways were identified by KEGG pathway enrichment analysis. Moreover, we found 789 DEGs related to transcription factors. Finally, according to the results of qRT-PCR, the expression levels of the 20 unigenes tested were consistent with the results of next-generation sequencing. CONCLUSIONS In the present study, we identified a large set of cDNA unigenes from C. oleifera annotated using public databases. Further studies of DEGs involved in metabolic pathways related to drought stress and transcription will facilitate the discovery of novel genes involved in resistance to drought stress in this commercially important plant.
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Affiliation(s)
- Bin Dong
- South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Agriculture Industry Business Polytechnic, Guangzhou, Guangdong, China
| | - Bin Wu
- DRIGEN Company Limited, Shenzhen, Guangdong, China
| | - Wenhong Hong
- South China Agricultural University, Guangzhou, Guangdong, China
| | - Xiuping Li
- South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Agriculture Industry Business Polytechnic, Guangzhou, Guangdong, China
| | - Zhuo Li
- The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Li Xue
- South China Agricultural University, Guangzhou, Guangdong, China
- * E-mail: (YH); (LX)
| | - Yongfang Huang
- South China Agricultural University, Guangzhou, Guangdong, China
- * E-mail: (YH); (LX)
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47
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Zhang X, Liu X, Zhang D, Tang H, Sun B, Li C, Hao L, Liu C, Li Y, Shi Y, Xie X, Song Y, Wang T, Li Y. Genome-wide identification of gene expression in contrasting maize inbred lines under field drought conditions reveals the significance of transcription factors in drought tolerance. PLoS One 2017; 12:e0179477. [PMID: 28700592 PMCID: PMC5507481 DOI: 10.1371/journal.pone.0179477] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 05/31/2017] [Indexed: 11/19/2022] Open
Abstract
Drought is a major threat to maize growth and production. Understanding the molecular regulation network of drought tolerance in maize is of great importance. In this study, two maize inbred lines with contrasting drought tolerance were tested in the field under natural soil drought and well-watered conditions. In addition, the transcriptomes of their leaves was analyzed by RNA-Seq. In total, 555 and 2,558 genes were detected to specifically respond to drought in the tolerant and the sensitive line, respectively, with a more positive regulation tendency in the tolerant genotype. Furthermore, 4,700, 4,748, 4,403 and 4,288 genes showed differential expression between the two lines under moderate drought, severe drought and their well-watered controls, respectively. Transcription factors were enriched in both genotypic differentially expressed genes and specifically responsive genes of the tolerant line. It was speculated that the genotype-specific response of 20 transcription factors in the tolerance line and the sustained genotypically differential expression of 22 transcription factors might enhance tolerance to drought in maize. Our results provide new insight into maize drought tolerance-related regulation systems and provide gene resources for subsequent studies and drought tolerance improvement.
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Affiliation(s)
- Xiaojing Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuyang Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dengfeng Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huaijun Tang
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Baocheng Sun
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Chunhui Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Luyang Hao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cheng Liu
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Yongxiang Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunsu Shi
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoqing Xie
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Yanchun Song
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianyu Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Seeve CM, Cho IJ, Hearne LB, Srivastava GP, Joshi T, Smith DO, Sharp RE, Oliver MJ. Water-deficit-induced changes in transcription factor expression in maize seedlings. PLANT, CELL & ENVIRONMENT 2017; 40:686-701. [PMID: 28039925 DOI: 10.1111/pce.12891] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/16/2016] [Accepted: 12/19/2016] [Indexed: 05/15/2023]
Abstract
Plants tolerate water deficits by regulating gene networks controlling cellular and physiological traits to modify growth and development. Transcription factor (TF)-directed regulation of transcription within these gene networks is key to eliciting appropriate responses. In this study, reverse transcription quantitative PCR (RT-qPCR) was used to examine the abundance of 618 transcripts from 536 TF genes in individual root and shoot tissues of maize seedlings grown in vermiculite under well-watered (water potential of -0.02 MPa) and water-deficit conditions (water potentials of -0.3 and -1.6 MPa). A linear mixed model identified 433 TF transcripts representing 392 genes that differed significantly in abundance in at least one treatment, including TFs that intersect growth and development and environmental stress responses. TFs were extensively differentially regulated across stressed maize seedling tissues. Hierarchical clustering revealed TFs with stress-induced increased abundance in primary root tips that likely regulate root growth responses to water deficits, possibly as part of abscisic acid and/or auxin-dependent signaling pathways. Ten of these TFs were selected for validation in nodal root tips of drought-stressed field-grown plants (late V1 to early V2 stage). Changes in abundance of these TF transcripts under a field drought were similar to those observed in the seedling system.
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Affiliation(s)
- Candace M Seeve
- Plant Genetics Research Unit, USDA-ARS, Columbia, MO, 65211, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA
| | - In-Jeong Cho
- Plant Genetics Research Unit, USDA-ARS, Columbia, MO, 65211, USA
| | - Leonard B Hearne
- Statistics Department, University of Missouri, Columbia, MO, 65211, USA
| | | | - Trupti Joshi
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, 65211, USA
- Informatics Institute and Christopher S Bond Life Science Center, Columbia, MO, 65211, USA
| | - Dante O Smith
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Robert E Sharp
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Melvin J Oliver
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
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Al Khateeb W, Al Shalabi A, Schroeder D, Musallam I. Phenotypic and molecular variation in drought tolerance of Jordanian durum wheat ( Triticum durum Desf.) landraces. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:311-319. [PMID: 28461720 PMCID: PMC5391366 DOI: 10.1007/s12298-017-0434-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 03/06/2017] [Accepted: 03/16/2017] [Indexed: 05/04/2023]
Abstract
Drought is considered one of the major constraints of plant growth and productivity worldwide. Plants respond to drought through different mechanisms including physiological, biochemical, and gene expression modulation. Studying these mechanisms will provide better understanding of drought response mechanisms and will help breeders in developing new cultivars. In this study, growth, biochemical, and molecular responses of four wheat (Triticum durum Desf.) landraces to drought stress (300 mM mannitol) were investigated at the seedling stage. Reverse transcription-polymerase chain reaction was used to assess gene expression level for a drought stress responsive gene (DHN15.1). Germination percentage, shoot length, root length, and root number for all T. durum landraces were decreased significantly under drought stress. However, drought stress caused an increase in proline content, lipid peroxidation level, and DHN15.1 transcript level. According to the studied traits, the Karak landrace showed long shoots (48% relative to its control), the longest roots (45% relative to its control) and the highest proline content (483% relative to its control). The results indicate that from the landraces studied, Karak may be selected as the most tolerant wheat landrace and may help in wheat breeding programs for adaptation to drought-prone environments.
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Affiliation(s)
- Wesam Al Khateeb
- Department of Biological Sciences, Yarmouk University, Irbid, Jordan
| | - Ala’a Al Shalabi
- Department of Biological Sciences, Yarmouk University, Irbid, Jordan
| | - Dana Schroeder
- Department of Biological Sciences, University of Manitoba, Winnipeg, Canada
| | - Iyad Musallam
- Biodiversity and Medicinal Plants Department, National Center for Agricultural Research and Extension, Amman, Jordan
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50
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Sun T, Li M, Shao Y, Yu L, Ma F. Comprehensive Genomic Identification and Expression Analysis of the Phosphate Transporter (PHT) Gene Family in Apple. FRONTIERS IN PLANT SCIENCE 2017; 8:426. [PMID: 28424713 PMCID: PMC5371654 DOI: 10.3389/fpls.2017.00426] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 03/13/2017] [Indexed: 05/03/2023]
Abstract
Elemental phosphorus (Pi) is essential to plant growth and development. The family of phosphate transporters (PHTs) mediates the uptake and translocation of Pi inside the plants. Members include five sub-cellular phosphate transporters that play different roles in Pi uptake and transport. We searched the Genome Database for Rosaceae and identified five clusters of phosphate transporters in apple (Malus domestica), including 37 putative genes. The MdPHT1 family contains 14 genes while MdPHT2 has two, MdPHT3 has seven, MdPHT4 has 11, and MdPHT5 has three. Our overview of this gene family focused on structure, chromosomal distribution and localization, phylogenies, and motifs. These genes displayed differential expression patterns in various tissues. For example, expression was high for MdPHT1;12, MdPHT3;6, and MdPHT3;7 in the roots, and was also increased in response to low-phosphorus conditions. In contrast, MdPHT4;1, MdPHT4;4, and MdPHT4;10 were expressed only in the leaves while transcript levels of MdPHT1;4, MdPHT1;12, and MdPHT5;3 were highest in flowers. In general, these 37 genes were regulated significantly in either roots or leaves in response to the imposition of phosphorus and/or drought stress. The results suggest that members of the PHT family function in plant adaptations to adverse growing environments. Our study will lay a foundation for better understanding the PHT family evolution and exploring genes of interest for genetic improvement in apple.
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