51
|
Shavrukov Y, Zhumalin A, Serikbay D, Botayeva M, Otemisova A, Absattarova A, Sereda G, Sereda S, Shvidchenko V, Turbekova A, Jatayev S, Lopato S, Soole K, Langridge P. Expression Level of the DREB2-Type Gene, Identified with Amplifluor SNP Markers, Correlates with Performance, and Tolerance to Dehydration in Bread Wheat Cultivars from Northern Kazakhstan. FRONTIERS IN PLANT SCIENCE 2016; 7:1736. [PMID: 27917186 PMCID: PMC5114286 DOI: 10.3389/fpls.2016.01736] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 11/03/2016] [Indexed: 05/18/2023]
Abstract
A panel of 89 local commercial cultivars of bread wheat was tested in field trials in the dry conditions of Northern Kazakhstan. Two distinct groups of cultivars (six cultivars in each group), which had the highest and the lowest grain yield under drought were selected for further experiments. A dehydration test conducted on detached leaves indicated a strong association between rates of water loss in plants from the first group with highest grain yield production in the dry environment relative to the second group. Modern high-throughput Amplifluor Single Nucleotide Polymorphism (SNP) technology was applied to study allelic variations in a series of drought-responsive genes using 19 SNP markers. Genotyping of an SNP in the TaDREB5 (DREB2-type) gene using the Amplifluor SNP marker KATU48 revealed clear allele distribution across the entire panel of wheat accessions, and distinguished between the two groups of cultivars with high and low yield under drought. Significant differences in expression levels of TaDREB5 were revealed by qRT-PCR. Most wheat plants from the first group of cultivars with high grain yield showed slight up-regulation in the TaDREB5 transcript in dehydrated leaves. In contrast, expression of TaDREB5 in plants from the second group of cultivars with low grain yield was significantly down-regulated. It was found that SNPs did not alter the amino acid sequence of TaDREB5 protein. Thus, a possible explanation is that alternative splicing and up-stream regulation of TaDREB5 may be affected by SNP, but these hypotheses require additional analysis (and will be the focus of future studies).
Collapse
Affiliation(s)
- Yuri Shavrukov
- School of Agriculture, Food and Wine, Faculty of Sciences, University of AdelaideUrrbrae, SA, Australia
- School of Biological Sciences, Flinders University, Bedford ParkSA, Australia
- *Correspondence: Yuri Shavrukov, ;
| | - Aibek Zhumalin
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical UniversityAstana Kazakhstan
| | - Dauren Serikbay
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical UniversityAstana Kazakhstan
| | - Makpal Botayeva
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical UniversityAstana Kazakhstan
| | - Ainur Otemisova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical UniversityAstana Kazakhstan
| | | | - Grigoriy Sereda
- Karaganda Research Institute of Plant Industry and BreedingKaraganda, Kazakhstan
| | - Sergey Sereda
- Karaganda Research Institute of Plant Industry and BreedingKaraganda, Kazakhstan
| | - Vladimir Shvidchenko
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical UniversityAstana Kazakhstan
| | - Arysgul Turbekova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical UniversityAstana Kazakhstan
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical UniversityAstana Kazakhstan
| | - Sergiy Lopato
- School of Agriculture, Food and Wine, Faculty of Sciences, University of AdelaideUrrbrae, SA, Australia
| | - Kathleen Soole
- School of Biological Sciences, Flinders University, Bedford ParkSA, Australia
| | - Peter Langridge
- School of Agriculture, Food and Wine, Faculty of Sciences, University of AdelaideUrrbrae, SA, Australia
| |
Collapse
|
52
|
Iovieno P, Punzo P, Guida G, Mistretta C, Van Oosten MJ, Nurcato R, Bostan H, Colantuono C, Costa A, Bagnaresi P, Chiusano ML, Albrizio R, Giorio P, Batelli G, Grillo S. Transcriptomic Changes Drive Physiological Responses to Progressive Drought Stress and Rehydration in Tomato. FRONTIERS IN PLANT SCIENCE 2016; 7:371. [PMID: 27066027 PMCID: PMC4814702 DOI: 10.3389/fpls.2016.00371] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/10/2016] [Indexed: 05/07/2023]
Abstract
Tomato is a major crop in the Mediterranean basin, where the cultivation in the open field is often vulnerable to drought. In order to adapt and survive to naturally occurring cycles of drought stress and recovery, plants employ a coordinated array of physiological, biochemical, and molecular responses. Transcriptomic studies on tomato responses to drought and subsequent recovery are few in number. As the search for novel traits to improve the genetic tolerance to drought increases, a better understanding of these responses is required. To address this need we designed a study in which we induced two cycles of prolonged drought stress and a single recovery by rewatering in tomato. In order to dissect the complexity of plant responses to drought, we analyzed the physiological responses (stomatal conductance, CO2 assimilation, and chlorophyll fluorescence), abscisic acid (ABA), and proline contents. In addition to the physiological and metabolite assays, we generated transcriptomes for multiple points during the stress and recovery cycles. Cluster analysis of differentially expressed genes (DEGs) between the conditions has revealed potential novel components in stress response. The observed reduction in leaf gas exchanges and efficiency of the photosystem PSII was concomitant with a general down-regulation of genes belonging to the photosynthesis, light harvesting, and photosystem I and II category induced by drought stress. Gene ontology (GO) categories such as cell proliferation and cell cycle were also significantly enriched in the down-regulated fraction of genes upon drought stress, which may contribute to explain the observed growth reduction. Several histone variants were also repressed during drought stress, indicating that chromatin associated processes are also affected by drought. As expected, ABA accumulated after prolonged water deficit, driving the observed enrichment of stress related GOs in the up-regulated gene fractions, which included transcripts putatively involved in stomatal movements. This transcriptomic study has yielded promising candidate genes that merit further functional studies to confirm their involvement in drought tolerance and recovery. Together, our results contribute to a better understanding of the coordinated responses taking place under drought stress and recovery in adult plants of tomato.
Collapse
Affiliation(s)
- Paolo Iovieno
- National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici (CNR-IBBR) Portici, Italy
| | - Paola Punzo
- National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici (CNR-IBBR) Portici, Italy
| | - Gianpiero Guida
- National Research Council of Italy, Institute for Agricultural and Forestry Systems in the Mediterranean (CNR-ISAFoM) Ercolano, Italy
| | - Carmela Mistretta
- National Research Council of Italy, Institute for Agricultural and Forestry Systems in the Mediterranean (CNR-ISAFoM) Ercolano, Italy
| | | | - Roberta Nurcato
- National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici (CNR-IBBR) Portici, Italy
| | - Hamed Bostan
- Department of Agriculture, University of Naples "Federico II," Portici, Italy
| | - Chiara Colantuono
- Department of Agriculture, University of Naples "Federico II," Portici, Italy
| | - Antonello Costa
- National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici (CNR-IBBR) Portici, Italy
| | - Paolo Bagnaresi
- CREA - Council for Agricultural Research and Economics, Genomics Research Centre Fiorenzuola d'Arda, Italy
| | - Maria L Chiusano
- Department of Agriculture, University of Naples "Federico II," Portici, Italy
| | - Rossella Albrizio
- National Research Council of Italy, Institute for Agricultural and Forestry Systems in the Mediterranean (CNR-ISAFoM) Ercolano, Italy
| | - Pasquale Giorio
- National Research Council of Italy, Institute for Agricultural and Forestry Systems in the Mediterranean (CNR-ISAFoM) Ercolano, Italy
| | - Giorgia Batelli
- National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici (CNR-IBBR) Portici, Italy
| | - Stefania Grillo
- National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici (CNR-IBBR) Portici, Italy
| |
Collapse
|
53
|
Hepworth C, Doheny‐Adams T, Hunt L, Cameron DD, Gray JE. Manipulating stomatal density enhances drought tolerance without deleterious effect on nutrient uptake. THE NEW PHYTOLOGIST 2015; 208:336-41. [PMID: 26268722 PMCID: PMC4973681 DOI: 10.1111/nph.13598] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 07/07/2015] [Indexed: 05/18/2023]
Abstract
Manipulation of stomatal density was investigated as a potential tool for enhancing drought tolerance or nutrient uptake. Drought tolerance and soil water retention were assessed using Arabidopsis epidermal patterning factor mutants manipulated to have increased or decreased stomatal density. Root nutrient uptake via mass flow was monitored under differing plant watering regimes using nitrogen-15 ((15) N) isotope and mass spectrometry. Plants with less than half of their normal complement of stomata, and correspondingly reduced levels of transpiration, conserve soil moisture and are highly drought tolerant but show little or no reduction in shoot nitrogen concentrations especially when water availability is restricted. By contrast, plants with over twice the normal density of stomata have a greater capacity for nitrogen uptake, except when water availability is restricted. We demonstrate the possibility of producing plants with reduced transpiration which have increased drought tolerance, with little or no loss of nutrient uptake. We demonstrate that increasing transpiration can enhance nutrient uptake when water is plentiful.
Collapse
Affiliation(s)
- Christopher Hepworth
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldSheffieldS10 2TNUK
| | | | - Lee Hunt
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldSheffieldS10 2TNUK
| | - Duncan D. Cameron
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldS10 2TNUK
| | - Julie E. Gray
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldSheffieldS10 2TNUK
| |
Collapse
|
54
|
Großkinsky DK, Svensgaard J, Christensen S, Roitsch T. Plant phenomics and the need for physiological phenotyping across scales to narrow the genotype-to-phenotype knowledge gap. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5429-40. [PMID: 26163702 DOI: 10.1093/jxb/erv345] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plants are affected by complex genome×environment×management interactions which determine phenotypic plasticity as a result of the variability of genetic components. Whereas great advances have been made in the cost-efficient and high-throughput analyses of genetic information and non-invasive phenotyping, the large-scale analyses of the underlying physiological mechanisms lag behind. The external phenotype is determined by the sum of the complex interactions of metabolic pathways and intracellular regulatory networks that is reflected in an internal, physiological, and biochemical phenotype. These various scales of dynamic physiological responses need to be considered, and genotyping and external phenotyping should be linked to the physiology at the cellular and tissue level. A high-dimensional physiological phenotyping across scales is needed that integrates the precise characterization of the internal phenotype into high-throughput phenotyping of whole plants and canopies. By this means, complex traits can be broken down into individual components of physiological traits. Since the higher resolution of physiological phenotyping by 'wet chemistry' is inherently limited in throughput, high-throughput non-invasive phenotyping needs to be validated and verified across scales to be used as proxy for the underlying processes. Armed with this interdisciplinary and multidimensional phenomics approach, plant physiology, non-invasive phenotyping, and functional genomics will complement each other, ultimately enabling the in silico assessment of responses under defined environments with advanced crop models. This will allow generation of robust physiological predictors also for complex traits to bridge the knowledge gap between genotype and phenotype for applications in breeding, precision farming, and basic research.
Collapse
Affiliation(s)
- Dominik K Großkinsky
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Højbakkegård Allé 13, 2630 Taastrup, Denmark
| | - Jesper Svensgaard
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Højbakkegård Allé 13, 2630 Taastrup, Denmark
| | - Svend Christensen
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Højbakkegård Allé 13, 2630 Taastrup, Denmark
| | - Thomas Roitsch
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Højbakkegård Allé 13, 2630 Taastrup, Denmark Global Change Research Centre, Czech Globe AS CR, v.v.i.., Drásov 470, Cz-664 24 Drásov, Czech Republic
| |
Collapse
|
55
|
Ain QU, Rasheed A, Anwar A, Mahmood T, Imtiaz M, Mahmood T, Xia X, He Z, Quraishi UM. Genome-wide association for grain yield under rainfed conditions in historical wheat cultivars from Pakistan. FRONTIERS IN PLANT SCIENCE 2015; 6:743. [PMID: 26442056 PMCID: PMC4585131 DOI: 10.3389/fpls.2015.00743] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 08/31/2015] [Indexed: 05/18/2023]
Abstract
Genome-wide association studies (GWAS) were undertaken to identify SNP markers associated with yield and yield-related traits in 123 Pakistani historical wheat cultivars evaluated during 2011-2014 seasons under rainfed field conditions. The population was genotyped by using high-density Illumina iSelect 90K single nucleotide polymorphism (SNP) assay, and finally 14,960 high quality SNPs were used in GWAS. Population structure examined using 1000 unlinked markers identified seven subpopulations (K = 7) that were representative of different breeding programs in Pakistan, in addition to local landraces. Forty four stable marker-trait associations (MTAs) with -log p > 4 were identified for nine yield-related traits. Nine multi-trait MTAs were found on chromosomes 1AL, 1BS, 2AL, 2BS, 2BL, 4BL, 5BL, 6AL, and 6BL, and those on 5BL and 6AL were stable across two seasons. Gene annotation and syntey identified that 14 trait-associated SNPs were linked to genes having significant importance in plant development. Favorable alleles for days to heading (DH), plant height (PH), thousand grain weight (TGW), and grain yield (GY) showed minor additive effects and their frequencies were slightly higher in cultivars released after 2000. However, no selection pressure on any favorable allele was identified. These genomic regions identified have historically contributed to achieve yield gains from 2.63 million tons in 1947 to 25.7 million tons in 2015. Future breeding strategies can be devised to initiate marker assisted breeding to accumulate these favorable alleles of SNPs associated with yield-related traits to increase grain yield. Additionally, in silico identification of 454-contigs corresponding to MTAs will facilitate fine mapping and subsequent cloning of candidate genes and functional marker development.
Collapse
Affiliation(s)
- Qurat-ul Ain
- Molecular Plant Breeding, Department of Plant Sciences, Quaid-i-Azam UniversityIslamabad, Pakistan
| | - Awais Rasheed
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- International Maize and Wheat Improvement Center (CIMMYT), C/O Chinese Academy of Agricultural SciencesBeijing, China
| | - Alia Anwar
- Molecular Plant Breeding, Department of Plant Sciences, Quaid-i-Azam UniversityIslamabad, Pakistan
| | - Tariq Mahmood
- Higher Education Commission, Research and DevelopmentIslamabad, Pakistan
| | - Muhammad Imtiaz
- International Maize and Wheat Improvement Center (CIMMYT), C/O National Agriculture Research CenterIslamabad, Pakistan
| | - Tariq Mahmood
- Molecular Plant Breeding, Department of Plant Sciences, Quaid-i-Azam UniversityIslamabad, Pakistan
| | - Xianchun Xia
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- International Maize and Wheat Improvement Center (CIMMYT), C/O Chinese Academy of Agricultural SciencesBeijing, China
| | - Umar M. Quraishi
- Molecular Plant Breeding, Department of Plant Sciences, Quaid-i-Azam UniversityIslamabad, Pakistan
- *Correspondence: Umar M. Quraishi, Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| |
Collapse
|