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Zhu J, Zhou H, Fan Y, Guo Y, Zhang M, Shabala S, Zhao C, Lv C, Guo B, Wang F, Zhou M, Xu R. HvNCX, a prime candidate gene for the novel qualitative locus qS7.1 associated with salinity tolerance in barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:9. [PMID: 36656369 PMCID: PMC9852152 DOI: 10.1007/s00122-023-04267-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
A major QTL (qS7.1) for salinity damage score and Na+ exclusion was identified on chromosome 7H from a barley population derived from a cross between a cultivated variety and a wild accession. qS7.1 was fine-mapped to a 2.46 Mb physical interval and HvNCX encoding a sodium/calcium exchanger is most likely the candidate gene. Soil salinity is one of the major abiotic stresses affecting crop yield. Developing salinity-tolerant varieties is critical for minimizing economic penalties caused by salinity and providing solutions for global food security. Many genes/QTL for salt tolerance have been reported in barley, but only a few of them have been cloned. In this study, a total of 163 doubled haploid lines from a cross between a cultivated barley variety Franklin and a wild barley accession TAM407227 were used to map QTL for salinity tolerance. Four significant QTL were identified for salinity damage scores. One (qS2.1) was located on 2H, determining 7.5% of the phenotypic variation. Two (qS5.1 and qS5.2) were located on 5H, determining 5.3-11.7% of the phenotypic variation. The most significant QTL was found on 7H, explaining 27.8% of the phenotypic variation. Two QTL for Na+ content in leaves under salinity stress were detected on chromosomes 1H (qNa1.1) and 7H(qNa7.1). qS7.1 was fine-mapped to a 2.46 Mb physical interval using F4 recombinant inbred lines. This region contains 23 high-confidence genes, with HvNCX which encodes a sodium/calcium exchanger being most likely the candidate gene. HvNCX was highly induced by salinity stress and showed a greater expression level in the sensitive parent. Multiple nucleotide substitutions and deletions/insertions in the promoter sequence of HvNCX were found between the two parents. cDNA sequencing of the HvNCX revealed that the difference between the two parents is conferred by a single Ala77/Pro77 amino acid substitution, which is located on the transmembrane domain. These findings open new prospects for improving salinity tolerance in barley by targeting a previously unexplored trait.
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Affiliation(s)
- Juan Zhu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, 225009, China
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, Prospect, TAS, 7250, Australia
| | - Hui Zhou
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, 225009, China
| | - Yun Fan
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, Prospect, TAS, 7250, Australia
| | - Yu Guo
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, 225009, China
| | - Mengna Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, 225009, China
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, Prospect, TAS, 7250, Australia
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, 528000, China
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
| | - Chenchen Zhao
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, Prospect, TAS, 7250, Australia
| | - Chao Lv
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, 225009, China
| | - Baojian Guo
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, 225009, China
| | - Feifei Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, 225009, China
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, Prospect, TAS, 7250, Australia.
| | - Rugen Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, 225009, China.
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Overview of Identified Genomic Regions Associated with Various Agronomic and Physiological Traits in Barley under Abiotic Stresses. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12105189] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Climate change has caused breeders to focus on varieties that are able to grow under unfavorable conditions, such as drought, high and low temperatures, salinity, and other stressors. In recent decades, progress in biotechnology and its related tools has provided opportunities to dissect and decipher the genetic basis of tolerance to various stress conditions. One such approach is the identification of genomic regions that are linked with specific or multiple characteristics. Cereal crops have a key role in supplying the energy required for human and animal populations. However, crop products are dramatically affected by various environmental stresses. Barley (Hordeum vulgare L.) is one of the oldest domesticated crops that is cultivated globally. Research has shown that, compared with other cereals, barley is well adapted to various harsh environmental conditions. There is ample literature regarding these responses to abiotic stressors, as well as the genomic regions associated with the various morpho-physiological and biochemical traits of stress tolerance. This review focuses on (i) identifying the tolerance mechanisms that are important for stable growth and development, and (ii) the applicability of QTL mapping and association analysis in identifying genomic regions linked with stress-tolerance traits, in order to help breeders in marker-assisted selection (MAS) to quickly screen tolerant germplasms in their breeding cycles. Overall, the information presented here will inform and assist future barley breeding programs.
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Manik SMN, Quamruzzaman M, Zhao C, Johnson P, Hunt I, Shabala S, Zhou M. Genome-Wide Association Study Reveals Marker Trait Associations (MTA) for Waterlogging-Triggered Adventitious Roots and Aerenchyma Formation in Barley. Int J Mol Sci 2022; 23:ijms23063341. [PMID: 35328762 PMCID: PMC8954902 DOI: 10.3390/ijms23063341] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/16/2022] [Indexed: 12/31/2022] Open
Abstract
Waterlogging is an environmental stress, which severely affects barley growth and development. Limited availability of oxygen in the root zone negatively affects the metabolism of the whole plant. Adventitious roots (AR) and root cortical aerenchyma (RCA) formation are the most important adaptive traits that contribute to a plant's ability to survive in waterlogged soil conditions. This study used a genome-wide association (GWAS) approach using 18,132 single nucleotide polymorphisms (SNPs) in a panel of 697 barley genotypes to reveal marker trait associations (MTA) conferring the above adaptive traits. Experiments were conducted over two consecutive years in tanks filled with soil and then validated in field experiments. GWAS analysis was conducted using general linear models (GLM), mixed linear models (MLM), and fixed and random model circulating probability unification models (FarmCPU model), with the FarmCPU showing to be the best suited model. Six and five significant (approximately -log10 (p) ≥ 5.5) MTA were identified for AR and RCA formation under waterlogged conditions, respectively. The highest -log10 (p) MTA for adventitious root and aerenchyma formation were approximately 9 and 8 on chromosome 2H and 4H, respectively. The combination of different MTA showed to be more effective in forming RCA and producing more AR under waterlogging stress. Genes from major facilitator superfamily (MFS) transporter and leucine-rich repeat (LRR) families for AR formation, and ethylene responsive factor (ERF) family genes and potassium transporter family genes for RCA formation were the potential candidate genes involved under waterlogging conditions. Several genotypes, which performed consistently well under different conditions, can be used in breeding programs to develop waterlogging-tolerant varieties.
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Affiliation(s)
- S. M. Nuruzzaman Manik
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (S.M.N.M.); (M.Q.); (C.Z.); (P.J.); (I.H.); (S.S.)
| | - Md Quamruzzaman
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (S.M.N.M.); (M.Q.); (C.Z.); (P.J.); (I.H.); (S.S.)
| | - Chenchen Zhao
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (S.M.N.M.); (M.Q.); (C.Z.); (P.J.); (I.H.); (S.S.)
| | - Peter Johnson
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (S.M.N.M.); (M.Q.); (C.Z.); (P.J.); (I.H.); (S.S.)
| | - Ian Hunt
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (S.M.N.M.); (M.Q.); (C.Z.); (P.J.); (I.H.); (S.S.)
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (S.M.N.M.); (M.Q.); (C.Z.); (P.J.); (I.H.); (S.S.)
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (S.M.N.M.); (M.Q.); (C.Z.); (P.J.); (I.H.); (S.S.)
- Correspondence:
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Wang L, Xie J, Mou C, Jiao Y, Dou Y, Zheng H. Transcriptomic Analysis of the Interaction Between FLOWERING LOCUS T Induction and Photoperiodic Signaling in Response to Spaceflight. Front Cell Dev Biol 2022; 9:813246. [PMID: 35178402 PMCID: PMC8844200 DOI: 10.3389/fcell.2021.813246] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/21/2021] [Indexed: 01/05/2023] Open
Abstract
Spaceflight has an impact on the growth and development of higher plants at both the vegetative stage and reproductive stage. A great deal of information has been available on the vegetative stage in space, but relatively little is known about the influence of spaceflight on plants at the reproductive stage. In this study, we constructed transgenic Arabidopsis thaliana plants expressing the flowering control gene, FLOWERING LOCUS T (FT), together with the green fluorescent protein gene (GFP) under control of a heat shock-inducible promoter (HSP17.4), by which we induced FT expression inflight through remote controlling heat shock (HS) treatment. Inflight photography data showed that induction of FT expression in transgenic plants in space under non-inductive short-day conditions could promote flowering and reduce the length of the inflorescence stem in comparison with that of wild-type plants under the same conditions. Whole-genome microarray analysis of gene expression changes in leaves of wild-type and these transgenic plants grown under the long-day and short-day photoperiod conditions in space indicated that the function of the photoperiod-related spaceflight responsive genes is mainly involved in protein synthesis and post-translation protein modulation, notably protein phosphorylation. In addition, changes of the circadian component of gene expression in response to spaceflight under different photoperiods indicated that roles of the circadian oscillator could act as integrators of spaceflight response and photoperiodic signals in Arabidopsis plants grown in space.
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Affiliation(s)
- Lihua Wang
- Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Junyan Xie
- Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chenghong Mou
- Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuwei Jiao
- Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yanhui Dou
- Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Huiqiong Zheng
- Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
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Saradadevi GP, Das D, Mangrauthia SK, Mohapatra S, Chikkaputtaiah C, Roorkiwal M, Solanki M, Sundaram RM, Chirravuri NN, Sakhare AS, Kota S, Varshney RK, Mohannath G. Genetic, Epigenetic, Genomic and Microbial Approaches to Enhance Salt Tolerance of Plants: A Comprehensive Review. BIOLOGY 2021; 10:biology10121255. [PMID: 34943170 PMCID: PMC8698797 DOI: 10.3390/biology10121255] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 12/17/2022]
Abstract
Simple Summary Globally, soil salinity, which refers to salt-affected soils, is increasing due to various environmental factors and human activities. Soil salinity poses one of the most serious challenges in the field of agriculture as it significantly reduces the growth and yield of crop plants, both quantitatively and qualitatively. Over the last few decades, several studies have been carried out to understand plant biology in response to soil salinity stress with a major emphasis on genetic and other hereditary components. Based on the outcome of these studies, several approaches are being followed to enhance plants’ ability to tolerate salt stress while still maintaining reasonable levels of crop yields. In this manuscript, we comprehensively list and discuss various biological approaches being followed and, based on the recent advances in the field of molecular biology, we propose some new approaches to improve salinity tolerance of crop plants. The global scientific community can make use of this information for the betterment of crop plants. This review also highlights the importance of maintaining global soil health to prevent several crop plant losses. Abstract Globally, soil salinity has been on the rise owing to various factors that are both human and environmental. The abiotic stress caused by soil salinity has become one of the most damaging abiotic stresses faced by crop plants, resulting in significant yield losses. Salt stress induces physiological and morphological modifications in plants as a result of significant changes in gene expression patterns and signal transduction cascades. In this comprehensive review, with a major focus on recent advances in the field of plant molecular biology, we discuss several approaches to enhance salinity tolerance in plants comprising various classical and advanced genetic and genetic engineering approaches, genomics and genome editing technologies, and plant growth-promoting rhizobacteria (PGPR)-based approaches. Furthermore, based on recent advances in the field of epigenetics, we propose novel approaches to create and exploit heritable genome-wide epigenetic variation in crop plants to enhance salinity tolerance. Specifically, we describe the concepts and the underlying principles of epigenetic recombinant inbred lines (epiRILs) and other epigenetic variants and methods to generate them. The proposed epigenetic approaches also have the potential to create additional genetic variation by modulating meiotic crossover frequency.
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Affiliation(s)
- Gargi Prasad Saradadevi
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Hyderabad 500078, India; (G.P.S.); (S.M.)
| | - Debajit Das
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, India; (D.D.); (C.C.)
| | - Satendra K. Mangrauthia
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Sridev Mohapatra
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Hyderabad 500078, India; (G.P.S.); (S.M.)
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, India; (D.D.); (C.C.)
| | - Manish Roorkiwal
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India;
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
| | - Manish Solanki
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Raman Meenakshi Sundaram
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Neeraja N. Chirravuri
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Akshay S. Sakhare
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Suneetha Kota
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
- Correspondence: (S.K.); (R.K.V.); (G.M.); Tel.: +91-40-245-91268 (S.K.); +91-84-556-83305 (R.K.V.); +91-40-66303697 (G.M.)
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India;
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
- Correspondence: (S.K.); (R.K.V.); (G.M.); Tel.: +91-40-245-91268 (S.K.); +91-84-556-83305 (R.K.V.); +91-40-66303697 (G.M.)
| | - Gireesha Mohannath
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Hyderabad 500078, India; (G.P.S.); (S.M.)
- Correspondence: (S.K.); (R.K.V.); (G.M.); Tel.: +91-40-245-91268 (S.K.); +91-84-556-83305 (R.K.V.); +91-40-66303697 (G.M.)
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Sayed MA, Tarawneh R, Youssef HM, Pillen K, Börner A. Detection and Verification of QTL for Salinity Tolerance at Germination and Seedling Stages Using Wild Barley Introgression Lines. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112246. [PMID: 34834608 PMCID: PMC8624391 DOI: 10.3390/plants10112246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
Salinity is one of the major environmental factors that negatively affect crop development, particularly at the early growth stage of a plant and consequently the final yield. Therefore, a set of 50 wild barley (Hordeum vulgare ssp. spontaneum, Hsp) introgression lines (ILs) was used to detect QTL alleles improving germination and seedling growth under control, 75 mM, and 150 mM NaCl conditions. Large variation was observed for germination and seedling growth related traits that were highly heritable under salinity stress. In addition, highly significant differences were obtained for five salinity tolerance indices and between treatments as well. A total of 90 and 35 significant QTL were identified for ten investigated traits and for tolerance indices, respectively. The Hsp introgression alleles are involved in improving salinity tolerance at forty (43.9%) out of 90 QTL including introgression lines S42IL-109 (2H), S42IL-116 (4H), S42IL-132 (6H), S42IL-133 (7H), S42IL-148 (6H), and S42IL-176 (5H). Interestingly, seven exotic QTL alleles were successfully validated in the wild barley ILs including S42IL-127 (5H), 139 (7H), 125 (5H), 117 (4H), 118 (4H), 121 (4H), and 137 (7H). We conclude that the barley introgression lines contain numerous germination and seedling growth-improving novel QTL alleles, which are effective under salinity conditions.
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Affiliation(s)
- Mohammed Abdelaziz Sayed
- Agronomy Department, Faculty of Agriculture, Assiut University, Assiut 71526, Egypt
- Resources Genetics and Reproduction, Gene Bank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, D-06466 Seeland, Germany;
| | - Rasha Tarawneh
- Resources Genetics and Reproduction, Gene Bank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, D-06466 Seeland, Germany;
| | - Helmy Mohamed Youssef
- Faculty of Agriculture, Cairo University, Giza 12613, Egypt;
- Plant Breeding, Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany;
| | - Klaus Pillen
- Plant Breeding, Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany;
| | - Andreas Börner
- Resources Genetics and Reproduction, Gene Bank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, D-06466 Seeland, Germany;
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Borrego-Benjumea A, Carter A, Zhu M, Tucker JR, Zhou M, Badea A. Genome-Wide Association Study of Waterlogging Tolerance in Barley ( Hordeum vulgare L.) Under Controlled Field Conditions. FRONTIERS IN PLANT SCIENCE 2021; 12:711654. [PMID: 34512694 PMCID: PMC8427447 DOI: 10.3389/fpls.2021.711654] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/21/2021] [Indexed: 06/01/2023]
Abstract
Waterlogging is one of the main abiotic stresses severely reducing barley grain yield. Barley breeding programs focusing on waterlogging tolerance require an understanding of genetic loci and alleles in the current germplasm. In this study, 247 worldwide spring barley genotypes grown under controlled field conditions were genotyped with 35,926 SNPs with minor allele frequency (MAF) > 0.05. Significant phenotypic variation in each trait, including biomass, spikes per plant, grains per plant, kernel weight per plant, plant height and chlorophyll content, was observed. A genome-wide association study (GWAS) based on linkage disequilibrium (LD) for waterlogging tolerance was conducted. Population structure analysis divided the population into three subgroups. A mixed linkage model using both population structure and kinship matrix (Q+K) was performed. We identified 17 genomic regions containing 51 significant waterlogging-tolerance-associated markers for waterlogging tolerance response, accounting for 5.8-11.5% of the phenotypic variation, with a majority of them localized on chromosomes 1H, 2H, 4H, and 5H. Six novel QTL were identified and eight potential candidate genes mediating responses to abiotic stresses were located at QTL associated with waterlogging tolerance. To our awareness, this is the first GWAS for waterlogging tolerance in a worldwide barley collection under controlled field conditions. The marker-trait associations could be used in the marker-assisted selection of waterlogging tolerance and will facilitate barley breeding.
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Affiliation(s)
- Ana Borrego-Benjumea
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Adam Carter
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Min Zhu
- College of Agriculture, Yangzhou University, Yangzhou, China
| | - James R. Tucker
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Ana Badea
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
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Karahara I, Horie T. Functions and structure of roots and their contributions to salinity tolerance in plants. BREEDING SCIENCE 2021; 71:89-108. [PMID: 33762879 PMCID: PMC7973495 DOI: 10.1270/jsbbs.20123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/15/2020] [Indexed: 05/03/2023]
Abstract
Soil salinity is an increasing threat to the productivity of glycophytic crops worldwide. The root plays vital roles under various stress conditions, including salinity, as well as has diverse functions in non-stress soil environments. In this review, we focus on the essential functions of roots such as in ion homeostasis mediated by several different membrane transporters and signaling molecules under salinity stress and describe recent advances in the impacts of quantitative trait loci (QTLs) or genetic loci (and their causal genes, if applicable) on salinity tolerance. Furthermore, we introduce important literature for the development of barriers against the apoplastic flow of ions, including Na+, as well as for understanding the functions and components of the barrier structure under salinity stress.
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Affiliation(s)
- Ichirou Karahara
- Department of Biology, Faculty of Science, University of Toyama, Toyama 930-8555, Japan
| | - Tomoaki Horie
- Division of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda, Nagano 386-8567, Japan
- Corresponding author (e-mail: )
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Saade S, Brien C, Pailles Y, Berger B, Shahid M, Russell J, Waugh R, Negrão S, Tester M. Dissecting new genetic components of salinity tolerance in two-row spring barley at the vegetative and reproductive stages. PLoS One 2020; 15:e0236037. [PMID: 32701981 PMCID: PMC7377408 DOI: 10.1371/journal.pone.0236037] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 06/27/2020] [Indexed: 11/18/2022] Open
Abstract
Soil salinity imposes an agricultural and economic burden that may be alleviated by identifying the components of salinity tolerance in barley, a major crop and the most salt tolerant cereal. To improve our understanding of these components, we evaluated a diversity panel of 377 two-row spring barley cultivars during both the vegetative, in a controlled environment, and the reproductive stages, in the field. In the controlled environment, a high-throughput phenotyping platform was used to assess the growth-related traits under both control and saline conditions. In the field, the agronomic traits were measured from plots irrigated with either fresh or saline water. Association mapping for the different components of salinity tolerance enabled us to detect previously known associations, such as HvHKT1;5. Using an "interaction model", which took into account the interaction between treatment (control and salt) and genetic markers, we identified several loci associated with yield components related to salinity tolerance. We also observed that the two developmental stages did not share genetic regions associated with the components of salinity tolerance, suggesting that different mechanisms play distinct roles throughout the barley life cycle. Our association analysis revealed that genetically defined regions containing known flowering genes (Vrn-H3, Vrn-H1, and HvNAM-1) were responsive to salt stress. We identified a salt-responsive locus (7H, 128.35 cM) that was associated with grain number per ear, and suggest a gene encoding a vacuolar H+-translocating pyrophosphatase, HVP1, as a candidate. We also found a new QTL on chromosome 3H (139.22 cM), which was significant for ear number per plant, and a locus on chromosome 2H (141.87 cM), previously identified using a nested association mapping population, which associated with a yield component and interacted with salinity stress. Our study is the first to evaluate a barley diversity panel for salinity stress under both controlled and field conditions, allowing us to identify contributions from new components of salinity tolerance which could be used for marker-assisted selection when breeding for marginal and saline regions.
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Affiliation(s)
- Stephanie Saade
- Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Chris Brien
- School of Agriculture, Food and Wine, Waite Research Precinct, University of Adelaide, Urrbrae, South Australia, Australia
- School of Information Technology and Mathematical Sciences, University of South Australia, Adelaide, South Australia, Australia
- The Plant Accelerator, Australian Plant Phenomics Facility, Waite Research Precinct, University of Adelaide, Urrbrae, South Australia, Australia
| | - Yveline Pailles
- Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Bettina Berger
- School of Agriculture, Food and Wine, Waite Research Precinct, University of Adelaide, Urrbrae, South Australia, Australia
- The Plant Accelerator, Australian Plant Phenomics Facility, Waite Research Precinct, University of Adelaide, Urrbrae, South Australia, Australia
| | - Mohammad Shahid
- International Center for Biosaline Agriculture (ICBA), Dubai, United Arab Emirates
| | - Joanne Russell
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland
| | - Robbie Waugh
- School of Agriculture, Food and Wine, Waite Research Precinct, University of Adelaide, Urrbrae, South Australia, Australia
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland
- Division of Plant Sciences, School of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, Scotland
| | - Sónia Negrão
- School of Biology and Environmental Sciences, University College Dublin, Belfield, Dublin, Ireland
| | - Mark Tester
- Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Gill MB, Zeng F, Shabala L, Zhang G, Yu M, Demidchik V, Shabala S, Zhou M. Identification of QTL Related to ROS Formation under Hypoxia and Their Association with Waterlogging and Salt Tolerance in Barley. Int J Mol Sci 2019; 20:E699. [PMID: 30736310 PMCID: PMC6387252 DOI: 10.3390/ijms20030699] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/01/2019] [Accepted: 02/04/2019] [Indexed: 01/19/2023] Open
Abstract
Waterlogging is a serious environmental problem that limits agricultural production in low-lying rainfed areas around the world. The major constraint that plants face in a waterlogging situation is the reduced oxygen availability. Accordingly, all previous efforts of plant breeders focused on traits providing adequate supply of oxygen to roots under waterlogging conditions, such as enhanced aerenchyma formation or reduced radial oxygen loss. However, reduced oxygen concentration in waterlogged soils also leads to oxygen deficiency in plant tissues, resulting in an excessive accumulation of reactive oxygen species (ROS) in plants. To the best of our knowledge, this trait has never been targeted in breeding programs and thus represents an untapped resource for improving plant performance in waterlogged soils. To identify the quantitative trait loci (QTL) for ROS tolerance in barley, 187 double haploid (DH) lines from a cross between TX9425 and Naso Nijo were screened for superoxide anion (O₂•-) and hydrogen peroxide (H₂O₂)-two major ROS species accumulated under hypoxia stress. We show that quantifying ROS content after 48 h hypoxia could be a fast and reliable approach for the selection of waterlogging tolerant barley genotypes. The same QTL on chromosome 2H was identified for both O₂•- (QSO.TxNn.2H) and H₂O₂ (QHP.TxNn.2H) contents. This QTL was located at the same position as the QTL for the overall waterlogging and salt tolerance reported in previous studies, explaining 23% and 24% of the phenotypic variation for O₂•- and H₂O2 contents, respectively. The analysis showed a causal association between ROS production and both waterlogging and salt stress tolerance. Waterlogging and salinity are two major abiotic factors affecting crop production around the globe and frequently occur together. The markers associated with this QTL could potentially be used in future breeding programs to improve waterlogging and salinity tolerance.
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Affiliation(s)
- Muhammad Bilal Gill
- International Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China.
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Tas 7005, Australia.
| | - Fanrong Zeng
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Lana Shabala
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Tas 7005, Australia.
| | - Guoping Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Min Yu
- International Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China.
| | - Vadim Demidchik
- International Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China.
- Department of Plant Cell Biology and Bioengineering, Biological Faculty, Belarusian State University, 222030 Minsk, Belarus.
| | - Sergey Shabala
- International Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China.
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Tas 7005, Australia.
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Tas 7005, Australia.
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11
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Wang J, Yang J, Hua W, Wu X, Zhu J, Shang Y, Zhou M. QTL Mapping Reveals the Relationship between Pasting Properties and Malt Extract in Barley. Int J Mol Sci 2018; 19:ijms19113559. [PMID: 30424480 PMCID: PMC6275068 DOI: 10.3390/ijms19113559] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 10/27/2018] [Accepted: 10/30/2018] [Indexed: 11/16/2022] Open
Abstract
Pasting properties are important characteristics of barley starch from a processing standpoint. Many studies reported the close relationship between pasting properties and malting quality, especially malt extract. However, most conclusions were derived from the correlation between pasting properties and malting quality using a set of cultivars or breeding lines. In this study, a doubled haploid population of 150 lines from a cross between a Japanese malting barley and a Chinese feed barley was grown in four different environments (two sites × two years). Based on average values from all different environments, 17 significant quantitative trait loci (QTL) were identified for pasting properties. The genetic variance explained by these QTL varied from 7.0 to 23.2%. Most QTL controlling pasting properties were located on 1H, 2H, 5H, and 7H. Results confirmed the linkage between pasting properties and malt extract, with most of the QTL for pasting properties becoming nonsignificant when using malt extract as a covariate. Breakdown showed the closest correlation with malt extract. Molecular markers closely linked to the QTL can be used to select desired pasting properties to improve malting quality.
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Affiliation(s)
- Junmei Wang
- Institute of Crop and Nuclear Technology Utilization, Jinghuan, Hangzhou 310021, China.
| | - Jianming Yang
- Institute of Crop and Nuclear Technology Utilization, Jinghuan, Hangzhou 310021, China.
| | - Wei Hua
- Institute of Crop and Nuclear Technology Utilization, Jinghuan, Hangzhou 310021, China.
| | - Xiaojian Wu
- Institute of Crop and Nuclear Technology Utilization, Jinghuan, Hangzhou 310021, China.
| | - Jinghuan Zhu
- Institute of Crop and Nuclear Technology Utilization, Jinghuan, Hangzhou 310021, China.
| | - Yi Shang
- Institute of Crop and Nuclear Technology Utilization, Jinghuan, Hangzhou 310021, China.
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, Tasmania 6250, Australia.
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12
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Türkösi E, Darko E, Rakszegi M, Molnár I, Molnár-Láng M, Cseh A. Development of a new 7BS.7HL winter wheat-winter barley Robertsonian translocation line conferring increased salt tolerance and (1,3;1,4)-β-D-glucan content. PLoS One 2018; 13:e0206248. [PMID: 30395616 PMCID: PMC6218033 DOI: 10.1371/journal.pone.0206248] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/09/2018] [Indexed: 01/01/2023] Open
Abstract
Interspecific hybridization between bread wheat (Triticum aestivum, 2n = 42) and related species allows the transfer of agronomic and quality traits, whereby subsequent generations comprise an improved genetic background and can be directly applied in wheat breeding programmes. While wild relatives are frequently used as sources of agronomically favourable traits, cultivated species can also improve wheat quality and stress resistance. A salt-tolerant 'Asakaze'/'Manas' 7H disomic addition line (2n = 44) with elevated β-glucan content, but with low fertility and an unstable genetic background was developed in an earlier wheat-barley prebreeding programme. The aim of the present study was to take this hybridization programme further and transfer the favourable barley traits into a more stable genetic background. Taking advantage of the breakage-fusion mechanism of univalent chromosomes, the 'Rannaya' winter wheat 7B monosomic line was used as female partner to the 7H addition line male, leading to the development of a compensating wheat/barley Robertsonian translocation line (7BS.7HL centric fusion, 2n = 42) exhibiting higher salt tolerance and elevated grain β-glucan content. Throughout the crossing programme, comprising the F1-F4 generations, genomic in situ hybridization, fluorescence in situ hybridization and chromosome-specific molecular markers were used to trace and identify the wheat and barley chromatin. Investigations on salt tolerance during germination and on the (1,3;1,4)-β-D-glucan (mixed-linkage glucan [MLG]) content of the seeds confirmed the salt tolerance and elevated grain MLG content of the translocation line, which can be directly applied in current wheat breeding programmes.
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Affiliation(s)
- Edina Türkösi
- Department of Plant Genetic Resources, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Eva Darko
- Department of Plant Physiology, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Marianna Rakszegi
- Cereal Breeding Department, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - István Molnár
- Maize Breeding Department, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Márta Molnár-Láng
- Department of Plant Genetic Resources, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - András Cseh
- Molecular Breeding Department, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
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13
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Gill MB, Zeng F, Shabala L, Zhang G, Fan Y, Shabala S, Zhou M. Cell-Based Phenotyping Reveals QTL for Membrane Potential Maintenance Associated with Hypoxia and Salinity Stress Tolerance in Barley. FRONTIERS IN PLANT SCIENCE 2017; 8:1941. [PMID: 29201033 PMCID: PMC5696338 DOI: 10.3389/fpls.2017.01941] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 10/27/2017] [Indexed: 05/18/2023]
Abstract
Waterlogging and salinity are two major abiotic stresses that hamper crop production world-wide resulting in multibillion losses. Plant abiotic stress tolerance is conferred by many interrelated mechanisms. Amongst these, the cell's ability to maintain membrane potential (MP) is considered to be amongst the most crucial traits, a positive relationship between the ability of plants to maintain highly negative MP and its tolerance to both salinity and waterlogging stress. However, no attempts have been made to identify quantitative trait loci (QTL) conferring this trait. In this study, the microelectrode MIFE technique was used to measure the plasma membrane potential of epidermal root cells of 150 double haploid (DH) lines of barley (Hordeum vulgare L.) from a cross between a Chinese landrace TX9425 and Japanese malting cultivar Naso Nijo under hypoxic conditions. A major QTL for the MP in the epidermal root cells in hypoxia-exposed plants was identified. This QTL was located on 2H, at a similar position to the QTL for waterlogging and salinity tolerance reported in previous studies. Further analysis confirmed that MP showed a significant contribution to both waterlogging and salinity tolerance. The fact that the QTL for MP was controlled by a single major QTL illustrates the power of the single-cell phenotyping approach and opens prospects for fine mapping this QTL and thus being more effective in marker assisted selection.
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Affiliation(s)
- Muhammad B. Gill
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- School of Land and Food, University of Tasmania, Hobart, TAS, Australia
| | - Fanrong Zeng
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Lana Shabala
- School of Land and Food, University of Tasmania, Hobart, TAS, Australia
| | - Guoping Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yun Fan
- School of Land and Food, University of Tasmania, Hobart, TAS, Australia
| | - Sergey Shabala
- School of Land and Food, University of Tasmania, Hobart, TAS, Australia
| | - Meixue Zhou
- School of Land and Food, University of Tasmania, Hobart, TAS, Australia
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14
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Angessa TT, Zhang XQ, Zhou G, Broughton S, Zhang W, Li C. Early growth stages salinity stress tolerance in CM72 x Gairdner doubled haploid barley population. PLoS One 2017. [PMID: 28640858 PMCID: PMC5480976 DOI: 10.1371/journal.pone.0179715] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A doubled haploid (DH) population of barley (Hordeum vulgare L.) generated from salinity tolerant genotype CM72 and salinity sensitive variety Gairdner was studied for salinity stress tolerance at germination, seedling emergence and first leaf full expansion growth stages. Germination study was conducted with deionized water, 150 mM and 300 mM NaCl treatments. Seedling stage salinity tolerance was conducted with three treatments: control, 150 mM NaCl added at seedling emergence and first leaf full expansion growth stages. Results from this study revealed transgressive phenotypic segregations for germination percentage and biomass at seedling stage. Twelve QTL were identified on chromosomes 2H-6H each explaining 10-25% of the phenotypic variations. A QTL located at 176.5 cM on chromosome 3H was linked with fresh weight per plant and dry weight per plant in salinity stress induced at first leaf full expansion growth stage, and dry weight per plant in salinity stress induced at seedling emergence. A stable QTL for germination at both 150 and 300 mM salinity stress was mapped on chromosome 2H but distantly located from a QTL linked with seedling stage salinity stress tolerance. QTL, associated markers and genotypes identified in this study play important roles in developing salinity stress tolerant barley varieties.
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Affiliation(s)
- Tefera Tolera Angessa
- Western Barley Genetics Alliance, School of Veterinary and Life Sciences (VLS), Murdoch University, Murdoch, WA, Australia
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, School of Veterinary and Life Sciences (VLS), Murdoch University, Murdoch, WA, Australia
| | - Gaofeng Zhou
- Western Barley Genetics Alliance, School of Veterinary and Life Sciences (VLS), Murdoch University, Murdoch, WA, Australia
| | - Sue Broughton
- Grains Industry, Department of Agriculture and Food WA, South Perth, WA, Australia
| | - Wenying Zhang
- Hubei Collaborative Innovation Centre for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, Hubei, China
- * E-mail: (CL); (WZ)
| | - Chengdao Li
- Western Barley Genetics Alliance, School of Veterinary and Life Sciences (VLS), Murdoch University, Murdoch, WA, Australia
- Grains Industry, Department of Agriculture and Food WA, South Perth, WA, Australia
- * E-mail: (CL); (WZ)
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15
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Zhang X, Shabala S, Koutoulis A, Shabala L, Zhou M. Meta-analysis of major QTL for abiotic stress tolerance in barley and implications for barley breeding. PLANTA 2017; 245:283-295. [PMID: 27730410 DOI: 10.1007/s00425-016-2605-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/04/2016] [Indexed: 05/24/2023]
Abstract
We projected meta-QTL (MQTL) for drought, salinity, and waterlogging tolerance to the physical map of barley through meta-analysis. The positions of these MQTL were refined and candidate genes were identified. Drought, salinity and waterlogging are three major abiotic stresses limiting barley yield worldwide. Breeding for abiotic stress-tolerant crops has drawn increased attention, and a large number of quantitative trait loci (QTL) for drought, salinity, and waterlogging tolerance in barley have been detected. However, very few QTL have been successfully used in marker-assisted selection (MAS) in breeding. In this study, we summarized 632 QTL for drought, salinity and waterlogging tolerance in barley. Among all these QTL, only 195 major QTL were used to conduct meta-analysis to refine QTL positions for MAS. Meta-analysis was used to map the summarized major QTL for drought, salinity, and waterlogging tolerance from different mapping populations on the barley physical map. The positions of identified meta-QTL (MQTL) were used to search for candidate genes for drought, salinity, and waterlogging tolerance in barley. Both MQTL3H.4 and MQTL6H.2 control drought tolerance in barley. Fine-mapped QTL for salinity tolerance, HvNax4 and HvNax3, were validated on MQTL1H.4 and MQTL7H.2, respectively. MQTL2H.1 and MQTL5H.3 were also the target regions for improving salinity tolerance in barley. MQTL4H.4 is the main region controlling waterlogging tolerance in barley with fine-mapped QTL for aerenchyma formation under waterlogging conditions. Detected and refined MQTL and candidate genes are crucial for future successful MAS in barley breeding.
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Affiliation(s)
- Xuechen Zhang
- School of Land and Food, University of Tasmania, P.O. Box 46, Kings Meadows, Tasmania, TAS 7249, Australia
| | - Sergey Shabala
- School of Land and Food, University of Tasmania, P.O. Box 46, Kings Meadows, Tasmania, TAS 7249, Australia
| | - Anthony Koutoulis
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
| | - Lana Shabala
- School of Land and Food, University of Tasmania, P.O. Box 46, Kings Meadows, Tasmania, TAS 7249, Australia
| | - Meixue Zhou
- School of Land and Food, University of Tasmania, P.O. Box 46, Kings Meadows, Tasmania, TAS 7249, Australia.
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16
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Liu X, Fan Y, Mak M, Babla M, Holford P, Wang F, Chen G, Scott G, Wang G, Shabala S, Zhou M, Chen ZH. QTLs for stomatal and photosynthetic traits related to salinity tolerance in barley. BMC Genomics 2017; 18:9. [PMID: 28049416 PMCID: PMC5210286 DOI: 10.1186/s12864-016-3380-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 12/06/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stomata regulate photosynthesis and transpiration, and these processes are critical for plant responses to abiotic stresses such as salinity. A barley double haploid population with 108 lines derived from a cross between CM72 (salt-tolerant) and Gairdner (salt-sensitive) was used to detect quantitative trait loci (QTLs) associated with stomatal and photosynthetic traits related to salinity tolerance. RESULTS A total of 11 significant QTLs (LOD > 3.0) and 11 tentative QTLs (2.5 < LOD < 3.0) were identified. These QTLs are distributed on all the seven chromosomes, except 5H and explain 9.5-17.3% of the phenotypic variation. QTLs for biomass, intercellular CO2 concentration, transpiration rate and stomatal conductance under control conditions co-localised together. A QTL for biomass also co-located with one for transpiration rate under salinity stress. A linkage was found between stomatal pore area and gas exchange. A QTL for salinity tolerance also co-localised with QTLs for grain yield and biomass on chromosome 3H. Based on the draft barley genome, the candidate genes for salinity tolerance at this locus are proposed. CONCLUSIONS The lack of major QTLs for gas exchange and stomatal traits under control and saline conditions indicates a complex relationship between salinity and leaf gas exchange due to the fact that these complex quantitative traits are under the control of multiple genes.
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Affiliation(s)
- Xiaohui Liu
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751 Australia
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072 China
| | - Yun Fan
- School of Land and Food and Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7249 Australia
| | - Michelle Mak
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751 Australia
| | - Mohammad Babla
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751 Australia
| | - Paul Holford
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751 Australia
| | - Feifei Wang
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751 Australia
- School of Land and Food and Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7249 Australia
| | - Guang Chen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Grace Scott
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751 Australia
| | - Gang Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072 China
| | - Sergey Shabala
- School of Land and Food and Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7249 Australia
| | - Meixue Zhou
- School of Land and Food and Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7249 Australia
| | - Zhong-Hua Chen
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751 Australia
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