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Wang W, Huang S, Wang Z, Cao P, Luo M, Wang F. Unraveling wheat's response to salt stress during early growth stages through transcriptomic analysis and co-expression network profiling. BMC Genom Data 2024; 25:36. [PMID: 38609855 PMCID: PMC11015659 DOI: 10.1186/s12863-024-01221-1] [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: 08/15/2023] [Accepted: 03/14/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Soil salinization is one of the vital factors threatening the world's food security. To reveal the biological mechanism of response to salt stress in wheat, this study was conducted to resolve the transcription level difference to salt stress between CM6005 (salt-tolerant) and KN9204 (salt-sensitive) at the germination and seedling stage. RESULTS To investigate the molecular mechanism underlying salt tolerance in wheat, we conducted comprehensive transcriptome analyses at the seedling and germination stages. Two wheat cultivars, CM6005 (salt-tolerant) and KN9204 (salt-sensitive) were subjected to salt treatment, resulting in a total of 24 transcriptomes. Through expression-network analysis, we identified 17 modules, 16 and 13 of which highly correlate with salt tolerance-related phenotypes in the germination and seedling stages, respectively. Moreover, we identified candidate Hub genes associated with specific modules and explored their regulatory relationships using co-expression data. Enrichment analysis revealed specific enrichment of gibberellin-related terms and pathways in CM6005, highlighting the potential importance of gibberellin regulation in enhancing salt tolerance. In contrast, KN9204 exhibited specific enrichment in glutathione-related terms and activities, suggesting the involvement of glutathione-mediated antioxidant mechanisms in conferring resistance to salt stress. Additionally, glucose transport was found to be a fundamental mechanism for salt tolerance during wheat seedling and germination stages, indicating its potential universality in wheat. Wheat plants improve their resilience and productivity by utilizing adaptive mechanisms like adjusting osmotic balance, bolstering antioxidant defenses, accumulating compatible solutes, altering root morphology, and regulating hormones, enabling them to better withstand extended periods of salt stress. CONCLUSION Through utilizing transcriptome-level analysis employing WGCNA, we have revealed a potential regulatory mechanism that governs the response to salt stress and recovery in wheat cultivars. Furthermore, we have identified key candidate central genes that play a crucial role in this mechanism. These central genes are likely to be vital components within the gene expression network associated with salt tolerance. The findings of this study strongly support the molecular breeding of salt-tolerant wheat, particularly by utilizing the genetic advancements based on CM6005 and KN9204.
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Affiliation(s)
- Wei Wang
- Cangzhou Academy of Agriculture and Forestry Sciences, 061001, Cangzhou, Hebei, China.
- Hebei Key Laboratory of Drought-Alkali Tolerance in Wheat, 061001, Cangzhou, Hebei, China.
| | - Sufang Huang
- Cangzhou Academy of Agriculture and Forestry Sciences, 061001, Cangzhou, Hebei, China
- Hebei Key Laboratory of Drought-Alkali Tolerance in Wheat, 061001, Cangzhou, Hebei, China
| | - Zhi Wang
- Cangzhou Academy of Agriculture and Forestry Sciences, 061001, Cangzhou, Hebei, China
- Hebei Key Laboratory of Drought-Alkali Tolerance in Wheat, 061001, Cangzhou, Hebei, China
| | - Pingping Cao
- Cangzhou Academy of Agriculture and Forestry Sciences, 061001, Cangzhou, Hebei, China
- Hebei Key Laboratory of Drought-Alkali Tolerance in Wheat, 061001, Cangzhou, Hebei, China
| | - Meng Luo
- Shanghai Majorbio Bio-pharm Technology Co., Ltd, 200120, Shanghai, China
| | - Fengzhi Wang
- Cangzhou Academy of Agriculture and Forestry Sciences, 061001, Cangzhou, Hebei, China.
- Hebei Key Laboratory of Drought-Alkali Tolerance in Wheat, 061001, Cangzhou, Hebei, China.
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Zhang X, Wang H, Yang M, Liu R, Zhang X, Jia Z, Li P. Natural variation in ZmNAC087 contributes to total root length regulation in maize seedlings under salt stress. BMC PLANT BIOLOGY 2023; 23:392. [PMID: 37580686 PMCID: PMC10424409 DOI: 10.1186/s12870-023-04393-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/31/2023] [Indexed: 08/16/2023]
Abstract
Soil salinity poses a significant challenge to crop growth and productivity, particularly affecting the root system, which is vital for water and nutrient uptake. To identify genetic factors that influence root elongation in stressful environments, we conducted a genome-wide association study (GWAS) to investigate the natural variation associated with total root length (TRL) under salt stress and normal conditions in maize seedlings. Our study identified 69 genetic variants associated with 38 candidate genes, among which a specific single nucleotide polymorphism (SNP) in ZmNAC087 was significantly associated with TRL under salt stress. Transient expression and transactivation assays revealed that ZmNAC087 encodes a nuclear-localized protein with transactivation activity. Further candidate gene association analysis showed that non-coding variations in ZmNAC087 promoter contribute to differential ZmNAC087 expression among maize inbred lines, potentially influencing the variation in salt-regulated TRL. In addition, through nucleotide diversity analysis, neutrality tests, and coalescent simulation, we demonstrated that ZmNAC087 underwent selection during maize domestication and improvement. These findings highlight the significance of natural variation in ZmNAC087, particularly the favorable allele, in maize salt tolerance, providing theoretical basis and valuable genetic resources for the development of salt-tolerant maize germplasm.
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Affiliation(s)
- Xiaomin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Sanya Institute, Henan University, Sanya, 572025, China
| | - Houmiao Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Mengling Yang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Runxiao Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Zhongtao Jia
- State Key Laboratory of Nutrient Use and Management (SKL-NUM), College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China.
| | - Pengcheng Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
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Pasam RK, Kant S, Thoday-Kennedy E, Dimech A, Joshi S, Keeble-Gagnere G, Forrest K, Tibbits J, Hayden M. Haplotype-Based Genome-Wide Association Analysis Using Exome Capture Assay and Digital Phenotyping Identifies Genetic Loci Underlying Salt Tolerance Mechanisms in Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:2367. [PMID: 37375992 DOI: 10.3390/plants12122367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023]
Abstract
Soil salinity can impose substantial stress on plant growth and cause significant yield losses. Crop varieties tolerant to salinity stress are needed to sustain yields in saline soils. This requires effective genotyping and phenotyping of germplasm pools to identify novel genes and QTL conferring salt tolerance that can be utilised in crop breeding schemes. We investigated a globally diverse collection of 580 wheat accessions for their growth response to salinity using automated digital phenotyping performed under controlled environmental conditions. The results show that digitally collected plant traits, including digital shoot growth rate and digital senescence rate, can be used as proxy traits for selecting salinity-tolerant accessions. A haplotype-based genome-wide association study was conducted using 58,502 linkage disequilibrium-based haplotype blocks derived from 883,300 genome-wide SNPs and identified 95 QTL for salinity tolerance component traits, of which 54 were novel and 41 overlapped with previously reported QTL. Gene ontology analysis identified a suite of candidate genes for salinity tolerance, some of which are already known to play a role in stress tolerance in other plant species. This study identified wheat accessions that utilise different tolerance mechanisms and which can be used in future studies to investigate the genetic and genic basis of salinity tolerance. Our results suggest salinity tolerance has not arisen from or been bred into accessions from specific regions or groups. Rather, they suggest salinity tolerance is widespread, with small-effect genetic variants contributing to different levels of tolerance in diverse, locally adapted germplasm.
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Affiliation(s)
- Raj K Pasam
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | - Surya Kant
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC 3400, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
| | | | - Adam Dimech
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | - Sameer Joshi
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC 3400, Australia
| | | | - Kerrie Forrest
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | - Josquin Tibbits
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | - Matthew Hayden
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
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Abdul Aziz M, Masmoudi K. Insights into the Transcriptomics of Crop Wild Relatives to Unravel the Salinity Stress Adaptive Mechanisms. Int J Mol Sci 2023; 24:9813. [PMID: 37372961 DOI: 10.3390/ijms24129813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/29/2023] Open
Abstract
The narrow genomic diversity of modern cultivars is a major bottleneck for enhancing the crop's salinity stress tolerance. The close relatives of modern cultivated plants, crop wild relatives (CWRs), can be a promising and sustainable resource to broaden the diversity of crops. Advances in transcriptomic technologies have revealed the untapped genetic diversity of CWRs that represents a practical gene pool for improving the plant's adaptability to salt stress. Thus, the present study emphasizes the transcriptomics of CWRs for salinity stress tolerance. In this review, the impacts of salt stress on the plant's physiological processes and development are overviewed, and the transcription factors (TFs) regulation of salinity stress tolerance is investigated. In addition to the molecular regulation, a brief discussion on the phytomorphological adaptation of plants under saline environments is provided. The study further highlights the availability and use of transcriptomic resources of CWR and their contribution to pangenome construction. Moreover, the utilization of CWRs' genetic resources in the molecular breeding of crops for salinity stress tolerance is explored. Several studies have shown that cytoplasmic components such as calcium and kinases, and ion transporter genes such as Salt Overly Sensitive 1 (SOS1) and High-affinity Potassium Transporters (HKTs) are involved in the signaling of salt stress, and in mediating the distribution of excess Na+ ions within the plant cells. Recent comparative analyses of transcriptomic profiling through RNA sequencing (RNA-Seq) between the crops and their wild relatives have unraveled several TFs, stress-responsive genes, and regulatory proteins for generating salinity stress tolerance. This review specifies that the use of CWRs transcriptomics in combination with modern breeding experimental approaches such as genomic editing, de novo domestication, and speed breeding can accelerate the CWRs utilization in the breeding programs for enhancing the crop's adaptability to saline conditions. The transcriptomic approaches optimize the crop genomes with the accumulation of favorable alleles that will be indispensable for designing salt-resilient crops.
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Affiliation(s)
- Mughair Abdul Aziz
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Khaled Masmoudi
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates
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5
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Zhang X, Jiang X, Zhang Y, Ren J, Feng J, Quan W. Identification of QTL for reducing loss of grain yield under salt stress conditions in bi-parental populations derived from wheat landrace Hongmangmai. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:49. [PMID: 36913045 DOI: 10.1007/s00122-023-04290-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/26/2022] [Indexed: 06/18/2023]
Abstract
A novel QTL (QSt.nftec-2BL) was mapped to a 0.7 cM interval on chromosome 2B. Plants carrying QSt.nftec-2BL produced higher grain yields by up to 21.4% than otherwise in salinized fields. Wheat yield has been limited by soil salinity in many wheat-growing areas globally. The wheat landrace Hongmangmai (HMM) possesses salt tolerance as it produced higher grain yields than other tested wheat varieties including Early Premium (EP) under salt stresses. To detect QTL underlying this tolerance, wheat cross EP × HMM was chosen to serve as mapping population that was homozygous at Ppd (photoperiod response gene), Rht (reduced plant height gene) and Vrn (vernalization gene); thus, interference with QTL detection by these loci could be minimized. QTL mapping was conducted firstly using 102 recombinant inbred lines (RILs) that were selected from the EP × HMM population (827 RILs) for similarity in grain yield under non-saline condition. Under salt stresses, however, the 102 RILs varied significantly in grain yield. These RILs were genotyped using a 90 K SNP (single nucleotide polymorphism) array; consequently, a QTL (QSt.nftec-2BL) was detected on chromosome 2B. Then, using 827 RILs and new simple sequence repeat (SSR) markers developed according to the reference sequence IWGSC RefSeq v1.0, location of QSt.nftec-2BL was refined to a 0.7 cM (6.9 Mb) interval flanked by SSR markers 2B-557.23 and 2B-564.09. Selection for QSt.nftec-2BL was performed based on the flanking markers using two bi-parental wheat populations. Trials for validating effectiveness of the selection were conducted in salinized fields in two geographical areas and two crop seasons, demonstrating that wheat plants with the salt-tolerant allele in homozygous status at QSt.nftec-2BL produced higher grain yields by up to 21.4% than otherwise.
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Affiliation(s)
- Xiang Zhang
- National Fisheries Technology Extension Center, Beijing, 100125, People's Republic of China
| | - Xu Jiang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, People's Republic of China
- Liaoning Provincial Key Laboratory of Forest Protection, Liaoning Academy of Forestry Science, Shenyang, 110032, People's Republic of China
| | - Yibin Zhang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, People's Republic of China
| | - Junda Ren
- Beijing University of Agriculture, Beijing, 102206, People's Republic of China
| | - Jing Feng
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
| | - Wei Quan
- Institute of Hybrid Wheat, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, People's Republic of China.
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6
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Benaouda S, Stöcker T, Schoof H, Léon J, Ballvora A. Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat. BMC PLANT BIOLOGY 2023; 23:25. [PMID: 36631761 PMCID: PMC9835304 DOI: 10.1186/s12870-022-03986-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The transition from vegetative to floral phase is the result of complex crosstalk of exogenous and endogenous floral integrators. This critical physiological event is the response to environmental interaction, which causes biochemical cascades of reactions at different internal tissues, organs, and releases signals that make the plant moves from vegetative status to a reproductive phase. This network controlling flowering time is not deciphered largely in bread wheat. In this study, a comparative transcriptome analysis at a transition time in combination with genetic mapping was used to identify responsible genes in a stage and tissue-specific manner. For this reason, two winter cultivars that have been bred in Germany showing contrasting and stable heading time in different environments were selected for the analysis. RESULTS In total, 670 and 1075 differentially expressed genes in the shoot apical meristem and leaf tissue, respectively, could be identified in 23 QTL intervals for the heading date. In the transition apex, Histone methylation H3-K36 and regulation of circadian rhythm are both controlled by the same homoeolog genes mapped in QTL TaHd112, TaHd124, and TaHd137. TaAGL14 gene that identifies the floral meristem was mapped in TaHd054 in the double ridge. In the same stage, the homoeolog located on chromosome 7D of FLOWERING TIME LOCUS T mapped on chr 7B, which evolved an antagonist function and acts as a flowering repressor was uncovered. The wheat orthologue of transcription factor ASYMMETRIC LEAVES 1 (AS1) was identified in the late reproductive stage and was mapped in TaHd102, which is strongly associated with heading date. Deletion of eight nucleotides in the AS1 promoter could be identified in the binding site of the SUPPRESSOR OF CONSTANS OVEREXPRESSION 1 (SOC1) gene in the late flowering cultivar. Both proteins AS1 and SOC1 are inducing flowering time in response to gibberellin biosynthesis. CONCLUSION The global transcriptomic at the transition phase uncovered stage and tissue-specific genes mapped in QTL of heading date in winter wheat. In response to Gibberellin signaling, wheat orthologous transcription factor AS1 is expressed in the late reproductive phase of the floral transition. The locus harboring this gene is the strongest QTL associated with the heading date trait in the German cultivars. Consequently, we conclude that this is another indication of the Gibberellin biosynthesis as the mechanism behind the heading variation in wheat.
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Affiliation(s)
- Salma Benaouda
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, University of Bonn, Bonn, Germany
| | - Tyll Stöcker
- Institute for Crop Science and Resource Conservation, Chair of Crop Bioinformatics, University of Bonn, Bonn, Germany
| | - Heiko Schoof
- Institute for Crop Science and Resource Conservation, Chair of Crop Bioinformatics, University of Bonn, Bonn, Germany
| | - Jens Léon
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, University of Bonn, Bonn, Germany
| | - Agim Ballvora
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, University of Bonn, Bonn, Germany
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Khodaeiaminjan M, Knoch D, Ndella Thiaw MR, Marchetti CF, Kořínková N, Techer A, Nguyen TD, Chu J, Bertholomey V, Doridant I, Gantet P, Graner A, Neumann K, Bergougnoux V. Genome-wide association study in two-row spring barley landraces identifies QTL associated with plantlets root system architecture traits in well-watered and osmotic stress conditions. FRONTIERS IN PLANT SCIENCE 2023; 14:1125672. [PMID: 37077626 PMCID: PMC10106628 DOI: 10.3389/fpls.2023.1125672] [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: 12/16/2022] [Accepted: 03/15/2023] [Indexed: 05/03/2023]
Abstract
Water availability is undoubtedly one of the most important environmental factors affecting crop production. Drought causes a gradual deprivation of water in the soil from top to deep layers and can occur at diverse stages of plant development. Roots are the first organs that perceive water deficit in soil and their adaptive development contributes to drought adaptation. Domestication has contributed to a bottleneck in genetic diversity. Wild species or landraces represent a pool of genetic diversity that has not been exploited yet in breeding program. In this study, we used a collection of 230 two-row spring barley landraces to detect phenotypic variation in root system plasticity in response to drought and to identify new quantitative trait loci (QTL) involved in root system architecture under diverse growth conditions. For this purpose, young seedlings grown for 21 days in pouches under control and osmotic-stress conditions were phenotyped and genotyped using the barley 50k iSelect SNP array, and genome-wide association studies (GWAS) were conducted using three different GWAS methods (MLM GAPIT, FarmCPU, and BLINK) to detect genotype/phenotype associations. In total, 276 significant marker-trait associations (MTAs; p-value (FDR)< 0.05) were identified for root (14 and 12 traits under osmotic-stress and control conditions, respectively) and for three shoot traits under both conditions. In total, 52 QTL (multi-trait or identified by at least two different GWAS approaches) were investigated to identify genes representing promising candidates with a role in root development and adaptation to drought stress.
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Affiliation(s)
- Mortaza Khodaeiaminjan
- Czech Advanced Technology and Research Institute, Palacký University in Olomouc, Olomouc, Czechia
- *Correspondence: Mortaza Khodaeiaminjan, ; Véronique Bergougnoux,
| | - Dominic Knoch
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | | - Cintia F. Marchetti
- Czech Advanced Technology and Research Institute, Palacký University in Olomouc, Olomouc, Czechia
| | - Nikola Kořínková
- Czech Advanced Technology and Research Institute, Palacký University in Olomouc, Olomouc, Czechia
| | - Alexie Techer
- Czech Advanced Technology and Research Institute, Palacký University in Olomouc, Olomouc, Czechia
| | - Thu D. Nguyen
- Czech Advanced Technology and Research Institute, Palacký University in Olomouc, Olomouc, Czechia
| | - Jianting Chu
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Valentin Bertholomey
- Limagrain Field Seeds, Traits and Technologies, Groupe Limagrain Centre de Recherche, Chappes, France
| | - Ingrid Doridant
- Limagrain Field Seeds, Traits and Technologies, Groupe Limagrain Centre de Recherche, Chappes, France
| | - Pascal Gantet
- Czech Advanced Technology and Research Institute, Palacký University in Olomouc, Olomouc, Czechia
- Unité Mixte de Recherche DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Andreas Graner
- Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Kerstin Neumann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Véronique Bergougnoux
- Czech Advanced Technology and Research Institute, Palacký University in Olomouc, Olomouc, Czechia
- *Correspondence: Mortaza Khodaeiaminjan, ; Véronique Bergougnoux,
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Javid S, Bihamta MR, Omidi M, Abbasi AR, Alipour H, Ingvarsson PK. Genome-Wide Association Study (GWAS) and genome prediction of seedling salt tolerance in bread wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2022; 22:581. [PMID: 36513980 PMCID: PMC9746167 DOI: 10.1186/s12870-022-03936-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Salinity tolerance in wheat is imperative for improving crop genetic capacity in response to the expanding phenomenon of soil salinization. However, little is known about the genetic foundation underlying salinity tolerance at the seedling growth stage of wheat. Herein, a GWAS analysis was carried out by the random-SNP-effect mixed linear model (mrMLM) multi-locus model to uncover candidate genes responsible for salt tolerance at the seedling stage in 298 Iranian bread wheat accessions, including 208 landraces and 90 cultivars. RESULTS A total of 29 functional marker-trait associations (MTAs) were detected under salinity, 100 mM NaCl (sodium chloride). Of these, seven single nucleotide polymorphisms (SNPs) including rs54146, rs257, rs37983, rs18682, rs55629, rs15183, and rs63185 with R2 ≥ 10% were found to be linked with relative water content, root fresh weight, root dry weight, root volume, shoot high, proline, and shoot potassium (K+), respectively. Further, a total of 27 candidate genes were functionally annotated to be involved in response to the saline environment. Most of these genes have key roles in photosynthesis, response to abscisic acid, cell redox homeostasis, sucrose and carbohydrate metabolism, ubiquitination, transmembrane transport, chromatin silencing, and some genes harbored unknown functions that all together may respond to salinity as a complex network. For genomic prediction (GP), the genomic best linear unbiased prediction (GBLUP) model reflected genetic effects better than both bayesian ridge regression (BRR) and ridge regression-best linear unbiased prediction (RRBLUP), suggesting GBLUP as a favorable tool for wheat genomic selection. CONCLUSION The SNPs and candidate genes identified in the current work can be used potentially for developing salt-tolerant varieties at the seedling growth stage by marker-assisted selection.
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Affiliation(s)
- Saeideh Javid
- Department of Agronomy and Plant Breeding, University of Tehran, Karaj, Iran
| | | | - Mansour Omidi
- Department of Agronomy and Plant Breeding, University of Tehran, Karaj, Iran
| | - Ali Reza Abbasi
- Department of Agronomy and Plant Breeding, University of Tehran, Karaj, Iran
| | - Hadi Alipour
- Department of Plant Production and Genetics, Urmia University, Urmia, Iran
| | - Pär K Ingvarsson
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Guo X, Wu C, Wang D, Wang G, Jin K, Zhao Y, Tian J, Deng Z. Conditional QTL mapping for seed germination and seedling traits under salt stress and candidate gene prediction in wheat. Sci Rep 2022; 12:21010. [PMID: 36471100 PMCID: PMC9722660 DOI: 10.1038/s41598-022-25703-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Breeding new wheat varieties with salt resistance is one of the best ways to solve a constraint on the sustainability and expansion of wheat cultivation. Therefore, understanding the molecular components or genes related to salt tolerance must contribute to the cultivation of salt-tolerant varieties. The present study used a recombinant inbred line (RIL) population to genetically dissect the effects of different salt stress concentrations on wheat seed germination and seedling traits using two quantitative trait locus (QTL) mapping methods. A total of 31 unconditional and 11 conditional QTLs for salt tolerance were identified on 11 chromosomes explaining phenotypic variation (PVE) ranging from 2.01 to 65.76%. Of these, 15 major QTLs were found accounting for more than 10% PVE. QTL clusters were detected on chromosomes 2A and 3B in the marker intervals 'wPt-8328 and wPt-2087' and 'wPt-666008 and wPt-3620', respectively, involving more than one salt tolerance trait. QRdw3B and QSfw3B.2 were most consistent in two or more salt stress treatments. 16 candidate genes associated with salt tolerance were predicted in wheat. These results could be useful to improve salt tolerance by marker-assisted selection (MAS) and shed new light on understanding the genetic basis of salt tolerance in wheat.
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Affiliation(s)
- Xin Guo
- grid.440622.60000 0000 9482 4676State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Group of Wheat Quality Breeding, Agronomy College, Shandong Agricultural University, Tai’an, Shandong People’s Republic of China ,Taiyuan Agro-Tech Extension and Service Center, 030000 Taiyuan, Shanxi People’s Republic of China
| | - Chongning Wu
- grid.440622.60000 0000 9482 4676State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Group of Wheat Quality Breeding, Agronomy College, Shandong Agricultural University, Tai’an, Shandong People’s Republic of China
| | - Dehua Wang
- grid.440622.60000 0000 9482 4676State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Group of Wheat Quality Breeding, Agronomy College, Shandong Agricultural University, Tai’an, Shandong People’s Republic of China
| | - Guanying Wang
- grid.440622.60000 0000 9482 4676State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Group of Wheat Quality Breeding, Agronomy College, Shandong Agricultural University, Tai’an, Shandong People’s Republic of China
| | - Kaituo Jin
- grid.440622.60000 0000 9482 4676State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Group of Wheat Quality Breeding, Agronomy College, Shandong Agricultural University, Tai’an, Shandong People’s Republic of China
| | - Yingjie Zhao
- grid.440622.60000 0000 9482 4676State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Group of Wheat Quality Breeding, Agronomy College, Shandong Agricultural University, Tai’an, Shandong People’s Republic of China
| | - Jichun Tian
- grid.440622.60000 0000 9482 4676State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Group of Wheat Quality Breeding, Agronomy College, Shandong Agricultural University, Tai’an, Shandong People’s Republic of China
| | - Zhiying Deng
- grid.440622.60000 0000 9482 4676State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Group of Wheat Quality Breeding, Agronomy College, Shandong Agricultural University, Tai’an, Shandong People’s Republic of China
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10
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Validation of a QTL on Chromosome 1DS Showing a Major Effect on Salt Tolerance in Winter Wheat. Int J Mol Sci 2022; 23:ijms232213745. [PMID: 36430224 PMCID: PMC9691212 DOI: 10.3390/ijms232213745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/28/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
Salt stress is one the most destructive abiotic stressors, causing yield losses in wheat worldwide. A prerequisite for improving salt tolerance is the identification of traits for screening genotypes and uncovering causative genes. Two populations of F3 lines developed from crosses between sensitive and tolerant parents were tested for salt tolerance at the seedling stage. Based on their response, the offspring were classified as salt sensitive and tolerant. Under saline conditions, tolerant genotypes showed lower Na+ and proline content but higher K+, higher chlorophyll content, higher K+/Na+ ratio, higher PSII activity levels, and higher photochemical efficiency, and were selected for further molecular analysis. Five stress responsive QTL identified in a previous study were validated in the populations. A QTL on the short arm of chromosome 1D showed large allelic effects in several salt tolerant related traits. An expression analysis of associated candidate genes showed that TraesCS1D02G052200 and TraesCS5B02G368800 had the highest expression in most tissues. Furthermore, qRT-PCR expression analysis revealed that ZIP-7 had higher differential expressions under saline conditions compared to KefC, AtABC8 and 6-SFT. This study provides information on the genetic and molecular basis of salt tolerance that could be useful in development of salt-tolerant wheat varieties.
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11
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Khan RWA, Khan RSA, Awan FS, Akrem A, Iftikhar A, Anwar FN, Alzahrani HAS, Alsamadany H, Iqbal RK. Genome-wide association studies of seedling quantitative trait loci against salt tolerance in wheat. Front Genet 2022; 13:946869. [PMID: 36159962 PMCID: PMC9492296 DOI: 10.3389/fgene.2022.946869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Salinity is one of the significant factors in decreasing wheat yield and quality. To counter this, it is necessary to develop salt-tolerant wheat varieties through conventional and advanced molecular techniques. The current study identified quantitative trait loci in response to salt stress among worldwide landraces and improved varieties of wheat at the seedling stage. A total of 125 landraces and wheat varieties were subjected to salt treatment (50, 100, and 150 mM) with control. Morphological seedling traits, i.e., shoot length, root length, and fresh and dry shoot and root weights for salinity tolerance were observed to assess salt tolerance and genetic analysis using SNP data through DArT-seq. The results showed that, at the seedling stage, 150 mM NaCl treatment decreased shoot length, root length, and fresh and dry weights of the shoot and root. The root length and dry root weight were the most affected traits at the seedling stage. Effective 4417 SNPs encompassing all the chromosomes of the wheat genome with marker density, i.e., 37%, fall in genome B, genome D (32%), and genome A (31%). Five loci were found on four chromosomes 6B, 6D, 7A, and 7D, showing strong associations with the root length, fresh shoot weight, fresh root weight, and dry root weight at the p < 0.03 significance level. The positive correlation was found among all morphological traits under study.
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Affiliation(s)
- Rao Waqar Ahmad Khan
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Rao Sohail Ahmad Khan
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Faisal Saeed Awan
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
- *Correspondence: Faisal Saeed Awan, , ; Rana Khalid Iqbal,
| | - Ahmed Akrem
- Botany Division, Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
| | - Arslan Iftikhar
- Department of Physiology, Faculty of Life Sciences, Government College University, Faisalabad, Pakistan
| | | | - Hind A. S. Alzahrani
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Hameed Alsamadany
- Department of Biological Sciences, Faculty of Science, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Rana Khalid Iqbal
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
- *Correspondence: Faisal Saeed Awan, , ; Rana Khalid Iqbal,
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12
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A Large-Scale Genomic Association Analysis Identifies the Candidate Genes Regulating Salt Tolerance in Cucumber ( Cucumis sativus L.) Seedlings. Int J Mol Sci 2022; 23:ijms23158260. [PMID: 35897836 PMCID: PMC9332819 DOI: 10.3390/ijms23158260] [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: 06/08/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 02/04/2023] Open
Abstract
Salt stress seriously restricts plant growth and development, affects yield and quality, and thus becomes an urgent problem to be solved in cucumber stress resistance breeding. Mining salt tolerance genes and exploring the molecular mechanism of salt tolerance could accelerate the breeding of cucumber germplasm with excellent salt stress tolerance. In this study, 220 cucumber core accessions were used for Genome-Wide Association Studies (GWAS) and the identification of salt tolerance genes. The salinity injury index that was collected in two years showed significant differences among the core germplasm. A total of seven loci that were associated with salt tolerance in cucumber seedlings were repeatedly detected, which were located on Chr.2 (gST2.1), Chr.3 (gST3.1 and gST3.2), Chr.4 (gST4.1 and gST4.2), Chr.5 (gST5.1), and Chr.6 (gST6.1). Within these loci, 62 genes were analyzed, and 5 candidate genes (CsaV3_2G035120, CsaV3_3G023710, CsaV3_4G033150, CsaV3_5G023530, and CsaV3_6G009810) were predicted via the functional annotation of Arabidopsis homologous genes, haplotype of extreme salt-tolerant accessions, and qRT-PCR. These results provide a guide for further research on salt tolerance genes and molecular mechanisms of cucumber seedlings.
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13
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Hussain B, Akpınar BA, Alaux M, Algharib AM, Sehgal D, Ali Z, Aradottir GI, Batley J, Bellec A, Bentley AR, Cagirici HB, Cattivelli L, Choulet F, Cockram J, Desiderio F, Devaux P, Dogramaci M, Dorado G, Dreisigacker S, Edwards D, El-Hassouni K, Eversole K, Fahima T, Figueroa M, Gálvez S, Gill KS, Govta L, Gul A, Hensel G, Hernandez P, Crespo-Herrera LA, Ibrahim A, Kilian B, Korzun V, Krugman T, Li Y, Liu S, Mahmoud AF, Morgounov A, Muslu T, Naseer F, Ordon F, Paux E, Perovic D, Reddy GVP, Reif JC, Reynolds M, Roychowdhury R, Rudd J, Sen TZ, Sukumaran S, Ozdemir BS, Tiwari VK, Ullah N, Unver T, Yazar S, Appels R, Budak H. Capturing Wheat Phenotypes at the Genome Level. FRONTIERS IN PLANT SCIENCE 2022; 13:851079. [PMID: 35860541 PMCID: PMC9289626 DOI: 10.3389/fpls.2022.851079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world's most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public-private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence.
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Affiliation(s)
- Babar Hussain
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | | | - Michael Alaux
- Université Paris-Saclay, INRAE, URGI, Versailles, France
| | - Ahmed M. Algharib
- Department of Environment and Bio-Agriculture, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Zulfiqar Ali
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan, Pakistan
| | - Gudbjorg I. Aradottir
- Department of Pathology, The National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Arnaud Bellec
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Alison R. Bentley
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Halise B. Cagirici
- Crop Improvement and Genetics Research, USDA, Agricultural Research Service, Albany, CA, United States
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Fred Choulet
- French National Research Institute for Agriculture, Food and the Environment, INRAE, GDEC, Clermont-Ferrand, France
| | - James Cockram
- The John Bingham Laboratory, The National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Francesca Desiderio
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Pierre Devaux
- Research & Innovation, Florimond Desprez Group, Cappelle-en-Pévèle, France
| | - Munevver Dogramaci
- USDA, Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Gabriel Dorado
- Department of Bioquímica y Biología Molecular, Campus Rabanales C6-1-E17, Campus de Excelencia Internacional Agroalimentario (ceiA3), Universidad de Córdoba, Córdoba, Spain
| | | | - David Edwards
- University of Western Australia, Perth, WA, Australia
| | - Khaoula El-Hassouni
- State Plant Breeding Institute, The University of Hohenheim, Stuttgart, Germany
| | - Kellye Eversole
- International Wheat Genome Sequencing Consortium (IWGSC), Bethesda, MD, United States
| | - Tzion Fahima
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, ACT, Australia
| | - Sergio Gálvez
- Department of Languages and Computer Science, ETSI Informática, Campus de Teatinos, Universidad de Málaga, Andalucía Tech, Málaga, Spain
| | - Kulvinder S. Gill
- Department of Crop Science, Washington State University, Pullman, WA, United States
| | - Liubov Govta
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Alvina Gul
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Goetz Hensel
- Center of Plant Genome Engineering, Heinrich-Heine-Universität, Düsseldorf, Germany
- Division of Molecular Biology, Centre of Region Haná for Biotechnological and Agriculture Research, Czech Advanced Technology and Research Institute, Palacký University, Olomouc, Czechia
| | - Pilar Hernandez
- Institute for Sustainable Agriculture (IAS-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Córdoba, Spain
| | | | - Amir Ibrahim
- Crop and Soil Science, Texas A&M University, College Station, TX, United States
| | | | | | - Tamar Krugman
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Yinghui Li
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Shuyu Liu
- Crop and Soil Science, Texas A&M University, College Station, TX, United States
| | - Amer F. Mahmoud
- Department of Plant Pathology, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Alexey Morgounov
- Food and Agriculture Organization of the United Nations, Riyadh, Saudi Arabia
| | - Tugdem Muslu
- Molecular Biology, Genetics and Bioengineering, Sabanci University, Istanbul, Turkey
| | - Faiza Naseer
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Etienne Paux
- French National Research Institute for Agriculture, Food and the Environment, INRAE, GDEC, Clermont-Ferrand, France
| | - Dragan Perovic
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Gadi V. P. Reddy
- USDA-Agricultural Research Service, Southern Insect Management Research Unit, Stoneville, MS, United States
| | - Jochen Christoph Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Matthew Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Rajib Roychowdhury
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Jackie Rudd
- Crop and Soil Science, Texas A&M University, College Station, TX, United States
| | - Taner Z. Sen
- Crop Improvement and Genetics Research, USDA, Agricultural Research Service, Albany, CA, United States
| | | | | | | | - Naimat Ullah
- Institute of Biological Sciences (IBS), Gomal University, D. I. Khan, Pakistan
| | - Turgay Unver
- Ficus Biotechnology, Ostim Teknopark, Ankara, Turkey
| | - Selami Yazar
- General Directorate of Research, Ministry of Agriculture, Ankara, Turkey
| | | | - Hikmet Budak
- Montana BioAgriculture, Inc., Missoula, MT, United States
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14
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Negisho K, Shibru S, Matros A, Pillen K, Ordon F, Wehner G. Association Mapping of Drought Tolerance Indices in Ethiopian Durum Wheat ( Triticum turgidum ssp. durum). FRONTIERS IN PLANT SCIENCE 2022; 13:838088. [PMID: 35693182 PMCID: PMC9178276 DOI: 10.3389/fpls.2022.838088] [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: 12/17/2021] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Ethiopia is a major producer of durum wheat in sub-Saharan Africa. However, its production is prone to drought stress as it is fully dependent on rain, which is erratic and unpredictable. This study aimed to detect marker-trait associations (MTAs) and quantitative trait loci (QTLs) related to indices. Six drought tolerance indices, i.e., drought susceptibility index (DSI), geometric mean productivity (GMP), relative drought index (RDI), stress tolerance index (STI), tolerance index (TOL), and yield stability index (YSI) were calculated from least-square means (lsmeans) of grain yield (GY) and traits significantly (p < 0.001) correlated with grain yield (GY) under field drought stress (FDS) and field non-stress (FNS) conditions. GY, days to grain filling (DGF), soil plant analysis development (SPAD) chlorophyll meter, seeds per spike (SPS), harvest index (HI), and thousand kernel weight (TKW) were used to calculate DSI, GMP, RDI, STI, TOL, and YSI drought indices. Accessions, DW084, DW082, DZ004, C037, and DW092 were selected as the top five drought-tolerant based on DSI, RDI, TOL, and YSI combined ranking. Similarly, C010, DW033, DW080, DW124-2, and C011 were selected as stable accessions based on GMP and STI combined ranking. A total of 184 MTAs were detected linked with drought indices at -log10p ≥ 4.0,79 of which were significant at a false discovery rate (FDR) of 5%. Based on the linkage disequilibrium (LD, r 2 ≥ 0.2), six of the MTAs with a positive effect on GY-GMP were detected on chromosomes 2B, 3B, 4A, 5B, and 6B, explaining 14.72, 10.07, 26.61, 21.16, 21.91, and 22.21% of the phenotypic variance, respectively. The 184 MTAs were clustered into 102 QTLs. Chromosomes 1A, 2B, and 7A are QTL hotspots with 11 QTLs each. These chromosomes play a key role in drought tolerance and respective QTL may be exploited by marker-assisted selection for improving drought stress tolerance in wheat.
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Affiliation(s)
- Kefyalew Negisho
- National Agricultural Biotechnology Research Center, Ethiopian Institute of Agricultural Research (EIAR), Holeta, Ethiopia
| | - Surafel Shibru
- Melkassa Research Center, Ethiopian Institute of Agricultural Research (EIAR), Melkassa, Ethiopia
| | - Andrea Matros
- Julius Kühn Institute (JKI), Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Martin Luther University, Halle, Germany
| | - Frank Ordon
- Julius Kühn Institute (JKI), Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Gwendolin Wehner
- Julius Kühn Institute (JKI), Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
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15
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Hasseb NM, Sallam A, Karam MA, Gao L, Wang RRC, Moursi YS. High-LD SNP markers exhibiting pleiotropic effects on salt tolerance at germination and seedlings stages in spring wheat. PLANT MOLECULAR BIOLOGY 2022; 108:585-603. [PMID: 35217965 PMCID: PMC8967789 DOI: 10.1007/s11103-022-01248-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 01/25/2022] [Indexed: 06/01/2023]
Abstract
Salt tolerance at germination and seedling growth stages was investigated. GWAS revealed nine genomic regions with pleiotropic effects on salt tolerance. Salt tolerant genotypes were identified for future breeding program. With 20% of the irrigated land worldwide affected by it, salinity is a serious threat to plant development and crop production. While wheat is the most stable food source worldwide, it has been classified as moderately tolerant to salinity. In several crop plants; such as barley, maize and rice, it has been shown that salinity tolerance at seed germination and seedling establishment is under polygenic control. As yield was the ultimate goal of breeders and geneticists, less attention has been paid to understanding the genetic architecture of salt tolerance at early stages. Thus, the genetic control of salt tolerance at these stages is poorly understood relative to the late stages. In the current study, 176 genotypes of spring wheat were tested for salinity tolerance at seed germination and seedling establishment. Genome-Wide Association Study (GWAS) has been used to identify the genomic regions/genes conferring salt tolerance at seed germination and seedling establishment. Salinity stress negatively impacted all germination and seedling development parameters. A set of 137 SNPs showed significant association with the traits of interest. Across the whole genome, 33 regions showed high linkage disequilibrium (LD). These high LD regions harbored 15 SNPs with pleiotropic effect (i.e. SNPs that control more than one trait). Nine genes belonging to different functional groups were found to be associated with the pleiotropic SNPs. Noteworthy, chromosome 2B harbored the gene TraesCS2B02G135900 that acts as a potassium transporter. Remarkably, one SNP marker, reported in an early study, associated with salt tolerance was validated in this study. Our findings represent potential targets of genetic manipulation to understand and improve salinity tolerance in wheat.
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Affiliation(s)
- Nouran M Hasseb
- Department of Botany, Faculty of Science, Fayoum University, Fayoum, 63514, Egypt
| | - Ahmed Sallam
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt.
| | - Mohamed A Karam
- Department of Botany, Faculty of Science, Fayoum University, Fayoum, 63514, Egypt
| | - Liangliang Gao
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State Univ, Manhattan, KS, 66502, USA
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Buxin Road 97, Dapeng-District, Shenzhen, 518120, Guangdong, China
| | - Richard R C Wang
- USDA-ARS Forage and Range Research Lab, Utah State University, Logan, UT, 84322-6300, USA
| | - Yasser S Moursi
- Department of Botany, Faculty of Science, Fayoum University, Fayoum, 63514, Egypt
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16
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Kumar P, Choudhary M, Halder T, Prakash NR, Singh V, V. VT, Sheoran S, T. RK, Longmei N, Rakshit S, Siddique KHM. Salinity stress tolerance and omics approaches: revisiting the progress and achievements in major cereal crops. Heredity (Edinb) 2022; 128:497-518. [DOI: 10.1038/s41437-022-00516-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 02/07/2023] Open
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17
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Sharma DL, Bhoite R, Reeves K, Forrest K, Smith R, Dowla MANNU. Genome-wide superior alleles, haplotypes and candidate genes associated with tolerance on sodic-dispersive soils in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1113-1128. [PMID: 34985536 PMCID: PMC8942925 DOI: 10.1007/s00122-021-04021-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
The pleiotropic SNPs/haplotypes, overlapping genes (metal ion binding, photosynthesis), and homozygous/biallelic SNPs and transcription factors (HTH myb-type and BHLH) hold great potential for improving wheat yield potential on sodic-dispersive soils. Sodic-dispersive soils have multiple subsoil constraints including poor soil structure, alkaline pH and subsoil toxic elemental ion concentration, affecting growth and development in wheat. Tolerance is required at all developmental stages to enhance wheat yield potential on such soils. An in-depth investigation of genome-wide associations was conducted using a field phenotypic data of 206 diverse Focused Identification of Germplasm Strategy (FIGS) wheat lines for two consecutive years from different sodic and non-sodic plots and the exome targeted genotyping by sequencing (tGBS) assay. A total of 39 quantitative trait SNPs (QTSs), including 18 haplotypes were identified on chromosome 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 5A, 5D, 6B, 7A, 7B, 7D for yield and yield-components tolerance. Among these, three QTSs had common associations for multiple traits, indicating pleiotropism and four QTSs had close associations for multiple traits, within 32.38 Mb. The overlapping metal ion binding (Mn, Ca, Zn and Al) and photosynthesis genes and transcription factors (PHD-, Dof-, HTH myb-, BHLH-, PDZ_6-domain) identified are known to be highly regulated during germination, maximum stem elongation, anthesis, and grain development stages. The homozygous/biallelic SNPs having allele frequency above 30% were identified for yield and crop establishment/plants m-2. These SNPs correspond to HTH myb-type and BHLH transcription factors, brassinosteroid signalling pathway, kinase activity, ATP and chitin binding activity. These resources are valuable in haplotype-based breeding and genome editing to improve yield potential on sodic-dispersive soils.
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Affiliation(s)
- Darshan Lal Sharma
- Department of Primary Industries and Regional Development, 3 Baron-Hay Ct, South Perth, WA, 6151, Australia.
- College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia.
| | - Roopali Bhoite
- Department of Primary Industries and Regional Development, 3 Baron-Hay Ct, South Perth, WA, 6151, Australia.
- College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia.
| | - Karyn Reeves
- Department of Primary Industries and Regional Development, 3 Baron-Hay Ct, South Perth, WA, 6151, Australia
| | - Kerrie Forrest
- Centre for AgriBioscience, Agriculture Victoria, Bundoora, AgriBioVIC, Australia
| | - Rosemary Smith
- Department of Primary Industries and Regional Development, 3 Baron-Hay Ct, South Perth, WA, 6151, Australia
| | - Mirza A N N U Dowla
- Department of Primary Industries and Regional Development, 3 Baron-Hay Ct, South Perth, WA, 6151, Australia
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18
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Quamruzzaman M, Manik SMN, Shabala S, Cao F, Zhou M. Genome-wide association study reveals a genomic region on 5AL for salinity tolerance in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:709-721. [PMID: 34797396 DOI: 10.1007/s00122-021-03996-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Soil salinity is a major threat to crop productivity and quality worldwide. In order to reduce the negative effects of salinity stress, it is important to understand the genetic basis of salinity tolerance. Identifying new salinity tolerance QTL or genes is crucial for breeders to pyramid different tolerance mechanisms to improve crop adaptability to salinity. Being one of the major cereal crops, wheat is known as a salt-sensitive glycophyte and subject to substantial yield losses when grown in the presence of salt. In this study, both pot and tank experiments were conducted to investigate the genotypic variation present in 328 wheat varieties in their salinity tolerance at the vegetative stage. A Genome-Wide Association Studies (GWAS) were carried out to identify QTL conferring salinity tolerance through a mixed linear model. Six, five and eight significant marker-trait associations (MTAs) were identified from pot experiments, tank experiments and average damage scores, respectively. These markers are located on the wheat chromosomes 1B, 2B, 2D, 3A, 4B, and 5A. These tolerance alleles were additive in their effects and, when combined, increased tolerance to salinity. Candidate genes identified in these QTL regions encoded a diverse class of proteins involved in salinity tolerance in plants. A Na+/H+ exchanger and a potassium transporter on chromosome 5A (IWB30519) will be of a potential value for improvement of salt tolerance of wheat cultivars using marker assisted selection programs. Some useful genotypes, which showed consistent tolerance in different trials, can also be effectively used in breeding programs.
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Affiliation(s)
- Md Quamruzzaman
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Australia
| | | | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Australia
- International Research Centre for Environmental Membrane Biology, Foshan University, Chancheng, China
| | - Fangbin Cao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Australia.
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, China.
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Saini DK, Chopra Y, Singh J, Sandhu KS, Kumar A, Bazzer S, Srivastava P. Comprehensive evaluation of mapping complex traits in wheat using genome-wide association studies. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:1. [PMID: 37309486 PMCID: PMC10248672 DOI: 10.1007/s11032-021-01272-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Genome-wide association studies (GWAS) are effectively applied to detect the marker trait associations (MTAs) using whole genome-wide variants for complex quantitative traits in different crop species. GWAS has been applied in wheat for different quality, biotic and abiotic stresses, and agronomic and yield-related traits. Predictions for marker-trait associations are controlled with the development of better statistical models taking population structure and familial relatedness into account. In this review, we have provided a detailed overview of the importance of association mapping, population design, high-throughput genotyping and phenotyping platforms, advancements in statistical models and multiple threshold comparisons, and recent GWA studies conducted in wheat. The information about MTAs utilized for gene characterization and adopted in breeding programs is also provided. In the literature that we surveyed, as many as 86,122 wheat lines have been studied under various GWA studies reporting 46,940 loci. However, further utilization of these is largely limited. The future breakthroughs in area of genomic selection, multi-omics-based approaches, machine, and deep learning models in wheat breeding after exploring the complex genetic structure with the GWAS are also discussed. This is a most comprehensive study of a large number of reports on wheat GWAS and gives a comparison and timeline of technological developments in this area. This will be useful to new researchers or groups who wish to invest in GWAS.
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Affiliation(s)
- Dinesh K. Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | - Yuvraj Chopra
- College of Agriculture, Punjab Agricultural University, Ludhiana, 141004 India
| | - Jagmohan Singh
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Karansher S. Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163 USA
| | - Anand Kumar
- Department of Genetics and Plant Breeding, Chandra Shekhar Azad University of Agriculture and Technology, Kanpur, 202002 India
| | - Sumandeep Bazzer
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
| | - Puja Srivastava
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
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Genome-wide association analysis of chickpea germplasms differing for salinity tolerance based on DArTseq markers. PLoS One 2021; 16:e0260709. [PMID: 34852014 PMCID: PMC8635330 DOI: 10.1371/journal.pone.0260709] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/15/2021] [Indexed: 11/19/2022] Open
Abstract
Soil salinity is significant abiotic stress that severely limits global crop production. Chickpea (Cicer arietinum L.) is an important grain legume that plays a substantial role in nutritional food security, especially in the developing world. This study used a chickpea population collected from the International Center for Agricultural Research in the Dry Area (ICARDA) genebank using the focused identification of germplasm strategy. The germplasm included 186 genotypes with broad Asian and African origins and genotyped with 1856 DArTseq markers. We conducted phenotyping for salinity in the field (Arish, Sinai, Egypt) and greenhouse hydroponic experiments at 100 mM NaCl concentration. Based on the performance in both hydroponic and field experiments, we identified seven genotypes from Azerbaijan and Pakistan (IGs: 70782, 70430, 70764, 117703, 6057, 8447, and 70249) as potential sources for high salinity tolerance. Multi-trait genome-wide association analysis (mtGWAS) detected one locus on chromosome Ca4 at 10618070 bp associated with salinity tolerance under hydroponic and field conditions. In addition, we located another locus specific to the hydroponic system on chromosome Ca2 at 30537619 bp. Gene annotation analysis revealed the location of rs5825813 within the Embryogenesis-associated protein (EMB8-like), while the location of rs5825939 is within the Ribosomal Protein Large P0 (RPLP0). Utilizing such markers in practical breeding programs can effectively improve the adaptability of current chickpea cultivars in saline soil. Moreover, researchers can use our markers to facilitate the incorporation of new genes into commercial cultivars.
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Siddiqui MN, Teferi TJ, Ambaw AM, Gabi MT, Koua P, Léon J, Ballvora A. New drought-adaptive loci underlying candidate genes on wheat chromosome 4B with improved photosynthesis and yield responses. PHYSIOLOGIA PLANTARUM 2021; 173:2166-2180. [PMID: 34549429 DOI: 10.1111/ppl.13566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
Flag leaf serves as an essential source of assimilates during grain filling, thereby contributing to grain yield up to 48%. Thus, high-throughput phenotyping of flag leaves is crucial to determine their physiological and genetic basis of yield formation and drought adaptation. Here, we utilized 200 wheat cultivars to identify drought-adaptive loci underlying candidate genes associated with flag leaf biomass and photosynthesis-related traits using a genome-wide association study (GWAS). GWAS revealed 21 significant marker-trait associations for key photosynthetic traits in response to drought stress. Analysis of linkage disequilibrium (LD) in these SNPs intervals discovered 103 significant SNPs that established distinct LD blocks containing a total of 382 candidate genes putatively involved in physiological processes, including photosynthesis and water responses. Further, in silico transcript analysis identified two candidate genes in locus AX-580365925 on chromosome 4B, those were found to be highly expressed under drought and associated with proton-transporting ATP synthase activity and stress response pathways. Accordingly, we identified significant allelic haplotype differences on this same locus. The tolerant haplotype (higher chlorophyll content under drought) representing major allele was more abundant and stably increased photosynthetic efficiency and yield under drought scenarios. Collectively, this study offers new adaptive loci and beneficial alleles to reshape the flag leaf physiological and associated photosynthetic components for better yield and sustainability to water-deficit stress.
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Affiliation(s)
- Md Nurealam Siddiqui
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Tesfaye J Teferi
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
| | - Abebaw M Ambaw
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
| | - Melesech T Gabi
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
| | - Patrice Koua
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
| | - Jens Léon
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
- Field Lab Campus Klein-Altendorf, University of Bonn, Rheinbach, Germany
| | - Agim Ballvora
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
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Pal N, Saini DK, Kumar S. Meta-QTLs, ortho-MQTLs and candidate genes for the traits contributing to salinity stress tolerance in common wheat ( Triticum aestivum L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2767-2786. [PMID: 35035135 PMCID: PMC8720133 DOI: 10.1007/s12298-021-01112-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 12/04/2021] [Accepted: 12/07/2021] [Indexed: 05/20/2023]
Abstract
A meta-analysis of QTLs associated with the traits contributing to salinity tolerance was undertaken in wheat to detect consensus and robust meta-QTLs (MQTLs) using 844 known QTLs retrieved from 26 earlier studies. A consensus map with a total length of 4621.56 cM including 7710 markers was constructed using 21 individual linkage maps and three previously published integrated genetic maps. Out of 844 QTLs, 571 QTLs were projected on the consensus map which gave origin to 100 MQTLs. Interestingly, 49 MQTLs were co-located with marker-trait associations reported in wheat genome-wide association studies for the traits contributing to salinity stress tolerance. Five potential MQTLs associated with the major salinity-responsive traits were also identified to be utilized in the breeding programme. In the resulted MQTLs, the average confidence interval (CI, 3.58 cM) was reduced up to 4.16 folds compared to the mean CI of the initial QTLs. Furthermore, as many as 617 gene models including 81 most likely candidate genes (CGs) were identified in the high confidence MQTL regions. These most likely CGs encoded proteins mainly belonging to the following families: B-box-type zinc finger, cytochrome P450 protein, pentatricopeptide repeat, phospholipid/glycerol acyltransferase, F-box protein, small auxin-up RNA, UDP-glucosyltransferase, glutathione S-transferase protein, etc. In addition, ortho-MQTL analysis based on synteny among wheat, rice and barley was also performed which permitted the identification of six ortho-MQTLs among these three cereals. This meta-analysis defines a genome-wide landscape on the most stable and consistent loci associated with reliable molecular markers and candidate genes for salinity tolerance in wheat. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01112-0.
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Affiliation(s)
- Neeraj Pal
- Department of Molecular Biology and Genetic Engineering, G. B. Pant, University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab 141004 India
| | - Sundip Kumar
- Department of Molecular Biology and Genetic Engineering, G. B. Pant, University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
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23
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Borjigin C, Schilling RK, Jewell N, Brien C, Sanchez-Ferrero JC, Eckermann PJ, Watson-Haigh NS, Berger B, Pearson AS, Roy SJ. Identifying the genetic control of salinity tolerance in the bread wheat landrace Mocho de Espiga Branca. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:1148-1160. [PMID: 34600599 DOI: 10.1071/fp21140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
Salinity tolerance in bread wheat is frequently reported to be associated with low leaf sodium (Na+) concentrations. However, the Portuguese landrace, Mocho de Espiga Branca, accumulates significantly higher leaf Na+ but has comparable salinity tolerance to commercial bread wheat cultivars. To determine the genetic loci associated with the salinity tolerance of this landrace, an F2 mapping population was developed by crossing Mocho de Espiga Branca with the Australian cultivar Gladius. The population was phenotyped for 19 salinity tolerance subtraits using both non-destructive and destructive techniques. Genotyping was performed using genotyping-by-sequencing (GBS). Genomic regions associated with salinity tolerance were detected on chromosomes 1A, 1D, 4B and 5A for the subtraits of relative and absolute growth rate (RGR, AGR respectively), and on chromosome 2A, 2B, 4D and 5D for Na+, potassium (K+) and chloride (Cl-) accumulation. Candidate genes that encode proteins associated with salinity tolerance were identified within the loci including Na+/H+ antiporters, K+ channels, H+-ATPase, calcineurin B-like proteins (CBLs), CBL-interacting protein kinases (CIPKs), calcium dependent protein kinases (CDPKs) and calcium-transporting ATPase. This study provides a new insight into the genetic control of salinity tolerance in a Na+ accumulating bread wheat to assist with the future development of salt tolerant cultivars.
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Affiliation(s)
- Chana Borjigin
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Rhiannon K Schilling
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia; and Department of Primary Industries and Regions, South Australian Research and Development Institute, Urrbrae, SA 5064, Australia
| | - Nathaniel Jewell
- School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia; and Australian Plant Phenomics Facility, The Plant Accelerator, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Chris Brien
- School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia; and Australian Plant Phenomics Facility, The Plant Accelerator, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Juan Carlos Sanchez-Ferrero
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Paul J Eckermann
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Nathan S Watson-Haigh
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia; and South Australian Genomics Centre, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Bettina Berger
- School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia; and Australian Plant Phenomics Facility, The Plant Accelerator, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Allison S Pearson
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia; and ARC Centre of Excellence in Plant Energy Biology, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Stuart J Roy
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia; and ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, The University of Adelaide, PMB1, Glen Osmond, SA 5064, Australia
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Luo Q, Hu P, Yang G, Li H, Liu L, Wang Z, Li B, Li Z, Zheng Q. Mapping QTL for seedling morphological and physiological traits under normal and salt treatments in a RIL wheat population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2991-3011. [PMID: 34095960 DOI: 10.1007/s00122-021-03872-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/25/2021] [Indexed: 06/12/2023]
Abstract
The genetic basis of 27 seedling traits under normal and salt treatments was fully analyzed in a RIL wheat population, and seven QTL intervals were validated in two other genetic populations. Soil salinity seriously constrains wheat (Triticum aestivum L.) production globally by influencing its growth and development. To explore the genetic basis of salt tolerance in wheat, a recombinant inbred line (RIL) population derived from a cross between high-yield wheat cultivar Zhongmai 175 (ZM175) and salt-tolerant cultivar Xiaoyan 60 (XY60) was used to map QTL for seedling traits under normal and salt treatments based on a high-density genetic linkage map. A total of 158 stable additive QTL for 27 morphological and physiological traits were identified and distributed on all wheat chromosomes except 3A and 4D. They explained 2.35-46.43% of the phenotypic variation with a LOD score range of 2.61-40.38. The alleles from XY60 increased corresponding traits for 100 QTL, while the alleles from ZM175 had positive effects for the other 58 QTL. Nearly half of the QTL (78/158) were mapped in nine QTL clusters on chromosomes 2A, 2B, 2D, 4B, 5A, 5B, 5D, and 7D (2), respectively. To prove the reliability and potentiality in molecular marker-assisted selection (MAS), seven QTL intervals were validated in two other genetic populations. Besides additive QTL, 94 pairs of loci were detected with significant epistatic effect and 20 QTL were found to interact with treatment. This study provides a full elucidation of the genetic basis of seedling traits (especially root system-related traits) associated with salt tolerance in wheat, and the developed kompetitive allele-specific PCR markers closely linked to stable QTL would supply strong supports to MAS in salt-tolerant wheat breeding.
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Affiliation(s)
- Qiaoling Luo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Pan Hu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guotang Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongwei Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Liqin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zishan Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bin Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhensheng Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qi Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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25
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Genome-wide association mapping reveals key genomic regions for physiological and yield-related traits under salinity stress in wheat (Triticum aestivum L.). Genomics 2021; 113:3198-3215. [PMID: 34293475 DOI: 10.1016/j.ygeno.2021.07.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 06/27/2021] [Accepted: 07/13/2021] [Indexed: 11/21/2022]
Abstract
A genome-wide association study (GWAS) was conducted using six different multi-locus GWAS models and 35K SNP array to demarcate genomic regions underlying reproductive stage salinity tolerance. Marker-trait association analysis was performed for salt tolerance indices (STI) of 11 morpho-physiological traits, and the actual concentrations of Na+ and K+, and the Na+/K+ ratio in flag leaf. A total of 293 significantly associated quantitative trait nucleotides (QTNs) for 14 morpho-physiological traits were identified. Of these 293 QTNs, 12 major QTNs with R2 ≥ 10.0% were detected in three or more GWAS models. Novel major QTNs were identified for plant height, number of effective tillers, biomass, grain yield, thousand grain weight, Na+ and K+ content, and the Na+/K+ ratio in flag leaf. Moreover, 48 candidate genes were identified from the associated genomic regions. The QTNs identified in this study could potentially be targeted for improving salinity tolerance in wheat.
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Quan X, Liu J, Zhang N, Xie C, Li H, Xia X, He W, Qin Y. Genome-Wide Association Study Uncover the Genetic Architecture of Salt Tolerance-Related Traits in Common Wheat ( Triticum aestivum L.). Front Genet 2021; 12:663941. [PMID: 34093656 PMCID: PMC8172982 DOI: 10.3389/fgene.2021.663941] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/24/2021] [Indexed: 01/13/2023] Open
Abstract
Soil salinity is a serious threat to wheat yield affecting sustainable agriculture. Although salt tolerance is important for plant establishment at seedling stage, its genetic architecture remains unclear. In the present study, we have evaluated eight salt tolerance-related traits at seedling stage and identified the loci for salt tolerance by genome-wide association study (GWAS). This GWAS panel comprised 317 accessions and was genotyped with the wheat 90 K single-nucleotide polymorphism (SNP) chip. In total, 37 SNPs located at 16 unique loci were identified, and each explained 6.3 to 18.6% of the phenotypic variations. Among these, six loci were overlapped with previously reported genes or quantitative trait loci, whereas the other 10 were novel. Besides, nine loci were detected for two or more traits, indicating that the salt-tolerance genetic architecture is complex. Furthermore, five candidate genes were identified for salt tolerance-related traits, including kinase family protein, E3 ubiquitin-protein ligase-like protein, and transmembrane protein. SNPs identified in this study and the accessions with more favorable alleles could further enhance salt tolerance in wheat breeding. Our results are useful for uncovering the genetic mechanism of salt tolerance in wheat at seeding stage.
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Affiliation(s)
- Xiaoyan Quan
- Department of Biological Science, School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Jindong Liu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ning Zhang
- Department of Biological Science, School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Chunjuan Xie
- Department of Biological Science, School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Hongmei Li
- Department of Biological Science, School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenxing He
- Department of Biological Science, School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Yuxiang Qin
- Department of Biological Science, School of Biological Science and Technology, University of Jinan, Jinan, China
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27
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Tao R, Ding J, Li C, Zhu X, Guo W, Zhu M. Evaluating and Screening of Agro-Physiological Indices for Salinity Stress Tolerance in Wheat at the Seedling Stage. FRONTIERS IN PLANT SCIENCE 2021; 12:646175. [PMID: 33868346 PMCID: PMC8044411 DOI: 10.3389/fpls.2021.646175] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 03/09/2021] [Indexed: 05/26/2023]
Abstract
Soil salinity is a worldwide issue that affects wheat production. A comprehensive understanding of salt-tolerance mechanisms and the selection of reliable screening indices are crucial for breeding salt-tolerant wheat cultivars. In this study, 30 wheat genotypes (obtained from a rapid selection of 96 original varieties) were chosen to investigate the existing screening methods and clarify the salinity tolerance mechanisms in wheat. Ten-day-old seedlings were treated with 150 mM NaCl. Eighteen agronomic and physiological parameters were measured. The results indicated that the effects of salinity on the agronomic and physiological traits were significant. Salinity stress significantly decreased K+ content and K+/Na+ ratio in the whole plant, while the leaf K+/Na+ ratio was the strongest determinant of salinity tolerance and had a significantly positive correlation with salt tolerance. In contrast, salinity stress significantly increased Na+ concentration and relative gene expression (TaHKT1;5, TaSOS1, and TaAKT1-like). The Na+ transporter gene (TaHKT1;5) showed a significantly greater increase in expression than the K+ transporter gene (TaAKT1-like). We concluded that Na+ exclusion rather than K+ retention contributed to an optimal leaf K+/Na+ ratio. Furthermore, the present exploration revealed that, under salt stress, tolerant accessions had higher shoot water content, shoot dry weight and lower stomatal density, leaf sap osmolality, and a significantly negative correlation was observed between salt tolerance and stomatal density. This indicated that changes in stomata density may represent a fundamental mechanism by which a plant may optimize water productivity and maintain growth under saline conditions. Taken together, the leaf K+/Na+ ratio and stomatal density can be used as reliable screening indices for salt tolerance in wheat at the seedling stage.
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Affiliation(s)
- Rongrong Tao
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, China
| | - Jinfeng Ding
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, China
- Co-Innovation Centre for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Chunyan Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, China
- Co-Innovation Centre for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Xinkai Zhu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, China
- Co-Innovation Centre for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Wenshan Guo
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, China
- Co-Innovation Centre for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Min Zhu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, China
- Co-Innovation Centre for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
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Li L, Peng Z, Mao X, Wang J, Li C, Chang X, Jing R. Genetic insights into natural variation underlying salt tolerance in wheat. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1135-1150. [PMID: 33130904 DOI: 10.1093/jxb/eraa500] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 10/26/2020] [Indexed: 05/06/2023]
Abstract
Developing salt-tolerant crop varieties is one of the important approaches to cope with increasing soil salinization worldwide. In this study, a diversity panel of 323 wheat accessions and 150 doubled haploid lines were phenotyped for salt-responsive morphological and physiological traits across two growth stages. The comprehensive salt tolerance of each wheat accession was evaluated based on principal component analysis. A total of 269 associated loci for salt-responsive traits and/or salt tolerance indices were identified by genome-wide association studies using 395 675 single nucleotide polymorphisms, among which 22 overlapping loci were simultaneously identified by biparental quantitative trait loci mapping. Two novel candidate genes ROOT NUMBER 1 (TaRN1) and ROOT NUMBER 2 (TaRN2) involved in root responses to salt stress fell within overlapping loci, showing different expression patterns and a frameshift mutation (in TaRN2) in contrasting salt-tolerant wheat genotypes. Moreover, the decline in salt tolerance of Chinese wheat varieties was observed from genetic and phenotypic data. We demonstrate that a haplotype controlling root responses to salt stress has been diminished by strong selection for grain yield, which highlights that linkage drag constrains the salt tolerance of Chinese wheat. This study will facilitate salt-tolerant wheat breeding in terms of elite germplasm, favorable alleles and selection strategies.
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Affiliation(s)
- Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhi Peng
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Chang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Genome-wide association study in hexaploid wheat identifies novel genomic regions associated with resistance to root lesion nematode (Pratylenchus thornei). Sci Rep 2021; 11:3572. [PMID: 33574377 PMCID: PMC7878755 DOI: 10.1038/s41598-021-80996-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/30/2020] [Indexed: 01/30/2023] Open
Abstract
Root lesion nematode (RLN; Pratylenchus thornei) causes extensive yield losses in wheat worldwide and thus pose serious threat to global food security. Reliance on fumigants (such as methyl bromide) and nematicides for crop protection has been discouraged due to environmental concerns. Hence, alternative environment friendly control measures like finding and deployment of resistance genes against Pratylenchus thornei are of significant importance. In the present study, genome-wide association study (GWAS) was performed using single-locus and multi-locus methods. In total, 143 wheat genotypes collected from pan-Indian wheat cultivation states were used for nematode screening. Genotypic data consisted of > 7K SNPs with known genetic positions on the high-density consensus map was used for association analysis. Principal component analysis indicated the existence of sub-populations with no major structuring of populations due to the origin. Altogether, 25 significant marker trait associations were detected with - log10 (p value) > 4.0. Three large linkage disequilibrium blocks and the corresponding haplotypes were found to be associated with significant SNPs. In total, 37 candidate genes with nine genes having a putative role in disease resistance (F-box-like domain superfamily, Leucine-rich repeat, cysteine-containing subtype, Cytochrome P450 superfamily, Zinc finger C2H2-type, RING/FYVE/PHD-type, etc.) were identified. Genomic selection was conducted to investigate how well one could predict the phenotype of the nematode count without performing the screening experiments. Prediction value of r = 0.40 to 0.44 was observed when 56 to 70% of the population was used as a training set. This is the first report where GWAS has been conducted to find resistance against root lesion nematode (P. thornei) in Indian wheat germplasm.
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Hu P, Zheng Q, Luo Q, Teng W, Li H, Li B, Li Z. Genome-wide association study of yield and related traits in common wheat under salt-stress conditions. BMC PLANT BIOLOGY 2021; 21:27. [PMID: 33413113 PMCID: PMC7792188 DOI: 10.1186/s12870-020-02799-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 12/16/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND Soil salinization is a major threat to wheat production. It is essential to understand the genetic basis of salt tolerance for breeding and selecting new salt-tolerant cultivars that have the potential to increase wheat yield. RESULT In this study, a panel of 191 wheat accessions was subjected to genome wide association study (GWAS) to identify SNP markers linked with adult-stage characters. The population was genotyped by Wheat660K SNP array and eight phenotype traits were investigated under low and high salinity environments for three consecutive years. A total of 389 SNPs representing 11 QTLs were significantly associated with plant height, spike number, spike length, grain number, thousand kernels weight, yield and biological mass under different salt treatments, with the phenotypic explanation rate (R2) ranging from 9.14 to 50.45%. Of these, repetitive and pleiotropic loci on chromosomes 4A, 5A, 5B and 7A were significantly linked to yield and yield related traits such as thousand kernels weight, spike number, spike length, grain number and so on under low salinity conditions. Spike length-related loci were mainly located on chromosomes 1B, 3B, 5B and 7A under different salt treatments. Two loci on chromosome 4D and 5A were related with plant height in low and high salinity environment, respectively. Three salt-tolerant related loci were confirmed to be important in two bi-parental populations. Distribution of favorable haplotypes indicated that superior haplotypes of pleiotropic loci on group-5 chromosomes were strongly selected and had potential for increasing wheat salt tolerance. A total of 14 KASP markers were developed for nine loci associating with yield and related traits to improve the selection efficiency of wheat salt-tolerance breeding. CONCLUSION Utilizing a Wheat660K SNPs chip, QTLs for yield and its related traits were detected under salt treatment in a natural wheat population. Important salt-tolerant related loci were validated in RIL and DH populations. This study provided reliable molecular markers that could be crucial for marker-assisted selection in wheat salt tolerance breeding programs.
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Affiliation(s)
- Pan Hu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qi Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Qiaoling Luo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wan Teng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hongwei Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bin Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhensheng Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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Luo Q, Zheng Q, Hu P, Liu L, Yang G, Li H, Li B, Li Z. Mapping QTL for agronomic traits under two levels of salt stress in a new constructed RIL wheat population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:171-189. [PMID: 32995899 DOI: 10.1007/s00122-020-03689-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 09/16/2020] [Indexed: 06/11/2023]
Abstract
QTL for 15 agronomic traits under two levels of salt stress in dry salinity field were mapped in a new constructed RIL population utilizing a Wheat55K SNP array. Furthermore, eight QTL were validated in a collected natural population. Soil salinity is one of the major abiotic stresses causing serious impact on crop growth, development and yield. As one of the three most important crops in the world, bread wheat (Triticum aestivum L.) is severely affected by salinity, too. In this study, an F7 recombinant inbred line (RIL) population derived from a cross between high-yield wheat cultivar Zhongmai 175 and salt-tolerant cultivar Xiaoyan 60 was constructed. The adult stage performances of the RIL population and their parent lines under low and high levels of salt stress were evaluated for three consecutive growing seasons. Utilizing a Wheat55K SNP array, a high-density genetic linkage map spinning 3250.71 cM was constructed. QTL mapping showed that 90 stable QTL for 15 traits were detected, and they were distributed on all wheat chromosomes except 4D, 6B and 7D. These QTL individually explained 2.34-32.43% of the phenotypic variation with LOD values ranging from 2.68 to 47.15. It was found that four QTL clusters were located on chromosomes 2D, 3D, 4B and 6A, respectively. Notably, eight QTL from the QTL clusters were validated in a collected natural population. Among them, QPh-4B was deduced to be an allele of Rht-B1. In addition, three kompetitive allele-specific PCR (KASP) markers derived from SNPs were successfully designed for three QTL clusters. This study provides an important base for salt-tolerant QTL (gene) cloning in wheat, and the markers, especially the KASP markers, will be useful for marker-assisted selection in salt-tolerant wheat breeding.
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Affiliation(s)
- Qiaoling Luo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qi Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Pan Hu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Liqin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guotang Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongwei Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bin Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhensheng Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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Asif MA, Garcia M, Tilbrook J, Brien C, Dowling K, Berger B, Schilling RK, Short L, Trittermann C, Gilliham M, Fleury D, Roy SJ, Pearson AS. Identification of salt tolerance QTL in a wheat RIL mapping population using destructive and non-destructive phenotyping. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:131-140. [PMID: 32835651 DOI: 10.1071/fp20167] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Bread wheat (Triticum aestivum L.) is one of the most important food crops, however it is only moderately tolerant to salinity stress. To improve wheat yield under saline conditions, breeding for improved salinity tolerance of wheat is needed. We have identified nine quantitative trail loci (QTL) for different salt tolerance sub-traits in a recombinant inbred line (RIL) population, derived from the bi-parental cross of Excalibur × Kukri. This population was screened for salinity tolerance subtraits using a combination of both destructive and non-destructive phenotyping. Genotyping by sequencing (GBS) was used to construct a high-density genetic linkage map, consisting of 3236 markers, and utilised for mapping QTL. Of the nine mapped QTL, six were detected under salt stress, including QTL for maintenance of shoot growth under salinity (QG(1-5).asl-5A, QG(1-5).asl-7B) sodium accumulation (QNa.asl-2A), chloride accumulation (QCl.asl-2A, QCl.asl-3A) and potassium:sodium ratio (QK:Na.asl-2DS2). Potential candidate genes within these QTL intervals were shortlisted using bioinformatics tools. These findings are expected to facilitate the breeding of new salt tolerant wheat cultivars.
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Affiliation(s)
- Muhammad A Asif
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and School of Agriculture, Food and Wine & Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Melissa Garcia
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and School of Agriculture, Food and Wine & Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia; and ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, The University of Adelaide, PMB1, Glen Osmond, SA 5064, Australia
| | - Joanne Tilbrook
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and School of Agriculture, Food and Wine & Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Chris Brien
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and Australian Plant Phenomics Facility, The Plant Accelerator, The University of Adelaide, SA 5064, Australia; and School of Information Technology and Mathematical Sciences, The University of South Australia, GPO Box 2471, Adelaide, SA 5001, Australia
| | - Kate Dowling
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and Australian Plant Phenomics Facility, The Plant Accelerator, The University of Adelaide, SA 5064, Australia
| | - Bettina Berger
- School of Agriculture, Food and Wine & Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia; and Australian Plant Phenomics Facility, The Plant Accelerator, The University of Adelaide, SA 5064, Australia
| | - Rhiannon K Schilling
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and School of Agriculture, Food and Wine & Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Laura Short
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and School of Agriculture, Food and Wine & Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Christine Trittermann
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and School of Agriculture, Food and Wine & Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Matthew Gilliham
- School of Agriculture, Food and Wine & Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia; and ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Delphine Fleury
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and School of Agriculture, Food and Wine & Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia; and ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, The University of Adelaide, PMB1, Glen Osmond, SA 5064, Australia; and Innolea, 6 chemin de Panedautes, 31700, Mondonville, France
| | - Stuart J Roy
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and School of Agriculture, Food and Wine & Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia; and ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, The University of Adelaide, PMB1, Glen Osmond, SA 5064, Australia; and Corresponding author.
| | - Allison S Pearson
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and School of Agriculture, Food and Wine & Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia; and ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
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Wang X, Guan P, Xin M, Wang Y, Chen X, Zhao A, Liu M, Li H, Zhang M, Lu L, Zhang J, Ni Z, Yao Y, Hu Z, Peng H, Sun Q. Genome-wide association study identifies QTL for thousand grain weight in winter wheat under normal- and late-sown stressed environments. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:143-157. [PMID: 33030571 DOI: 10.1007/s00122-020-03687-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 09/16/2020] [Indexed: 05/27/2023]
Abstract
GWAS identified stable loci for TGW and stress tolerance in winter wheat based on two sowing conditions, which will provide opportunities for developing new cultivars with high yield and yield stability. Wheat is an important food crop widely cultivated in the world. Breeding new varieties with high yields and superior adaptability is the main goal of modern wheat breeding program. In order to determine the marker-trait associations (MATs), a set of 688 diverse winter wheat accessions were subjected to genome-wide association study (GWAS) using the wheat 90K array. Field trials under normal-sown (NS) and late-sown (LS) conditions were conducted for thousand grain weight (TGW) and stress susceptibility index (SSI) at three different sites across two consecutive years. A total of 179 (NS) and 158 (LS) MATs corresponded with TGW; of these, 16 and 6 stable MATs for TGWNS and TGWLS were identified on chromosomes 1B, 2B, 3A, 3B, 5A, 5B, 5D, 6B, and 7D across at least three environments. Notably, a QTL hot spot controlling TGW under NS and LS conditions was found on chromosome 5A (140-142 cM). Moreover, 8 of 228 stable MATs on chromosomes 4B, 5A, and 5D for SSI were detected. A haplotype block associated with TGW and SSI was located on chromosome 5A at 91 cM, nearby the vernalization gene VRN-A1. Additionally, analysis of wheat varieties from the different eras revealed that the grain weight and stress tolerance are not improved concurrently. Overall, our results provide promising alleles controlling grain weight and stress tolerance (particularly for thermotolerance) for wheat breeders, which can be used in marker-assisted selection for improving grain yield and yield stability in wheat.
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Affiliation(s)
- Xiaobo Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Panfeng Guan
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yongfa Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xiyong Chen
- Hebei Crop Genetic Breeding Laboratory, Institute of Cereal and Oil Crops of Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Aiju Zhao
- Hebei Crop Genetic Breeding Laboratory, Institute of Cereal and Oil Crops of Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Manshuang Liu
- Agronomy College, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hongxia Li
- Agronomy College, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Mingyi Zhang
- Institute of Wheat, Shanxi Academy of Agricultural Sciences, Linfen, 041000, China
| | - Lahu Lu
- Institute of Wheat, Shanxi Academy of Agricultural Sciences, Linfen, 041000, China
| | - Jinbo Zhang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
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Plewiński P, Ćwiek-Kupczyńska H, Rudy E, Bielski W, Rychel-Bielska S, Stawiński S, Barzyk P, Krajewski P, Naganowska B, Wolko B, Książkiewicz M. Innovative transcriptome-based genotyping highlights environmentally responsive genes for phenology, growth and yield in a non-model grain legume. PLANT, CELL & ENVIRONMENT 2020; 43:2680-2698. [PMID: 32885839 DOI: 10.1111/pce.13880] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/21/2020] [Accepted: 08/22/2020] [Indexed: 06/11/2023]
Abstract
The narrow-leafed lupin, Lupinus angustifolius L., is a grain legume crop, cultivated both as a green manure and as a source of protein for animal feed and human food production. During its domestication process, numerous agronomic traits were improved, however, only two trait-related genes were identified hitherto, both by linkage mapping. Genome-wide association studies (GWAS), exploiting genomic sequencing, did not select any novel candidate gene. In the present study, an innovative method of 3'-end reduced representation transcriptomic profiling, a massive analysis of cDNA ends, has been used for genotyping of 126 L. angustifolius lines surveyed by field phenotyping. Significant genotype × environment interactions were identified for all phenology and yield traits analysed. Principal component analysis of population structure evidenced European domestication bottlenecks, visualized by clustering of breeding materials and cultivars. GWAS provided contribution towards deciphering vernalization pathway in legumes, and, apart from highlighting known domestication loci (Ku/Julius and mol), designated novel candidate genes for L. angustifolius traits. Early phenology was associated with genes from vernalization, cold-responsiveness and phosphatidylinositol signalling pathways whereas high yield with genes controlling photosynthesis performance and abiotic stress (drought or heat) tolerance. PCR-based toolbox was developed and validated to enable tracking desired alleles in marker-assisted selection. Narrow-leafed lupin was genotyped with an innovative method of transcriptome profiling and phenotyped for phenology, growth and yield traits in field. Early phenology was found associated with genes from cold-response, vernalization and phosphatidylinositol signalling pathways, whereas high yield with genes running photosystem II and drought or heat stress response. Key loci were supplied with PCR-based toolbox for marker-assisted selection.
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Affiliation(s)
- Piotr Plewiński
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Hanna Ćwiek-Kupczyńska
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Elżbieta Rudy
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Wojciech Bielski
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Sandra Rychel-Bielska
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Stanisław Stawiński
- Department in Przebędowo, Plant Breeding Smolice Ltd., Murowana Goślina, Poland
| | - Paweł Barzyk
- Department in Wiatrowo, Poznań Plant Breeding Ltd., Wiatrowo, Poland
| | - Paweł Krajewski
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Barbara Naganowska
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Bogdan Wolko
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Michał Książkiewicz
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
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Duarte-Delgado D, Dadshani S, Schoof H, Oyiga BC, Schneider M, Mathew B, Léon J, Ballvora A. Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes. BMC PLANT BIOLOGY 2020; 20:428. [PMID: 32938380 PMCID: PMC7493341 DOI: 10.1186/s12870-020-02616-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/19/2020] [Indexed: 05/17/2023]
Abstract
BACKGROUND Bread wheat is one of the most important crops for the human diet, but the increasing soil salinization is causing yield reductions worldwide. Improving salt stress tolerance in wheat requires the elucidation of the mechanistic basis of plant response to this abiotic stress factor. Although several studies have been performed to analyze wheat adaptation to salt stress, there are still some gaps to fully understand the molecular mechanisms from initial signal perception to the onset of responsive tolerance pathways. The main objective of this study is to exploit the dynamic salt stress transcriptome in underlying QTL regions to uncover candidate genes controlling salt stress tolerance in bread wheat. The massive analysis of 3'-ends sequencing protocol was used to analyze leave samples at osmotic and ionic phases. Afterward, stress-responsive genes overlapping QTL for salt stress-related traits in two mapping populations were identified. RESULTS Among the over-represented salt-responsive gene categories, the early up-regulation of calcium-binding and cell wall synthesis genes found in the tolerant genotype are presumably strategies to cope with the salt-related osmotic stress. On the other hand, the down-regulation of photosynthesis-related and calcium-binding genes, and the increased oxidative stress response in the susceptible genotype are linked with the greater photosynthesis inhibition at the osmotic phase. The specific up-regulation of some ABC transporters and Na+/Ca2+ exchangers in the tolerant genotype at the ionic stage indicates their involvement in mechanisms of sodium exclusion and homeostasis. Moreover, genes related to protein synthesis and breakdown were identified at both stress phases. Based on the linkage disequilibrium blocks, salt-responsive genes within QTL intervals were identified as potential components operating in pathways leading to salt stress tolerance. Furthermore, this study conferred evidence of novel regions with transcription in bread wheat. CONCLUSION The dynamic transcriptome analysis allowed the comparison of osmotic and ionic phases of the salt stress response and gave insights into key molecular mechanisms involved in the salt stress adaptation of contrasting bread wheat genotypes. The leveraging of the highly contiguous chromosome-level reference genome sequence assembly facilitated the QTL dissection by targeting novel candidate genes for salt tolerance.
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Affiliation(s)
| | - Said Dadshani
- INRES-Plant Breeding, University of Bonn, Bonn, Germany
| | - Heiko Schoof
- INRES-Crop Bioinformatics, University of Bonn, Bonn, Germany
| | | | | | - Boby Mathew
- INRES-Plant Breeding, University of Bonn, Bonn, Germany
| | - Jens Léon
- INRES-Plant Breeding, University of Bonn, Bonn, Germany
| | - Agim Ballvora
- INRES-Plant Breeding, University of Bonn, Bonn, Germany.
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Chaurasia S, Singh AK, Songachan LS, Sharma AD, Bhardwaj R, Singh K. Multi-locus genome-wide association studies reveal novel genomic regions associated with vegetative stage salt tolerance in bread wheat (Triticum aestivum L.). Genomics 2020; 112:4608-4621. [PMID: 32771624 DOI: 10.1016/j.ygeno.2020.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/27/2020] [Accepted: 08/04/2020] [Indexed: 10/23/2022]
Abstract
Soil salinity is one of the typical abiotic stresses affecting sustainability of wheat production worldwide. In the present study, we performed a 35 K SNP genotyping assay on association panel of 135 diverse wheat genotypes evaluated for vegetative stage tolerance in hydroponics. Association analyses using five multi-locus GWAS models revealed 42 reliable QTNs for 10 salt tolerance associated traits. Among these 42 reliable QTNs, 9, 17 and 16 QTNs were associated with physiological, biomass and shoot ionic traits respectively. Novel major QTNs were identified for chlorophyll content, shoot fresh weight, seedling total biomass, Na+ and K+ concentration and Na+/K+ ratio in shoots. Further, 10 major QTNs showed significant effect on the corresponding salt tolerance traits. Gene ontology analysis of the associated genomic regions identified 58 candidate genes. The information generated in this study will be of potential value for improvement of salt tolerance of wheat cultivars using marker assisted selection.
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Affiliation(s)
- Shiksha Chaurasia
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India; Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Amit Kumar Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India.
| | - L S Songachan
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Axma Dutt Sharma
- Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
| | - Rakesh Bhardwaj
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
| | - Kuldeep Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
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37
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Li B. Identification of Genes Conferring Plant Salt Tolerance using GWAS: Current Success and Perspectives. PLANT & CELL PHYSIOLOGY 2020; 61:1419-1426. [PMID: 32484868 DOI: 10.1093/pcp/pcaa073] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 05/25/2020] [Indexed: 06/11/2023]
Abstract
An understanding of the molecular mechanisms that underlie plant salt tolerance is important for both economic and scientific interests. Genome-wide association study (GWAS) is a promising approach to pinpoint genes that confer plant salt tolerance. With the advancement of supporting technology and methodology, GWAS has enabled the discovery of genes that play central roles in regulating plant salt tolerance in the past decade. Here, I highlight recent successful GWAS work in unveiling the molecular factors underlying plant salt tolerance and discuss the concerns and opportunities in conducting such experiments. It is anticipated that GWAS will be increasingly successful in the identification of key genes that are useful for crop improvement.
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Affiliation(s)
- Bo Li
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou 730000, China
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38
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Gupta PK, Balyan HS, Sharma S, Kumar R. Genetics of yield, abiotic stress tolerance and biofortification in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1569-1602. [PMID: 32253477 DOI: 10.1007/s00122-020-03583-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/13/2020] [Indexed: 05/18/2023]
Abstract
A review of the available literature on genetics of yield and its component traits, tolerance to abiotic stresses and biofortification should prove useful for future research in wheat in the genomics era. The work reviewed in this article mainly covers the available information on genetics of some important quantitative traits including yield and its components, tolerance to abiotic stresses (heat, drought, salinity and pre-harvest sprouting = PHS) and biofortification (Fe/Zn and phytate contents with HarvestPlus Program) in wheat. Major emphasis is laid on the recent literature on QTL interval mapping and genome-wide association studies, giving lists of known QTL and marker-trait associations. Candidate genes for different traits and the cloned and characterized genes for yield traits along with the molecular mechanism are also described. For each trait, an account of the present status of marker-assisted selection has also been included. The details of available results have largely been presented in the form of tables; some of these tables are included as supplementary files.
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Affiliation(s)
- Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India.
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
| | - Rahul Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
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39
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Oyiga BC, Palczak J, Wojciechowski T, Lynch JP, Naz AA, Léon J, Ballvora A. Genetic components of root architecture and anatomy adjustments to water-deficit stress in spring barley. PLANT, CELL & ENVIRONMENT 2020; 43:692-711. [PMID: 31734943 DOI: 10.1111/pce.13683] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/06/2019] [Accepted: 11/13/2019] [Indexed: 05/26/2023]
Abstract
Roots perform vital roles for adaptation and productivity under water-deficit stress, even though their specific functions are poorly understood. In this study, the genetic control of the nodal-root architectural and anatomical response to water deficit were investigated among diverse spring barley accessions. Water deficit induced substantial variations in the nodal root traits. The cortical, stele, and total root cross-sectional areas of the main-shoot nodal roots decreased under water deficit, but increased in the tiller nodal roots. Root xylem density and arrested nodal roots increased under water deficit, with the formation of root suberization/lignification and large cortical aerenchyma. Genome-wide association study implicated 11 QTL intervals in the architectural and anatomical nodal root response to water deficit. Among them, three and four QTL intervals had strong effects across seasons and on both root architectural and anatomical traits, respectively. Genome-wide epistasis analysis revealed 44 epistatically interacting SNP loci. Further analyses showed that these QTL intervals contain important candidate genes, including ZIFL2, MATE, and PPIB, whose functions are shown to be related to the root adaptive response to water deprivation in plants. These results give novel insight into the genetic architectures of barley nodal root response to soil water deficit stress in the fields, and thus offer useful resources for root-targeted marker-assisted selection.
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Affiliation(s)
| | | | - Tobias Wojciechowski
- Forschungszentrum Jülich, Institute for Bio- and Geosciences (Plant Sciences), Bonn, Germany
| | - Jonathan P Lynch
- Department of Plant Science, The Pennsylvania State, State College, Pennsylvania
| | - Ali A Naz
- INRES-Plant Breeding, University of Bonn, Bonn, Germany
| | - Jens Léon
- INRES-Plant Breeding, University of Bonn, Bonn, Germany
| | - Agim Ballvora
- INRES-Plant Breeding, University of Bonn, Bonn, Germany
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40
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Plewiński P, Książkiewicz M, Rychel-Bielska S, Rudy E, Wolko B. Candidate Domestication-Related Genes Revealed by Expression Quantitative Trait Loci Mapping of Narrow-Leafed Lupin ( Lupinus angustifolius L.). Int J Mol Sci 2019; 20:ijms20225670. [PMID: 31726789 PMCID: PMC6888189 DOI: 10.3390/ijms20225670] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/08/2019] [Accepted: 11/09/2019] [Indexed: 12/12/2022] Open
Abstract
The last century has witnessed rapid domestication of the narrow-leafed lupin (Lupinus angustifolius L.) as a grain legume crop, exploiting discovered alleles conferring low-alkaloid content (iucundus), vernalization independence (Ku and Julius), and reduced pod shattering (lentus and tardus). In this study, a L. angustifolius mapping population was subjected to massive analysis of cDNA ends (MACE). The MACE yielded 4185 single nucleotide polymorphism (SNP) markers for linkage map improvement and 30,595 transcriptomic profiles for expression quantitative trait loci (eQTL) mapping. The eQTL highlighted a high number of cis- and trans-regulated alkaloid biosynthesis genes with gene expression orchestrated by a regulatory agent localized at iucundus locus, supporting the concept that ETHYLENE RESPONSIVE TRANSCRIPTION FACTOR RAP2-7 may control low-alkaloid phenotype. The analysis of Ku shed light on the vernalization response via FLOWERING LOCUS T and FD regulon in L. angustifolius, providing transcriptomic evidence for the contribution of several genes acting in C-repeat binding factor (CBF) cold responsiveness and in UDP-glycosyltransferases pathways. Research on lentus selected a DUF1218 domain protein as a candidate gene controlling the orientation of the sclerified endocarp and a homolog of DETOXIFICATION14 for purplish hue of young pods. An ABCG transporter was identified as a hypothetical contributor to sclerenchyma fortification underlying tardus phenotype.
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41
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Lin Y, Yi X, Tang S, Chen W, Wu F, Yang X, Jiang X, Shi H, Ma J, Chen G, Chen G, Zheng Y, Wei Y, Liu Y. Dissection of Phenotypic and Genetic Variation of Drought-Related Traits in Diverse Chinese Wheat Landraces. THE PLANT GENOME 2019; 12:1-14. [PMID: 33016597 DOI: 10.3835/plantgenome2019.03.0025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 08/30/2019] [Indexed: 05/10/2023]
Abstract
Variations in 16 seedling traits under normal and drought conditions were investigated. Extremely resistant and sensitive accessions were identified for future analyses. Under normal and drought conditions, 57 and 29 QTL were identified, respectively. A total of 77 candidate genes were identified, and four were validated by qRT-PCR. Drought is one of the most important abiotic stressors affecting wheat (Triticum aestivum L.) production. To improve wheat yield, a better understanding of the genetic control of traits governing drought resistance is paramount. Here, using 645 wheat landraces, we evaluated 16 seedling traits related to root and shoot growth and water content under normal and drought (induced by polyethylene glycol) conditions. Extremely resistant and sensitive accessions were identified for future drought-resistance breeding and further genetic analyses. A genome-wide association study was performed for the 16 traits using 52,118 diversity arrays technology sequencing (DArT-seq) markers. A total of 57 quantitative trait loci (QTL) were detected for seven traits under normal conditions, whereas 29 QTL were detected for eight traits under drought conditions. On the basis of these markers, we identified 56 candidate genes for six seedling traits under normal conditions, and 21 candidate genes for seven seedling traits under drought conditions. Four candidate genes were validated under normal and drought conditions using quantitative reverse transcription polymerase chain reaction (qRT-PCR) data. The co-localization of the flowering date and drought-related traits indicates that the regulatory networks of flowering may also respond to drought stress or are associated with the correlated responses of these traits. The phenotypic and genetic elucidation of drought-related traits will assist future gene discovery efforts and provide a basis for breeding drought-resistant wheat cultivars.
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Affiliation(s)
- Yu Lin
- Triticeae Research Institute, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Xin Yi
- College of Environmental Sciences, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Si Tang
- Triticeae Research Institute, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Wei Chen
- Triticeae Research Institute, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Fangkun Wu
- Triticeae Research Institute, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Xilan Yang
- Triticeae Research Institute, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Xiaojun Jiang
- Triticeae Research Institute, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Haoran Shi
- Triticeae Research Institute, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Guangdeng Chen
- Triticeae Research Institute, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Guoyue Chen
- College of resources, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
| | - Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural Univ., Wenjiang, Chengdu, 611130, China
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42
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Genc Y, Taylor J, Lyons G, Li Y, Cheong J, Appelbee M, Oldach K, Sutton T. Bread Wheat With High Salinity and Sodicity Tolerance. FRONTIERS IN PLANT SCIENCE 2019; 10:1280. [PMID: 31695711 PMCID: PMC6817574 DOI: 10.3389/fpls.2019.01280] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/13/2019] [Indexed: 05/20/2023]
Abstract
Soil salinity and sodicity are major constraints to global cereal production, but breeding for tolerance has been slow. Narrow gene pools, over-emphasis on the sodium (Na+) exclusion mechanism, little attention to osmotic stress/tissue tolerance mechanism(s) in which accumulation of inorganic ions such as Na+ is implicated, and lack of a suitable screening method have impaired progress. The aims of this study were to discover novel genes for Na+ accumulation using genome-wide association studies, compare growth responses to salinity and sodicity in low-Na+ bread Westonia with Nax1 and Nax2 genes and high-Na+ bread wheat Baart-46, and evaluate growth responses to salinity and sodicity in bread wheats with varying leaf Na+ concentrations. The novel high-Na+ bread wheat germplasm, MW#293, had higher grain yield under salinity and sodicity, in absolute and relative terms, than the other bread wheat entries tested. Genes associated with high Na+ accumulation in bread wheat were identified, which may be involved in tissue tolerance/osmotic adjustment. As most modern bread wheats are efficient at excluding Na+, further reduction in plant Na+ is unlikely to provide agronomic benefit. The salinity and sodicity tolerant germplasm MW#293 provides an opportunity for the development of future salinity/sodicity tolerant bread wheat.
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Affiliation(s)
- Yusuf Genc
- South Australian Research and Development Institute, Adelaide, SA, Australia
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Julian Taylor
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Graham Lyons
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Yongle Li
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Judy Cheong
- South Australian Research and Development Institute, Adelaide, SA, Australia
| | | | - Klaus Oldach
- South Australian Research and Development Institute, Adelaide, SA, Australia
| | - Tim Sutton
- South Australian Research and Development Institute, Adelaide, SA, Australia
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
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Abdel Latef AAH, Kordrostami M, Zakir A, Zaki H, Saleh OM. Eustress with H 2O 2 Facilitates Plant Growth by Improving Tolerance to Salt Stress in Two Wheat Cultivars. PLANTS (BASEL, SWITZERLAND) 2019; 8:E303. [PMID: 31461870 PMCID: PMC6783893 DOI: 10.3390/plants8090303] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/16/2019] [Accepted: 08/19/2019] [Indexed: 12/27/2022]
Abstract
In this study, the positive role of hydrogen peroxide (H2O2) pretreatment in mitigating the adverse impacts of seawater stress has been evaluated in two wheat (Triticum aestivum L.) cultivars, namely Gemmiza 11 as a salt-sensitive and Misr 1 as a salt-tolerant cultivar, with contrasting phenotypes in response to the salinity stress. Under normal conditions, wheat seeds eustress with H2O2 have shown significant effects on the improvement of plant growth parameters, such as dry weight and root and shoot lengths. Under salt stress conditions, seeds eustress with H2O2 have shown a reduction in damage to plant growth and physiological parameters as compared to the seeds kept as un-primed in both wheat cultivars. In addition, eustress of seeds with H2O2 has induced an increment in the pigments content, proline level and mineral uptake (K+, Ca2+ and Mg2+). Moreover, seeds eustress with H2O2 have shown significant decrement in Na+ content uptake in plants and that subsequently reduced lipid peroxidation. Seawater stress has increased the activity of the antioxidant system based on catalase (CAT), peroxidase (POD) and ascorbate peroxidase (APX) in both cultivars, except POD in Gemmiza 11. Similarly, the application of H2O2 has further enhanced the activity of the antioxidant system in stressed plants and this enhancement of the antioxidant system further reduced Na+ content in plants and subsequently increased the growth parameters. Results of inter-simple sequence repeat (ISSR) markers have shown clear differentiation among the treatments and have provided strong evidence in support of the hypothesis proposed in this study that H2O2 eustress improves seed tolerance and enhances plant growth parameters under seawater stress.
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Affiliation(s)
- Arafat Abdel Hamed Abdel Latef
- Botany and Microbiology Department, Faculty of Science, South Valley University, 83523 Qena, Egypt.
- Biology Department, Turabah University College, Taif University, Turabah Branch, 21955 Taif, Saudi Arabia.
| | - Mojtaba Kordrostami
- Department of Plant Biotechnology, Faculty of Agricultural Sciences, University of Guilan, P.O. Box 41635-1314 Rasht, Iran
- Rice Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 41996-13475 Rasht, Iran
| | - Ali Zakir
- Department of Environmental Sciences, COMSATS University Islamabad, Vehari-Campus, Vehari 61100, Pakistan
| | - Hoida Zaki
- Botany and Microbiology Department, Faculty of Science, South Valley University, 83523 Qena, Egypt
| | - Osama Moseilhy Saleh
- National Products Department, National Centre for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority, Nasr City, 11787 Cairo, Egypt
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44
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Oyiga BC, Ogbonnaya FC, Sharma RC, Baum M, Léon J, Ballvora A. Genetic and transcriptional variations in NRAMP-2 and OPAQUE1 genes are associated with salt stress response in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:323-346. [PMID: 30392081 PMCID: PMC6349800 DOI: 10.1007/s00122-018-3220-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 10/24/2018] [Indexed: 05/02/2023]
Abstract
SNP alleles on chromosomes 4BL and 6AL are associated with sensitivity to salt tolerance in wheat and upon validation can be exploited in the development of salt-tolerant wheat varieties. The dissection of the genetic and molecular components of salt stress response offers strong opportunities toward understanding and improving salt tolerance in crops. In this study, GWAS was employed to identify a total of 106 SNP loci (R2 = 0.12-63.44%) linked to salt stress response in wheat using leaf chlorophyll fluorescence, grain quality and shoot ionic (Na+ and K+ ions) attributes. Among them, 14 SNP loci individually conferred pleiotropic effects on multiple independent salinity tolerance traits including loci at 99.04 cM (R2 ≥ 14.7%) and 68.45 cM (R2 ≥ 4.10%) on chromosomes 6AL and 4BL, respectively, that influenced shoot Na+-uptake, shoot K+/Na+ ratio, and specific energy fluxes for absorption (ABS/RC) and dissipation (DIo/RC). Analysis of the open reading frame (ORF) containing the SNP markers revealed that they are orthologous to genes involved in photosynthesis and plant stress (salt) response. Further transcript abundance and qRT-PCR analyses indicated that the genes are mostly up-regulated in salt-tolerant and down-regulated in salt-sensitive wheat genotypes including NRAMP-2 and OPAQUE1 genes on 4BL and 6AL, respectively. Both genes showed highest differential expression between contrasting genotypes when expressions of all the genes within their genetic intervals were analyzed. Possible cis-acting regulatory elements and coding sequence variation that may be involved in salt stress response were also identified in both genes. This study identified genetic and molecular components of salt stress response that are associated with Na+-uptake, shoot Na+/K+ ratio, ABS/RC, DIo/RC, and grain quality traits and upon functional validation would facilitate the development of gene-specific markers that could be deployed to improve salinity tolerance in wheat.
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Affiliation(s)
- Benedict C Oyiga
- INRES-Pflanzenzuchtung, Rheinische Friedrich-Wilhelms-Universitat, Bonn, Germany
- Center for Development Research (ZEF), Rheinische Friedrich-Wilhelms-Universitat, Bonn, Germany
| | | | - Ram C Sharma
- International Center for Agricultural Research in the Dry Areas (ICARDA), Tashkent, Uzbekistan
| | - Michael Baum
- International Centre for Agricultural Research in the Dry Areas (ICARDA), Al Irfane, 10112, Rabat, Morocco
| | - Jens Léon
- INRES-Pflanzenzuchtung, Rheinische Friedrich-Wilhelms-Universitat, Bonn, Germany
| | - Agim Ballvora
- INRES-Pflanzenzuchtung, Rheinische Friedrich-Wilhelms-Universitat, Bonn, Germany.
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Wang J, Mao X, Wang R, Li A, Zhao G, Zhao J, Jing R. Identification of wheat stress-responding genes and TaPR-1-1 function by screening a cDNA yeast library prepared following abiotic stress. Sci Rep 2019; 9:141. [PMID: 30644420 PMCID: PMC6333785 DOI: 10.1038/s41598-018-37859-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 12/06/2018] [Indexed: 11/29/2022] Open
Abstract
Abiotic stress significantly impacts growth and yield of crop plants. It is imperative for crop improvement to discover and utilize stress-tolerant functional genes. In this study, genes responding to abiotic stresses, such as freezing, salt and osmotic stress, were screened from a cDNA yeast library that was constructed from the drought- and heat-tolerant wheat variety Hanxuan 10. After screening for surviving clones we isolated 7,249, 4,313 and 4,469 raw sequences, corresponding to 4,695, 2,641 and 2,771 genes following each treatment. Venn diagrams revealed 377 overlapping genes. GO analysis suggested that these genes were mainly involved in the metabolic and stress signal pathways. KEGG pathway enrichment analysis indicated that the isolated genes predominantly belonged to pathways concerning energy and metabolism. Overlapping gene TaPR-1-1 within the pathogenesis-related (PR) protein family was selected for detailed characterization. Although previous studies had shown that PR genes function during pathogen attack, our results demonstrated that TaPR-1-1 expression was also induced by freezing, salinity, and osmotic stresses. Overexpression in yeast and Arabidopsis showed that TaPR-1-1 conferred tolerance to these stresses. We concluded that screening cDNA yeast libraries following abiotic stress is an efficient way to identify stress-tolerance genes.
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Affiliation(s)
- Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ruitong Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ang Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guangyao Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jinfeng Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Morton MJL, Awlia M, Al‐Tamimi N, Saade S, Pailles Y, Negrão S, Tester M. Salt stress under the scalpel - dissecting the genetics of salt tolerance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:148-163. [PMID: 30548719 PMCID: PMC6850516 DOI: 10.1111/tpj.14189] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 11/28/2018] [Accepted: 11/30/2018] [Indexed: 05/08/2023]
Abstract
Salt stress limits the productivity of crops grown under saline conditions, leading to substantial losses of yield in saline soils and under brackish and saline irrigation. Salt tolerant crops could alleviate these losses while both increasing irrigation opportunities and reducing agricultural demands on dwindling freshwater resources. However, despite significant efforts, progress towards this goal has been limited, largely because of the genetic complexity of salt tolerance for agronomically important yield-related traits. Consequently, the focus is shifting to the study of traits that contribute to overall tolerance, thus breaking down salt tolerance into components that are more genetically tractable. Greater consideration of the plasticity of salt tolerance mechanisms throughout development and across environmental conditions furthers this dissection. The demand for more sophisticated and comprehensive methodologies is being met by parallel advances in high-throughput phenotyping and sequencing technologies that are enabling the multivariate characterisation of vast germplasm resources. Alongside steady improvements in statistical genetics models, forward genetics approaches for elucidating salt tolerance mechanisms are gaining momentum. Subsequent quantitative trait locus and gene validation has also become more accessible, most recently through advanced techniques in molecular biology and genomic analysis, facilitating the translation of findings to the field. Besides fuelling the improvement of established crop species, this progress also facilitates the domestication of naturally salt tolerant orphan crops. Taken together, these advances herald a promising era of discovery for research into the genetics of salt tolerance in plants.
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Affiliation(s)
- Mitchell J. L. Morton
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Kingdom of Saudi Arabia
| | - Mariam Awlia
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Kingdom of Saudi Arabia
| | - Nadia Al‐Tamimi
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Kingdom of Saudi Arabia
| | - Stephanie Saade
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Kingdom of Saudi Arabia
| | - Yveline Pailles
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Kingdom of Saudi Arabia
| | - Sónia Negrão
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Kingdom of Saudi Arabia
| | - Mark Tester
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Kingdom of Saudi Arabia
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Chatterjee P, Kanagendran A, Samaddar S, Pazouki L, Sa TM, Niinemets Ü. Inoculation of Brevibacterium linens RS16 in Oryza sativa genotypes enhanced salinity resistance: Impacts on photosynthetic traits and foliar volatile emissions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 645:721-732. [PMID: 30031330 PMCID: PMC6354898 DOI: 10.1016/j.scitotenv.2018.07.187] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 07/14/2018] [Accepted: 07/14/2018] [Indexed: 05/05/2023]
Abstract
The emission of volatiles in response to salt stress in rice cultivars has not been studied much to date. Studies addressing the regulation of stress induced volatile emission by halotolerant plant growth promoting bacteria containing ACC (1-aminocyclopropane-1-carboxylate) deaminase are also limited. The objective of the present study was to investigate the salt alleviation potential of bacteria by regulating photosynthetic characteristics and volatile emissions in rice cultivars, and to compare the effects of the bacteria inoculation and salt responses between two rice genotypes. The interactive effects of soil salinity (0, 50, and 100 mM NaCl) and inoculation with Brevibacterium linens RS16 on ACC accumulation, ACC oxidase activity, carbon assimilation and stress volatile emissions after stress application were studied in the moderately salt resistant (FL478) and the salt-sensitive (IR29) rice (Oryza sativa L.) cultivars. It was observed that salt stress reduced foliage photosynthetic rate, but induced foliage ACC accumulation, foliage ACC oxidase activity, and the emissions of all the major classes of volatile organic compounds (VOCs) including the lipoxygenase pathway volatiles, light-weight oxygenated volatiles, long-chained saturated aldehydes, benzenoids, geranylgeranyl diphosphate pathway products, and mono- and sesquiterpenes. All these characteristics scaled up quantitatively with increasing salt stress. The effects of salt stress were more pronounced in the salt-sensitive genotype IR29 compared to the moderately salt resistant FL478 genotype. However, the bacterial inoculation significantly enhanced photosynthesis, and decreased ACC accumulation and the ACC oxidase activity, and VOC emissions both in control and salt-treated plants. Taken together, these results suggested that the ACC deaminase-containing Brevibacterium linens RS16 reduces the temporal regulation of VOC emissions and increases the plant physiological activity by reducing the availability of ethylene precursor ACC and the ACC oxidase activity under salt stress.
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Affiliation(s)
- Poulami Chatterjee
- Department of Environmental and Biological Chemistry, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea
| | - Arooran Kanagendran
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51006, Estonia
| | - Sandipan Samaddar
- Department of Environmental and Biological Chemistry, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea
| | - Leila Pazouki
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51006, Estonia; Department of Biology, University of Louisville, Louisville, KY 40292, USA
| | - Tong-Min Sa
- Department of Environmental and Biological Chemistry, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea.
| | - Ülo Niinemets
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51006, Estonia; Estonian Academy of Sciences, Kohtu 6, 10130 Tallinn, Estonia.
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48
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Lehnert H, Serfling A, Friedt W, Ordon F. Genome-Wide Association Studies Reveal Genomic Regions Associated With the Response of Wheat ( Triticum aestivum L.) to Mycorrhizae Under Drought Stress Conditions. FRONTIERS IN PLANT SCIENCE 2018; 9:1728. [PMID: 30568663 PMCID: PMC6290350 DOI: 10.3389/fpls.2018.01728] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 11/07/2018] [Indexed: 05/06/2023]
Abstract
In the majority of wheat growing areas worldwide, the incidence of drought stress has increased significantly resulting in a negative impact on plant development and grain yield. Arbuscular mycorrhizal symbiosis is known to improve drought stress tolerance of wheat. However, quantitative trait loci (QTL) involved in the response to drought stress conditions in the presence of mycorrhizae are largely unknown. Therefore, a diverse set consisting of 94 bread wheat genotypes was phenotyped under drought stress and well watered conditions in the presence and absence of mycorrhizae. Grain yield and yield components, drought stress related traits as well as response to mycorrhizae were assessed. In parallel, wheat accessions were genotyped by using the 90k iSelect chip, resulting in a set of 15511 polymorphic and mapped SNP markers, which were used for genome-wide association studies (GWAS). In general, drought stress tolerance of wheat was significantly increased in the presence of mycorrhizae compared to drought stress tolerance in the absence of mycorrhizae. However, genotypes differed in their response to mycorrhizae under drought stress conditions. Several QTL regions on different chromosomes were detected associated with grain yield and yield components under drought stress conditions. Furthermore, two genome regions on chromosomes 3D and 7D were found to be significantly associated with the response to mycorrhizae under drought stress conditions. Overall, the results reveal that inoculation of wheat with mycorrhizal fungi significantly improves drought stress tolerance and that QTL regions associated with the response to mycorrhizae under drought stress conditions exist in wheat. Further research is necessary to validate detected QTL regions. However, this study may be the starting point for the identification of candidate genes associated with drought stress tolerance and response to mycorrhizae under drought stress conditions. Maybe in future, these initial results will help to contribute to use mycorrhizal fungi effectively in agriculture and combine new approaches i.e., use of genotypic variation in response to mycorrhizae under drought stress conditions with existing drought tolerance breeding programs to develop new drought stress tolerant genotypes.
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Affiliation(s)
- Heike Lehnert
- Institute of Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute (JKI), Quedlinburg, Germany
| | - Albrecht Serfling
- Institute of Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute (JKI), Quedlinburg, Germany
| | - Wolfgang Friedt
- IFZ Research Centre for Biosystems, Land Use and Nutrition, Plant Breeding Department, Justus Liebig University, Gießen, Germany
| | - Frank Ordon
- Institute of Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute (JKI), Quedlinburg, Germany
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Zatybekov A, Abugalieva S, Didorenko S, Rsaliyev A, Turuspekov Y. GWAS of a soybean breeding collection from South East and South Kazakhstan for resistance to fungal diseases. Vavilovskii Zhurnal Genet Selektsii 2018. [DOI: 10.18699/vj18.392] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Soybean (Glycine max(L.) Merr) is an essential food, feed, and technical culture. In Kazakhstan the area under soybean is increasing every year, helping to solve the problem of protein deficiency in human nutrition and animal feeding. One of the main problems of soybean production is fungal diseases causing yields losses of up to 30 %. Modern genomic studies can be applied to facilitate efficient breeding research for improvement of soybean fungal disease tolerance. Therefore, the objective of this genome-wide association study (GWAS) was analysis of a soybean collection consisting of 182 accessions in relation to fungal diseases in the conditions of South East and South Kazakhstan. Field evaluation of the soybean collection suggested thatFusariumspp. andCercospora sojinaaffected plants in the South region (RIBSP), andSeptoria glycines– in the South East region (KRIAPP). The major objective of the study was identification of QTL associated with resistance to fusarium root rot (FUS), frogeye leaf spot (FLS), and brown spot (BS). GWAS using 4 442 SNP (single nucleotide polymorphism) markers of Illumina iSelect array allowed for identification of fifteen marker trait associations (MTA) resistant to the three diseases at two different stages of growth. Two QTL both for FUS (chromosomes 13 and 17) and BS (chromosomes 14 and 17) were genetically mapped, including one presumably novel QTL for BS (chromosome 17). Also, five presumably novel QTL for FLS were genetically mapped on chromosomes 2, 7, and 15. The results can be used for improvement of the local breeding projects based on marker-assisted selection approach.
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Mansouri M, Naghavi MR, Alizadeh H, Mohammadi-Nejad G, Mousavi SA, Salekdeh GH, Tada Y. Transcriptomic analysis of Aegilops tauschii during long-term salinity stress. Funct Integr Genomics 2018; 19:13-28. [PMID: 29931612 DOI: 10.1007/s10142-018-0623-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 03/17/2018] [Accepted: 06/07/2018] [Indexed: 10/28/2022]
Abstract
Aegilops tauschii is the diploid progenitor of the bread wheat D-genome. It originated from Iran and is a source of abiotic stress tolerance genes. However, little is known about the molecular events of salinity tolerance in Ae. tauschii. This study investigates the leaf transcriptional changes associated with long-term salt stress. Total RNA extracted from leaf tissues of control and salt-treated samples was sequenced using the Illumina technology, and more than 98 million high-quality reads were assembled into 255,446 unigenes with an average length of 1398 bp and an N50 of 2269 bp. Functional annotation of the unigenes showed that 93,742 (36.69%) had at least a significant BLAST hit in the SwissProt database, while 174,079 (68.14%) showed significant similarity to proteins in the NCBI nr database. Differential expression analysis identified 4506 salt stress-responsive unigenes. Bioinformatic analysis of the differentially expressed unigenes (DEUs) revealed a number of biological processes and pathways involved in the establishment of ion homeostasis, signaling processes, carbohydrate metabolism, and post-translational modifications. Fine regulation of starch and sucrose content may be important features involved in salt tolerance in Ae. tauschii. Moreover, 82% of DEUs mapped to the D-subgenome, including known QTL for salt tolerance, and these DEUs showed similar salt stress responses in other accessions of Ae. tauschii. These results could provide fundamental insight into the regulatory process underlying salt tolerance in Ae. tauschii and wheat and facilitate identification of genes involved in their salt tolerance mechanisms.
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Affiliation(s)
- Mehdi Mansouri
- Department of Agricultural Biotechnology, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mohammad Reza Naghavi
- Agronomy and Plant Breeding Department, Agricultural & Natural Resources College, University of Tehran, Karaj, 31587-11167, Iran.
| | - Hoshang Alizadeh
- Agronomy and Plant Breeding Department, Agricultural & Natural Resources College, University of Tehran, Karaj, 31587-11167, Iran
| | - Ghasem Mohammadi-Nejad
- Department of Agronomy and plant Breeding, College of Agriculture and Center of Excellence for Abiotic Stress in Cereal Crop, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Seyed Ahmad Mousavi
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran
| | - Yuichi Tada
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo, 192-0982, Japan.
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