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Sallam A, Awadalla RA, Elshamy MM, Börner A, Heikal YM. Genome-wide analysis for root and leaf architecture traits associated with drought tolerance at the seedling stage in a highly ecologically diverse wheat population. Comput Struct Biotechnol J 2024; 23:870-882. [PMID: 38356657 PMCID: PMC10864764 DOI: 10.1016/j.csbj.2024.01.020] [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: 11/29/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
Drought stress occurred at early growth stages in wheat affecting the following growth stages. Therefore, selecting promising drought-tolerant genotypes with highly adapted traits at the seedling stage is an important task for wheat breeders and geneticists. Few research efforts were conducted on the genetic control for drought-adaptive traits at the seedling stage in wheat. In this study, a set of 146 highly diverse spring wheat core collections representing 28 different countries was evaluated under drought stress at the seedling stage. All genotypes were exposed to drought stress for 13 days by water withholding. Leaf traits including seedling length, leaf wilting, days to wilting, leaf area, and leaf rolling were scored. Moreover, root traits such as root length, maximum width, emergence angle, tip angle, and number of roots were scored. Considerable significant genetic variation was found among all genotypes tested in these experiments. The heritability estimates ranged from 0.74 (leaf witling) to 0.99 (root tip angle). A set of nine genotypes were selected and considered drought-tolerant genotypes. Among all leaf traits, shoot length had significant correlations with all root traits under drought stress. The 146 genotypes were genotyped using the Infinium Wheat 15 K single nucleotide polymorphism (SNP) array and diversity arrays technology (DArT) marker platform. The result of genotyping revealed 12,999 SNPs and 2150 DArT markers which were used to run a genome-wide association study (GWAS). The results of GWAS revealed 169 markers associated with leaf and root traits under drought stress. Out of the 169 markers, 82 were considered major quantitative trait loci (QTL). The GWAS revealed 95 candidate genes were identified with 53 genes showing evidence for drought tolerance in wheat, while the remaining candidate genes were considered novel. No shared markers were found between leaf and root traits. The results of the study provided mapping novel markers associated with new root traits at the seedling stage. Also, the selected genotypes from different countries could be employed in future wheat breeding programs not only for improving adaptive drought-tolerant traits but also for expanding genetic diversity.
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Affiliation(s)
- Ahmed Sallam
- Resources Genetics and Reproduction, Department GenBank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben D-06466 Stadt Seeland, Germany
- Department of Genetics, Faculty of Agriculture, Assiut University, 71526 Assiut, Egypt
| | - Rawan A. Awadalla
- Botany Department, Faculty of Science, Mansoura University, 35516 Mansoura, Egypt
| | - Maha M. Elshamy
- Botany Department, Faculty of Science, Mansoura University, 35516 Mansoura, Egypt
| | - Andreas Börner
- Resources Genetics and Reproduction, Department GenBank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben D-06466 Stadt Seeland, Germany
| | - Yasmin M. Heikal
- Botany Department, Faculty of Science, Mansoura University, 35516 Mansoura, Egypt
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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: 49] [Impact Index Per Article: 24.5] [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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Francki MG, Stainer GS, Walker E, Rebetzke GJ, Stefanova KT, French RJ. Phenotypic Evaluation and Genetic Analysis of Seedling Emergence in a Global Collection of Wheat Genotypes ( Triticum aestivum L.) Under Limited Water Availability. FRONTIERS IN PLANT SCIENCE 2021; 12:796176. [PMID: 35003185 PMCID: PMC8739788 DOI: 10.3389/fpls.2021.796176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
The challenge in establishing an early-sown wheat crop in southern Australia is the need for consistently high seedling emergence when sowing deep in subsoil moisture (>10 cm) or into dry top-soil (4 cm). However, the latter is strongly reliant on a minimum soil water availability to ensure successful seedling emergence. This study aimed to: (1) evaluate 233 Australian and selected international wheat genotypes for consistently high seedling emergence under limited soil water availability when sown in 4 cm of top-soil in field and glasshouse (GH) studies; (2) ascertain genetic loci associated with phenotypic variation using a genome-wide association study (GWAS); and (3) compare across loci for traits controlling coleoptile characteristics, germination, dormancy, and pre-harvest sprouting. Despite significant (P < 0.001) environment and genotype-by-environment interactions within and between field and GH experiments, eight genotypes that included five cultivars, two landraces, and one inbred line had consistently high seedling emergence (mean value > 85%) across nine environments. Moreover, 21 environment-specific quantitative trait loci (QTL) were detected in GWAS analysis on chromosomes 1B, 1D, 2B, 3A, 3B, 4A, 4B, 5B, 5D, and 7D, indicating complex genetic inheritance controlling seedling emergence. We aligned QTL for known traits and individual genes onto the reference genome of wheat and identified 16 QTL for seedling emergence in linkage disequilibrium with coleoptile length, width, and cross-sectional area, pre-harvest sprouting and dormancy, germination, seed longevity, and anthocyanin development. Therefore, it appears that seedling emergence is controlled by multifaceted networks of interrelated genes and traits regulated by different environmental cues.
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Affiliation(s)
- Michael G. Francki
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Grantley S. Stainer
- Department of Primary Industries and Regional Development, Merredin, WA, Australia
| | - Esther Walker
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Gregory J. Rebetzke
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Katia T. Stefanova
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Robert J. French
- Department of Primary Industries and Regional Development, Merredin, WA, Australia
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Post-Anthesis Mobilization of Stem Assimilates in Wheat under Induced Stress. SUSTAINABILITY 2021. [DOI: 10.3390/su13115940] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Stem reserves in grain crops are considered important in grain filling under post-anthesis stress in the absence/low availability of photosynthetic assimilates. Considerable variation is present among genotypes for stem reserve translocation in wheat. Therefore, this study aimed to exploit the phenotypic variation for stem reserve translocation in wheat under control and chemically induced stress conditions. The phenotypic variation among six parents and their corresponding direct cross combinations was evaluated under induced stress conditions. The results signify the presence of considerable variation between treatments, genotypes, and treatment-genotype interactions. The parent LLR-20 depicted the highest translocation of dry matter and contribution of post-anthesis assimilates under induced-stress conditions. Similarly, cross combinations Nacozari × LLR22, Nacozari × LLR 20, Nacozari × Parula, Nacozari × LLR 21, LLR 22 × LLR 21, and LLR 20 × LLR 21 showed higher source-sink accumulation under induced-stress conditions. The selected parents and cross combinations can be further utilized in the breeding program to strengthen the genetic basis for stress tolerance in wheat.
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Konstantinov DK, Zubairova US, Ermakov AA, Doroshkov AV. Comparative transcriptome profiling of a resistant vs susceptible bread wheat ( Triticum aestivum L.) cultivar in response to water deficit and cold stress. PeerJ 2021; 9:e11428. [PMID: 34026365 PMCID: PMC8123233 DOI: 10.7717/peerj.11428] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 04/19/2021] [Indexed: 11/28/2022] Open
Abstract
Bread wheat (Triticum aestivum L.) is one of the most important agricultural plants wearing abiotic stresses, such as water deficit and cold, that cause its productivity reduction. Since resistance to abiotic factors is a multigenic trait, therefore modern genome-wide approaches can help to involve various genetic material in breeding. One technique is full transcriptome analysis that reveals groups of stress response genes serving marker-assisted selection markers. Comparing transcriptome profiles of the same genetic material under several stresses is essential and makes the whole picture. Here, we addressed this by studying the transcriptomic response to water deficit and cold stress for two evolutionarily distant bread wheat varieties: stress-resistant cv. Saratovskaya 29 (S29) and stress-sensitive cv. Yanetzkis Probat (YP). For the first time, transcriptomes for these cultivars grown under abiotic stress conditions were obtained using Illumina based MACE technology. We identified groups of genes involved in response to cold and water deficiency stresses, including responses to each stress factor and both factors simultaneously that may be candidates for resistance genes. We discovered a core group of genes that have a similar pattern of stress-induced expression changes. The particular expression pattern was revealed not only for the studied varieties but also for the published transcriptomic data on cv. Jing 411 and cv. Fielder. Comparative transcriptome profiling of cv. S29 and cv. YP in response to water deficit and cold stress confirmed the hypothesis that stress-induced expression change is unequal within a homeologous gene group. As a rule, at least one changed significantly while the others had a relatively lower expression. Also, we found several SNPs distributed throughout the genomes of cv. S29 and cv. YP and distinguished the studied varieties from each other and the reference cv. Chinese Spring. Our results provide new data for genomics-assisted breeding of stress-tolerant wheat cultivars.
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Affiliation(s)
- Dmitrii K Konstantinov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.,Novosibirsk State University, Novosibirsk, Russian Federation
| | - Ulyana S Zubairova
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.,Novosibirsk State University, Novosibirsk, Russian Federation
| | - Anton A Ermakov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Alexey V Doroshkov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.,Novosibirsk State University, Novosibirsk, Russian Federation
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Jatayev S, Sukhikh I, Vavilova V, Smolenskaya SE, Goncharov NP, Kurishbayev A, Zotova L, Absattarova A, Serikbay D, Hu YG, Borisjuk N, Gupta NK, Jacobs B, de Groot S, Koekemoer F, Alharthi B, Lethola K, Cu DT, Schramm C, Anderson P, Jenkins CLD, Soole KL, Shavrukov Y, Langridge P. Green revolution 'stumbles' in a dry environment: Dwarf wheat with Rht genes fails to produce higher grain yield than taller plants under drought. PLANT, CELL & ENVIRONMENT 2020; 43:2355-2364. [PMID: 32515827 DOI: 10.1111/pce.13819] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/03/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Satyvaldy Jatayev
- Faculty of Agronomy, S. Seifullin Kazakh Agro-Technical University, Nur-Sultan, Kazakhstan
| | - Igor Sukhikh
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Valeriya Vavilova
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Svetlana E Smolenskaya
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Nikolay P Goncharov
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Akhylbek Kurishbayev
- Faculty of Agronomy, S. Seifullin Kazakh Agro-Technical University, Nur-Sultan, Kazakhstan
| | - Lyudmila Zotova
- Faculty of Agronomy, S. Seifullin Kazakh Agro-Technical University, Nur-Sultan, Kazakhstan
| | - Aiman Absattarova
- Faculty of Agronomy, S. Seifullin Kazakh Agro-Technical University, Nur-Sultan, Kazakhstan
| | - Dauren Serikbay
- Faculty of Agronomy, S. Seifullin Kazakh Agro-Technical University, Nur-Sultan, Kazakhstan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Yin-Gang Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Nikolai Borisjuk
- School of Life Science, Huaian Normal University, Huai'an, China
| | | | - Bertus Jacobs
- LongReach Plant Breeders Management Pty Ltd, Lonsdale, South Australia, Australia
| | | | | | - Badr Alharthi
- College of Science and Engineering (Biological Sciences), Flinders University, Bedford Park, South Australia, Australia
| | - Katso Lethola
- College of Science and Engineering (Biological Sciences), Flinders University, Bedford Park, South Australia, Australia
| | - Dan T Cu
- College of Science and Engineering (Biological Sciences), Flinders University, Bedford Park, South Australia, Australia
| | - Carly Schramm
- College of Science and Engineering (Biological Sciences), Flinders University, Bedford Park, South Australia, Australia
| | - Peter Anderson
- College of Science and Engineering (Biological Sciences), Flinders University, Bedford Park, South Australia, Australia
| | - Colin L D Jenkins
- College of Science and Engineering (Biological Sciences), Flinders University, Bedford Park, South Australia, Australia
| | - Kathleen L Soole
- College of Science and Engineering (Biological Sciences), Flinders University, Bedford Park, South Australia, Australia
| | - Yuri Shavrukov
- College of Science and Engineering (Biological Sciences), Flinders University, Bedford Park, South Australia, Australia
| | - Peter Langridge
- Wheat Initiative, Julius-Kühn-Institute, Berlin, Germany
- University of Adelaide, Urrbrae, South Australia, Australia
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Badr A, El-Shazly HH, Tarawneh RA, Börner A. Screening for Drought Tolerance in Maize ( Zea mays L.) Germplasm Using Germination and Seedling Traits under Simulated Drought Conditions. PLANTS (BASEL, SWITZERLAND) 2020; 9:E565. [PMID: 32365550 PMCID: PMC7284379 DOI: 10.3390/plants9050565] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/19/2020] [Accepted: 04/21/2020] [Indexed: 11/17/2022]
Abstract
Maize is known to be susceptible to drought stress, which negatively affects vegetative growth and biomass production, as well as the formation of reproductive organs and yield parameters. In this study, 27 responsive traits of germination (G) and seedlings growth were evaluated for 40 accessions of the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) germplasm collection, under no stress and simulated drought stress treatments by 10%, 15%, and 20% of polyethylene glycol (PEG). The three treatments significantly reduced G% and retarded seedlings growth, particularly the 15% and 20% PEG treatments; these two treatments also resulted in a significant increase of abnormal seedlings (AS). The heritability (H2) and correlations of the traits were estimated, and drought tolerance indices (DTIs) were calculated for traits and accessions. The H2 of G% values were reduced, and H2 for AS% increased as the PEG stress increased. Positive correlations were found between most trait pairs, particularly shoot and root traits, with 48 highly significant correlations under no stress and 25 highly significant correlations under the 10% PEG treatments, particularly for shoot and root traits. The medium to high heritability of shoot and root seedling traits provides a sound basis for further genetic analyses. PCA analysis clearly grouped accessions with high DTIs together and the accessions with low DTIs together, indicating that the DTI indicates the stress tolerance level of maize germplasm. However, the resemblance in DTI values does not clearly reflect the origin or taxonomic assignments to subspecies and varieties of the examined accessions.
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Affiliation(s)
- Abdelfattah Badr
- Botany and Microbiology Department, Faculty of Science, Helwan University, Cairo 11790, Egypt
| | - Hanaa H. El-Shazly
- Biological and Geological Sciences Department, Faculty of Education, Ain Shams University, Cairo 11341, Egypt;
| | - Rasha A. Tarawneh
- Gene Bank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Corrensstr. 3, D-06466 Seeland, OT Gatersleben, Germany;
| | - Andreas Börner
- Gene Bank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Corrensstr. 3, D-06466 Seeland, OT Gatersleben, Germany;
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