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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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Kang Y, Alahmad S, Haeften SV, Akinlade O, Tong J, Dinglasan E, Voss-Fels KP, Potgieter AB, Borrell AK, Makhoul M, Obermeier C, Snowdon R, Mace E, Jordan DR, Hickey LT. Mapping quantitative trait loci for seminal root angle in a selected durum wheat population. THE PLANT GENOME 2024:e20490. [PMID: 39044485 DOI: 10.1002/tpg2.20490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Seminal root angle (SRA) is an important root architectural trait associated with drought adaptation in cereal crops. To date, all attempts to dissect the genetic architecture of SRA in durum wheat (Triticum durum Desf.) have used large association panels or structured mapping populations. Identifying changes in allele frequency generated by selection provides an alternative genetic mapping approach that can increase the power and precision of QTL detection. This study aimed to map quantitative trait loci (QTL) for SRA by genotyping durum lines created through divergent selection using a combination of marker-assisted selection (MAS) for the major SRA QTL (qSRA-6A) and phenotypic selection for SRA over multiple generations. The created 11 lines (BC1F2:5) were genotyped with genome-wide single-nucleotide polymorphism (SNP) markers to map QTL by identifying markers that displayed segregation distortion significantly different from the Mendelian expectation. QTL regions were further assessed in an independent validation population to confirm their associations with SRA. The experiment revealed 14 genomic regions under selection, 12 of which have not previously been reported for SRA. Five regions, including qSRA-6A, were confirmed in the validation population. The genomic regions identified in this study indicate that the genetic control of SRA is more complex than previously anticipated. Our study demonstrates that selection mapping is a powerful approach to complement genome-wide association studies for QTL detection. Moreover, the verification of qSRA-6A in an elite genetic background highlights the potential for MAS, although it is necessary to combine additional QTL to develop new cultivars with extreme SRA phenotypes.
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Affiliation(s)
- Yichen Kang
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia
| | - Samir Alahmad
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia
| | - Shanice V Haeften
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia
| | - Oluwaseun Akinlade
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia
| | - Jingyang Tong
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia
| | - Eric Dinglasan
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia
| | - Kai P Voss-Fels
- Department of Grapevine Breeding, Geisenheim University, Geisenheim, Germany
| | - Andries B Potgieter
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Gatton, Queensland, Australia
| | - Andrew K Borrell
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Hermitage Research Facility, Warwick, Queensland, Australia
| | - Manar Makhoul
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Gießen, Germany
| | - Christian Obermeier
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Gießen, Germany
| | - Rod Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Gießen, Germany
| | - Emma Mace
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Hermitage Research Facility, Warwick, Queensland, Australia
| | - David R Jordan
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Hermitage Research Facility, Warwick, Queensland, Australia
| | - Lee T Hickey
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia
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Schierenbeck M, Alqudah AM, Thabet SG, Avogadro EG, Dietz JI, Simón MR, Börner A. Natural allelic variation confers diversity in the regulation of flag leaf traits in wheat. Sci Rep 2024; 14:13316. [PMID: 38858489 PMCID: PMC11164900 DOI: 10.1038/s41598-024-64161-x] [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: 11/08/2023] [Accepted: 06/05/2024] [Indexed: 06/12/2024] Open
Abstract
Flag leaf (FL) dimension has been reported as a key ecophysiological aspect for boosting grain yield in wheat. A worldwide winter wheat panel consisting of 261 accessions was tested to examine the phenotypical variation and identify quantitative trait nucleotides (QTNs) with candidate genes influencing FL morphology. To this end, four FL traits were evaluated during the early milk stage under two growing seasons at the Leibniz Institute of Plant Genetics and Crop Plant Research. The results showed that all leaf traits (Flag leaf length, width, area, and length/width ratio) were significantly influenced by the environments, genotypes, and environments × genotypes interactions. Then, a genome-wide association analysis was performed using 17,093 SNPs that showed 10 novel QTNs that potentially play a role in modulating FL morphology in at least two environments. Further analysis revealed 8 high-confidence candidate genes likely involved in these traits and showing high expression values from flag leaf expansion until its senescence and also during grain development. An important QTN (wsnp_RFL_Contig2177_1500201) was associated with FL width and located inside TraesCS3B02G047300 at chromosome 3B. This gene encodes a major facilitator, sugar transporter-like, and showed the highest expression values among the candidate genes reported, suggesting their positive role in controlling flag leaf and potentially being involved in photosynthetic assimilation. Our study suggests that the detection of novel marker-trait associations and the subsequent elucidation of the genetic mechanism influencing FL morphology would be of interest for improving plant architecture, light capture, and photosynthetic efficiency during grain development.
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Affiliation(s)
- Matías Schierenbeck
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, 06466, Seeland, Germany.
- Faculty of Agricultural Sciences and Forestry, National University of La Plata, La Plata, Argentina.
- CONICET CCT La Plata, La Plata, Argentina.
| | - Ahmad Mohammad Alqudah
- Biological Science Program, Department of Biological and Environmental Sciences, College of Art and Science, Qatar University, Doha, Qatar.
| | - Samar Gamal Thabet
- Department of Botany, Faculty of Science, Fayoum University, Fayoum, Egypt
| | - Evangelina Gabriela Avogadro
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
| | - Juan Ignacio Dietz
- CONICET CCT La Plata, La Plata, Argentina
- EEA INTA Bordenave, Ruta 76 km 36, Bordenave, Argentina
| | - María Rosa Simón
- Faculty of Agricultural Sciences and Forestry, National University of La Plata, La Plata, Argentina
- CONICET CCT La Plata, La Plata, Argentina
| | - Andreas Börner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
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Alrajhi A, Alharbi S, Beecham S, Alotaibi F. Regulation of root growth and elongation in wheat. FRONTIERS IN PLANT SCIENCE 2024; 15:1397337. [PMID: 38835859 PMCID: PMC11148372 DOI: 10.3389/fpls.2024.1397337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/06/2024] [Indexed: 06/06/2024]
Abstract
Currently, the control of rhizosphere selection on farms has been applied to achieve enhancements in phenotype, extending from improvements in single root characteristics to the dynamic nature of entire crop systems. Several specific signals, regulatory elements, and mechanisms that regulate the initiation, morphogenesis, and growth of new lateral or adventitious root species have been identified, but much more work remains. Today, phenotyping technology drives the development of root traits. Available models for simulation can support all phenotyping decisions (root trait improvement). The detection and use of markers for quantitative trait loci (QTLs) are effective for enhancing selection efficiency and increasing reproductive genetic gains. Furthermore, QTLs may help wheat breeders select the appropriate roots for efficient nutrient acquisition. Single-nucleotide polymorphisms (SNPs) or alignment of sequences can only be helpful when they are associated with phenotypic variation for root development and elongation. Here, we focus on major root development processes and detail important new insights recently generated regarding the wheat genome. The first part of this review paper discusses the root morphology, apical meristem, transcriptional control, auxin distribution, phenotyping of the root system, and simulation models. In the second part, the molecular genetics of the wheat root system, SNPs, TFs, and QTLs related to root development as well as genome editing (GE) techniques for the improvement of root traits in wheat are discussed. Finally, we address the effect of omics strategies on root biomass production and summarize existing knowledge of the main molecular mechanisms involved in wheat root development and elongation.
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Affiliation(s)
- Abdullah Alrajhi
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- Sustainable Infrastructure and Resource Management, University of South Australia, University of South Australia Science, Technology, Engineering, and Mathematics (UniSA STEM), Mawson Lakes, SA, Australia
| | - Saif Alharbi
- The National Research and Development Center for Sustainable Agriculture (Estidamah), Riyadh, Saudi Arabia
| | - Simon Beecham
- Sustainable Infrastructure and Resource Management, University of South Australia, University of South Australia Science, Technology, Engineering, and Mathematics (UniSA STEM), Mawson Lakes, SA, Australia
| | - Fahad Alotaibi
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
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Hafeez A, Ali S, Javed MA, Iqbal R, Khan MN, Çiğ F, Sabagh AE, Abujamel T, Harakeh S, Ercisli S, Ali B. Breeding for water-use efficiency in wheat: progress, challenges and prospects. Mol Biol Rep 2024; 51:429. [PMID: 38517566 DOI: 10.1007/s11033-024-09345-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 02/12/2024] [Indexed: 03/24/2024]
Abstract
Drought poses a significant challenge to wheat production globally, leading to substantial yield losses and affecting various agronomic and physiological traits. The genetic route offers potential solutions to improve water-use efficiency (WUE) in wheat and mitigate the negative impacts of drought stress. Breeding for drought tolerance involves selecting desirable plants such as efficient water usage, deep root systems, delayed senescence, and late wilting point. Biomarkers, automated and high-throughput techniques, and QTL genes are crucial in enhancing breeding strategies and developing wheat varieties with improved resilience to water scarcity. Moreover, the role of root system architecture (RSA) in water-use efficiency is vital, as roots play a key role in nutrient and water uptake. Genetic engineering techniques offer promising avenues to introduce desirable RSA traits in wheat to enhance drought tolerance. These technologies enable targeted modifications in DNA sequences, facilitating the development of drought-tolerant wheat germplasm. The article highlighted the techniques that could play a role in mitigating drought stress in wheat.
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Affiliation(s)
- Aqsa Hafeez
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Shehzad Ali
- Department of Environmental Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Ammar Javed
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Rashid Iqbal
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63000, Pakistan
| | - Muhammad Nauman Khan
- Department of Botany, Islamia College Peshawar, Peshawar, 25120, Pakistan
- Biology Laboratory, University Public School, University of Peshawar, Peshawar, 25120, Pakistan
| | - Fatih Çiğ
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt, 56100, Turkey
| | - Ayman El Sabagh
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt, 56100, Turkey
| | - Turki Abujamel
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Steve Harakeh
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Yousef Abdullatif Jameel Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Sezai Ercisli
- Department of Horticulture, Agricultural Faculty, Ataturk University, Erzurum, 25240, Türkiye
- HGF Agro, Ata Teknokent, Erzurum, 25240, Türkiye
| | - Baber Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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Bhoite R, Han Y, Chaitanya AK, Varshney RK, Sharma DL. Genomic approaches to enhance adaptive plasticity to cope with soil constraints amidst climate change in wheat. THE PLANT GENOME 2024; 17:e20358. [PMID: 37265088 DOI: 10.1002/tpg2.20358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/09/2023] [Accepted: 05/09/2023] [Indexed: 06/03/2023]
Abstract
Climate change is varying the availability of resources, soil physicochemical properties, and rainfall events, which collectively determines soil physical and chemical properties. Soil constraints-acidity (pH < 6), salinity (pH ≤ 8.5), sodicity, and dispersion (pH > 8.5)-are major causes of wheat yield loss in arid and semiarid cropping systems. To cope with changing environments, plants employ adaptive strategies such as phenotypic plasticity, a key multifaceted trait, to promote shifts in phenotypes. Adaptive strategies for constrained soils are complex, determined by key functional traits and genotype × environment × management interactions. The understanding of the molecular basis of stress tolerance is particularly challenging for plasticity traits. Advances in sequencing and high-throughput genomics technologies have identified functional alleles in gene-rich regions, haplotypes, candidate genes, mechanisms, and in silico gene expression profiles at various growth developmental stages. Our review focuses on favorable alleles for enhanced gene expression, quantitative trait loci, and epigenetic regulation of plant responses to soil constraints, including heavy metal stress and nutrient limitations. A strategy is then described for quantitative traits in wheat by investigating significant alleles and functional characterization of variants, followed by gene validation using advanced genomic tools, and marker development for molecular breeding and genome editing. Moreover, the review highlights the progress of gene editing in wheat, multiplex gene editing, and novel alleles for smart control of gene expression. Application of these advanced genomic technologies to enhance plasticity traits along with soil management practices will be an effective tool to build yield, stability, and sustainability on constrained soils in the face of climate change.
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Affiliation(s)
- Roopali Bhoite
- Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia, Australia
| | - Yong Han
- Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Perth, Western Australia, Australia
| | - Alamuru Krishna Chaitanya
- Grains Genetics Portfolio, University of Southern Queensland, Centre for Crop Health, Toowoomba, Queensland, Australia
| | - Rajeev K Varshney
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Perth, Western Australia, Australia
| | - Darshan Lal Sharma
- Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Perth, Western Australia, Australia
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Valladares García AP, Desiderio F, Simeone R, Ravaglia S, Ciorba R, Fricano A, Guerra D, Blanco A, Cattivelli L, Mazzucotelli E. QTL mapping for kernel-related traits in a durum wheat x T. dicoccum segregating population. FRONTIERS IN PLANT SCIENCE 2023; 14:1253385. [PMID: 37849841 PMCID: PMC10577384 DOI: 10.3389/fpls.2023.1253385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/28/2023] [Indexed: 10/19/2023]
Abstract
Durum wheat breeding relies on grain yield improvement to meet its upcoming demand while coping with climate change. Kernel size and shape are the determinants of thousand kernel weight (TKW), which is a key component of grain yield, and the understanding of the genetic control behind these traits supports the progress in yield potential. The present study aimed to dissect the genetic network responsible for kernel size components (length, width, perimeter, and area) and kernel shape traits (width-to-length ratio and formcoefficient) as well as their relationships with kernel weight, plant height, and heading date in durum wheat. Quantitative Trait Locus (QTL) mapping was performed on a segregating population of 110 recombinant inbred lines, derived from a cross between the domesticated emmer wheat accession MG5323 and the durum wheat cv. Latino, evaluated in four different environments. A total of 24 QTLs stable across environments were found and further grouped in nine clusters on chromosomes 2A, 2B, 3A, 3B, 4B, 6B, and 7A. Among them, a QTL cluster on chromosome 4B was associated with kernel size traits and TKW, where the parental MG5323 contributed the favorable alleles, highlighting its potential to improve durum wheat germplasm. The physical positions of the clusters, defined by the projection on the T. durum reference genome, overlapped with already known genes (i.e., BIG GRAIN PROTEIN 1 on chromosome 4B). These results might provide genome-based guidance for the efficient exploitation of emmer wheat diversity in wheat breeding, possibly through yield-related molecular markers.
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Affiliation(s)
- Ana Paola Valladares García
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, Valencia, Spain
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Francesca Desiderio
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Rosanna Simeone
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Bari, Italy
| | | | - Roberto Ciorba
- Council for Agricultural Research and Economics (CREA) - Research Centre for Olive, Fruit and Citrus Crops, Rome, Italy
| | - Agostino Fricano
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Davide Guerra
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Antonio Blanco
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Bari, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
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Urbanavičiūtė I, Bonfiglioli L, Pagnotta MA. Phenotypic and Genotypic Diversity of Roots Response to Salt in Durum Wheat Seedlings. PLANTS (BASEL, SWITZERLAND) 2023; 12:412. [PMID: 36679125 PMCID: PMC9865824 DOI: 10.3390/plants12020412] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/03/2023] [Accepted: 01/11/2023] [Indexed: 06/17/2023]
Abstract
Soil salinity is a serious threat to food production now and in the near future. In this study, the root system of six durum wheat genotypes, including one highly salt-tolerant (J. Khetifa) used as a check genotype, was evaluated, by a high-throughput phenotyping system, under control and salt conditions at the seedling stage. Genotyping was performed using 11 SSR markers closely linked with genome regions associated with root traits. Based on phenotypic cluster analysis, genotypes were grouped differently under control and salt conditions. Under control conditions, genotypes were clustered mainly due to a root angle, while under salt stress, genotypes were grouped according to their capacity to maintain higher roots length, volume, and surface area, as J. Khetifa, Sebatel, and Azeghar. SSR analysis identified a total of 42 alleles, with an average of about three alleles per marker. Moreover, quite a high number of Private alleles in total, 18 were obtained. The UPGMA phenogram of the Nei (1972) genetic distance clusters for 11 SSR markers and all phenotypic data under control conditions discriminate genotypes almost into the same groups. The study revealed as the combination of high-throughput systems for phenotyping with SSR markers for genotyping it's a useful tool to provide important data for the selection of suitable parental lines for salt-tolerance breeding. Nevertheless, the narrow root angle, which is an important trait in drought tolerance, is not a good indicator of salt tolerance. Instated for salt tolerance is more important the amount of roots.
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Kou X, Han W, Kang J. Responses of root system architecture to water stress at multiple levels: A meta-analysis of trials under controlled conditions. FRONTIERS IN PLANT SCIENCE 2022; 13:1085409. [PMID: 36570905 PMCID: PMC9780461 DOI: 10.3389/fpls.2022.1085409] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 11/28/2022] [Indexed: 05/31/2023]
Abstract
Plants are exposed to increasingly severe drought events and roots play vital roles in maintaining plant survival, growth, and reproduction. A large body of literature has investigated the adaptive responses of root traits in various plants to water stress and these studies have been reviewed in certain groups of plant species at a certain scale. Nevertheless, these responses have not been synthesized at multiple levels. This paper screened over 2000 literatures for studies of typical root traits including root growth angle, root depth, root length, root diameter, root dry weight, root-to-shoot ratio, root hair length and density and integrates their drought responses at genetic and morphological scales. The genes, quantitative trait loci (QTLs) and hormones that are involved in the regulation of drought response of the root traits were summarized. We then statistically analyzed the drought responses of root traits and discussed the underlying mechanisms. Moreover, we highlighted the drought response of 1-D and 2-D root length density (RLD) distribution in the soil profile. This paper will provide a framework for an integrated understanding of root adaptive responses to water deficit at multiple scales and such insights may provide a basis for selection and breeding of drought tolerant crop lines.
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Affiliation(s)
- Xinyue Kou
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Weihua Han
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Jian Kang
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
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Esposito S, Taranto F, Vitale P, Ficco DBM, Colecchia SA, Stevanato P, De Vita P. Unlocking the molecular basis of wheat straw composition and morphological traits through multi-locus GWAS. BMC PLANT BIOLOGY 2022; 22:519. [PMID: 36344939 PMCID: PMC9641881 DOI: 10.1186/s12870-022-03900-6] [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: 01/31/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Rapid reductions in emissions from fossil fuel burning are needed to curb global climate change. Biofuel production from crop residues can contribute to reducing the energy crisis and environmental deterioration. Wheat is a renewable source for biofuels owing to the low cost and high availability of its residues. Thus, identifying candidate genes controlling these traits is pivotal for efficient biofuel production. Here, six multi-locus genome-wide association (ML-GWAS) models were applied using 185 tetraploid wheat accessions to detect quantitative trait nucleotides (QTNs) for fifteen traits associated with biomass composition. RESULTS Among the 470 QTNs, only 72 identified by at least two models were considered as reliable. Among these latter, 16 also showed a significant effect on the corresponding trait (p.value < 0.05). Candidate genes survey carried out within 4 Mb flanking the QTNs, revealed putative biological functions associated with lipid transfer and metabolism, cell wall modifications, cell cycle, and photosynthesis. Four genes encoded as Cellulose Synthase (CeSa), Anaphase promoting complex (APC/C), Glucoronoxylan 4-O Methyltransferase (GXM) and HYPONASTIC LEAVES1 (HYL1) might be responsible for an increase in cellulose, and natural and acid detergent fiber (NDF and ADF) content in tetraploid wheat. In addition, the SNP marker RFL_Contig3228_2154 associated with the variation in stem solidness (Q.Scsb-3B) was validated through two molecular methods (High resolution melting; HRM and RNase H2-dependent PCR; rhAMP). CONCLUSIONS The study provides new insights into the genetic basis of biomass composition traits on tetraploid wheat. The application of six ML-GWAS models on a panel of diverse wheat genotypes represents an efficient approach to dissect complex traits with low heritability such as wheat straw composition. The discovery of genes/genomic regions associated with biomass production and straw quality parameters is expected to accelerate the development of high-yielding wheat varieties useful for biofuel production.
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Affiliation(s)
- Salvatore Esposito
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA - Council for Agricultural Research and Economics, 71122 Foggia, Italy
| | - Francesca Taranto
- Institute of Biosciences and Bioresources, (CNR-IBBR), 70126 Bari, Italy
| | - Paolo Vitale
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA - Council for Agricultural Research and Economics, 71122 Foggia, Italy
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, 71122 Foggia, Italy
| | - Donatella Bianca Maria Ficco
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA - Council for Agricultural Research and Economics, 71122 Foggia, Italy
| | - Salvatore Antonio Colecchia
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA - Council for Agricultural Research and Economics, 71122 Foggia, Italy
| | - Piergiorgio Stevanato
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Padova, Legnaro Italy
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA - Council for Agricultural Research and Economics, 71122 Foggia, Italy
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11
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El Gataa Z, Samir K, Tadesse W. Genetic Dissection of Drought Tolerance of Elite Bread Wheat ( Triticum aestivum L.) Genotypes Using Genome Wide Association Study in Morocco. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11202705. [PMID: 36297729 PMCID: PMC9611990 DOI: 10.3390/plants11202705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/01/2022] [Accepted: 10/03/2022] [Indexed: 06/01/2023]
Abstract
Drought is one of the most important yield-limiting factors in Morocco. Identification and deployment of drought-tolerant wheat varieties are important to cope with the challenge of terminal moisture stress and increase wheat productivity. A panel composed of 200 elite spring bread wheat genotypes was phenotyped for yield and agronomic traits for 2 years (2020 and 2021) in Morocco under rainfed and irrigated environments. The panel was genotyped using 20K SNPs and, after filtration, a total of 15,735 SNP markers were used for a genome-wide association study (GWAS) using a mixed linear model (MLM) to identify marker-trait associations (MTA) and putative genes associated with grain yield and yield-related traits under rainfed and irrigated conditions. Significant differences were observed among the elite genotypes for grain yield and yield-related traits. Grain yield performance ranged from 0.97 to 6.16 t/ha under rainfed conditions at Sidi Al-Aidi station and from 3.31 to 9.38 t/h under irrigated conditions at Sidi Al-Aidi station, while Grain yield at Merchouch station ranged from 2.32 to 6.16 t/h under rainfed condition. A total of 159 MTAs (p < 0.001) and 46 genes were discovered, with 67 MTAs recorded under rainfed conditions and 37 MTAs recorded under irrigated conditions at the Sidi Al-Aidi station, while 55 MTAs were recorded under rainfed conditions at Merchouch station. The marker ‘BobWhite_c2988_493’ on chromosome 2B was significantly correlated with grain yield under rainfed conditions. Under irrigated conditions, the marker ‘AX-94653560’ on chromosome 2D was significantly correlated with grain yield at Sidi Al-Aidi station. The maker ‘RAC875_c17918_321’ located on chromosome 4A, associated with grain yield was linked with the gene TraesCS4A02G322700, which encodes for F-box domain-containing protein. The markers and candidate genes discovered in this study should be further validated for their potential use in marker-assisted selection to generate high-yielding wheat genotypes with drought tolerance.
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Affiliation(s)
- Zakaria El Gataa
- The International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat 10080, Morocco
- Faculty of Sciences Ben M’sick, University Hassan II of Casablanca, Casablanca 7955, Morocco
| | - Karima Samir
- Faculty of Sciences Ben M’sick, University Hassan II of Casablanca, Casablanca 7955, Morocco
| | - Wuletaw Tadesse
- The International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat 10080, Morocco
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12
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Leigh FJ, Wright TIC, Horsnell RA, Dyer S, Bentley AR. Progenitor species hold untapped diversity for potential climate-responsive traits for use in wheat breeding and crop improvement. Heredity (Edinb) 2022; 128:291-303. [PMID: 35383318 PMCID: PMC9076643 DOI: 10.1038/s41437-022-00527-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/13/2022] [Accepted: 03/15/2022] [Indexed: 01/07/2023] Open
Abstract
Climate change will have numerous impacts on crop production worldwide necessitating a broadening of the germplasm base required to source and incorporate novel traits. Major variation exists in crop progenitor species for seasonal adaptation, photosynthetic characteristics, and root system architecture. Wheat is crucial for securing future food and nutrition security and its evolutionary history and progenitor diversity offer opportunities to mine favourable functional variation in the primary gene pool. Here we provide a review of the status of characterisation of wheat progenitor variation and the potential to use this knowledge to inform the use of variation in other cereal crops. Although significant knowledge of progenitor variation has been generated, we make recommendations for further work required to systematically characterise underlying genetics and physiological mechanisms and propose steps for effective use in breeding. This will enable targeted exploitation of useful variation, supported by the growing portfolio of genomics and accelerated breeding approaches. The knowledge and approaches generated are also likely to be useful across wider crop improvement.
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Affiliation(s)
- Fiona J Leigh
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Tally I C Wright
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Richard A Horsnell
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Sarah Dyer
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Alison R Bentley
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK. .,International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico.
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13
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Ma J, Zhao D, Tang X, Yuan M, Zhang D, Xu M, Duan Y, Ren H, Zeng Q, Wu J, Han D, Li T, Jiang L. Genome-Wide Association Study on Root System Architecture and Identification of Candidate Genes in Wheat (Triticum aestivum L.). Int J Mol Sci 2022; 23:ijms23031843. [PMID: 35163763 PMCID: PMC8836572 DOI: 10.3390/ijms23031843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 02/04/2023] Open
Abstract
The root tissues play important roles in water and nutrient acquisition, environmental adaptation, and plant development. In this study, a diversity panel of 388 wheat accessions was collected to investigate nine root system architecture (RSA) traits at the three-leaf stage under two growing environments: outdoor pot culture (OPC) and indoor pot culture (IPC). Phenotypic analysis revealed that root development was faster under OPC than that under IPC and a significant correlation was observed between the nine RSA traits. The 660K single-nucleotide polymorphism (SNP) chip was used for a genome-wide association study (GWAS). Significant SNPs with a threshold of −log10 (p-value) ≥ 4 were considered. Thus, 36 quantitative trait loci (QTLs), including 13 QTL clusters that were associated with more than one trait, were detected, and 31 QTLs were first identified. The QTL clusters on chromosomes 3D and 5B were associated with four and five RSA traits, respectively. Two candidate genes, TraesCS2A01G516200 and TraesCS7B01G036900, were found to be associated with more than one RSA trait using haplotype analysis, and preferentially expressed in the root tissues. These favourable alleles for RSA traits identified in this study may be useful to optimise the root system in wheat.
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Affiliation(s)
- Jianhui Ma
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.M.); (D.Z.); (X.T.); (M.Y.); (D.Z.); (M.X.); (Y.D.); (H.R.)
| | - Dongyang Zhao
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.M.); (D.Z.); (X.T.); (M.Y.); (D.Z.); (M.X.); (Y.D.); (H.R.)
| | - Xiaoxiao Tang
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.M.); (D.Z.); (X.T.); (M.Y.); (D.Z.); (M.X.); (Y.D.); (H.R.)
| | - Meng Yuan
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.M.); (D.Z.); (X.T.); (M.Y.); (D.Z.); (M.X.); (Y.D.); (H.R.)
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang 712100, China; (Q.Z.); (J.W.); (D.H.)
| | - Daijing Zhang
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.M.); (D.Z.); (X.T.); (M.Y.); (D.Z.); (M.X.); (Y.D.); (H.R.)
| | - Mengyuan Xu
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.M.); (D.Z.); (X.T.); (M.Y.); (D.Z.); (M.X.); (Y.D.); (H.R.)
| | - Yingze Duan
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.M.); (D.Z.); (X.T.); (M.Y.); (D.Z.); (M.X.); (Y.D.); (H.R.)
| | - Haiyue Ren
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.M.); (D.Z.); (X.T.); (M.Y.); (D.Z.); (M.X.); (Y.D.); (H.R.)
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang 712100, China; (Q.Z.); (J.W.); (D.H.)
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang 712100, China; (Q.Z.); (J.W.); (D.H.)
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang 712100, China; (Q.Z.); (J.W.); (D.H.)
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence: (T.L.); (L.J.)
| | - Lina Jiang
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.M.); (D.Z.); (X.T.); (M.Y.); (D.Z.); (M.X.); (Y.D.); (H.R.)
- Correspondence: (T.L.); (L.J.)
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14
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Hu D, He S, Jia Y, Nazir MF, Sun G, Geng X, Pan Z, Wang L, Chen B, Li H, Ge Y, Pang B, Du X. Genome-wide association study for seedling biomass-related traits in Gossypium arboreum L. BMC PLANT BIOLOGY 2022; 22:54. [PMID: 35086471 PMCID: PMC8793229 DOI: 10.1186/s12870-022-03443-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 01/11/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND Seedling stage plant biomass is usually used as an auxiliary trait to study plant growth and development or stress adversities. However, few molecular markers and candidate genes of seedling biomass-related traits were found in cotton. RESULT Here, we collected 215 Gossypium arboreum accessions, and investigated 11 seedling biomass-related traits including the fresh weight, dry weight, water content, and root shoot ratio. A genome-wide association study (GWAS) utilizing 142,5003 high-quality SNPs identified 83 significant associations and 69 putative candidate genes. Furthermore, the transcriptome profile of the candidate genes emphasized higher expression of Ga03G1298, Ga09G2054, Ga10G1342, Ga11G0096, and Ga11G2490 in four representative cotton accessions. The relative expression levels of those five genes were further verified by qRT-PCR. CONCLUSIONS The significant SNPs, candidate genes identified in this study are expected to lay a foundation for studying the molecular mechanism for early biomass development and related traits in Asian cotton.
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Affiliation(s)
- Daowu Hu
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Shoupu He
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Yinhua Jia
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Mian Faisal Nazir
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Gaofei Sun
- Anyang Institute of Technology, Anyang, 455000, China
| | - Xiaoli Geng
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Zhaoe Pan
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Liru Wang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Baojun Chen
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Hongge Li
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Yuting Ge
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Baoyin Pang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Xiongming Du
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China.
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Daryani P, Darzi Ramandi H, Dezhsetan S, Mirdar Mansuri R, Hosseini Salekdeh G, Shobbar ZS. Pinpointing genomic regions associated with root system architecture in rice through an integrative meta-analysis approach. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:81-106. [PMID: 34623472 DOI: 10.1007/s00122-021-03953-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Applying an integrated meta-analysis approach led to identification of meta-QTLs/ candidate genes associated with rice root system architecture, which can be used in MQTL-assisted breeding/ genetic engineering of root traits. Root system architecture (RSA) is an important factor for facilitating water and nutrient uptake from deep soils and adaptation to drought stress conditions. In the present research, an integrated meta-analysis approach was employed to find candidate genes and genomic regions involved in rice RSA traits. A whole-genome meta-analysis was performed for 425 initial QTLs reported in 34 independent experiments controlling RSA traits under control and drought stress conditions in the previous twenty years. Sixty-four consensus meta-QTLs (MQTLs) were detected, unevenly distributed on twelve rice chromosomes. The confidence interval (CI) of the identified MQTLs was obtained as 0.11-14.23 cM with an average of 3.79 cM, which was 3.88 times narrower than the mean CI of the original QTLs. Interestingly, 52 MQTLs were co-located with SNP peak positions reported in rice genome-wide association studies (GWAS) for root morphological traits. The genes located in these RSA-related MQTLs were detected and explored to find the drought-responsive genes in the rice root based on the RNA-seq and microarray data. Multiple RSA and drought tolerance-associated genes were found in the MQTLs including the genes involved in auxin biosynthesis or signaling (e.g. YUCCA, WOX, AUX/IAA, ARF), root angle (DRO1-related genes), lateral root development (e.g. DSR, WRKY), root diameter (e.g. OsNAC5), plant cell wall (e.g. EXPA), and lignification (e.g. C4H, PAL, PRX and CAD). The genes located within both the SNP peak positions and the QTL-overview peaks for RSA are suggested as novel candidate genes for further functional analysis. The promising candidate genes and MQTLs can be used as basis for genetic engineering and MQTL-assisted breeding of root phenotypes to improve yield potential, stability and performance in a water-stressed environment.
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Affiliation(s)
- Parisa Daryani
- Department of Agronomy & Plant Breeding, University of Mohaghegh Ardabili, Ardabil, Iran
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), 31535-1897, Karaj, Iran
| | - Hadi Darzi Ramandi
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Sara Dezhsetan
- Department of Agronomy & Plant Breeding, University of Mohaghegh Ardabili, Ardabil, Iran.
| | - Raheleh Mirdar Mansuri
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), 31535-1897, Karaj, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), 31535-1897, Karaj, Iran
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Zahra-Sadat Shobbar
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), 31535-1897, Karaj, Iran.
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16
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Soriano JM, Colasuonno P, Marcotuli I, Gadaleta A. Meta-QTL analysis and identification of candidate genes for quality, abiotic and biotic stress in durum wheat. Sci Rep 2021; 11:11877. [PMID: 34088972 PMCID: PMC8178383 DOI: 10.1038/s41598-021-91446-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/25/2021] [Indexed: 11/15/2022] Open
Abstract
The genetic improvement of durum wheat and enhancement of plant performance often depend on the identification of stable quantitative trait loci (QTL) and closely linked molecular markers. This is essential for better understanding the genetic basis of important agronomic traits and identifying an effective method for improving selection efficiency in breeding programmes. Meta-QTL analysis is a useful approach for dissecting the genetic basis of complex traits, providing broader allelic coverage and higher mapping resolution for the identification of putative molecular markers to be used in marker-assisted selection. In the present study, extensive QTL meta-analysis was conducted on 45 traits of durum wheat, including quality and biotic and abiotic stress-related traits. A total of 368 QTL distributed on all 14 chromosomes of genomes A and B were projected: 171 corresponded to quality-related traits, 127 to abiotic stress and 71 to biotic stress, of which 318 were grouped in 85 meta-QTL (MQTL), 24 remained as single QTL and 26 were not assigned to any MQTL. The number of MQTL per chromosome ranged from 4 in chromosomes 1A and 6A to 9 in chromosome 7B; chromosomes 3A and 7A showed the highest number of individual QTL (4), and chromosome 7B the highest number of undefined QTL (4). The recently published genome sequence of durum wheat was used to search for candidate genes within the MQTL peaks. This work will facilitate cloning and pyramiding of QTL to develop new cultivars with specific quantitative traits and speed up breeding programs.
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Affiliation(s)
- Jose Miguel Soriano
- Sustainable Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), 25198, Lleida, Spain.
| | - Pasqualina Colasuonno
- Department of Agricultural and Environmental Science, University of Bari 'Aldo Moro', Via G. Amendola 165/A, 70126, Bari, Italy
| | - Ilaria Marcotuli
- Department of Agricultural and Environmental Science, University of Bari 'Aldo Moro', Via G. Amendola 165/A, 70126, Bari, Italy.
| | - Agata Gadaleta
- Department of Agricultural and Environmental Science, University of Bari 'Aldo Moro', Via G. Amendola 165/A, 70126, Bari, Italy
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Comparative Analysis Based on Transcriptomics and Metabolomics Data Reveal Differences between Emmer and Durum Wheat in Response to Nitrogen Starvation. Int J Mol Sci 2021; 22:ijms22094790. [PMID: 33946478 PMCID: PMC8124848 DOI: 10.3390/ijms22094790] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/04/2022] Open
Abstract
Mounting evidence indicates the key role of nitrogen (N) on diverse processes in plant, including development and defense. Using a combined transcriptomics and metabolomics approach, we studied the response of seedlings to N starvation of two different tetraploid wheat genotypes from the two main domesticated subspecies: emmer and durum wheat. We found that durum wheat exhibits broader and stronger response in comparison to emmer as seen from the expression pattern of both genes and metabolites and gene enrichment analysis. They showed major differences in the responses to N starvation for transcription factor families, emmer showed differential reduction in the levels of primary metabolites while durum wheat exhibited increased levels of most of them to N starvation. The correlation-based networks, including the differentially expressed genes and metabolites, revealed tighter regulation of metabolism in durum wheat in comparison to emmer. We also found that glutamate and γ-aminobutyric acid (GABA) had highest values of centrality in the metabolic correlation network, suggesting their critical role in the genotype-specific response to N starvation of emmer and durum wheat, respectively. Moreover, this finding indicates that there might be contrasting strategies associated to GABA and glutamate signaling modulating shoot vs. root growth in the two different wheat subspecies.
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18
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Fatima I, Gao Y, Xu X, Jin J, Duan S, Zhen W, Xie C, Ma J. Genome-Wide Association Mapping of Seedling Biomass and Root Traits Under Different Water Conditions in Wheat. Front Genet 2021; 12:663557. [PMID: 33912219 PMCID: PMC8072265 DOI: 10.3389/fgene.2021.663557] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/02/2021] [Indexed: 11/13/2022] Open
Abstract
Drought is a major threat to global wheat production. In this study, an association panel containing 200 Chinese wheat germplasms was used for genome-wide association studies (GWASs) of genetic loci associated with eight root and seedling biomass traits under normal water and osmotic stress conditions. The following traits were investigated in wheat seedlings at the four-leaf stage: root length (RL), root number (RN), root fresh weight (RFW), root dry weight (RDW), shoot fresh weight (SFW), shoot dry weight (SDW), total fresh weight (TFW), and total dry weight (TDW). A total of 323 and 286 SNPs were detected under two water environments, respectively. Some of these SNPs were near known loci for root traits. Eleven SNPs on chromosomes 1B, 2B, 4B, and 2D had pleiotropic effects on multiple traits under different water conditions. Further analysis indicated that several genes located inside the 4 Mb LD block on each side of these 11 SNPs were known to be associated with plant growth and development and thus may be candidate genes for these loci. Results from this study increased our understanding of the genetic architecture of root and seedling biomass traits under different water conditions and will facilitate the development of varieties with better drought tolerance.
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Affiliation(s)
- Iza Fatima
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yutian Gao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Xiangru Xu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jingjing Jin
- College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Shuonan Duan
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Wenchao Zhen
- College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Chaojie Xie
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jun Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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Colasuonno P, Marcotuli I, Gadaleta A, Soriano JM. From Genetic Maps to QTL Cloning: An Overview for Durum Wheat. PLANTS (BASEL, SWITZERLAND) 2021; 10:315. [PMID: 33562160 PMCID: PMC7914919 DOI: 10.3390/plants10020315] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/26/2021] [Accepted: 02/02/2021] [Indexed: 12/17/2022]
Abstract
Durum wheat is one of the most important cultivated cereal crops, providing nutrients to humans and domestic animals. Durum breeding programs prioritize the improvement of its main agronomic traits; however, the majority of these traits involve complex characteristics with a quantitative inheritance (quantitative trait loci, QTL). This can be solved with the use of genetic maps, new molecular markers, phenotyping data of segregating populations, and increased accessibility to sequences from next-generation sequencing (NGS) technologies. This allows for high-density genetic maps to be developed for localizing candidate loci within a few Kb in a complex genome, such as durum wheat. Here, we review the identified QTL, fine mapping, and cloning of QTL or candidate genes involved in the main traits regarding the quality and biotic and abiotic stresses of durum wheat. The current knowledge on the used molecular markers, sequence data, and how they changed the development of genetic maps and the characterization of QTL is summarized. A deeper understanding of the trait architecture useful in accelerating durum wheat breeding programs is envisioned.
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Affiliation(s)
- Pasqualina Colasuonno
- Department of Agricultural and Environmental Science, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A, 70126 Bari, Italy; (P.C.); (I.M.)
| | - Ilaria Marcotuli
- Department of Agricultural and Environmental Science, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A, 70126 Bari, Italy; (P.C.); (I.M.)
| | - Agata Gadaleta
- Department of Agricultural and Environmental Science, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A, 70126 Bari, Italy; (P.C.); (I.M.)
| | - Jose Miguel Soriano
- Sustainable Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), 25198 Lleida, Spain
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20
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Regulation of Sixth Seminal Root Formation by Jasmonate in Triticum aestivum L. PLANTS 2021; 10:plants10020219. [PMID: 33498738 PMCID: PMC7911905 DOI: 10.3390/plants10020219] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 01/08/2023]
Abstract
A well-developed root system is an important characteristic of crop plants, which largely determines their productivity, especially under conditions of water and nutrients deficiency. Being Poaceous, wheat has more than one seminal root. The number of grown seminal roots varies in different wheat accessions and is regulated by environmental factors. Currently, the molecular mechanisms determining the number of germinated seminal roots remain poorly understood. The analysis of the root system development in germinating seeds of genetically modified hexaploid wheat plants with altered activity of jasmonate biosynthesis pathway and seeds exogenously treated with methyl jasmonate revealed the role of jasmonates in the regulation of sixth seminal root development. This regulatory effect strongly depends on the jasmonate concentration and the duration of the exposure to this hormone. The maximum stimulatory effect of exogenously applied methyl jasmonate on the formation of the sixth seminal root was achieved at 200 μM concentration after 48 h of treatment. Further increase in concentration and exposure time does not increase the stimulating effect. While 95% of non-transgenic plants under non-stress conditions possess five or fewer seminal roots, the number of plants with developed sixth seminal root reaches up to 100% when selected transgenic lines are treated with methyl jasmonate.
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21
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Alemu A, Feyissa T, Maccaferri M, Sciara G, Tuberosa R, Ammar K, Badebo A, Acevedo M, Letta T, Abeyo B. Genome-wide association analysis unveils novel QTLs for seminal root system architecture traits in Ethiopian durum wheat. BMC Genomics 2021; 22:20. [PMID: 33407083 PMCID: PMC7789649 DOI: 10.1186/s12864-020-07320-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetic improvement of root system architecture is essential to improve water and nutrient use efficiency of crops or to boost their productivity under stress or non-optimal soil conditions. One hundred ninety-two Ethiopian durum wheat accessions comprising 167 historical landraces and 25 modern cultivars were assembled for GWAS analysis to identify QTLs for root system architecture (RSA) traits and genotyped with a high-density 90 K wheat SNP array by Illumina. RESULTS Using a non-roll, paper-based root phenotyping platform, a total of 2880 seedlings and 14,947 seminal roots were measured at the three-leaf stage to collect data for total root length (TRL), total root number (TRN), root growth angle (RGA), average root length (ARL), bulk root dry weight (RDW), individual root dry weight (IRW), bulk shoot dry weight (SDW), presence of six seminal roots per seedling (RT6) and root shoot ratio (RSR). Analysis of variance revealed highly significant differences between accessions for all RSA traits. Four major (- log10P ≥ 4) and 34 nominal (- log10P ≥ 3) QTLs were identified and grouped in 16 RSA QTL clusters across chromosomes. A higher number of significant RSA QTL were identified on chromosome 4B particularly for root vigor traits (root length, number and/or weight). CONCLUSIONS After projecting the identified QTLs on to a high-density tetraploid consensus map along with previously reported RSA QTL in both durum and bread wheat, fourteen nominal QTLs were found to be novel and could potentially be used to tailor RSA in elite lines. The major RGA QTLs on chromosome 6AL detected in the current study and reported in previous studies is a good candidate for cloning the causative underlining sequence and identifying the beneficial haplotypes able to positively affect yield under water- or nutrient-limited conditions.
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Affiliation(s)
- Admas Alemu
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia. .,Department of Biology, Debre Tabor University, Debra Tabor, Ethiopia.
| | - Tileye Feyissa
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Giuseppe Sciara
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Karim Ammar
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Ayele Badebo
- International Maize and Wheat Improvement Center (CIMMYT), Addis Ababa, Ethiopia
| | - Maricelis Acevedo
- International Programs, College of Agriculture and Life Sciences, Cornell University, New York City, NY, USA
| | - Tesfaye Letta
- Oromia Agricultural Research Institute, Addis Ababa, Ethiopia
| | - Bekele Abeyo
- International Maize and Wheat Improvement Center (CIMMYT), Addis Ababa, Ethiopia
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22
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Nazari M, Riebeling S, Banfield CC, Akale A, Crosta M, Mason-Jones K, Dippold MA, Ahmed MA. Mucilage Polysaccharide Composition and Exudation in Maize From Contrasting Climatic Regions. FRONTIERS IN PLANT SCIENCE 2020; 11:587610. [PMID: 33363554 PMCID: PMC7752898 DOI: 10.3389/fpls.2020.587610] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 11/18/2020] [Indexed: 05/28/2023]
Abstract
Mucilage, a gelatinous substance comprising mostly polysaccharides, is exuded by maize nodal and underground root tips. Although mucilage provides several benefits for rhizosphere functions, studies on the variation in mucilage amounts and its polysaccharide composition between genotypes are still lacking. In this study, eight maize (Zea mays L.) genotypes from different globally distributed agroecological zones were grown under identical abiotic conditions in a randomized field experiment. Mucilage exudation amount, neutral sugars and uronic acids were quantified. Galactose (∼39-42%), fucose (∼22-30%), mannose (∼11-14%), and arabinose (∼8-11%) were the major neutral sugars in nodal root mucilage. Xylose (∼1-4%), and glucose (∼1-4%) occurred only in minor proportions. Glucuronic acid (∼3-5%) was the only uronic acid detected. The polysaccharide composition differed significantly between maize genotypes. Mucilage exudation was 135 and 125% higher in the Indian (900 M Gold) and Kenyan (DH 02) genotypes than in the central European genotypes, respectively. Mucilage exudation was positively associated with the vapor pressure deficit of the genotypes' agroecological zone. The results indicate that selection for environments with high vapor pressure deficit may favor higher mucilage exudation, possibly because mucilage can delay the onset of hydraulic failure during periods of high vapor pressure deficit. Genotypes from semi-arid climates might offer sources of genetic material for beneficial mucilage traits.
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Affiliation(s)
- Meisam Nazari
- Division of Biogeochemistry of Agroecosystems, Georg-August University of Göttingen, Göttingen, Germany
| | - Sophie Riebeling
- Division of Biogeochemistry of Agroecosystems, Georg-August University of Göttingen, Göttingen, Germany
| | - Callum C. Banfield
- Division of Biogeochemistry of Agroecosystems, Georg-August University of Göttingen, Göttingen, Germany
| | - Asegidew Akale
- Chair of Soil Physics, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Margherita Crosta
- Chair of Soil Physics, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Kyle Mason-Jones
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Michaela A. Dippold
- Division of Biogeochemistry of Agroecosystems, Georg-August University of Göttingen, Göttingen, Germany
| | - Mutez Ali Ahmed
- Division of Biogeochemistry of Agroecosystems, Georg-August University of Göttingen, Göttingen, Germany
- Chair of Soil Physics, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
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23
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Arriagada O, Marcotuli I, Gadaleta A, Schwember AR. Molecular Mapping and Genomics of Grain Yield in Durum Wheat: A Review. Int J Mol Sci 2020; 21:ijms21197021. [PMID: 32987666 PMCID: PMC7582296 DOI: 10.3390/ijms21197021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 02/07/2023] Open
Abstract
Durum wheat is the most relevant cereal for the whole of Mediterranean agriculture, due to its intrinsic adaptation to dryland and semi-arid environments and to its strong historical cultivation tradition. It is not only relevant for the primary production sector, but also for the food industry chains associated with it. In Mediterranean environments, wheat is mostly grown under rainfed conditions and the crop is frequently exposed to environmental stresses, with high temperatures and water scarcity especially during the grain filling period. For these reasons, and due to recurrent disease epidemics, Mediterranean wheat productivity often remains under potential levels. Many studies, using both linkage analysis (LA) and a genome-wide association study (GWAS), have identified the genomic regions controlling the grain yield and the associated markers that can be used for marker-assisted selection (MAS) programs. Here, we have summarized all the current studies identifying quantitative trait loci (QTLs) and/or candidate genes involved in the main traits linked to grain yield: kernel weight, number of kernels per spike and number of spikes per unit area.
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Affiliation(s)
- Osvin Arriagada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, 306-22 Santiago, Chile;
| | - Ilaria Marcotuli
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, 70121 Bari, Italy; (I.M.); (A.G.)
| | - Agata Gadaleta
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, 70121 Bari, Italy; (I.M.); (A.G.)
| | - Andrés R. Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, 306-22 Santiago, Chile;
- Correspondence: ; Tel.: +56-223544123
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24
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Li T, Ma J, Zou Y, Chen G, Ding P, Zhang H, Yang C, Mu Y, Tang H, Liu Y, Jiang Q, Chen G, Qi P, Wei Y, Zheng Y, Lan X. Quantitative trait loci for seeding root traits and the relationships between root and agronomic traits in common wheat. Genome 2019; 63:27-36. [PMID: 31580743 DOI: 10.1139/gen-2019-0116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A completely developed and vigorous root system can provide a stable platform for aboveground plant organs. To identify loci controlling root traits that could be used in wheat (Triticum aestivum L.) breeding, 199 recombinant inbred lines were used to measure and analyze eight root traits. A total of 18 quantitative trait loci (QTL) located on chromosomes 1A, 2A, 2B, 2D, 4B, 4D, 6A, 7A, and 7B were identified. The phenotypic variation explained by these 18 QTL ranged from 3.27% to 11.75%, and the logarithm of odds scores ranged from 2.50 to 6.58. A comparison of physical intervals indicated several new QTL for root traits were identified. In addition, significant correlations between root and agronomic traits were detected and discussed. The results presented in this study, along with those of previous reports, suggest that chromosomes 2 and 7 likely play important roles in the growth and development of wheat roots.
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Affiliation(s)
- Ting Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Yaya Zou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
| | - Puyang Ding
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Han Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Congcong Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
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25
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Shorinola O, Kaye R, Golan G, Peleg Z, Kepinski S, Uauy C. Genetic Screening for Mutants with Altered Seminal Root Numbers in Hexaploid Wheat Using a High-Throughput Root Phenotyping Platform. G3 (BETHESDA, MD.) 2019; 9:2799-2809. [PMID: 31352407 PMCID: PMC6723138 DOI: 10.1534/g3.119.400537] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 07/23/2019] [Indexed: 12/23/2022]
Abstract
Roots are the main channel for water and nutrient uptake in plants. Optimization of root architecture provides a viable strategy to improve nutrient and water uptake efficiency and maintain crop productivity under water-limiting and nutrient-poor conditions. We know little, however, about the genetic control of root development in wheat, a crop supplying 20% of global calorie and protein intake. To improve our understanding of the genetic control of seminal root development in wheat, we conducted a high-throughput screen for variation in seminal root number using an exome-sequenced mutant population derived from the hexaploid wheat cultivar Cadenza. The screen identified seven independent mutants with homozygous and stably altered seminal root number phenotypes. One mutant, Cadenza0900, displays a recessive extra seminal root number phenotype, while six mutants (Cadenza0062, Cadenza0369, Cadenza0393, Cadenza0465, Cadenza0818 and Cadenza1273) show lower seminal root number phenotypes most likely originating from defects in the formation and activation of seminal root primordia. Segregation analysis in F2 populations suggest that the phenotype of Cadenza0900 is controlled by multiple loci whereas the Cadenza0062 phenotype fits a 3:1 mutant:wild-type segregation ratio characteristic of dominant single gene action. This work highlights the potential to use the sequenced wheat mutant population as a forward genetic resource to uncover novel variation in agronomic traits, such as seminal root architecture.
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Affiliation(s)
- Oluwaseyi Shorinola
- Bioscience Eastern and Central Africa - International Livestock Research Institute, Nairobi, PO Box 30709, Kenya
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ryan Kaye
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK, and
| | - Guy Golan
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Zvi Peleg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Stefan Kepinski
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK, and
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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26
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Li L, Xu Y, Ren Y, Guo Z, Li J, Tong Y, Lin T, Cui D. Comparative Proteomic Analysis Provides Insights into the Regulatory Mechanisms of Wheat Primary Root Growth. Sci Rep 2019; 9:11741. [PMID: 31409818 PMCID: PMC6692329 DOI: 10.1038/s41598-019-47926-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 07/26/2019] [Indexed: 12/22/2022] Open
Abstract
Plant roots are vital for acquiring nutrients and water from soil. However, the mechanisms regulating root growth in hexaploid wheat remain to be elucidated. Here, an integrated comparative proteome study on the roots of two varieties and their descendants with contrasting root phenotypes was performed. A total of 80 differentially expressed proteins (DEPs) associated with the regulation of primary root growth were identified, including two plant steroid biosynthesis related proteins and nine class III peroxidases. Real-time PCR analysis showed that brassinosteroid (BR) biosynthesis pathway was significantly elevated in long-root plants compared with those short-root plants. Moreover, O2.- and H2O2 were distributed abundantly in both the root meristematic and elongation zones of long root plants, but only in the meristematic zone of short-root plants. The differential distribution of reactive oxygen species (ROS) in the root tips of different genotypes may be caused by the differential expression of peroxidases. Taken together, our results suggest that the regulation of wheat primary root growth is closely related to BR biosynthesis pathway and BR-mediated ROS distribution.
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Affiliation(s)
- Le Li
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
| | - Yanhua Xu
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
- Shangqiu Normal University, Shangqiu, China
| | - Yongzhe Ren
- College of Agronomy, Henan Agricultural University, Zhengzhou, China.
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China.
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China.
| | - Zhanyong Guo
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
| | - Jingjing Li
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
| | - Yiping Tong
- State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Tongbao Lin
- College of Agronomy, Henan Agricultural University, Zhengzhou, China.
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China.
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China.
| | - Dangqun Cui
- College of Agronomy, Henan Agricultural University, Zhengzhou, China.
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China.
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China.
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27
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Soriano JM, Alvaro F. Discovering consensus genomic regions in wheat for root-related traits by QTL meta-analysis. Sci Rep 2019; 9:10537. [PMID: 31332216 PMCID: PMC6646344 DOI: 10.1038/s41598-019-47038-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 07/09/2019] [Indexed: 11/25/2022] Open
Abstract
Root system architecture is crucial for wheat adaptation to drought stress, but phenotyping for root traits in breeding programmes is difficult and time-consuming owing to the belowground characteristics of the system. Identifying quantitative trait loci (QTLs) and linked molecular markers and using marker-assisted selection is an efficient way to increase selection efficiency and boost genetic gains in breeding programmes. Hundreds of QTLs have been identified for different root traits in the last few years. In the current study, consensus QTL regions were identified through QTL meta-analysis. First, a consensus map comprising 7352 markers was constructed. For the meta-analysis, 754 QTLs were retrieved from the literature and 634 of them were projected onto the consensus map. Meta-analysis grouped 557 QTLs in 94 consensus QTL regions, or meta-QTLs (MQTLs), and 18 QTLs remained as singletons. The recently published genome sequence of wheat was used to search for gene models within the MQTL peaks. As a result, gene models for 68 of the 94 Root_MQTLs were found, 35 of them related to root architecture and/or drought stress response. This work will facilitate QTL cloning and pyramiding to develop new cultivars with specific root architecture for coping with environmental constraints.
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Affiliation(s)
- Jose Miguel Soriano
- Sustainable Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), Lleida, Spain.
| | - Fanny Alvaro
- Sustainable Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), Lleida, Spain
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28
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Khasanova A, Lovell JT, Bonnette J, Weng X, Jenkins J, Yoshinaga Y, Schmutz J, Juenger TE. The Genetic Architecture of Shoot and Root Trait Divergence Between Mesic and Xeric Ecotypes of a Perennial Grass. FRONTIERS IN PLANT SCIENCE 2019; 10:366. [PMID: 31019518 PMCID: PMC6458277 DOI: 10.3389/fpls.2019.00366] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/08/2019] [Indexed: 05/16/2023]
Abstract
Environmental heterogeneity can drive patterns of functional trait variation and lead to the formation of locally adapted ecotypes. Plant ecotypes are often differentiated by suites of correlated root and shoot traits that share common genetic, developmental, and physiological relationships. For instance, although plant water loss is largely governed by shoot systems, root systems determine water access and constrain shoot water status. To evaluate the genetic basis of root and shoot trait divergence, we developed a recombinant inbred population derived from mesic and xeric ecotypes of the perennial grass Panicum hallii. Our study sheds light on the genetic architecture underlying the relationships between root and shoot traits. We identified several genomic "hotspots" which control suites of correlated root and shoot traits, thus indicating genetic coordination between plant organ systems in the process of ecotypic divergence. Genomic regions of colocalized quantitative trait locus (QTL) for the majority of shoot and root growth related traits were independent of colocalized QTL for shoot and root resource acquisition traits. The allelic effects of individual QTL underscore ecological specialization for drought adaptation between ecotypes and reveal possible hybrid breakdown through epistatic interactions. These results have implications for understanding the factors constraining or facilitating local adaptation in plants.
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Affiliation(s)
- Albina Khasanova
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
| | - John T. Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Jason Bonnette
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
| | - Xiaoyu Weng
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Yuko Yoshinaga
- United States Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Thomas E. Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
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29
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N’Diaye A, Haile JK, Nilsen KT, Walkowiak S, Ruan Y, Singh AK, Clarke FR, Clarke JM, Pozniak CJ. Haplotype Loci Under Selection in Canadian Durum Wheat Germplasm Over 60 Years of Breeding: Association With Grain Yield, Quality Traits, Protein Loss, and Plant Height. FRONTIERS IN PLANT SCIENCE 2018; 9:1589. [PMID: 30455711 PMCID: PMC6230583 DOI: 10.3389/fpls.2018.01589] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/15/2018] [Indexed: 05/21/2023]
Abstract
Durum wheat was introduced in the southern prairies of western Canada in the late nineteenth century. Breeding efforts have mainly focused on improving quality traits to meet the pasta industry demands. For this study, 192 durum wheat lines were genotyped using the Illumina 90K Infinium iSelect assay, and resulted in a total of 14,324 polymorphic SNPs. Genetic diversity changed over time, declining during the first 20 years of breeding in Canada, then increased in the late 1980s and early 1990s. We scanned the genome for signatures of selection, using the total variance Fst-based outlier detection method (Lositan), the hierarchical island model (Arlequin) and the Bayesian genome scan method (BayeScan). A total of 407 outliers were identified and clustered into 84 LD-based haplotype loci, spanning all 14 chromosomes of the durum wheat genome. The association analysis detected 54 haplotype loci, of which 39% contained markers with a complete reversal of allelic state. This tendency to fixation of favorable alleles corroborates the success of the Canadian durum wheat breeding programs over time. Twenty-one haplotype loci were associated with multiple traits. In particular, hap_4B_1 explained 20.6, 17.9 and 16.6% of the phenotypic variance of pigment loss, pasta b∗ and dough extensibility, respectively. The locus hap_2B_9 explained 15.9 and 17.8% of the variation of protein content and protein loss, respectively. All these pleiotropic haplotype loci offer breeders the unique opportunity for further improving multiple traits, facilitating marker-assisted selection in durum wheat, and could help in identifying genes as functional annotations of the wheat genome become available.
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Affiliation(s)
- Amidou N’Diaye
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jemanesh K. Haile
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kirby T. Nilsen
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Sean Walkowiak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yuefeng Ruan
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Swift Current, SK, Canada
| | - Asheesh K. Singh
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Fran R. Clarke
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Swift Current, SK, Canada
| | - John M. Clarke
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Curtis J. Pozniak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
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De Vita P, Avio L, Sbrana C, Laidò G, Marone D, Mastrangelo AM, Cattivelli L, Giovannetti M. Genetic markers associated to arbuscular mycorrhizal colonization in durum wheat. Sci Rep 2018; 8:10612. [PMID: 30006562 PMCID: PMC6045686 DOI: 10.1038/s41598-018-29020-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/04/2018] [Indexed: 11/09/2022] Open
Abstract
In this work we investigated the variability and the genetic basis of susceptibility to arbuscular mycorrhizal (AM) colonization of wheat roots. The mycorrhizal status of wild, domesticated and cultivated tetraploid wheat accessions, inoculated with the AM species Funneliformis mosseae, was evaluated. In addition, to detect genetic markers in linkage with chromosome regions involved in AM root colonization, a genome wide association analysis was carried out on 108 durum wheat varieties and two AM fungal species (F. mosseae and Rhizoglomus irregulare). Our findings showed that a century of breeding on durum wheat and the introgression of Reduced height (Rht) genes associated with increased grain yields did not select against AM symbiosis in durum wheat. Seven putative Quantitative Trait Loci (QTLs) linked with durum wheat mycorrhizal susceptibility in both experiments, located on chromosomes 1A, 2B, 5A, 6A, 7A and 7B, were detected. The individual QTL effects (r2) ranged from 7 to 16%, suggesting a genetic basis for this trait. Marker functional analysis identified predicted proteins with potential roles in host-parasite interactions, degradation of cellular proteins, homeostasis regulation, plant growth and disease/defence. The results of this work emphasize the potential for further enhancement of root colonization exploiting the genetic variability present in wheat.
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Affiliation(s)
- Pasquale De Vita
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Cerealicoltura e Colture Industriali, S.S. 673 km 25 + 200, 71121, Foggia, Italy.
| | - Luciano Avio
- Dipartimento di Scienze Agrarie, Alimentari e Agro-Ambientali, Università di Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | | | - Giovanni Laidò
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Cerealicoltura e Colture Industriali, S.S. 673 km 25 + 200, 71121, Foggia, Italy
| | - Daniela Marone
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Cerealicoltura e Colture Industriali, S.S. 673 km 25 + 200, 71121, Foggia, Italy
| | - Anna M Mastrangelo
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Cerealicoltura e Colture Industriali, S.S. 673 km 25 + 200, 71121, Foggia, Italy
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Cerealicoltura e Colture Industriali, Via Stezzano 24, 24126, Bergamo, Italy
| | - Luigi Cattivelli
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Genomica e Bioinformatica, Via San Protaso 302, 29017, Fiorenzuola d'Arda, (PC), Italy
| | - Manuela Giovannetti
- Dipartimento di Scienze Agrarie, Alimentari e Agro-Ambientali, Università di Pisa, Via del Borghetto 80, 56124, Pisa, Italy
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Ren Y, Qian Y, Xu Y, Zou C, Liu D, Zhao X, Zhang A, Tong Y. Characterization of QTLs for Root Traits of Wheat Grown under Different Nitrogen and Phosphorus Supply Levels. FRONTIERS IN PLANT SCIENCE 2017; 8:2096. [PMID: 29312372 PMCID: PMC5732362 DOI: 10.3389/fpls.2017.02096] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 11/24/2017] [Indexed: 05/21/2023]
Abstract
Root is important in acquiring nutrients from soils. Developing marker-assisted selection for wheat root traits can help wheat breeders to select roots desirable for efficient acquisition of nutrients. A recombinant inbred line (RIL) population derived from wheat varieties Xiaoyan 54 and Jing 411 was used to detect QTLs for maximum root length and root dry weight (RDW) under control, low nitrogen and low phosphorus conditions in hydrophobic culture (HC). We totally detected 17 QTLs for the investigated root traits located at 13 loci on 11 chromosomes. These loci differentially expressed under different nutrient supplying levels. The RILs simultaneously harboring positive alleles or negative alleles of the most significant three QTLs for RDW, qRDW.CK-2A, qRDW.CK-2D, and qRDW.CK-3B, were selected for soil column culture (SC) trial to verify the effects of these QTLs under soil conditions. The RILs pyramiding the positive alleles not only had significantly higher shoot dry weight, RDW, nitrogen and phosphorus uptake in all the three treatments of the HC trial, but also had significantly higher RDW distribution in both the top- and sub-soils in the SC trial than those pyramiding the negative alleles. These results suggested that QTL analysis based on hydroponic culture can provide useful information for molecular design of wheat with large and deep root system.
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Affiliation(s)
- Yongzhe Ren
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
| | | | - Yanhua Xu
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
| | - ChunQin Zou
- China Agricultural University, Beijing, China
| | - Dongcheng Liu
- State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Xueqiang Zhao
- State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Aimin Zhang
- State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yiping Tong
- State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Sciences, Chinese Academy of Sciences, Beijing, China
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Kulkarni M, Soolanayakanahally R, Ogawa S, Uga Y, Selvaraj MG, Kagale S. Drought Response in Wheat: Key Genes and Regulatory Mechanisms Controlling Root System Architecture and Transpiration Efficiency. Front Chem 2017; 5:106. [PMID: 29259968 PMCID: PMC5723305 DOI: 10.3389/fchem.2017.00106] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/07/2017] [Indexed: 12/24/2022] Open
Abstract
Abiotic stresses such as, drought, heat, salinity, and flooding threaten global food security. Crop genetic improvement with increased resilience to abiotic stresses is a critical component of crop breeding strategies. Wheat is an important cereal crop and a staple food source globally. Enhanced drought tolerance in wheat is critical for sustainable food production and global food security. Recent advances in drought tolerance research have uncovered many key genes and transcription regulators governing morpho-physiological traits. Genes controlling root architecture and stomatal development play an important role in soil moisture extraction and its retention, and therefore have been targets of molecular breeding strategies for improving drought tolerance. In this systematic review, we have summarized evidence of beneficial contributions of root and stomatal traits to plant adaptation to drought stress. Specifically, we discuss a few key genes such as, DRO1 in rice and ERECTA in Arabidopsis and rice that were identified to be the enhancers of drought tolerance via regulation of root traits and transpiration efficiency. Additionally, we highlight several transcription factor families, such as, ERF (ethylene response factors), DREB (dehydration responsive element binding), ZFP (zinc finger proteins), WRKY, and MYB that were identified to be both positive and negative regulators of drought responses in wheat, rice, maize, and/or Arabidopsis. The overall aim of this review is to provide an overview of candidate genes that have been identified as regulators of drought response in plants. The lack of a reference genome sequence for wheat and non-transgenic approaches for manipulation of gene functions in wheat in the past had impeded high-resolution interrogation of functional elements, including genes and QTLs, and their application in cultivar improvement. The recent developments in wheat genomics and reverse genetics, including the availability of a gold-standard reference genome sequence and advent of genome editing technologies, are expected to aid in deciphering of the functional roles of genes and regulatory networks underlying adaptive phenological traits, and utilizing the outcomes of such studies in developing drought tolerant cultivars.
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Affiliation(s)
- Manoj Kulkarni
- Canadian Wheat Improvement Flagship Program, National Research Council Canada (NRC-CNRC), Saskatoon, SK, Canada
| | - Raju Soolanayakanahally
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
| | - Satoshi Ogawa
- Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yusaku Uga
- Institute of Crop Science (NICS), National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Michael G. Selvaraj
- Agrobioversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Sateesh Kagale
- Canadian Wheat Improvement Flagship Program, National Research Council Canada (NRC-CNRC), Saskatoon, SK, Canada
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