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Nouraei S, Mia MS, Liu H, Turner NC, Khan JM, Yan G. Proteomic analysis of near-isogenic lines reveals key biomarkers on wheat chromosome 4B conferring drought tolerance. THE PLANT GENOME 2024; 17:e20343. [PMID: 37199103 DOI: 10.1002/tpg2.20343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/05/2023] [Accepted: 03/27/2023] [Indexed: 05/19/2023]
Abstract
Drought is a major constraint for wheat production that is receiving increased attention due to global climate change. This study conducted isobaric tags for relative and absolute quantitation proteomic analysis on near-isogenic lines to shed light on the underlying mechanism of qDSI.4B.1 quantitative trait loci (QTL) on the short arm of chromosome 4B conferring drought tolerance in wheat. Comparing tolerant with susceptible isolines, 41 differentially expressed proteins were identified to be responsible for drought tolerance with a p-value of < 0.05 and fold change >1.3 or <0.7. These proteins were mainly enriched in hydrogen peroxide metabolic activity, reactive oxygen species metabolic activity, photosynthetic activity, intracellular protein transport, cellular macromolecule localization, and response to oxidative stress. Prediction of protein interactions and pathways analysis revealed the interaction between transcription, translation, protein export, photosynthesis, and carbohydrate metabolism as the most important pathways responsible for drought tolerance. The five proteins, including 30S ribosomal protein S15, SRP54 domain-containing protein, auxin-repressed protein, serine hydroxymethyltransferase, and an uncharacterized protein with encoding genes on 4BS, were suggested as candidate proteins responsible for drought tolerance in qDSI.4B.1 QTL. The gene coding SRP54 protein was also one of the differentially expressed genes in our previous transcriptomic study.
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Affiliation(s)
- Sina Nouraei
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, Western Australia, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Western Australia, Australia
| | - Md Sultan Mia
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Western Australia, Australia
- Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
| | - Hui Liu
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, Western Australia, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Western Australia, Australia
| | - Neil C Turner
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, Western Australia, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Western Australia, Australia
| | - Javed M Khan
- Proteomics International, Crawley, Western Australia, Australia
- Harry Perkins Institute of Medical Research, QEII Medical Centre, The University of Western Australia, Crawley, Western Australia, Australia
| | - Guijun Yan
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, Western Australia, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Western Australia, Australia
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2
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Halder T, Stroeher E, Liu H, Chen Y, Yan G, Siddique KHM. Protein biomarkers for root length and root dry mass on chromosomes 4A and 7A in wheat. J Proteomics 2024; 291:105044. [PMID: 37931703 DOI: 10.1016/j.jprot.2023.105044] [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: 08/25/2023] [Revised: 10/16/2023] [Accepted: 10/22/2023] [Indexed: 11/08/2023]
Abstract
Improving the wheat (Triticum aestivum L.) root system is important for enhancing grain yield and climate resilience. Total root length (RL) and root dry mass (RM) significantly contribute to water and nutrient acquisition directly impacting grain yield and stress tolerance. This study used label-free quantitative proteomics to identify proteins associated with RL and RM in wheat near-isogenic lines (NILs). NIL pair 6 had 113 and NIL pair 9 had 30 differentially abundant proteins (DAPs). Three of identified DAPs located within the targeted genomic regions (GRs) of NIL pairs 6 (qDT.4A.1) and 9 (QHtscc.ksu-7A), showed consistent gene expressions at the protein and mRNA transcription (qRT-PCR) levels for asparagine synthetase (TraesCS4A02G109900), signal recognition particle 19 kDa protein (TraesCS7A02G333600) and 3,4-dihydroxy-2-butanone 4-phosphate synthase (TraesCS7A02G415600). This study discovered, for the first time, the involvement of these proteins as candidate biomarkers for increased RL and RM in wheat. However, further functional validation is required to ascertain their practical applicability in wheat root breeding. SIGNIFICANCE OF THE STUDY: Climate change has impacted global demand for wheat (Triticum aestivum L.). Root traits such as total root length (RL) and root dry mass (RM) are crucial for water and nutrient uptake and tolerance to abiotic stresses such as drought, salinity, and nutrient imbalance in wheat. Improving RL and RM could significantly enhance wheat grain yield and climate resilience. However, breeding for these traits has been limited by lack of appropriate root phenotyping methods, advanced genotypes, and the complex nature of the wheat genome. In this study, we used a semi-hydroponic root phenotyping system to collect accurate root data, near-isogenic lines (NILs; isolines with similar genetic backgrounds but contrasting target genomic regions (GRs)) and label-free quantitative proteomics to explore the molecular mechanisms underlying high RL and RM in wheat. We identified differentially abundant proteins (DAPs) and their molecular pathways in NIL pairs 6 (GR: qDT.4A.1) and 9 (GR: QHtscc.ksu-7A), providing a foundation for further molecular investigations. Furthermore, we identified three DAPs within the target GRs of the NIL pairs with differential expression at the transcript level, as confirmed by qRT-PCR analysis which could serve as candidate protein biomarkers for RL and RM improvement.
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Affiliation(s)
- Tanushree Halder
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; Department of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka 1207, Bangladesh.
| | - Elke Stroeher
- Centre for Microscopy, Characterisation & Analysis, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Hui Liu
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.
| | - Yinglong Chen
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Guijun Yan
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Kadambot H M Siddique
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.
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Xu S, Fei Y, Wang Y, Zhao W, Hou L, Cao Y, Wu M, Wu H. Identification of a Seed Vigor-Related QTL Cluster Associated with Weed Competitive Ability in Direct-Seeded Rice (Oryza Sativa L.). RICE (NEW YORK, N.Y.) 2023; 16:45. [PMID: 37831291 PMCID: PMC10575835 DOI: 10.1186/s12284-023-00664-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 09/30/2023] [Indexed: 10/14/2023]
Abstract
Direct seeding of rice (Oryza sativa L.) is a low-labor and sustainable cultivation method that is used worldwide. Seed vigor and early vigor are important traits associated with seedling stand density (SSD) and weed competitive ability (WCA), which are key factors in direct-seeded rice (DSR) cultivation systems. Here, we developed a set of chromosome segment substitution lines with Xiushui134 as receptor parent and Yangdao6 as donor parent and used these lines as a mapping population to identify quantitative trait loci (QTLs) for seed vigor, which we evaluated based on germinability-related indicators (germination percentage (GP), germination energy (GE), and germination index (GI)) and seedling vigor-related indicators (root number (RN), root length (RL), and shoot length (SL) at 14 days after imbibition) under controlled conditions in an incubator. Ten QTLs were detected across four chromosomes, of which a cluster of QTLs (qGP11, qGE11, qGI11, and qRL11) co-localized on Chr. 11 with high LOD values (12.03, 8.13, 7.14, and 8.75, respectively). Fine mapping narrowed down the QTL cluster to a 0.7-Mb interval between RM26797 and RM6680. Further analysis showed that the QTL cluster has a significant effect (p < 0.01) on early vigor under hydroponic culture (root length, total dry weight) and direct seeding conditions (tiller number, aboveground dry weight). Thus, our combined analysis revealed that the QTL cluster influenced both seed vigor and early vigor. Identifying favorable alleles at this QTL cluster could facilitate the improvement of SSD and WCA, thereby addressing both major factors in DSR cultivation systems.
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Affiliation(s)
- Shan Xu
- College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, 311300, Zhejiang, China
| | - Yuexin Fei
- College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, 311300, Zhejiang, China
| | - Yue Wang
- College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, 311300, Zhejiang, China
| | - Wenjia Zhao
- College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, 311300, Zhejiang, China
| | - Luyan Hou
- College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, 311300, Zhejiang, China
| | - Yujie Cao
- College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, 311300, Zhejiang, China
| | - Min Wu
- College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, 311300, Zhejiang, China
| | - Hongkai Wu
- College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, 311300, Zhejiang, China.
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Liu G, Liu D, Zhang A, Liu H, Mia MS, Mullan D, Yan G. Identification of KASP markers and candidate genes for drought tolerance in wheat using 90K SNP array genotyping of near-isogenic lines targeting a 4BS quantitative trait locus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:190. [PMID: 37584740 PMCID: PMC10432333 DOI: 10.1007/s00122-023-04438-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023]
Abstract
KEY MESSAGE This study identified a novel SNP and developed a highly efficient KASP marker for drought tolerance in wheat by genotyping NILs targeting a major QTL for drought tolerance using an SNP array and validation with commercial varieties. Common wheat (Triticum aestivum L.) is an important winter crop worldwide and a typical allopolyploid with a large and complex genome. With global warming, the environmental volatility and incidence of drought in wheat-producing areas will increase. Molecular markers for drought tolerance are urgently needed to enhance drought tolerance breeding. Here, we genotyped four near-isogenic line (NIL) pairs targeting a major QTL qDSI.4B.1 on wheat chromosome arm 4BS for drought tolerance using the 90K SNP Illumina iSelect array and discovered a single nucleotide polymorphism (SNP) (Excalibur_c100336_106) with consistent genotype-phenotype associations among all four NIL pairs and their parents. Then, we converted the SNP into a Kompetitive Allele-Specific PCR (KASP) marker, with an accuracy of 100% for the four NIL pairs and their parents and as high as 81.8% for the 44 tested wheat lines with known phenotypes collected from Australia and China. Two genes near this SNP were suggested as candidate genes for drought tolerance in wheat after checking the Chinese Spring reference genome annotation version 1.1. One gene, TraesCS4B02G085300, encodes an F-box protein reportedly related to the ABA network, a main pathway for drought tolerance, and another gene, TraesCS4B02G085400, encodes a calcineurin-like metallophos-phoesterase transmembrane protein, which participates in Ca2+-dependent phosphorylation regulatory system. Based on this work and previous research on pre-harvest sprouting, we established a quick and efficient general SQV-based approach for KASP marker development, integrating genotyping by SNP arrays (S) using NILs targeting major QTL for a specific trait (Q) and validating them with commercial varieties (V). The identified SNP and developed KASP marker could be applied to marker-assisted selection in drought breeding, and further study of the candidate genes may improve our understanding of drought tolerance in wheat.
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Affiliation(s)
- Guannan Liu
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
| | - Dongcheng Liu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agriculture University, Baoding, 071000 Hebei China
| | - Aimin Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agriculture University, Baoding, 071000 Hebei China
| | - Hui Liu
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
| | - Md Sultan Mia
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
| | - Daniel Mullan
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
- InterGrain Pty. Ltd., 19 Ambitious Link, Bibra Lake, WA 6163 Australia
| | - Guijun Yan
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
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Ferrari RC, Kawabata AB, Ferreira SS, Hartwell J, Freschi L. A matter of time: regulatory events behind the synchronization of C4 and crassulacean acid metabolism in Portulaca oleracea. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4867-4885. [PMID: 35439821 DOI: 10.1093/jxb/erac163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/14/2022] [Indexed: 06/14/2023]
Abstract
Portulaca species can switch between C4 and crassulacean acid metabolism (CAM) depending on environmental conditions. However, the regulatory mechanisms behind this rare photosynthetic adaptation remain elusive. Using Portulaca oleracea as a model system, here we investigated the involvement of the circadian clock, plant hormones, and transcription factors in coordinating C4 and CAM gene expression. Free-running experiments in constant conditions suggested that C4 and CAM gene expression are intrinsically connected to the circadian clock. Detailed time-course, drought, and rewatering experiments revealed distinct time frames for CAM induction and reversion (days versus hours, respectively), which were accompanied by changes in abscisic acid (ABA) and cytokinin metabolism and signaling. Exogenous ABA and cytokinins were shown to promote and repress CAM expression in P. oleracea, respectively. Moreover, the drought-induced decline in C4 transcript levels was completely recovered upon cytokinin treatment. The ABA-regulated transcription factor genes HB7, NFYA7, NFYC9, TT8, and ARR12 were identified as likely candidate regulators of CAM induction following this approach, whereas NFYC4 and ARR9 were connected to C4 expression patterns. Therefore, we provide insights into the signaling events controlling C4-CAM transitions in response to water availability and over the day/night cycle, highlighting candidate genes for future functional studies in the context of facultative C4-CAM photosynthesis.
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Affiliation(s)
- Renata Callegari Ferrari
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brasil
| | - Aline Bastos Kawabata
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brasil
| | - Sávio Siqueira Ferreira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brasil
| | - James Hartwell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Luciano Freschi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brasil
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6
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Nouraei S, Mia MS, Liu H, Turner NC, Yan G. Transcriptome Analyses of Near Isogenic Lines Reveal Putative Drought Tolerance Controlling Genes in Wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:857829. [PMID: 35422827 PMCID: PMC9005202 DOI: 10.3389/fpls.2022.857829] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/24/2022] [Indexed: 05/08/2023]
Abstract
Drought stress, especially at the grain-filling stage, is a major constraint for wheat production. Drought tolerance is a complex trait controlled by a large array of genes and pathways. This study conducted gene expression profiling on two pairs of near-isogenic lines (NILs) for an important qDSI.4B.1 QTL conferring drought tolerance on the short arm of chromosome 4B in wheat. Analysis showed 1,614 genome-wide differentially expressed genes (DEGs) between the tolerant and susceptible isolines in both NIL pairs. Six common DEGs were found between NIL1 and NIL2 at both 7 and 14 days after stress induction, with two of them having single nucleotide polymorphism (SNP) variants. These six genes that were confirmed by quantitative real-time PCR (qRT-PCR) expression analysis are considered candidate genes for drought tolerance mediated by qDSI.4B.1 QTL with their main contributions to gene regulation, cell elongation, protein quality control, secondary metabolism, and hormone signaling. These six candidate genes and the highest number of DEGs and variants (SNPs/indels) were located between 49 and 137 Mbp of 4BS, making this interval the most probable location for the qDSI.4B.1 locus. Additionally, 765 and 84 DEGs were detected as responsive genes to drought stress in tolerant and susceptible isolines, respectively. According to gene ontology (GO), protein phosphorylation, oxidation reduction, and regulation of transcription were top biological processes involved in the drought response and tolerance. These results provide insights into stress responses regulated by the 4BS locus and have identified candidate genes and genetic markers that can be used for fine mapping of the qDSI.4B.1 locus and, ultimately, in wheat breeding programs for drought tolerance.
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Affiliation(s)
- Sina Nouraei
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Md Sultan Mia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- Department of Primary Industries and Regional Development, Northam, WA, Australia
| | - Hui Liu
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Neil C. Turner
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Guijun Yan
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
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7
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Tsugawa H, Rai A, Saito K, Nakabayashi R. Metabolomics and complementary techniques to investigate the plant phytochemical cosmos. Nat Prod Rep 2021; 38:1729-1759. [PMID: 34668509 DOI: 10.1039/d1np00014d] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2021Plants and their associated microbial communities are known to produce millions of metabolites, a majority of which are still not characterized and are speculated to possess novel bioactive properties. In addition to their role in plant physiology, these metabolites are also relevant as existing and next-generation medicine candidates. Elucidation of the plant metabolite diversity is thus valuable for the successful exploitation of natural resources for humankind. Herein, we present a comprehensive review on recent metabolomics approaches to illuminate molecular networks in plants, including chemical isolation and enzymatic production as well as the modern metabolomics approaches such as stable isotope labeling, ultrahigh-resolution mass spectrometry, metabolome imaging (spatial metabolomics), single-cell analysis, cheminformatics, and computational mass spectrometry. Mass spectrometry-based strategies to characterize plant metabolomes through metabolite identification and annotation are described in detail. We also highlight the use of phytochemical genomics to mine genes associated with specialized metabolites' biosynthesis. Understanding the metabolic diversity through biotechnological advances is fundamental to elucidate the functions of the plant-derived specialized metabolome.
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Affiliation(s)
- Hiroshi Tsugawa
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. .,RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei, Tokyo 184-8588, Japan.,Graduate School of Medical Life Science, Yokohama City University, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Amit Rai
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. .,Plant Molecular Science Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. .,Plant Molecular Science Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Ryo Nakabayashi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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Bohra A, Kilian B, Sivasankar S, Caccamo M, Mba C, McCouch SR, Varshney RK. Reap the crop wild relatives for breeding future crops. Trends Biotechnol 2021; 40:412-431. [PMID: 34629170 DOI: 10.1016/j.tibtech.2021.08.009] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/30/2021] [Accepted: 08/30/2021] [Indexed: 02/07/2023]
Abstract
Crop wild relatives (CWRs) have provided breeders with several 'game-changing' traits or genes that have boosted crop resilience and global agricultural production. Advances in breeding and genomics have accelerated the identification of valuable CWRs for use in crop improvement. The enhanced genetic diversity of breeding pools carrying optimum combinations of favorable alleles for targeted crop-growing regions is crucial to sustain genetic gain. In parallel, growing sequence information on wild genomes in combination with precise gene-editing tools provide a fast-track route to transform CWRs into ideal future crops. Data-informed germplasm collection and management strategies together with adequate policy support will be equally important to improve access to CWRs and their sustainable use to meet food and nutrition security targets.
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Affiliation(s)
- Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR), 208024 Kanpur, India
| | | | - Shoba Sivasankar
- International Atomic Energy Agency (IAEA), Vienna International Centre, 1400 Vienna, Austria
| | | | - Chikelu Mba
- Food and Agriculture Organization of the United Nations (FAO), Rome 00153, Italy
| | - Susan R McCouch
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA.
| | - Rajeev K Varshney
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA 6150, Australia.
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Bhattarai R, Liu H, Siddique KHM, Yan G. Characterisation of a 4A QTL for Metribuzin Resistance in Wheat by Developing Near-Isogenic Lines. PLANTS (BASEL, SWITZERLAND) 2021; 10:1856. [PMID: 34579389 PMCID: PMC8466451 DOI: 10.3390/plants10091856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/26/2021] [Accepted: 09/05/2021] [Indexed: 11/17/2022]
Abstract
Wheat (Triticum aestivum L.) production is constantly affected by weeds in the farming system. Chemical-based weed management is widely practiced; broad-spectrum herbicides such as metribuzin have been successfully used to control weeds in Australia and elsewhere of the world. Breeding metribuzin-resistant wheat through genetic improvement is needed for effective control of weeds. Quantitative trait loci (QTLs) mapping efforts identified a major QTL on wheat chromosome 4A, explaining up to 20% of the phenotypic variance for metribuzin resistance. The quantitative nature of inheritance of this QTL signifies the importance of near-isogenic lines (NILs), which can convert a quantitative trait into a Mendelian factor for better resolution of the QTL. In the current study, NILs were developed using a heterogeneous inbred family method combined with a fast generation-cycling system in a population of Chuan Mai 25 (resistant) and Ritchie (susceptible). Seven pairs of NILs targeting the 4A QTL for metribuzin resistance were confirmed with a molecular marker and phenotyping. The resistant allele from the resistant parent increased metribuzin resistance by 63-85% (average 69%) compared with the susceptible allele from the susceptible parent. Segregation analysis in the NIL pairs for thousand grain weight (TGW) (g), biomass per plant (kg), tillers per plant, plant height (cm), yield per plant, and powdery mildew visual score (0-9) indicated that these traits were linked with metribuzin resistance. Similarly, TGW was observed to co-segregate with metribuzin resistance in most confirmed NILs, signifying that the two traits are controlled by closely linked genes. The most contrasting NILs can be further characterised by transcriptomic and proteomic analyses to identify the candidate genes responsible for metribuzin resistance.
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Affiliation(s)
- Rudra Bhattarai
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; (R.B.); (K.H.M.S.)
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Hui Liu
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; (R.B.); (K.H.M.S.)
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Kadambot H. M. Siddique
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; (R.B.); (K.H.M.S.)
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Guijun Yan
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; (R.B.); (K.H.M.S.)
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
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10
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Halder T, Liu H, Chen Y, Yan G, Siddique KHM. Identification of Candidate Genes for Root Traits Using Genotype-Phenotype Association Analysis of Near-Isogenic Lines in Hexaploid Wheat ( Triticum aestivum L.). Int J Mol Sci 2021; 22:3579. [PMID: 33808237 PMCID: PMC8038026 DOI: 10.3390/ijms22073579] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/09/2021] [Accepted: 03/25/2021] [Indexed: 11/17/2022] Open
Abstract
Global wheat (Triticum aestivum L.) production is constrained by different biotic and abiotic stresses, which are increasing with climate change. An improved root system is essential for adaptability and sustainable wheat production. In this study, 10 pairs of near-isogenic lines (NILs)-targeting four genomic regions (GRs) on chromosome arms 4BS, 4BL, 4AS, and 7AL of hexaploid wheat-were used to phenotype root traits in a semi-hydroponic system. Seven of the 10 NIL pairs significantly differed between their isolines for 11 root traits. The NIL pairs targeting qDSI.4B.1 GR varied the most, followed by the NIL pair targeting qDT.4A.1 and QHtscc.ksu-7A GRs. For pairs 5-7 targeting qDT.4A.1 GR, pair 6 significantly differed in the most root traits. Of the 4 NIL pairs targeting qDSI.4B.1 GR, pairs 2 and 4 significantly differed in 3 and 4 root traits, respectively. Pairs 9 and 10 targeting QHtscc.ksu-7A GR significantly differed in 1 and 4 root traits, respectively. Using the wheat 90K Illumina iSelect array, we identified 15 putative candidate genes associated with different root traits in the contrasting isolines, in which two UDP-glycosyltransferase (UGT)-encoding genes, TraesCS4A02G185300 and TraesCS4A02G442700, and a leucine-rich repeat receptor-like protein kinase (LRR-RLK)-encoding gene, TraesCS4A02G330900, also showed important functions for root trait control in other crops. This study characterized, for the first time, that these GRs control root traits in wheat, and identified candidate genes, although the candidate genes will need further confirmation and validation for marker-assisted wheat breeding.
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Affiliation(s)
- Tanushree Halder
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; (H.L.); (Y.C.); (G.Y.)
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka 1207, Bangladesh
| | - Hui Liu
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; (H.L.); (Y.C.); (G.Y.)
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Yinglong Chen
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; (H.L.); (Y.C.); (G.Y.)
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Guijun Yan
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; (H.L.); (Y.C.); (G.Y.)
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Kadambot H. M. Siddique
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; (H.L.); (Y.C.); (G.Y.)
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
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Bányai J, Maccaferri M, Láng L, Mayer M, Tóth V, Cséplő M, Pál M, Mészáros K, Vida G. Abiotic Stress Response of Near-Isogenic Spring Durum Wheat Lines under Different Sowing Densities. Int J Mol Sci 2021; 22:2053. [PMID: 33669605 PMCID: PMC7923076 DOI: 10.3390/ijms22042053] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/02/2021] [Accepted: 02/07/2021] [Indexed: 11/29/2022] Open
Abstract
A detailed study was made of changes in the plant development, morphology, physiology and yield biology of near-isogenic lines of spring durum wheat sown in the field with different plant densities in two consecutive years (2013-2014). An analysis was made of the drought tolerance of isogenic lines selected for yield QTLs (QYld.idw-2B and QYld.idw-3B), and the presence of QTL effects was examined in spring sowings. Comparisons were made of the traits of the isogenic pairs QYld.idw-3B++ and QYld.idw-3B-- both within and between the pairs. Changes in the polyamine content, antioxidant enzyme activity, chlorophyll content of the flag leaf and the normalized difference vegetation index (NDVI) of the plot were monitored in response to drought stress, and the relationship between these components and the yield was analyzed. In the case of moderate stress, differences between the NIL++ and NIL-- pairs appeared in the early dough stage, indicating that the QYld.idw-3B++ QTL region was able to maintain photosynthetic activity for a longer period, resulting in greater grain number and grain weight at the end of the growing period. The chlorophyll content of the flag leaf in phenophases Z77 and Z83 was significantly correlated with the grain number and grain weight of the main spike. The grain yield was greatly influenced by the treatment, while the genotype had a significant effect on the thousand-kernel weight and on the grain number and grain weight of the main spike. When the lines were compared in the non-irrigated treatment, significantly more grains and significantly higher grain weight were observed in the main spike in NIL++ lines, confirming the theory that the higher yields of the QYld.idw-3B++ lines when sown in spring and exposed to drought stress could be attributed to the positive effect of the "Kofa" QTL on chromosome 3B.
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Affiliation(s)
- Judit Bányai
- Centre for Agricultural Research, Agricultural Institute, ELKH, 2462 Martonvásár, Hungary; (L.L.); (M.M.); (V.T.); (M.C.); (M.P.); (K.M.); (G.V.)
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, 40126 Bologna, Italy;
| | - László Láng
- Centre for Agricultural Research, Agricultural Institute, ELKH, 2462 Martonvásár, Hungary; (L.L.); (M.M.); (V.T.); (M.C.); (M.P.); (K.M.); (G.V.)
| | - Marianna Mayer
- Centre for Agricultural Research, Agricultural Institute, ELKH, 2462 Martonvásár, Hungary; (L.L.); (M.M.); (V.T.); (M.C.); (M.P.); (K.M.); (G.V.)
| | - Viola Tóth
- Centre for Agricultural Research, Agricultural Institute, ELKH, 2462 Martonvásár, Hungary; (L.L.); (M.M.); (V.T.); (M.C.); (M.P.); (K.M.); (G.V.)
| | - Mónika Cséplő
- Centre for Agricultural Research, Agricultural Institute, ELKH, 2462 Martonvásár, Hungary; (L.L.); (M.M.); (V.T.); (M.C.); (M.P.); (K.M.); (G.V.)
| | - Magda Pál
- Centre for Agricultural Research, Agricultural Institute, ELKH, 2462 Martonvásár, Hungary; (L.L.); (M.M.); (V.T.); (M.C.); (M.P.); (K.M.); (G.V.)
| | - Klára Mészáros
- Centre for Agricultural Research, Agricultural Institute, ELKH, 2462 Martonvásár, Hungary; (L.L.); (M.M.); (V.T.); (M.C.); (M.P.); (K.M.); (G.V.)
| | - Gyula Vida
- Centre for Agricultural Research, Agricultural Institute, ELKH, 2462 Martonvásár, Hungary; (L.L.); (M.M.); (V.T.); (M.C.); (M.P.); (K.M.); (G.V.)
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12
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Liu H, Mullan D, Zhang C, Zhao S, Li X, Zhang A, Lu Z, Wang Y, Yan G. Major genomic regions responsible for wheat yield and its components as revealed by meta-QTL and genotype-phenotype association analyses. PLANTA 2020; 252:65. [PMID: 32970252 DOI: 10.1007/s00425-020-03466-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 09/12/2020] [Indexed: 12/17/2022]
Abstract
MAIN CONCLUSION Meta-QTL (MQTL) analysis was done for yield-related traits in wheat. Candidate genes were identified within the refined MQTL and further validated by genotype-phenotype association analysis. Extensive studies have been undertaken on quantitative trait locus/loci (QTL) for wheat yield and its component traits. This study conducted a meta-analysis of 381 QTL related to wheat yield under various environments, including irrigated, drought- and/or heat-stressed conditions. Markers flanking meta-QTL (MQTL) were mapped on the wheat reference genome for their physical positions. Putative candidate genes were examined for MQTL with a physical interval of less than 20 Mbp. A total of 86 MQTL were identified as responsible for yield, of which 34 were for irrigated environments, 39 for drought-stressed environments, 36 for heat-stressed environments, and 23 for both drought- and heat-stressed environments. The high-confidence genes within the physical positions of the MQTL flanking markers were screened in the reference genome RefSeq V1.0, which identified 210 putative candidate genes. The phenotypic data for 14 contrasting genotypes with either high or low yield performance-according to the Australian National Variety Trials-were associated with their genotypic data obtained through ddRAD sequencing, which validated 18 genes or gene clusters associated with MQTL that had important roles for wheat yield. The detected and refined MQTL and candidate genes will be useful for marker-assisted selection of high yield in wheat breeding.
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Affiliation(s)
- Hui Liu
- School of Plant Biology, Faculty of Science and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Daniel Mullan
- InterGrain Pty Ltd, 19 Ambitious Link, Bibra Lake, WA, 6163, Australia
| | - Chi Zhang
- Beijing Genomics Institute, Shenzhen, 518053, China
| | - Shancen Zhao
- Beijing Genomics Institute, Shenzhen, 518053, China
| | - Xin Li
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chicness Academy of Sciences, Beijing, 100101, China
| | - Aimin Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chicness Academy of Sciences, Beijing, 100101, China
| | - Zhanyuan Lu
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, No. 22, Yuquan Qu Zhaojun Lu, Hohhot, Inner Mongolia Autonomous Region, China
| | - Yong Wang
- Wheat Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Guijun Yan
- School of Plant Biology, Faculty of Science and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia.
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Khadka K, Raizada MN, Navabi A. Recent Progress in Germplasm Evaluation and Gene Mapping to Enable Breeding of Drought-Tolerant Wheat. FRONTIERS IN PLANT SCIENCE 2020; 11:1149. [PMID: 32849707 PMCID: PMC7417477 DOI: 10.3389/fpls.2020.01149] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 07/15/2020] [Indexed: 05/02/2023]
Abstract
There is a need to increase wheat productivity to meet the food demands of the ever-growing human population. However, accelerated development of high yielding varieties is hindered by drought, which is worsening due to climate change. In this context, germplasm diversity is central to the development of drought-tolerant wheat. Extensive collections of these genetic resources are conserved in national and international genebanks. In addition to phenotypic assessments, the use of advanced molecular techniques (e.g., genotype by sequencing) to identify quantitative trait loci (QTLs) for drought tolerance related traits is useful for genome- and marker-assisted selection based approaches. Therefore, to assist wheat breeders at a critical time, we searched the recent peer-reviewed literature (2011-current), first, to identify wheat germplasm observed to be useful genetic sources for drought tolerance, and second, to report QTLs associated with drought tolerance. Though many breeders limit the parents used in breeding programs to a familiar core collection, the results of this review show that larger germplasm collections have been sources of useful genes for drought tolerance in wheat. The review also demonstrates that QTLs for drought tolerance in wheat are associated with diverse physio-morphological traits, at different growth stages. Here, we also briefly discuss the potential of genome engineering/editing to improve drought tolerance in wheat. The use of CRISPR-Cas9 and other gene-editing technologies can be used to fine-tune the expression of genes controlling drought adaptive traits, while high throughput phenotyping (HTP) techniques can potentially accelerate the selection process. These efforts are empowered by wheat researcher consortia.
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Affiliation(s)
- Kamal Khadka
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
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Yan X, Wang S, Yang B, Zhang W, Cao Y, Shi Y, Sun D, Jing R. QTL mapping for flag leaf-related traits and genetic effect of QFLW-6A on flag leaf width using two related introgression line populations in wheat. PLoS One 2020; 15:e0229912. [PMID: 32191715 PMCID: PMC7082017 DOI: 10.1371/journal.pone.0229912] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 02/17/2020] [Indexed: 11/29/2022] Open
Abstract
The flag leaf is the main organ of photosynthesis during grain-filling period of wheat, and flag leaf-related traits affect plant morphology and yield potential. In this study, two BC3F6 introgression line (IL) populations derived from the common recipient parent Lumai 14 with Jing 411 and Shaanhan 8675, respectively, were used to map quantitative trait loci (QTL) for flag leaf length (FLL), flag leaf width (FLW), flag leaf area (FLA) and chlorophyll content (CC) at flowering stage and 15 and 20 days after anthesis (DAA) in 2016–2017 (E1) and 2017–2018 (E2) two environments. A total of 14 and 15 QTLs for flag leaf-related traits were detected in Lumai 14 / Jing 411 and Lumai 14 / Shaanhan 8675 populations, respectively. Among them, Both QFLW-6A and QFLA-6A were detected in Lumai 14 / Jing 411 population under E2 and in Lumai 14 / Shaanhan 8675 population under E1 and E2 environments, respectively. QCCS2-3A from Lumai 14 / Jing 411 population and QCCS3-1A, QFLL-4A and QFLL-6A from Lumai 14 / Shaanhan 8675 population were repeatedly identified under two tested environments. Moreover, eight QTL clusters controlling flag leaf-related traits were identified, which provided a genetic basis for significant correlations in phenotype among these traits. On the other hand, positive alleles of QFLW-6A for FLW detected in two populations were derived from their donors. Eighteen lines and 44 lines carried this QTL were found in Lumai 14 / Jing 411 and Lumai 14 / Shaanhan 8675 populations, respectively. The means of FLW in these lines were wider than that of the recipient parent, Lumai 14, in two environments, suggesting that QFLW-6A played an important role for increasing FLW. The IL 124 in Lumai 14 / Jing 411 population and the IL 59 and IL 127 in Lumai 14 / Shaanhan 8675 population had five, five and four donor chromosomal segments which carried no other QTL controlling FLW than QFLW-6A, respectively. And the FLWs of these lines were significantly greater than that of Lumai 14 under two environments. So these lines and their donor parent can be regarded as potential near-isogenic lines. Further, a synteny analysis found QFLW-6A was near the 574,283,851–574,283,613 bp fragment on chromosome 6A and 10 genes were in the range of 500 kb upstream and downstream of the fragment. These results provide the basis for identification of candidate gene and map-based cloning and functional verification of the QTL.
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Affiliation(s)
- Xue Yan
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Shuguang Wang
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Bin Yang
- Wheat Research Institute, Shanxi Academy of Agricultural Sciences, Linfen, Shanxi, China
| | - Wenjun Zhang
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Yaping Cao
- Wheat Research Institute, Shanxi Academy of Agricultural Sciences, Linfen, Shanxi, China
| | - Yugang Shi
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Daizhen Sun
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, China
- * E-mail: (DS); (RJ)
| | - Ruilian Jing
- Chinese Academy of Agricultural Sciences, Institute of Crop Science, Beijing, China
- * E-mail: (DS); (RJ)
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15
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Lu L, Liu H, Wu Y, Yan G. Development and Characterization of Near-Isogenic Lines Revealing Candidate Genes for a Major 7AL QTL Responsible for Heat Tolerance in Wheat. FRONTIERS IN PLANT SCIENCE 2020; 11:1316. [PMID: 32983205 PMCID: PMC7485290 DOI: 10.3389/fpls.2020.01316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/11/2020] [Indexed: 05/22/2023]
Abstract
Wheat is one of the most important food crops in the world, but as a cool-season crop, it is more prone to heat stress, which severely affects crop production and grain quality. Heat tolerance in wheat is a quantitative trait, and the genes underlying reported quantitative trait loci (QTL) have rarely been identified. Near-isogenic lines (NILs) with a common genetic background but differing at a particular locus could turn quantitative traits into a Mendelian factor; therefore, they are suitable material for identifying candidate genes for targeted locus/loci. In this study, we developed and characterized NILs from two populations Cascades × Tevere and Cascades × W156 targeting a major 7AL QTL responsible for heat tolerance. Molecular marker screening and phenotyping for SPAD chlorophyll content and grain-yield-related traits confirmed four pairs of wheat NILs that contrasted for heat-stress responses. Genotyping the NILs using a 90K Infinium iSelect SNP array revealed five single nucleotide polymorphism (SNP) markers within the QTL interval that were distinguishable between the isolines. Seven candidate genes linked to the SNPs were identified as related to heat tolerance, and involved in important processes and pathways in response to heat stress. The confirmed multiple pairs of NILs and identified candidate genes in this study are valuable resources and information for further fine-mapping to clone major genes for heat tolerance.
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Affiliation(s)
- Lu Lu
- Faculty of Science, UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Hui Liu
- Faculty of Science, UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- *Correspondence: Hui Liu, ; Guijun Yan,
| | - Yu Wu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Guijun Yan
- Faculty of Science, UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- *Correspondence: Hui Liu, ; Guijun Yan,
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Wang X, Liu H, Liu G, Mia MS, Siddique KHM, Yan G. Phenotypic and genotypic characterization of near-isogenic lines targeting a major 4BL QTL responsible for pre-harvest sprouting in wheat. BMC PLANT BIOLOGY 2019; 19:348. [PMID: 31399046 PMCID: PMC6688225 DOI: 10.1186/s12870-019-1961-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/06/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND Resistance to pre-harvest sprouting (PHS) is one of the major objectives in wheat breeding programs. However, the complex quantitative nature of this trait presents challenges when breeding for PHS resistance. Characterization of PHS using near-isogenic lines (NILs) targeting major quantitative trait locus/loci (QTL/QTLs) can be an effective strategy for the identification of responsible genes and underlying mechanisms. RESULTS In this study, multiple pairs of NILs were developed and confirmed for a major QTL located on the 4BL chromosome arm that contributes to PHS resistance in wheat, using a combined heterogeneous inbred family method and a fast generation cycling system. Phenotypic characterization of these confirmed NILs revealed significant differences in PHS resistance between the isolines, where the presence of the resistant allele increased the resistance to sprouting on spikes by 54.0-81.9% (average 70.8%) and reduced seed germination by 59.4-70.5% (average 66.2%). The 90 K SNP genotyping assay on the confirmed NIL pairs identified eight SNPs on 4BL, associated with five candidate genes; two of the candidate genes were related to seed dormancy. Agronomic traits in the NIL pairs were investigated; both plant height and grain number per spike were positively correlated with PHS susceptibility. CONCLUSIONS This study confirmed multiple pairs of NILs and identified SNPs between PHS isolines, which are valuable resources for further fine-mapping of this locus to clone the major genes for PHS resistance and investigate the possible functional regulation of these genes on important agronomic traits, such as plant height and grain number per spike.
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Affiliation(s)
- Xingyi Wang
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Hui Liu
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia.
| | - Guannan Liu
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Md Sultan Mia
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
- Plant Breeding Division, Bangladesh Agricultural Research Institute, Joydebpur, Gazipur, 1701, Bangladesh
| | - Kadambot H M Siddique
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Guijun Yan
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia.
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