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Fu C, Zhou Y, Liu A, Chen R, Yin L, Li C, Mao H. Genome-wide association study for seedling heat tolerance under two temperature conditions in bread wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2024; 24:430. [PMID: 38773371 PMCID: PMC11107014 DOI: 10.1186/s12870-024-05116-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 05/08/2024] [Indexed: 05/23/2024]
Abstract
BACKGROUND As the greenhouse effect intensifies, global temperatures are steadily increasing, posing a challenge to bread wheat (Triticum aestivum L.) production. It is imperative to comprehend the mechanism of high temperature tolerance in wheat and implement breeding programs to identify and develop heat-tolerant wheat germplasm and cultivars. RESULTS To identify quantitative trait loci (QTL) related to heat stress tolerance (HST) at seedling stage in wheat, a panel of 253 wheat accessions which were re-sequenced used to conduct genome-wide association studies (GWAS) using the factored spectrally transformed linear mixed models (FaST-LMM). For most accessions, the growth of seedlings was found to be inhibited under heat stress. Analysis of the phenotypic data revealed that under heat stress conditions, the main root length, total root length, and shoot length of seedlings decreased by 47.46%, 49.29%, and 15.19%, respectively, compared to those in normal conditions. However, 17 varieties were identified as heat stress tolerant germplasm. Through GWAS analysis, a total of 115 QTLs were detected under both heat stress and normal conditions. Furthermore, 15 stable QTL-clusters associated with heat response were identified. By combining gene expression, haplotype analysis, and gene annotation information within the physical intervals of the 15 QTL-clusters, two novel candidate genes, TraesCS4B03G0152700/TaWRKY74-B and TraesCS4B03G0501400/TaSnRK3.15-B, were responsive to temperature and identified as potential regulators of HST in wheat at the seedling stage. CONCLUSIONS This study conducted a detailed genetic analysis and successfully identified two genes potentially associated with HST in wheat at the seedling stage, laying a foundation to further dissect the regulatory mechanism underlying HST in wheat under high temperature conditions. Our finding could serve as genomic landmarks for wheat breeding aimed at improving adaptation to heat stress in the face of climate change.
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Affiliation(s)
- Chao Fu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ying Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ankui Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rui Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Li Yin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cong Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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2
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Chang-Brahim I, Koppensteiner LJ, Beltrame L, Bodner G, Saranti A, Salzinger J, Fanta-Jende P, Sulzbachner C, Bruckmüller F, Trognitz F, Samad-Zamini M, Zechner E, Holzinger A, Molin EM. Reviewing the essential roles of remote phenotyping, GWAS and explainable AI in practical marker-assisted selection for drought-tolerant winter wheat breeding. FRONTIERS IN PLANT SCIENCE 2024; 15:1319938. [PMID: 38699541 PMCID: PMC11064034 DOI: 10.3389/fpls.2024.1319938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/13/2024] [Indexed: 05/05/2024]
Abstract
Marker-assisted selection (MAS) plays a crucial role in crop breeding improving the speed and precision of conventional breeding programmes by quickly and reliably identifying and selecting plants with desired traits. However, the efficacy of MAS depends on several prerequisites, with precise phenotyping being a key aspect of any plant breeding programme. Recent advancements in high-throughput remote phenotyping, facilitated by unmanned aerial vehicles coupled to machine learning, offer a non-destructive and efficient alternative to traditional, time-consuming, and labour-intensive methods. Furthermore, MAS relies on knowledge of marker-trait associations, commonly obtained through genome-wide association studies (GWAS), to understand complex traits such as drought tolerance, including yield components and phenology. However, GWAS has limitations that artificial intelligence (AI) has been shown to partially overcome. Additionally, AI and its explainable variants, which ensure transparency and interpretability, are increasingly being used as recognised problem-solving tools throughout the breeding process. Given these rapid technological advancements, this review provides an overview of state-of-the-art methods and processes underlying each MAS, from phenotyping, genotyping and association analyses to the integration of explainable AI along the entire workflow. In this context, we specifically address the challenges and importance of breeding winter wheat for greater drought tolerance with stable yields, as regional droughts during critical developmental stages pose a threat to winter wheat production. Finally, we explore the transition from scientific progress to practical implementation and discuss ways to bridge the gap between cutting-edge developments and breeders, expediting MAS-based winter wheat breeding for drought tolerance.
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Affiliation(s)
- Ignacio Chang-Brahim
- Unit Bioresources, Center for Health & Bioresources, AIT Austrian Institute of Technology, Tulln, Austria
| | | | - Lorenzo Beltrame
- Unit Assistive and Autonomous Systems, Center for Vision, Automation & Control, AIT Austrian Institute of Technology, Vienna, Austria
| | - Gernot Bodner
- Department of Crop Sciences, Institute of Agronomy, University of Natural Resources and Life Sciences Vienna, Tulln, Austria
| | - Anna Saranti
- Human-Centered AI Lab, Department of Forest- and Soil Sciences, Institute of Forest Engineering, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Jules Salzinger
- Unit Assistive and Autonomous Systems, Center for Vision, Automation & Control, AIT Austrian Institute of Technology, Vienna, Austria
| | - Phillipp Fanta-Jende
- Unit Assistive and Autonomous Systems, Center for Vision, Automation & Control, AIT Austrian Institute of Technology, Vienna, Austria
| | - Christoph Sulzbachner
- Unit Assistive and Autonomous Systems, Center for Vision, Automation & Control, AIT Austrian Institute of Technology, Vienna, Austria
| | - Felix Bruckmüller
- Unit Assistive and Autonomous Systems, Center for Vision, Automation & Control, AIT Austrian Institute of Technology, Vienna, Austria
| | - Friederike Trognitz
- Unit Bioresources, Center for Health & Bioresources, AIT Austrian Institute of Technology, Tulln, Austria
| | | | - Elisabeth Zechner
- Verein zur Förderung einer nachhaltigen und regionalen Pflanzenzüchtung, Zwettl, Austria
| | - Andreas Holzinger
- Human-Centered AI Lab, Department of Forest- and Soil Sciences, Institute of Forest Engineering, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Eva M. Molin
- Unit Bioresources, Center for Health & Bioresources, AIT Austrian Institute of Technology, Tulln, Austria
- Human-Centered AI Lab, Department of Forest- and Soil Sciences, Institute of Forest Engineering, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
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3
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Wang Z, Lai X, Wang C, Yang H, Liu Z, Fan Z, Li J, Zhang H, Liu M, Zhang Y. Exploring the Drought Tolerant Quantitative Trait Loci in Spring Wheat. PLANTS (BASEL, SWITZERLAND) 2024; 13:898. [PMID: 38592925 PMCID: PMC10975456 DOI: 10.3390/plants13060898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/24/2024] [Accepted: 03/01/2024] [Indexed: 04/11/2024]
Abstract
Drought-induced stress poses a significant challenge to wheat throughout its growth, underscoring the importance of identifying drought-stable quantitative trait loci (QTLs) for enhancing grain yield. Here, we evaluated 18 yield-related agronomic and physiological traits, along with their drought tolerance indices, in a recombinant inbred line population derived from the XC7 × XC21 cross. These evaluations were conducted under both non-stress and drought-stress conditions. Drought stress significantly reduced grain weight per spike and grain yield per plot. Genotyping the recombinant inbred line population using the wheat 90K single nucleotide polymorphism array resulted in the identification of 131 QTLs associated with the 18 traits. Drought stress also exerted negative impacts on grain formation and filling, directly leading to reductions in grain weight per spike and grain yield per plot. Among the identified QTLs, 43 were specifically associated with drought tolerance across the 18 traits, with 6 showing direct linkages to drought tolerance in wheat. These results provide valuable insights into the genetic mechanisms governing wheat growth and development, as well as the traits contributing to the drought tolerance index. Moreover, they serve as a theoretical foundation for the development of new wheat cultivars having exceptional drought tolerance and high yield potentials under both drought-prone and drought-free conditions.
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Affiliation(s)
- Zhong Wang
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (C.W.); (Z.F.); (J.L.); (H.Z.)
- Key Laboratory of Crop Ecophysiology and Farming System in Desert Oasis Region, Ministry of Agriculture, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
- Xinjiang Crop Chemical Control Engineering Technology Research Center, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
| | - Xiangjun Lai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China;
| | - Chunsheng Wang
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (C.W.); (Z.F.); (J.L.); (H.Z.)
- Key Laboratory of Crop Ecophysiology and Farming System in Desert Oasis Region, Ministry of Agriculture, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
- Xinjiang Crop Chemical Control Engineering Technology Research Center, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
| | - Hongmei Yang
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
- Xinjiang Laboratory of Special Environmental Microbiology, Institute of Applied Microbiology, Urumqi 830091, China
| | - Zihui Liu
- Department of Biochemistry, Baoding University, Baoding 071000, China;
| | - Zheru Fan
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (C.W.); (Z.F.); (J.L.); (H.Z.)
- Key Laboratory of Crop Ecophysiology and Farming System in Desert Oasis Region, Ministry of Agriculture, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
- Xinjiang Crop Chemical Control Engineering Technology Research Center, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
| | - Jianfeng Li
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (C.W.); (Z.F.); (J.L.); (H.Z.)
- Key Laboratory of Crop Ecophysiology and Farming System in Desert Oasis Region, Ministry of Agriculture, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
- Xinjiang Crop Chemical Control Engineering Technology Research Center, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
| | - Hongzhi Zhang
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (C.W.); (Z.F.); (J.L.); (H.Z.)
- Key Laboratory of Crop Ecophysiology and Farming System in Desert Oasis Region, Ministry of Agriculture, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
- Xinjiang Crop Chemical Control Engineering Technology Research Center, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
| | - Manshuang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China;
| | - Yueqiang Zhang
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (C.W.); (Z.F.); (J.L.); (H.Z.)
- Key Laboratory of Crop Ecophysiology and Farming System in Desert Oasis Region, Ministry of Agriculture, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
- Xinjiang Crop Chemical Control Engineering Technology Research Center, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
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4
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Nouraei S, Mia MS, Liu H, Turner NC, Yan G. Genome-wide association study of drought tolerance in wheat (Triticum aestivum L.) identifies SNP markers and candidate genes. Mol Genet Genomics 2024; 299:22. [PMID: 38430317 PMCID: PMC10908643 DOI: 10.1007/s00438-024-02104-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: 07/09/2023] [Accepted: 01/11/2024] [Indexed: 03/03/2024]
Abstract
Drought stress poses a severe threat to global wheat production, necessitating an in-depth exploration of the genetic basis for drought tolerance associated traits. This study employed a 90 K SNP array to conduct a genome-wide association analysis, unravelling genetic determinants of key traits related to drought tolerance in wheat, namely plant height, root length, and root and shoot dry weight. Using the mixed linear model (MLM) method on 125 wheat accessions subjected to both well-watered and drought stress treatments, we identified 53 SNPs significantly associated with stress susceptibility (SSI) and tolerance indices (STI) for the targeted traits. Notably, chromosomes 2A and 3B stood out with ten and nine associated markers, respectively. Across 17 chromosomes, 44 unique candidate genes were pinpointed, predominantly located on the distal ends of 1A, 1B, 1D, 2A, 3A, 3B, 4A, 6A, 6B, 7A, 7B, and 7D chromosomes. These genes, implicated in diverse functions related to plant growth, development, and stress responses, offer a rich resource for future investigation. A clustering pattern emerged, notably with seven genes associated with SSI for plant height and four genes linked to both STI of plant height and shoot dry weight, converging on specific regions of chromosome arms of 2AS and 3BL. Additionally, shared genes encoding polygalacturonase, auxilin-related protein 1, peptide deformylase, and receptor-like kinase underscored the interconnectedness between plant height and shoot dry weight. In conclusion, our findings provide insights into the molecular mechanisms governing wheat drought tolerance, identifying promising genomic loci for further exploration and crop improvement strategies.
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Affiliation(s)
- Sina Nouraei
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Md Sultan Mia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
- Department of Primary Industries and Regional Development, 3 Baron-Hay Court, South Perth, WA, 6151, Australia
| | - Hui Liu
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia.
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia.
| | - Neil C Turner
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Guijun Yan
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia.
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia.
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5
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Guo J, Guo J, Li L, Bai X, Huo X, Shi W, Gao L, Dai K, Jing R, Hao C. Combined linkage analysis and association mapping identifies genomic regions associated with yield-related and drought-tolerance traits in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:250. [PMID: 37982873 DOI: 10.1007/s00122-023-04494-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 10/26/2023] [Indexed: 11/21/2023]
Abstract
KEY MESSAGE Combined linkage analysis and association mapping identified genomic regions associated with yield and drought tolerance, providing information to assist breeding for high yield and drought tolerance in wheat. Wheat (Triticum aestivum L.) is one of the most widely grown food crops and provides adequate amounts of protein to support human health. Drought stress is the most important abiotic stress constraining yield during the flowering and grain development periods. Precise targeting of genomic regions underlying yield- and drought tolerance-responsive traits would assist in breeding programs. In this study, two water treatments (well-watered, WW, and rain-fed water stress, WS) were applied, and five yield-related agronomic traits (plant height, PH; spike length, SL; spikelet number per spike, SNPS; kernel number per spike, KNPS; thousand kernel weight, TKW) and drought response values (DRVs) were used to characterize the drought sensitivity of each accession. Association mapping was performed on an association panel of 304 accessions, and linkage analysis was applied to a doubled haploid (DH) population of 152 lines. Eleven co-localized genomic regions associated with yield traits and DRV were identified in both populations. Many previously cloned key genes were located in these regions. In particular, a TKW-associated region on chromosome 2D was identified using both association mapping and linkage analysis and a key candidate gene, TraesCS2D02G142500, was detected based on gene annotation and differences in expression levels. Exonic SNPs were analyzed by sequencing the full length of TraesCS2D02G142500 in the association panel, and a rare haplotype, Hap-2, which reduced TKW to a lesser extent than Hap-1 under drought stress, and the Hap-2 varieties presented drought-insensitive. Altogether, this study provides fundamental insights into molecular targets for high yield and drought tolerance in wheat.
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Affiliation(s)
- Jie Guo
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, Shanxi, China
| | - Jiahui Guo
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, Shanxi, China
- College of Agronomy, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Long Li
- State Key Laboratory of Crop Gene Resources and Breeding/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xionghui Bai
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, Shanxi, China
| | - Xiaoyu Huo
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, Shanxi, China
| | - Weiping Shi
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, Shanxi, China
| | - Lifeng Gao
- State Key Laboratory of Crop Gene Resources and Breeding/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Keli Dai
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, Shanxi, China.
| | - Ruilian Jing
- State Key Laboratory of Crop Gene Resources and Breeding/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Chenyang Hao
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, Shanxi, China.
- State Key Laboratory of Crop Gene Resources and Breeding/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Tyrka M, Krajewski P, Bednarek PT, Rączka K, Drzazga T, Matysik P, Martofel R, Woźna-Pawlak U, Jasińska D, Niewińska M, Ługowska B, Ratajczak D, Sikora T, Witkowski E, Dorczyk A, Tyrka D. Genome-wide association mapping in elite winter wheat breeding for yield improvement. J Appl Genet 2023; 64:377-391. [PMID: 37120451 PMCID: PMC10457411 DOI: 10.1007/s13353-023-00758-8] [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: 12/11/2022] [Revised: 03/19/2023] [Accepted: 04/03/2023] [Indexed: 05/01/2023]
Abstract
Increased grain yield (GY) is the primary breeding target of wheat breeders. We performed the genome-wide association study (GWAS) on 168 elite winter wheat lines from an ongoing breeding program to identify the main determinants of grain yield. Sequencing of Diversity Array Technology fragments (DArTseq) resulted in 19,350 single-nucleotide polymorphism (SNP) and presence-absence variation (PAV) markers. We identified 15 main genomic regions located in ten wheat chromosomes (1B, 2B, 2D, 3A, 3D, 5A, 5B, 6A, 6B, and 7B) that explained from 7.9 to 20.3% of the variation in grain yield and 13.3% of the yield stability. Loci identified in the reduced genepool are important for wheat improvement using marker-assisted selection. We found marker-trait associations between three genes involved in starch biosynthesis and grain yield. Two starch synthase genes (TraesCS2B03G1238800 and TraesCS2D03G1048800) and a sucrose synthase gene (TraesCS3D03G0024300) were found in regions of QGy.rut-2B.2, QGy.rut-2D.1, and QGy.rut-3D, respectively. These loci and other significantly associated SNP markers found in this study can be used for pyramiding favorable alleles in high-yielding varieties or to improve the accuracy of prediction in genomic selection.
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Affiliation(s)
- Mirosław Tyrka
- Department of Biotechnology and Bioinformatics, Rzeszow University of Technology, Powstańców Warszawy 6, 35-959, Rzeszów, Poland.
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Piotr Tomasz Bednarek
- Plant Breeding and Acclimatization Institute - National Research Institute, Radzików, 05-870, Błonie, Poland
| | - Kinga Rączka
- Department of Biotechnology and Bioinformatics, Rzeszow University of Technology, Powstańców Warszawy 6, 35-959, Rzeszów, Poland
| | - Tadeusz Drzazga
- Małopolska Plant Breeding Ltd, Sportowa 21, 55-040, Kobierzyce, Poland
| | - Przemysław Matysik
- Plant Breeding Strzelce Group IHAR Ltd, Główna 20, 99-307, Strzelce, Poland
| | - Róża Martofel
- Poznań Plant Breeding Ltd, Kasztanowa 5, 63-004, Tulce, Poland
| | | | - Dorota Jasińska
- Poznań Plant Breeding Ltd, Kasztanowa 5, 63-004, Tulce, Poland
| | | | | | | | - Teresa Sikora
- DANKO Plant Breeders Ltd, Ks. Strzybnego 23, 47-411, Rudnik, Poland
| | - Edward Witkowski
- Plant Breeding Smolice Ltd, Smolice 146, 63-740, Kobylin, Poland
| | - Ada Dorczyk
- Plant Breeding Smolice Ltd, Smolice 146, 63-740, Kobylin, Poland
| | - Dorota Tyrka
- Department of Biotechnology and Bioinformatics, Rzeszow University of Technology, Powstańców Warszawy 6, 35-959, Rzeszów, Poland
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7
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Wirojsirasak W, Songsri P, Jongrungklang N, Tangphatsornruang S, Klomsa-ard P, Ukoskit K. A Large-Scale Candidate-Gene Association Mapping for Drought Tolerance and Agronomic Traits in Sugarcane. Int J Mol Sci 2023; 24:12801. [PMID: 37628982 PMCID: PMC10454574 DOI: 10.3390/ijms241612801] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/09/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
Dissection of the genetic loci controlling drought tolerance traits with a complex genetic inheritance is important for drought-tolerant sugarcane improvement. In this study, we conducted a large-scale candidate gene association study of 649 candidate genes in a sugarcane diversity panel to identify genetic variants underlying agronomic traits and drought tolerance indices evaluated in plant cane and ratoon cane under water-stressed (WS) and non-stressed (NS) environments. We identified 197 significant marker-trait associations (MTAs) in 141 candidate genes associated with 18 evaluated traits with the Bonferroni correction threshold (α = 0.05). Out of the total, 95 MTAs in 78 candidate genes and 62 MTAs in 58 candidate genes were detected under NS and WS conditions, respectively. Most MTAs were found only in specific water regimes and crop seasons. These MTAs explained 7.93-30.52% of phenotypic variation. Association mapping results revealed that 34, 59, and 104 MTAs involved physiological and molecular adaptation, phytohormone metabolism, and drought-inducible genes. They identified 19 pleiotropic genes associated with more than one trait and many genes related to drought tolerance indices. The genetic and genomic resources identified in this study will enable the combining of yield-related traits and sugar-related traits with agronomic value to optimize the yield of sugarcane cultivars grown under drought-stressed and non-stressed environments.
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Affiliation(s)
- Warodom Wirojsirasak
- Department of Biotechnology, Faculty of Science and Technology, Rangsit Campus, Thammasat University, Pathum Thani 12120, Thailand;
- Mitr Phol Innovation and Research Center, Chaiyaphum 36110, Thailand;
| | - Patcharin Songsri
- Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (P.S.); (N.J.)
- Northeast Thailand Cane and Sugar Research Center, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Nakorn Jongrungklang
- Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (P.S.); (N.J.)
- Northeast Thailand Cane and Sugar Research Center, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand;
| | | | - Kittipat Ukoskit
- Department of Biotechnology, Faculty of Science and Technology, Rangsit Campus, Thammasat University, Pathum Thani 12120, Thailand;
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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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9
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Gohar S, Sajjad M, Zulfiqar S, Liu J, Wu J, Rahman MU. Domestication of newly evolved hexaploid wheat—A journey of wild grass to cultivated wheat. Front Genet 2022; 13:1022931. [PMID: 36263418 PMCID: PMC9574122 DOI: 10.3389/fgene.2022.1022931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Domestication of wheat started with the dawn of human civilization. Since then, improvement in various traits including resistance to diseases, insect pests, saline and drought stresses, grain yield, and quality were improved through selections by early farmers and then planned hybridization after the discovery of Mendel’s laws. In the 1950s, genetic variability was created using mutagens followed by the selection of superior mutants. Over the last 3 decades, research was focused on developing superior hybrids, initiating marker-assisted selection and targeted breeding, and developing genetically modified wheat to improve the grain yield, tolerance to drought, salinity, terminal heat and herbicide, and nutritive quality. Acceptability of genetically modified wheat by the end-user remained a major hurdle in releasing into the environment. Since the beginning of the 21st century, changing environmental conditions proved detrimental to achieving sustainability in wheat production particularly in developing countries. It is suggested that high-tech phenotyping assays and genomic procedures together with speed breeding procedures will be instrumental in achieving food security beyond 2050.
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Affiliation(s)
- Sasha Gohar
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Muhammad Sajjad
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Sana Zulfiqar
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Jiajun Liu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China
| | - Jiajie Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China
- *Correspondence: Jiajie Wu, ; Mehboob-ur- Rahman,
| | - Mehboob-ur- Rahman
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
- *Correspondence: Jiajie Wu, ; Mehboob-ur- Rahman,
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10
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Melaku G, Guangfu H, Shilai Z, Labroo M, Rhodes B, Harold E, Hu F. Single marker analysis for leaf gas exchange traits from RILS of RD 23 (O. sativa L.) and O. longistaminata. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2022; 35:e00743. [PMID: 35707315 PMCID: PMC9189769 DOI: 10.1016/j.btre.2022.e00743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/16/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
Rice is frequently affected by drought. However, economic water usage by the crop less impacted the stress. Its improvement should thus rely on assessing and utilizing the genetic bases of Carbon balance and water use efficient traits. These days, sequence based analysis is widely used to identify the associated hotspot loci to a given trait of interest. For two cropping seasons, 135 Oryza sativa L./Oryza longistaminata RILs were phenotyped to four leaf physiological traits and single marker analysis was integrated to identify consistently and significantly correlated SNPs. Through the RADseq technique, 20,014 SNPs were identified from the phenotypically diversified lines and in particular, 20 SNPs were defined as significantly associated hotspot loci. This study therefore, implicated marker-trait associations for leaf physiological traits. And such significantly associated loci can be used as tools for marker assisted selection of the relatively drought tolerant and highly photosynthetic lines of perennial rice.
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Affiliation(s)
- Getachew Melaku
- Research Center of Perennial Rice Engineering and Technology in Yunnan, School of Agriculture, Yunnan University, Kunming 650091, China
- Agricultural Biotechnology Directorate of the Ethiopian Biotechnology Institute, 5954, Addis Ababa, Ethiopia
| | - Huang Guangfu
- Research Center of Perennial Rice Engineering and Technology in Yunnan, School of Agriculture, Yunnan University, Kunming 650091, China
| | - Zhang Shilai
- Research Center of Perennial Rice Engineering and Technology in Yunnan, School of Agriculture, Yunnan University, Kunming 650091, China
| | - Marlee Labroo
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801, U.S.A
| | - Brian Rhodes
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801, U.S.A
| | - Edward Harold
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801, U.S.A
| | - Fengyi Hu
- Research Center of Perennial Rice Engineering and Technology in Yunnan, School of Agriculture, Yunnan University, Kunming 650091, China
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11
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Tanin MJ, Saini DK, Sandhu KS, Pal N, Gudi S, Chaudhary J, Sharma A. Consensus genomic regions associated with multiple abiotic stress tolerance in wheat and implications for wheat breeding. Sci Rep 2022; 12:13680. [PMID: 35953529 PMCID: PMC9372038 DOI: 10.1038/s41598-022-18149-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/05/2022] [Indexed: 12/03/2022] Open
Abstract
In wheat, a meta-analysis was performed using previously identified QTLs associated with drought stress (DS), heat stress (HS), salinity stress (SS), water-logging stress (WS), pre-harvest sprouting (PHS), and aluminium stress (AS) which predicted a total of 134 meta-QTLs (MQTLs) that involved at least 28 consistent and stable MQTLs conferring tolerance to five or all six abiotic stresses under study. Seventy-six MQTLs out of the 132 physically anchored MQTLs were also verified with genome-wide association studies. Around 43% of MQTLs had genetic and physical confidence intervals of less than 1 cM and 5 Mb, respectively. Consequently, 539 genes were identified in some selected MQTLs providing tolerance to 5 or all 6 abiotic stresses. Comparative analysis of genes underlying MQTLs with four RNA-seq based transcriptomic datasets unravelled a total of 189 differentially expressed genes which also included at least 11 most promising candidate genes common among different datasets. The promoter analysis showed that the promoters of these genes include many stress responsiveness cis-regulatory elements, such as ARE, MBS, TC-rich repeats, As-1 element, STRE, LTR, WRE3, and WUN-motif among others. Further, some MQTLs also overlapped with as many as 34 known abiotic stress tolerance genes. In addition, numerous ortho-MQTLs among the wheat, maize, and rice genomes were discovered. These findings could help with fine mapping and gene cloning, as well as marker-assisted breeding for multiple abiotic stress tolerances in wheat.
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Affiliation(s)
- Mohammad Jafar Tanin
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India.
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Karansher Singh Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99163, USA
| | - Neeraj Pal
- Department of Molecular Biology and Genetic Engineering, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Santosh Gudi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Jyoti Chaudhary
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, Uttar Pradesh, India
| | - Achla Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
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12
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Tanin MJ, Saini DK, Sandhu KS, Pal N, Gudi S, Chaudhary J, Sharma A. Consensus genomic regions associated with multiple abiotic stress tolerance in wheat and implications for wheat breeding. Sci Rep 2022; 12:13680. [PMID: 35953529 DOI: 10.1101/2022.06.24.497482] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/05/2022] [Indexed: 05/20/2023] Open
Abstract
In wheat, a meta-analysis was performed using previously identified QTLs associated with drought stress (DS), heat stress (HS), salinity stress (SS), water-logging stress (WS), pre-harvest sprouting (PHS), and aluminium stress (AS) which predicted a total of 134 meta-QTLs (MQTLs) that involved at least 28 consistent and stable MQTLs conferring tolerance to five or all six abiotic stresses under study. Seventy-six MQTLs out of the 132 physically anchored MQTLs were also verified with genome-wide association studies. Around 43% of MQTLs had genetic and physical confidence intervals of less than 1 cM and 5 Mb, respectively. Consequently, 539 genes were identified in some selected MQTLs providing tolerance to 5 or all 6 abiotic stresses. Comparative analysis of genes underlying MQTLs with four RNA-seq based transcriptomic datasets unravelled a total of 189 differentially expressed genes which also included at least 11 most promising candidate genes common among different datasets. The promoter analysis showed that the promoters of these genes include many stress responsiveness cis-regulatory elements, such as ARE, MBS, TC-rich repeats, As-1 element, STRE, LTR, WRE3, and WUN-motif among others. Further, some MQTLs also overlapped with as many as 34 known abiotic stress tolerance genes. In addition, numerous ortho-MQTLs among the wheat, maize, and rice genomes were discovered. These findings could help with fine mapping and gene cloning, as well as marker-assisted breeding for multiple abiotic stress tolerances in wheat.
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Affiliation(s)
- Mohammad Jafar Tanin
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India.
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Karansher Singh Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99163, USA
| | - Neeraj Pal
- Department of Molecular Biology and Genetic Engineering, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Santosh Gudi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Jyoti Chaudhary
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, Uttar Pradesh, India
| | - Achla Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
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13
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Balla MY, Gorafi YSA, Kamal NM, Abdalla MGA, Tahir ISA, Tsujimoto H. Exploiting Wild Emmer Wheat Diversity to Improve Wheat A and B Genomes in Breeding for Heat Stress Adaptation. FRONTIERS IN PLANT SCIENCE 2022; 13:895742. [PMID: 35937332 PMCID: PMC9355596 DOI: 10.3389/fpls.2022.895742] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Wheat is highly sensitive to temperature beyond the optimum. To improve wheat adaptation to heat stress, the best option is to exploit the diversity of wild wheat progenitors. This study aimed to identify germplasm and quantitative trait loci associated with heat stress tolerance from wild emmer wheat diversity. We evaluated a diverse set of multiple derivative lines harboring chromosome segments from nine wild emmer wheat parents under four environments: two optimum environments at Tottori, Japan and Dongola, Sudan, one moderate heat stress environment, and one severe heat stress environment at Wad Medani, Sudan. Genome-wide association analysis was conducted with 13,312 SNP markers. Strong marker-trait associations (MTAs) were identified for chlorophyll content at maturity on chromosomes 1A and 5B: these MTAs explained 28.8 and 26.8% of the variation, respectively. A region on chromosome 3A (473.7-638.4 Mbp) contained MTAs controlling grain yield, under optimum and severe heat stress. Under severe heat stress, regions on chromosomes 3A (590.4-713.3 Mbp) controlled grain yield, biomass, days to maturity and thousand kernel weight, and on 3B (744.0-795.2 Mbp) grain yield and biomass. Heat tolerance efficiency (HTE) was controlled by three MTAs, one each on chromosomes 2A, 2B, and 5A under moderate heat stress and one MTA on chromosome 3A under severe heat stress. Some of the MTAs found here were previously reported, but the new ones originated from the wild emmer wheat genomes. The favorable alleles identified from wild emmer wheat were absent or rare in the elite durum wheat germplasm being bred for heat stress tolerance. This study provides potential genetic materials, alleles, MTAs, and quantitative trait loci for enhancing wheat adaptation to heat stress. The derivative lines studied here could be investigated to enhance other stress tolerance such as drought and salinity.
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Affiliation(s)
| | - Yasir Serag Alnor Gorafi
- Arid Land Research Center, Tottori University, Tottori, Japan
- Agricultural Research Corporation, Wad Medani, Sudan
| | - Nasrein Mohamed Kamal
- Arid Land Research Center, Tottori University, Tottori, Japan
- Agricultural Research Corporation, Wad Medani, Sudan
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14
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Negisho K, Shibru S, Matros A, Pillen K, Ordon F, Wehner G. Association Mapping of Drought Tolerance Indices in Ethiopian Durum Wheat ( Triticum turgidum ssp. durum). FRONTIERS IN PLANT SCIENCE 2022; 13:838088. [PMID: 35693182 PMCID: PMC9178276 DOI: 10.3389/fpls.2022.838088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Ethiopia is a major producer of durum wheat in sub-Saharan Africa. However, its production is prone to drought stress as it is fully dependent on rain, which is erratic and unpredictable. This study aimed to detect marker-trait associations (MTAs) and quantitative trait loci (QTLs) related to indices. Six drought tolerance indices, i.e., drought susceptibility index (DSI), geometric mean productivity (GMP), relative drought index (RDI), stress tolerance index (STI), tolerance index (TOL), and yield stability index (YSI) were calculated from least-square means (lsmeans) of grain yield (GY) and traits significantly (p < 0.001) correlated with grain yield (GY) under field drought stress (FDS) and field non-stress (FNS) conditions. GY, days to grain filling (DGF), soil plant analysis development (SPAD) chlorophyll meter, seeds per spike (SPS), harvest index (HI), and thousand kernel weight (TKW) were used to calculate DSI, GMP, RDI, STI, TOL, and YSI drought indices. Accessions, DW084, DW082, DZ004, C037, and DW092 were selected as the top five drought-tolerant based on DSI, RDI, TOL, and YSI combined ranking. Similarly, C010, DW033, DW080, DW124-2, and C011 were selected as stable accessions based on GMP and STI combined ranking. A total of 184 MTAs were detected linked with drought indices at -log10p ≥ 4.0,79 of which were significant at a false discovery rate (FDR) of 5%. Based on the linkage disequilibrium (LD, r 2 ≥ 0.2), six of the MTAs with a positive effect on GY-GMP were detected on chromosomes 2B, 3B, 4A, 5B, and 6B, explaining 14.72, 10.07, 26.61, 21.16, 21.91, and 22.21% of the phenotypic variance, respectively. The 184 MTAs were clustered into 102 QTLs. Chromosomes 1A, 2B, and 7A are QTL hotspots with 11 QTLs each. These chromosomes play a key role in drought tolerance and respective QTL may be exploited by marker-assisted selection for improving drought stress tolerance in wheat.
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Affiliation(s)
- Kefyalew Negisho
- National Agricultural Biotechnology Research Center, Ethiopian Institute of Agricultural Research (EIAR), Holeta, Ethiopia
| | - Surafel Shibru
- Melkassa Research Center, Ethiopian Institute of Agricultural Research (EIAR), Melkassa, Ethiopia
| | - Andrea Matros
- Julius Kühn Institute (JKI), Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Martin Luther University, Halle, Germany
| | - Frank Ordon
- Julius Kühn Institute (JKI), Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Gwendolin Wehner
- Julius Kühn Institute (JKI), Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
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15
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Genome-Wide Association Study Identifies Two Loci for Stripe Rust Resistance in a Durum Wheat Panel from Iran. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12104963] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Stripe rust (Puccinia striiformis f. sp. tritici (Pst)) is one of the most devastating fungal diseases of durum wheat (Triticum turgidum L. var. durum Desf.). Races of Pst with new virulence combinations are emerging more regularly on wheat-growing continents, which challenges wheat breeding for resistance. This study aimed to identify and characterize resistance to Pst races based on a genome-wide association study. GWAS is an approach to analyze the associations between a genome-wide set of single-nucleotide polymorphisms (SNPs) and target phenotypic traits. A total of 139 durum wheat accessions from Iran were evaluated at the seedling stage against isolates Pstv-37 and Pstv-40 of Pst and then genotyped using a 15K SNP chip. In total, 230 significant associations were identified across 14 chromosomes, of which 30 were associated with resistance to both isolates. Furthermore, 17 durum wheat landraces showed an immune response against both Pst isolates. The SNP markers and resistant accessions identified in this study may be useful in programs breeding durum wheat for stripe rust resistance.
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16
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Bhardwaj A, Devi P, Chaudhary S, Rani A, Jha UC, Kumar S, Bindumadhava H, Prasad PVV, Sharma KD, Siddique KHM, Nayyar H. 'Omics' approaches in developing combined drought and heat tolerance in food crops. PLANT CELL REPORTS 2022; 41:699-739. [PMID: 34223931 DOI: 10.1007/s00299-021-02742-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Global climate change will significantly increase the intensity and frequency of hot, dry days. The simultaneous occurrence of drought and heat stress is also likely to increase, influencing various agronomic characteristics, such as biomass and other growth traits, phenology, and yield-contributing traits, of various crops. At the same time, vital physiological traits will be seriously disrupted, including leaf water content, canopy temperature depression, membrane stability, photosynthesis, and related attributes such as chlorophyll content, stomatal conductance, and chlorophyll fluorescence. Several metabolic processes contributing to general growth and development will be restricted, along with the production of reactive oxygen species (ROS) that negatively affect cellular homeostasis. Plants have adaptive defense strategies, such as ROS-scavenging mechanisms, osmolyte production, secondary metabolite modulation, and different phytohormones, which can help distinguish tolerant crop genotypes. Understanding plant responses to combined drought/heat stress at various organizational levels is vital for developing stress-resilient crops. Elucidating the genomic, proteomic, and metabolic responses of various crops, particularly tolerant genotypes, to identify tolerance mechanisms will markedly enhance the continuing efforts to introduce combined drought/heat stress tolerance. Besides agronomic management, genetic engineering and molecular breeding approaches have great potential in this direction.
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Affiliation(s)
| | - Poonam Devi
- Department of Botany, Panjab University, Chandigarh, India
| | | | - Anju Rani
- Department of Botany, Panjab University, Chandigarh, India
| | | | - Shiv Kumar
- International Center for Agriculture Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - H Bindumadhava
- Dr. Marri Channa Reddy Foundation (MCRF), Hyderabad, India
| | | | | | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, India.
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17
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Itam MO, Mega R, Gorafi YSA, Yamasaki Y, Tahir ISA, Akashi K, Tsujimoto H. Genomic analysis for heat and combined heat-drought resilience in bread wheat under field conditions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:337-350. [PMID: 34655314 PMCID: PMC8741676 DOI: 10.1007/s00122-021-03969-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/06/2021] [Indexed: 05/02/2023]
Abstract
KEY MESSAGE GWAS on a bread wheat panel with high D genome diversity identified novel alleles and QTLs associated with resilience to combined heat and drought stress under natural field conditions. As heat (H) and drought stresses occur concurrently under field conditions, studying them separately offers limited opportunities for wheat improvement. Here, a wheat diversity panel containing Aegilops tauschii introgressions was evaluated under H and combined heat-drought (HD) stresses to identify quantitative trait loci (QTLs) associated with resilience to the stresses, and to assess the practicability of harnessing Ae. tauschii diversity for breeding for combined stress resilience. Using genome-wide analysis, we identified alleles and QTLs on chromosomes 3D, 5D, and 7A controlling grain yield (GY), kernel number per spike, and thousand-kernel weight, and on 3D (521-549 Mbp) controlling GY alone. A strong marker-trait association (MTA) for GY stability on chromosome 3D (508.3 Mbp) explained 20.3% of the variation. Leaf traits-canopy temperature, vegetation index, and carbon isotope composition-were controlled by five QTLs on 2D (23-96, 511-554, and 606-614 Mbp), 3D (155-171 Mbp), and 5D (407-413 Mbp); some of them were pleiotropic for GY and yield-related traits. Further analysis revealed candidate genes, including GA20ox, regulating GY stability, and CaaX prenyl protease 2, regulating canopy temperature at the flowering stage, under H and HD stresses. As genome-wide association studies under HD in field conditions are scarce, our results provide genomic landmarks for wheat breeding to improve adaptation to H and HD conditions under climate change.
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Affiliation(s)
- Michael O Itam
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan
| | - Ryosuke Mega
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | - Yasir S A Gorafi
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan
- Agricultural Research Corporation, Wheat Research Program, P.O. Box 126, Wad Medani, Sudan
| | - Yuji Yamasaki
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan
| | - Izzat S A Tahir
- Agricultural Research Corporation, Wheat Research Program, P.O. Box 126, Wad Medani, Sudan
| | - Kinya Akashi
- Faculty of Agriculture, Tottori University, Tottori, 680-8553, Japan
| | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.
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18
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Saini DK, Chopra Y, Singh J, Sandhu KS, Kumar A, Bazzer S, Srivastava P. Comprehensive evaluation of mapping complex traits in wheat using genome-wide association studies. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:1. [PMID: 37309486 PMCID: PMC10248672 DOI: 10.1007/s11032-021-01272-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Genome-wide association studies (GWAS) are effectively applied to detect the marker trait associations (MTAs) using whole genome-wide variants for complex quantitative traits in different crop species. GWAS has been applied in wheat for different quality, biotic and abiotic stresses, and agronomic and yield-related traits. Predictions for marker-trait associations are controlled with the development of better statistical models taking population structure and familial relatedness into account. In this review, we have provided a detailed overview of the importance of association mapping, population design, high-throughput genotyping and phenotyping platforms, advancements in statistical models and multiple threshold comparisons, and recent GWA studies conducted in wheat. The information about MTAs utilized for gene characterization and adopted in breeding programs is also provided. In the literature that we surveyed, as many as 86,122 wheat lines have been studied under various GWA studies reporting 46,940 loci. However, further utilization of these is largely limited. The future breakthroughs in area of genomic selection, multi-omics-based approaches, machine, and deep learning models in wheat breeding after exploring the complex genetic structure with the GWAS are also discussed. This is a most comprehensive study of a large number of reports on wheat GWAS and gives a comparison and timeline of technological developments in this area. This will be useful to new researchers or groups who wish to invest in GWAS.
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Affiliation(s)
- Dinesh K. Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | - Yuvraj Chopra
- College of Agriculture, Punjab Agricultural University, Ludhiana, 141004 India
| | - Jagmohan Singh
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Karansher S. Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163 USA
| | - Anand Kumar
- Department of Genetics and Plant Breeding, Chandra Shekhar Azad University of Agriculture and Technology, Kanpur, 202002 India
| | - Sumandeep Bazzer
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
| | - Puja Srivastava
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
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19
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Liu H, Mullan D, Zhao S, Zhang Y, Ye J, Wang Y, Zhang A, Zhao X, Liu G, Zhang C, Chan K, Lu Z, Yan G. Genomic regions controlling yield-related traits in spring wheat: A mini review and a case study for rainfed environments in Australia and China. Genomics 2022; 114:110268. [PMID: 35065191 DOI: 10.1016/j.ygeno.2022.110268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/11/2022] [Accepted: 01/15/2022] [Indexed: 01/17/2023]
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20
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Itam MO, Wahbi A, Fujimaki H, Tsujimoto H. Transpiration response of two bread wheat lines differing in drought resilience and their backcross parent under dry-down conditions. BREEDING SCIENCE 2021; 71:575-583. [PMID: 35087321 PMCID: PMC8784354 DOI: 10.1270/jsbbs.20154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 09/08/2021] [Indexed: 06/14/2023]
Abstract
Improving wheat productivity in drylands largely depends on how plants manage limited water resources. Using fraction of transpirable soil water threshold (FTSWTh) and drought stress response function, we characterized the water conservation traits of two wheat multiple synthetic derivative lines (MSD53 and MSD345) which both contain introgressed segments from Aegilops tauschii but differ in drought resilience. The lines and their backcross parent, 'Norin 61', were subjected to dry-down conditions. MSD53 had a higher FTSWTh for transpiration decrease than 'Norin 61' and MSD345. In terms of drought stress response function, MSD53 had the lowest threshold suction, suggesting a lower drought resilience capacity compared with MSD345. However, MSD53 exhibited an effective-water-use trait whereas MSD345 exhibited a water-saving trait under dry-down conditions. These results are consistent with the reported higher yield of MSD53 in comparison with MSD345 under drought stress in Sudan, and demonstrate that high FTSWTh supports effective water use for improved agricultural productivity in drylands. The differences in water conservation traits between the two MSD lines may be attributed to variation in introgressed segments, which can be further explored for drought resilience breeding.
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Affiliation(s)
- Michael O. Itam
- Arid Land Research Center, Tottori University, Tottori 680-0001, Japan
| | - Ammar Wahbi
- Arid Land Research Center, Tottori University, Tottori 680-0001, Japan
| | - Haruyuki Fujimaki
- Arid Land Research Center, Tottori University, Tottori 680-0001, Japan
| | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, Tottori 680-0001, Japan
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21
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Rufo R, López A, Lopes MS, Bellvert J, Soriano JM. Identification of Quantitative Trait Loci Hotspots Affecting Agronomic Traits and High-Throughput Vegetation Indices in Rainfed Wheat. FRONTIERS IN PLANT SCIENCE 2021; 12:735192. [PMID: 34616417 PMCID: PMC8489662 DOI: 10.3389/fpls.2021.735192] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/20/2021] [Indexed: 06/13/2023]
Abstract
Understanding the genetic basis of agronomic traits is essential for wheat breeding programs to develop new cultivars with enhanced grain yield under climate change conditions. The use of high-throughput phenotyping (HTP) technologies for the assessment of agronomic performance through drought-adaptive traits opens new possibilities in plant breeding. HTP together with a genome-wide association study (GWAS) mapping approach can be a useful method to dissect the genetic control of complex traits in wheat to enhance grain yield under drought stress. This study aimed to identify molecular markers associated with agronomic and remotely sensed vegetation index (VI)-related traits under rainfed conditions in bread wheat and to use an in silico candidate gene (CG) approach to search for upregulated CGs under abiotic stress. The plant material consisted of 170 landraces and 184 modern cultivars from the Mediterranean basin. The collection was phenotyped for agronomic and VI traits derived from multispectral images over 3 and 2 years, respectively. The GWAS identified 2,579 marker-trait associations (MTAs). The quantitative trait loci (QTL) overview index statistic detected 11 QTL hotspots involving more than one trait in at least 2 years. A CG analysis detected 12 CGs upregulated under abiotic stress in six QTL hotspots and 46 downregulated CGs in 10 QTL hotspots. The current study highlights the utility of VI to identify chromosome regions that contribute to yield and drought tolerance under rainfed Mediterranean conditions.
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Affiliation(s)
- Rubén Rufo
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
| | - Andrea López
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
| | - Marta S. Lopes
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
| | - Joaquim Bellvert
- Efficient Use of Water in Agriculture Program, Institute for Food and Agricultural Research and Technology (IRTA), Parc Científici TecnològicAgroalimentari de Gardeny (PCiTAL), Fruitcentre, Lleida, Spain
| | - Jose M. Soriano
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
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22
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Genome-wide association mapping reveals key genomic regions for physiological and yield-related traits under salinity stress in wheat (Triticum aestivum L.). Genomics 2021; 113:3198-3215. [PMID: 34293475 DOI: 10.1016/j.ygeno.2021.07.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 06/27/2021] [Accepted: 07/13/2021] [Indexed: 11/21/2022]
Abstract
A genome-wide association study (GWAS) was conducted using six different multi-locus GWAS models and 35K SNP array to demarcate genomic regions underlying reproductive stage salinity tolerance. Marker-trait association analysis was performed for salt tolerance indices (STI) of 11 morpho-physiological traits, and the actual concentrations of Na+ and K+, and the Na+/K+ ratio in flag leaf. A total of 293 significantly associated quantitative trait nucleotides (QTNs) for 14 morpho-physiological traits were identified. Of these 293 QTNs, 12 major QTNs with R2 ≥ 10.0% were detected in three or more GWAS models. Novel major QTNs were identified for plant height, number of effective tillers, biomass, grain yield, thousand grain weight, Na+ and K+ content, and the Na+/K+ ratio in flag leaf. Moreover, 48 candidate genes were identified from the associated genomic regions. The QTNs identified in this study could potentially be targeted for improving salinity tolerance in wheat.
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23
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Elhadi GMI, Kamal NM, Gorafi YSA, Yamasaki Y, Takata K, Tahir ISA, Itam MO, Tanaka H, Tsujimoto H. Exploitation of Tolerance of Wheat Kernel Weight and Shape-Related Traits from Aegilops tauschii under Heat and Combined Heat-Drought Stresses. Int J Mol Sci 2021; 22:1830. [PMID: 33673217 PMCID: PMC7917938 DOI: 10.3390/ijms22041830] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 12/25/2022] Open
Abstract
Kernel weight and shape-related traits are inherited stably and increase wheat yield. Narrow genetic diversity limits the progress of wheat breeding. Here, we evaluated kernel weight and shape-related traits and applied genome-wide association analysis to a panel of wheat multiple synthetic derivative (MSD) lines. The MSD lines harbored genomic fragments from Aegilops tauschii. These materials were grown under optimum conditions in Japan, as well as under heat and combined heat-drought conditions in Sudan. We aimed to explore useful QTLs for kernel weight and shape-related traits under stress conditions. These can be useful for enhancing yield under stress conditions. MSD lines possessed remarkable genetic variation for all traits under all conditions, and some lines showed better performance than the background parent Norin 61. We identified 82 marker trait associations (MTAs) under the three conditions; most of them originated from the D genome. All of the favorable alleles originated from Ae. tauschii. For the first time, we identified markers on chromosome 5D associated with a candidate gene encoding a RING-type E3 ubiquitin-protein ligase and expected to have a role in regulating wheat seed size. Our study provides important knowledge for the improvement of wheat yield under optimum and stress conditions. The results emphasize the importance of Ae. tauschii as a gene reservoir for wheat breeding.
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Affiliation(s)
- Gamila Mohamed Idris Elhadi
- United Graduate School of Agricultural Sciences, Tottori University, Tottori 680-8553, Japan; (G.M.I.E.); (M.O.I.)
| | - Nasrein Mohamed Kamal
- Arid Land Research Center, Tottori University, Tottori 680-0001, Japan; (N.M.K.); (Y.S.A.G.); (Y.Y.)
- Wheat Research Program, Agricultural Research Corporation, P.O. Box 126, Wad Medani, Sudan;
| | - Yasir Serag Alnor Gorafi
- Arid Land Research Center, Tottori University, Tottori 680-0001, Japan; (N.M.K.); (Y.S.A.G.); (Y.Y.)
- Wheat Research Program, Agricultural Research Corporation, P.O. Box 126, Wad Medani, Sudan;
| | - Yuji Yamasaki
- Arid Land Research Center, Tottori University, Tottori 680-0001, Japan; (N.M.K.); (Y.S.A.G.); (Y.Y.)
| | - Kanenori Takata
- National Agriculture and Food Research Organization, Fukuyama 721-8514, Japan;
| | - Izzat S. A. Tahir
- Wheat Research Program, Agricultural Research Corporation, P.O. Box 126, Wad Medani, Sudan;
| | - Michel O. Itam
- United Graduate School of Agricultural Sciences, Tottori University, Tottori 680-8553, Japan; (G.M.I.E.); (M.O.I.)
| | - Hiroyuki Tanaka
- Faculty of Agriculture, Tottori University, Tottori 680-8550, Japan;
| | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, Tottori 680-0001, Japan; (N.M.K.); (Y.S.A.G.); (Y.Y.)
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24
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Pradhan AK, Kumar S, Singh AK, Budhlakoti N, Mishra DC, Chauhan D, Mittal S, Grover M, Kumar S, Gangwar OP, Kumar S, Gupta A, Bhardwaj SC, Rai A, Singh K. Identification of QTLs/Defense Genes Effective at Seedling Stage Against Prevailing Races of Wheat Stripe Rust in India. Front Genet 2020; 11:572975. [PMID: 33329711 PMCID: PMC7728992 DOI: 10.3389/fgene.2020.572975] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/30/2020] [Indexed: 01/06/2023] Open
Abstract
Resistance in modern wheat cultivars for stripe rust is not long lasting due to the narrow genetic base and periodical evolution of new pathogenic races. Though nearly 83 Yr genes conferring resistance to stripe rust have been cataloged so far, few of them have been mapped and utilized in breeding programs. Characterization of wheat germplasm for novel sources of resistance and their incorporation into elite cultivars is required to achieve durable resistance and thus to minimize the yield losses. Here, a genome-wide association study (GWAS) was performed on a set of 391 germplasm lines with the aim to identify quantitative trait loci (QTL) using 35K Axiom® array. Phenotypic evaluation disease severity against four stripe rust pathotypes, i.e., 46S119, 110S119, 238S119, and 47S103 (T) at the seedling stage in a greenhouse providing optimal conditions was carried out consecutively for 2 years (2018 and 2019 winter season). We identified, a total of 17 promising QTl which passed FDR criteria. Moreover these 17 QTL identified in the current study were mapped at different genomic locations i.e. 1B, 2A, 2B, 2D, 3A, 3B, 3D, 4B, 5B and 6B. These 17 QTLs identified in the present study might play a key role in marker-assisted breeding for developing stripe rust resistant wheat cultivars.
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Affiliation(s)
- Anjan Kumar Pradhan
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sundeep Kumar
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Amit Kumar Singh
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Neeraj Budhlakoti
- Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dwijesh C Mishra
- Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Divya Chauhan
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Shikha Mittal
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Monendra Grover
- Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Suneel Kumar
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Om P Gangwar
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Subodh Kumar
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Arun Gupta
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Subhash C Bhardwaj
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Anil Rai
- Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Kuldeep Singh
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
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25
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Kumar S, Kumari J, Bhusal N, Pradhan AK, Budhlakoti N, Mishra DC, Chauhan D, Kumar S, Singh AK, Reynolds M, Singh GP, Singh K, Sareen S. Genome-Wide Association Study Reveals Genomic Regions Associated With Ten Agronomical Traits in Wheat Under Late-Sown Conditions. FRONTIERS IN PLANT SCIENCE 2020; 11:549743. [PMID: 33042178 PMCID: PMC7527491 DOI: 10.3389/fpls.2020.549743] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
Poor understanding of the genetic and molecular basis of heat tolerance component traits is a major bottleneck in designing heat tolerant wheat cultivars. The impact of terminal heat stress is generally reported in the case of late sown wheat. In this study, our aim was to identify genomic regions for various agronomic traits under late sown conditions by using genome-wide association approach. An association mapping panel of 205 wheat accessions was evaluated under late sown conditions at three different locations in India. Genotyping of the association panel revealed 15,886 SNPs, out of which 11,911 SNPs with exact physical locations on the wheat reference genome were used in association analysis. A total of 69 QTLs (10 significantly associated and 59 suggestive) were identified for ten different traits including productive tiller number (17), grain yield (14), plant height (12), grain filling rate (6), grain filling duration (5), days to physiological maturity (4), grain number (3), thousand grain weight (3), harvest index (3), and biomass (2). Out of these associated QTLs, 17 were novel for traits, namely PTL (3), GY (2), GFR (6), HI (3) and GNM (3). Moreover, five consistent QTLs across environments were identified for GY (4) and TGW (1). Also, 11 multi-trait SNPs and three hot spot regions on Chr1Ds, Chr2BS, Chr2DS harboring many QTLs for many traits were identified. In addition, identification of heat tolerant germplasm lines based on favorable alleles HD2888, IC611071, IC611273, IC75240, IC321906, IC416188, and J31-170 would facilitate their targeted introgression into popular wheat cultivars. The significantly associated QTLs identified in the present study can be further validated to identify robust markers for utilization in marker-assisted selection (MAS) for development of heat tolerant wheat cultivars.
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Affiliation(s)
- Sundeep Kumar
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Jyoti Kumari
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Nabin Bhusal
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | | | - Neeraj Budhlakoti
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Divya Chauhan
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Suneel Kumar
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Amit Kumar Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Mathew Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
| | | | - Kuldeep Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sindhu Sareen
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
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26
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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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27
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Rehman Arif MA, Attaria F, Shokat S, Akram S, Waheed MQ, Arif A, Börner A. Mapping of QTLs Associated with Yield and Yield Related Traits in Durum Wheat ( Triticum durum Desf.) Under Irrigated and Drought Conditions. Int J Mol Sci 2020; 21:ijms21072372. [PMID: 32235556 PMCID: PMC7177892 DOI: 10.3390/ijms21072372] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 11/16/2022] Open
Abstract
Global durum wheat consumption (Triticum durum Desf.) is ahead of its production. One reason for this is abiotic stress, e.g., drought. Breeding for resistance to drought is complicated by the lack of fast, reproducible screening techniques and the inability to routinely create defined and repeatable water stress conditions. Here, we report the first analysis of dissection of yield and yield-related traits in durum wheat in Pakistan, seeking to elucidate the genetic components of yield and agronomic traits. Analysis of several traits revealed a total of 221 (160 with logarithm of odds (LOD) > 2 ≤ 3 and 61 with LOD > 3) quantitative trait loci (QTLs) distributed on all fourteen durum wheat chromosomes, of which 109 (78 with LOD > 2 ≤ 3 and 31 with LOD > 3) were observed in 2016-17 (S1) and 112 (82 with LOD > 2 ≤ 3 and 30 with LOD > 3) were observed in 2017-18 (S2). Allelic profiles of yield QTLs on chromosome 2A and 7B indicate that allele A of Xgwm895 and allele B of Xbarc276 can enhance the Yd up to 6.16% in control and 5.27% under drought. Moreover, if combined, a yield gain of up to 11% would be possible.
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Affiliation(s)
- Mian Abdur Rehman Arif
- Nuclear Institute for Agriculture and Biology, Jhang Road, Faisalabad, 38000, Pakistan; (F.A.); (S.S.); (S.A.); (M.Q.W.); (A.A.)
- Correspondence:
| | - Fauzia Attaria
- Nuclear Institute for Agriculture and Biology, Jhang Road, Faisalabad, 38000, Pakistan; (F.A.); (S.S.); (S.A.); (M.Q.W.); (A.A.)
| | - Sajid Shokat
- Nuclear Institute for Agriculture and Biology, Jhang Road, Faisalabad, 38000, Pakistan; (F.A.); (S.S.); (S.A.); (M.Q.W.); (A.A.)
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Allé 13, DK-2630 Taastrup, Denmark
| | - Saba Akram
- Nuclear Institute for Agriculture and Biology, Jhang Road, Faisalabad, 38000, Pakistan; (F.A.); (S.S.); (S.A.); (M.Q.W.); (A.A.)
| | - Muhammad Qandeel Waheed
- Nuclear Institute for Agriculture and Biology, Jhang Road, Faisalabad, 38000, Pakistan; (F.A.); (S.S.); (S.A.); (M.Q.W.); (A.A.)
| | - Anjuman Arif
- Nuclear Institute for Agriculture and Biology, Jhang Road, Faisalabad, 38000, Pakistan; (F.A.); (S.S.); (S.A.); (M.Q.W.); (A.A.)
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, Seeland OT, 06466 Gatersleben, Germany;
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28
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Schmidt J, Tricker PJ, Eckermann P, Kalambettu P, Garcia M, Fleury D. Novel Alleles for Combined Drought and Heat Stress Tolerance in Wheat. FRONTIERS IN PLANT SCIENCE 2019; 10:1800. [PMID: 32082351 PMCID: PMC7005056 DOI: 10.3389/fpls.2019.01800] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/23/2019] [Indexed: 05/03/2023]
Abstract
Drought and heat waves commonly co-occur in many wheat-growing regions causing significant crop losses. The identification of stress associated quantitative trait loci, particularly those for yield, is problematic due to their association with plant phenology and the high genetic × environment interaction. Here we studied a panel of 315 diverse, spring type accessions of bread wheat (Triticum aestivum) in pots in a semi-controlled environment under combined drought and heat stress over 2 years. Importantly, we treated individual plants according to their flowering time. We found 134 out of the 145 identified loci for grain weight that were not associated with either plant phenology or plant height. The majority of loci uncovered here were novel, with favorable alleles widespread in Asian and African landraces providing opportunities for their incorporation into modern varieties through breeding. Using residual heterozygosity in lines from a nested association mapping population, we were able to rapidly develop near-isogenic lines for important target loci. One target locus on chromosome 6A contributed to higher grain weight, harvest index, thousand kernel weight, and grain number under drought and heat stress in field conditions consistent with allelic effects demonstrated in the genome-wide association study.
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