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Sallam A, Awadalla RA, Elshamy MM, Börner A, Heikal YM. Genome-wide analysis for root and leaf architecture traits associated with drought tolerance at the seedling stage in a highly ecologically diverse wheat population. Comput Struct Biotechnol J 2024; 23:870-882. [PMID: 38356657 PMCID: PMC10864764 DOI: 10.1016/j.csbj.2024.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
Drought stress occurred at early growth stages in wheat affecting the following growth stages. Therefore, selecting promising drought-tolerant genotypes with highly adapted traits at the seedling stage is an important task for wheat breeders and geneticists. Few research efforts were conducted on the genetic control for drought-adaptive traits at the seedling stage in wheat. In this study, a set of 146 highly diverse spring wheat core collections representing 28 different countries was evaluated under drought stress at the seedling stage. All genotypes were exposed to drought stress for 13 days by water withholding. Leaf traits including seedling length, leaf wilting, days to wilting, leaf area, and leaf rolling were scored. Moreover, root traits such as root length, maximum width, emergence angle, tip angle, and number of roots were scored. Considerable significant genetic variation was found among all genotypes tested in these experiments. The heritability estimates ranged from 0.74 (leaf witling) to 0.99 (root tip angle). A set of nine genotypes were selected and considered drought-tolerant genotypes. Among all leaf traits, shoot length had significant correlations with all root traits under drought stress. The 146 genotypes were genotyped using the Infinium Wheat 15 K single nucleotide polymorphism (SNP) array and diversity arrays technology (DArT) marker platform. The result of genotyping revealed 12,999 SNPs and 2150 DArT markers which were used to run a genome-wide association study (GWAS). The results of GWAS revealed 169 markers associated with leaf and root traits under drought stress. Out of the 169 markers, 82 were considered major quantitative trait loci (QTL). The GWAS revealed 95 candidate genes were identified with 53 genes showing evidence for drought tolerance in wheat, while the remaining candidate genes were considered novel. No shared markers were found between leaf and root traits. The results of the study provided mapping novel markers associated with new root traits at the seedling stage. Also, the selected genotypes from different countries could be employed in future wheat breeding programs not only for improving adaptive drought-tolerant traits but also for expanding genetic diversity.
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Affiliation(s)
- Ahmed Sallam
- Resources Genetics and Reproduction, Department GenBank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben D-06466 Stadt Seeland, Germany
- Department of Genetics, Faculty of Agriculture, Assiut University, 71526 Assiut, Egypt
| | - Rawan A. Awadalla
- Botany Department, Faculty of Science, Mansoura University, 35516 Mansoura, Egypt
| | - Maha M. Elshamy
- Botany Department, Faculty of Science, Mansoura University, 35516 Mansoura, Egypt
| | - Andreas Börner
- Resources Genetics and Reproduction, Department GenBank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben D-06466 Stadt Seeland, Germany
| | - Yasmin M. Heikal
- Botany Department, Faculty of Science, Mansoura University, 35516 Mansoura, Egypt
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2
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Neupane A, Tamburic-Llincic L, Brûlé-Babel A, McCartney C. QTL analysis of native Fusarium head blight and deoxynivalenol resistance in 'D8006W'/'Superior', soft white winter wheat population. BMC PLANT BIOLOGY 2024; 24:852. [PMID: 39256692 PMCID: PMC11389122 DOI: 10.1186/s12870-024-05536-0] [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: 04/12/2024] [Accepted: 08/21/2024] [Indexed: 09/12/2024]
Abstract
BACKGROUND Fusarium head blight (FHB), caused by Fusarium graminearum, is a major disease of wheat in North America. FHB infection causes fusarium damaged kernels (FDKs), accumulation of deoxynivalenol (DON) in the grain, and a reduction in quality and grain yield. Inheritance of FHB resistance is complex and involves multiple genes. The objective of this research was to identify QTL associated with native FHB and DON resistance in a 'D8006W'/'Superior', soft white winter wheat population. RESULTS Phenotyping was conducted in replicated FHB field disease nurseries across multiple environments and included assessments of morphological and FHB related traits. Parental lines had moderate FHB resistance, however, the population showed transgressive segregation. A 1913.2 cM linkage map for the population was developed with SNP markers from the wheat 90 K Infinium iSelect SNP array. QTL analysis detected major FHB resistance QTL on chromosomes 2D, 4B, 5A, and 7A across multiple environments, with resistance from both parents. Trait specific unique QTL were detected on chromosomes 1A (visual traits), 5D (FDK), 6B (FDK and DON), and 7D (DON). The plant height and days to anthesis QTL on chromosome 2D coincided with Ppd-D1 and were linked with FHB traits. The plant height QTL on chromosome 4B was also linked with FHB traits; however, the Rht-B1 locus did not segregate in the population. CONCLUSIONS This study identified several QTL, including on chromosome 2D linked with Ppd-D1, for FHB resistance in a native winter wheat germplasm.
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Affiliation(s)
- Anjan Neupane
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB, R3T 2N2, Canada.
- Present address: Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada.
| | - Ljiljana Tamburic-Llincic
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB, R3T 2N2, Canada
- Ridgetown Campus, University of Guelph, 120 Main Street East, Ridgetown, ON, N0P 2C0, Canada
| | - Anita Brûlé-Babel
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB, R3T 2N2, Canada
| | - Curt McCartney
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB, R3T 2N2, Canada
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
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Bruschi M, Bozzoli M, Ratti C, Sciara G, Goudemand E, Devaux P, Ormanbekova D, Forestan C, Corneti S, Stefanelli S, Castelletti S, Fusari E, Novi JB, Frascaroli E, Salvi S, Perovic D, Gadaleta A, Rubies-Autonell C, Sanguineti MC, Tuberosa R, Maccaferri M. Dissecting the genetic basis of resistance to Soil-borne cereal mosaic virus (SBCMV) in durum wheat by bi-parental mapping and GWAS. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:213. [PMID: 39222129 PMCID: PMC11369050 DOI: 10.1007/s00122-024-04709-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 08/04/2024] [Indexed: 09/04/2024]
Abstract
Soil-borne cereal mosaic virus (SBCMV), the causative agent of wheat mosaic, is a Furovirus challenging wheat production all over Europe. Differently from bread wheat, durum wheat shows greater susceptibility and stronger yield penalties, so identification and genetic characterization of resistance sources are major targets for durum genetics and breeding. The Sbm1 locus providing high level of resistance to SBCMV was mapped in bread wheat to the 5DL chromosome arm (Bass in Genome 49:1140-1148, 2006). This excluded the direct use of Sbm1 for durum wheat improvement. Only one major QTL has been mapped in durum wheat, namely QSbm.ubo-2B, on the 2BS chromosome region coincident with Sbm2, already known in bread wheat as reported (Bayles in HGCA Project Report, 2007). Therefore, QSbm.ubo-2B = Sbm2 is considered a pillar for growing durum in SBCMV-affected areas. Herein, we report the fine mapping of Sbm2 based on bi-parental mapping and GWAS, using the Infinium 90 K SNP array and high-throughput KASP®. Fine mapping pointed out a critical haploblock of 3.2 Mb defined by concatenated SNPs successfully converted to high-throughput KASP® markers coded as KUBO. The combination of KUBO-27, wPt-2106-ASO/HRM, KUBO-29, and KUBO-1 allows unequivocal tracing of the Sbm2-resistant haplotype. The interval harbors 52 high- and 41 low-confidence genes, encoding 17 cytochrome p450, three receptor kinases, two defensins, and three NBS-LRR genes. These results pave the way for Sbm2 positional cloning. Importantly, the development of Sbm2 haplotype tagging KASP® provides a valuable case study for improving efficacy of the European variety testing system and, ultimately, the decision-making process related to varietal characterization and choice.
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Affiliation(s)
- Martina Bruschi
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Matteo Bozzoli
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Claudio Ratti
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Giuseppe Sciara
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Ellen Goudemand
- S.A.S. Florimond-Desprez Veuve and Fils, BP41, 59242, Cappelle-en-Pévèle, France
| | - Pierre Devaux
- S.A.S. Florimond-Desprez Veuve and Fils, BP41, 59242, Cappelle-en-Pévèle, France
| | - Danara Ormanbekova
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Cristian Forestan
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Simona Corneti
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Sandra Stefanelli
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Sara Castelletti
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Elena Fusari
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Jad B Novi
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Elisabetta Frascaroli
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Silvio Salvi
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Dragan Perovic
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institut (JKI), Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Agata Gadaleta
- Department of Soil, Plant and Food Science (Di.S.S.P.A.), University of Bari 'Aldo Moro', 70126, Bari, Italy
| | - Concepcion Rubies-Autonell
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Maria Corinna Sanguineti
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Roberto Tuberosa
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy.
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Rivera-Burgos L, VanGessel C, Guedira M, Smith J, Marshall D, Jin Y, Rouse M, Brown-Guedira G. Fine mapping of stem rust resistance derived from soft red winter wheat cultivar AGS2000 to an NLR gene cluster on chromosome 6D. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:206. [PMID: 39158718 PMCID: PMC11333525 DOI: 10.1007/s00122-024-04702-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 07/27/2024] [Indexed: 08/20/2024]
Abstract
The Puccinia graminis f. sp. tritici (Pgt) Ug99-emerging virulent races present a major challenge to global wheat production. To meet present and future needs, new sources of resistance must be found. Identification of markers that allow tracking of resistance genes is needed for deployment strategies to combat highly virulent pathogen races. Field evaluation of a DH population located a QTL for stem rust (Sr) resistance, QSr.nc-6D from the breeding line MD01W28-08-11 to the distal region of chromosome arm 6DS where Sr resistance genes Sr42, SrCad, and SrTmp have been identified. A locus for seedling resistance to Pgt race TTKSK was identified in a DH population and an RIL population derived from the cross AGS2000 × LA95135. The resistant cultivar AGS2000 is in the pedigree of MD01W28-08-11 and our results suggest that it is the source of Sr resistance in this breeding line. We exploited published markers and exome capture data to enrich marker density in a 10 Mb region flanking QSr.nc-6D. Our fine mapping in heterozygous inbred families identified three markers co-segregating with resistance and delimited QSr.nc-6D to a 1.3 Mb region. We further exploited information from other genome assemblies and identified collinear regions of 6DS harboring clusters of NLR genes. Evaluation of KASP assays corresponding to our co-segregating SNP suggests that they can be used to track this Sr resistance in breeding programs. However, our results also underscore the challenges posed in identifying genes underlying resistance in such complex regions in the absence of genome sequence from the resistant genotypes.
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Affiliation(s)
- L Rivera-Burgos
- Plant Science Research Unit, USDA-ARS, North Carolina State University, Raleigh, NC, 27695, USA
| | - C VanGessel
- Department of Crop and Soil Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - M Guedira
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - J Smith
- Plant Science Research Unit, USDA-ARS, North Carolina State University, Raleigh, NC, 27695, USA
| | - D Marshall
- Plant Science Research Unit, USDA-ARS, North Carolina State University, Raleigh, NC, 27695, USA
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Y Jin
- Cereal Disease Laboratory, USDA-ARS, University of Minnesota, St. Paul, MN, 55108, USA
| | - M Rouse
- Cereal Disease Laboratory, USDA-ARS, University of Minnesota, St. Paul, MN, 55108, USA
- Sugarcane Production Research Unit, USDA-ARS, Canal Point, FL, 33438, USA
| | - G Brown-Guedira
- Plant Science Research Unit, USDA-ARS, North Carolina State University, Raleigh, NC, 27695, USA.
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA.
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5
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Cavalet-Giorsa E, González-Muñoz A, Athiyannan N, Holden S, Salhi A, Gardener C, Quiroz-Chávez J, Rustamova SM, Elkot AF, Patpour M, Rasheed A, Mao L, Lagudah ES, Periyannan SK, Sharon A, Himmelbach A, Reif JC, Knauft M, Mascher M, Stein N, Chayut N, Ghosh S, Perovic D, Putra A, Perera AB, Hu CY, Yu G, Ahmed HI, Laquai KD, Rivera LF, Chen R, Wang Y, Gao X, Liu S, Raupp WJ, Olson EL, Lee JY, Chhuneja P, Kaur S, Zhang P, Park RF, Ding Y, Liu DC, Li W, Nasyrova FY, Dvorak J, Abbasi M, Li M, Kumar N, Meyer WB, Boshoff WHP, Steffenson BJ, Matny O, Sharma PK, Tiwari VK, Grewal S, Pozniak CJ, Chawla HS, Ens J, Dunning LT, Kolmer JA, Lazo GR, Xu SS, Gu YQ, Xu X, Uauy C, Abrouk M, Bougouffa S, Brar GS, Wulff BBH, Krattinger SG. Origin and evolution of the bread wheat D genome. Nature 2024:10.1038/s41586-024-07808-z. [PMID: 39143210 DOI: 10.1038/s41586-024-07808-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 07/10/2024] [Indexed: 08/16/2024]
Abstract
Bread wheat (Triticum aestivum) is a globally dominant crop and major source of calories and proteins for the human diet. Compared with its wild ancestors, modern bread wheat shows lower genetic diversity, caused by polyploidisation, domestication and breeding bottlenecks1,2. Wild wheat relatives represent genetic reservoirs, and harbour diversity and beneficial alleles that have not been incorporated into bread wheat. Here we establish and analyse extensive genome resources for Tausch's goatgrass (Aegilops tauschii), the donor of the bread wheat D genome. Our analysis of 46 Ae. tauschii genomes enabled us to clone a disease resistance gene and perform haplotype analysis across a complex disease resistance locus, allowing us to discern alleles from paralogous gene copies. We also reveal the complex genetic composition and history of the bread wheat D genome, which involves contributions from genetically and geographically discrete Ae. tauschii subpopulations. Together, our results reveal the complex history of the bread wheat D genome and demonstrate the potential of wild relatives in crop improvement.
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Affiliation(s)
- Emile Cavalet-Giorsa
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Andrea González-Muñoz
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Naveenkumar Athiyannan
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Samuel Holden
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, British Columbia, Canada
| | - Adil Salhi
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Catherine Gardener
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Samira M Rustamova
- Institute of Molecular Biology and Biotechnologies, Ministry of Science and Education of the Republic of Azerbaijan, Baku, Azerbaijan
| | - Ahmed Fawzy Elkot
- Wheat Research Department, Field Crops Research Institute, Agricultural Research Center (ARC), Giza, Egypt
| | - Mehran Patpour
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | - Awais Rasheed
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- International Maize and Wheat Improvement Centre (CIMMYT), c/o CAAS, Beijing, China
| | - Long Mao
- State Key Laboratory of Crop Gene Resources and Breeding and National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Evans S Lagudah
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, Canberra, New South Wales, Australia
| | - Sambasivam K Periyannan
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, Canberra, New South Wales, Australia
- Centre for Crop Health School of Agriculture and Environmental Science, University of Southern Queensland, Toowoomba, Queensland, Australia
| | - Amir Sharon
- Institute for Cereal Crops Improvement, School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Manuela Knauft
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Noam Chayut
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Sreya Ghosh
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Dragan Perovic
- Julius Kuehn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Alexander Putra
- Bioscience Core Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ana B Perera
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Chia-Yi Hu
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Guotai Yu
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Hanin Ibrahim Ahmed
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Centre d'anthropobiologie et de génomique de Toulouse (CAGT), Laboratoire d'Anthropobiologie et d'Imagerie de Synthèse, CNRS UMR 5288, Faculté de Médecine de Purpan, Toulouse, France
| | - Konstanze D Laquai
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Luis F Rivera
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Renjie Chen
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Yajun Wang
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xin Gao
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - W John Raupp
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Eric L Olson
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Jong-Yeol Lee
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Peng Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, New South Wales, Australia
| | - Robert F Park
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, New South Wales, Australia
| | - Yi Ding
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, New South Wales, Australia
| | - Deng-Cai Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wanlong Li
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Firuza Y Nasyrova
- Institute of Botany, Plant Physiology and Genetics, Tajik National Academy of Sciences, Dushanbe, Tajikistan
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Mehrdad Abbasi
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, British Columbia, Canada
| | - Meng Li
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, British Columbia, Canada
| | - Naveen Kumar
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, British Columbia, Canada
| | - Wilku B Meyer
- Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa
| | - Willem H P Boshoff
- Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, USA
| | - Oadi Matny
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, USA
| | - Parva K Sharma
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Vijay K Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Surbhi Grewal
- Nottingham Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, UK
| | - Curtis J Pozniak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, Saskatoon, Saskatchewan, Canada
| | - Harmeet Singh Chawla
- University of Saskatchewan, Crop Development Centre, Agriculture Building, Saskatoon, Saskatchewan, Canada
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jennifer Ens
- University of Saskatchewan, Crop Development Centre, Agriculture Building, Saskatoon, Saskatchewan, Canada
| | - Luke T Dunning
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | | | - Gerard R Lazo
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, USDA-ARS, Albany, CA, USA
| | - Steven S Xu
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, USDA-ARS, Albany, CA, USA
| | - Yong Q Gu
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, USDA-ARS, Albany, CA, USA
| | - Xianyang Xu
- Peanut and Small Grains Research Unit, USDA-ARS, Stillwater, OK, USA
| | | | - Michael Abrouk
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Salim Bougouffa
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Gurcharn S Brar
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, British Columbia, Canada
- Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, Canada
| | - Brande B H Wulff
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Simon G Krattinger
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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6
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Burridge AJ, Winfield M, Przewieslik‐Allen A, Edwards KJ, Siddique I, Barral‐Arca R, Griffiths S, Cheng S, Huang Z, Feng C, Dreisigacker S, Bentley AR, Brown‐Guedira G, Barker GL. Development of a next generation SNP genotyping array for wheat. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2235-2247. [PMID: 38520342 PMCID: PMC11258986 DOI: 10.1111/pbi.14341] [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: 12/07/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 03/25/2024]
Abstract
High-throughput genotyping arrays have provided a cost-effective, reliable and interoperable system for genotyping hexaploid wheat and its relatives. Existing, highly cited arrays including our 35K Wheat Breeder's array and the Illumina 90K array were designed based on a limited amount of varietal sequence diversity and with imperfect knowledge of SNP positions. Recent progress in wheat sequencing has given us access to a vast pool of SNP diversity, whilst technological improvements have allowed us to fit significantly more probes onto a 384-well format Axiom array than previously possible. Here we describe a novel Axiom genotyping array, the 'Triticum aestivum Next Generation' array (TaNG), largely derived from whole genome skim sequencing of 204 elite wheat lines and 111 wheat landraces taken from the Watkins 'Core Collection'. We used a novel haplotype optimization approach to select SNPs with the highest combined varietal discrimination and a design iteration step to test and replace SNPs which failed to convert to reliable markers. The final design with 43 372 SNPs contains a combination of haplotype-optimized novel SNPs and legacy cross-platform markers. We show that this design has an improved distribution of SNPs compared to previous arrays and can be used to generate genetic maps with a significantly higher number of distinct bins than our previous array. We also demonstrate the improved performance of TaNGv1.1 for Genome-wide association studies (GWAS) and its utility for Copy Number Variation (CNV) analysis. The array is commercially available with supporting marker annotations and initial genotyping results freely available.
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Affiliation(s)
| | - Mark Winfield
- School of Biological SciencesUniversity of BristolBristolUK
| | | | | | - Imteaz Siddique
- Thermo Fisher Scientific3450 Central ExpresswaySanta ClaraCAUSA
| | | | | | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Zejian Huang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Cong Feng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | | | | | - Gina Brown‐Guedira
- Plant Science Research UnitUSDA Agricultural Research ServiceRaleighNCUSA
| | - Gary L. Barker
- School of Biological SciencesUniversity of BristolBristolUK
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7
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Ullah R, Yin M, Li S, Israr Y, Wu Z, Wang X, Yu J, Li B, Ni Z, Liang R. Genome-wide association study identifies loci and candidate genes for RVA parameters in wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1421924. [PMID: 39104845 PMCID: PMC11298398 DOI: 10.3389/fpls.2024.1421924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 06/24/2024] [Indexed: 08/07/2024]
Abstract
The gelatinization and retrogradation characteristics of wheat starch affect the eating quality of Chinese-style food. Rapid Visco Analyzer (RVA) parameters have been widely used as important indicators to evaluate and improve the quality of wheat starch. However, the genetic basis of RVA parameters remains to be further explored. In the present study, a natural population was genotyped using 90K single nucleotide polymorphism (SNP) arrays, and the RVA parameters of this population grown in five environments were evaluated. The results showed that 22,068 high-quality SNP markers were identified and distributed unequally on the chromosomes. According to the genetic distance, 214 wheat materials were divided into four groups. Except for the pasting temperature (PTT), six parameters followed a normal distribution. Based on the general linear model, 969 significant association SNPs were detected by genome-wide association studies (GWAS), and chromosomes 7A and 2B had the most associated SNPs. Breakdown viscosity (BV) was associated with the most SNPs (n = 238), followed by PTT (n = 186), peak viscosity (PV; n = 156), trough viscosity (TV; n = 127), and final viscosity (FV; n = 126). According to the average linkage disequilibrium (LD), 33 stable quantitative trait loci (QTLs) were identified for single parameters in multiple environments, of which 12 were associated with BV, followed by peak time (PT; n = 8) and PTT (n = 7). On the other hand, 67 pleiotropic QTLs were identified for multiple parameters. Three candidate genes-TasbeIIa, TasbeI, and TassIIa-were screened for phenotyping analysis. The grain width and the weight of the TasbeIIa and TaSSIIa knockout (KO) lines were significantly lower than those of the TasbeI KO lines and the control (CK). The KO lines had smaller endosperm cells, smaller A-type starch granules, and higher amylose content. The TasbeI KO lines showed normal RVA curves, while the TasbeIIa KO lines showed flat curves. However, the TaSSIIa lines failed to paste under the RVA temperatures. Conclusively, the SNPs/QTLs significantly associated with the RVA parameters and genetic resources with novel haplotypes could be used to improve the quality of wheat starch.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Rongqi Liang
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, China
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8
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Mandal R, He X, Singh G, Kabir MR, Joshi AK, Singh PK. Screening of CIMMYT and South Asian Bread Wheat Germplasm Reveals Marker-Trait Associations for Seedling Resistance to Septoria Nodorum Blotch. Genes (Basel) 2024; 15:890. [PMID: 39062669 PMCID: PMC11276481 DOI: 10.3390/genes15070890] [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: 06/14/2024] [Revised: 07/02/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024] Open
Abstract
Wheat (Triticum aestivum L.) production is adversely impacted by Septoria nodorum blotch (SNB), a fungal disease caused by Parastagonospora nodorum. Wheat breeders are constantly up against this biotic challenge as they try to create resistant cultivars. The genome-wide association study (GWAS) has become an efficient tool for identifying molecular markers linked with SNB resistance. This technique is used to acquire an understanding of the genetic basis of resistance and to facilitate marker-assisted selection. In the current study, a total of 174 bread wheat accessions from South Asia and CIMMYT were assessed for SNB reactions at the seedling stage in three greenhouse experiments at CIMMYT, Mexico. The results indicated that 129 genotypes were resistant to SNB, 39 were moderately resistant, and only 6 were moderately susceptible. The Genotyping Illumina Infinium 15K Bead Chip was used, and 11,184 SNP markers were utilized to identify marker-trait associations (MTAs) after filtering. Multiple tests confirmed the existence of significant MTAs on chromosomes 5B, 5A, and 3D, and the ones at Tsn1 on 5B were the most stable and conferred the highest phenotypic variation. The resistant genotypes identified in this study could be cultivated in South Asian countries as a preventative measure against the spread of SNB. This work also identified molecular markers of SNB resistance that could be used in future wheat breeding projects.
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Affiliation(s)
- Rupsanatan Mandal
- Visiting Scientist, International Maize and Wheat Improvement Center (CIMMYT), Texcoco 56237, Mexico;
- Department of Genetics and Plant Breeding, Uttar Banga Krishi Viswavidyalaya, Cooch Behar 736165, India
| | - Xinyao He
- International Maize and Wheat Improvement Centre, Texcoco 56237, Mexico;
| | - Gyanendra Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, India;
| | | | - Arun Kumar Joshi
- International Maize and Wheat Improvement Center (CIMMYT)-India Office, New Delhi 110012, India;
- Borlaug Institute for South Asia, New Delhi 110012, India
| | - Pawan Kumar Singh
- International Maize and Wheat Improvement Centre, Texcoco 56237, Mexico;
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9
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Gaur A, Jindal Y, Singh V, Tiwari R, Juliana P, Kaushik D, Kumar KJY, Ahlawat OP, Singh G, Sheoran S. GWAS elucidated grain yield genetics in Indian spring wheat under diverse water conditions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:177. [PMID: 38972024 DOI: 10.1007/s00122-024-04680-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 06/11/2024] [Indexed: 07/08/2024]
Abstract
KEY MESSAGE Underpinned natural variations and key genes associated with yield under different water regimes, and identified genomic signatures of genetic gain in the Indian wheat breeding program. A novel KASP marker for TKW under water stress was developed and validated. A comprehensive genome-wide association study was conducted on 300 spring wheat genotypes to elucidate the natural variations associated with grain yield and its eleven contributing traits under fully irrigated, restricted water, and simulated no water conditions. Utilizing the 35K Wheat Breeders' Array, we identified 1155 quantitative trait nucleotides (QTNs), with 207 QTNs exhibiting stability across diverse conditions. These QTNs were further delimited into 539 genomic regions using a genome-wide LD value of 3.0 Mbp, revealing pleiotropic control across traits and conditions. Sub-genome A was significantly associated with traits under irrigated conditions, while sub-genome B showed more QTNs under water stressed conditions. Favourable alleles with significantly associated QTNs were delineated, with a notable pyramiding effect for enhancing trait performance. Additionally, allele of only 921 QTNs significantly affected the population mean. Allele profiling highlighted C-306 as a most potential source of drought tolerance. Moreover, 762 genes overlapping significant QTNs were identified, narrowing down to 27 putative candidate genes overlapping 29 novel and functional SNPs expressing (≥ 0.5 tpm) relevance across various growth conditions. A new KASP assay was developed, targeting a gene TraesCS2A03G1123700 regulating thousand kernel weight under severe drought condition. Genomic selection models (GBLUP, BayesB, MxE, and R-Norm) demonstrated an average prediction accuracy of 0.06-0.58 across environments, indicating potential for trait selection. Retrospective analysis of the Indian wheat breeding program supported a genetic gain in GY at the rate of ca. 0.56% per breeding cycle, since 1960, supporting the identification of genomic signatures driving trait selection and genetic gain. These findings offer insight into improving the rate of genetic gain in wheat breeding programs globally.
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Affiliation(s)
- Arpit Gaur
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar, India
- Crop Improvement, ICAR- Indian Institute of Wheat and Barley Research, Karnal, India
| | - Yogesh Jindal
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar, India
| | - Vikram Singh
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar, India
| | - Ratan Tiwari
- Crop Improvement, ICAR- Indian Institute of Wheat and Barley Research, Karnal, India
| | | | - Deepak Kaushik
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar, India
| | | | - Om Parkash Ahlawat
- Crop Improvement, ICAR- Indian Institute of Wheat and Barley Research, Karnal, India
| | - Gyanendra Singh
- Crop Improvement, ICAR- Indian Institute of Wheat and Barley Research, Karnal, India
| | - Sonia Sheoran
- Crop Improvement, ICAR- Indian Institute of Wheat and Barley Research, Karnal, India.
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10
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Chen J, Zhang Y, Wei J, Hu X, Yin H, Liu W, Li D, Tian W, Hao Y, He Z, Fernie AR, Chen W. Beyond pathways: Accelerated flavonoids candidate identification and novel exploration of enzymatic properties using combined mapping populations of wheat. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2033-2050. [PMID: 38408119 PMCID: PMC11182594 DOI: 10.1111/pbi.14323] [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: 11/15/2023] [Revised: 02/06/2024] [Accepted: 02/12/2024] [Indexed: 02/28/2024]
Abstract
Although forward-genetics-metabolomics methods such as mGWAS and mQTL have proven effective in providing myriad loci affecting metabolite contents, they are somehow constrained by their respective constitutional flaws such as the hidden population structure for GWAS and insufficient recombinant rate for QTL. Here, the combination of mGWAS and mQTL was performed, conveying an improved statistical power to investigate the flavonoid pathways in common wheat. A total of 941 and 289 loci were, respectively, generated from mGWAS and mQTL, within which 13 of them were co-mapped using both approaches. Subsequently, the mGWAS or mQTL outputs alone and their combination were, respectively, utilized to delineate the metabolic routes. Using this approach, we identified two MYB transcription factor encoding genes and five structural genes, and the flavonoid pathway in wheat was accordingly updated. Moreover, we have discovered some rare-activity-exhibiting flavonoid glycosyl- and methyl-transferases, which may possess unique biological significance, and harnessing these novel catalytic capabilities provides potentially new breeding directions. Collectively, we propose our survey illustrates that the forward-genetics-metabolomics approaches including multiple populations with high density markers could be more frequently applied for delineating metabolic pathways in common wheat, which will ultimately contribute to metabolomics-assisted wheat crop improvement.
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Affiliation(s)
- Jie Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
- Yazhouwan National LaboratorySanyaChina
| | - Yueqi Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Jiaqi Wei
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
- Wuhan Academy of Agricultural SciencesWuhanChina
| | - Xin Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Huanran Yin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Wei Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Dongqin Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
| | - Wenfei Tian
- National Wheat Improvement Center, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yuanfeng Hao
- National Wheat Improvement Center, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | | | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
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11
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Sadeh R, Ben-David R, Herrmann I, Peleg Z. Spectral-genomic chain-model approach enhances the wheat yield component prediction under the Mediterranean climate. PHYSIOLOGIA PLANTARUM 2024; 176:e14480. [PMID: 39187437 DOI: 10.1111/ppl.14480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 08/28/2024]
Abstract
In light of the changing climate that jeopardizes future food security, genomic selection is emerging as a valuable tool for breeders to enhance genetic gains and introduce high-yielding varieties. However, predicting grain yield is challenging due to the genetic and physiological complexities involved and the effect of genetic-by-environment interactions on prediction accuracy. We utilized a chained model approach to address these challenges, breaking down the complex prediction task into simpler steps. A diversity panel with a narrow phenological range was phenotyped across three Mediterranean environments for various morpho-physiological and yield-related traits. The results indicated that a multi-environment model outperformed a single-environment model in prediction accuracy for most traits. However, prediction accuracy for grain yield was not improved. Thus, in an attempt to ameliorate the grain yield prediction accuracy, we integrated a spectral estimation of spike number, being a major wheat yield component, with genomic data. A machine learning approach was used for spike number estimation from canopy hyperspectral reflectance captured by an unmanned aerial vehicle. The spectral-based estimated spike number was utilized as a secondary trait in a multi-trait genomic selection, significantly improving grain yield prediction accuracy. Moreover, the ability to predict the spike number based on data from previous seasons implies that it could be applied to new trials at various scales, even in small plot sizes. Overall, we demonstrate here that incorporating a novel spectral-genomic chain-model workflow, which utilizes spectral-based phenotypes as a secondary trait, improves the predictive accuracy of wheat grain yield.
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Affiliation(s)
- Roy Sadeh
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Roi Ben-David
- Institute of Plant Sciences, Agriculture Research Organization (ARO)-Volcani Institute, Rishon LeZion, Israel
| | - Ittai Herrmann
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Zvi Peleg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
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12
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John-Bejai C, Trethowan R, Revell I, de Groot S, Shezi L, Koekemoer F, Diffey S, Lage J. Identifying the seeds of heterotic pools for Southern and Eastern Africa from global elite spring wheat germplasm. FRONTIERS IN PLANT SCIENCE 2024; 15:1398715. [PMID: 38993941 PMCID: PMC11236601 DOI: 10.3389/fpls.2024.1398715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 05/31/2024] [Indexed: 07/13/2024]
Abstract
Hybrid breeding can increase the competitiveness of wheat (Triticum aestivum L.) in Sub-Saharan Africa by fostering more public-private partnerships and promoting investment by the private sector. The benefit of hybrid wheat cultivars in South Africa has previously been demonstrated but due to the high cost of hybrid seed production, hybrid breeding has not received significant attention in the past decade. Considering the renewed commitment of the private sector to establish wheat as a hybrid crop globally, coupled with significant research investment into enhancement of outcrossing of wheat, hybrid wheat breeding in Southern and Eastern Africa should be revisited. Our study aimed to identify genetically distinct germplasm groups in spring wheat that would be useful in the establishment of heterotic pools targeting this region. Multi-environment yield testing of a large panel of F1 test hybrids, generated using global elite germplasm, was carried out between 2019 and 2020 in Argentina, Africa, Europe, and Australia. We observed significant genotype by environment interactions within our testing network, confirming the distinctiveness of African trial sites. Relatively high additive genetic variance was observed highlighting the contribution of parental genotypes to the grain yield of test hybrids. We explored the genetic architecture of these parents and the genetic factors underlying the value of parents appear to be associated with their genetic subgroup, with positive marker effects distributed throughout the genome. In testcrosses, elite germplasm from the International Maize and Wheat Improvement Center (CIMMYT) appear to be complementary to the genetically distinct germplasm bred in South Africa. The feasibility of achieving genetic gain via heterotic pool establishment and divergence, and by extension the viability of hybrid cultivars in Sub-Saharan Africa, is supported by the results of our study.
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Affiliation(s)
| | - Richard Trethowan
- The Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Narrabri, NSW, Australia
| | - Isobella Revell
- The Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Narrabri, NSW, Australia
| | | | - Lindani Shezi
- Wheat Breeding, Sensako (Syngenta), Bethlehem, South Africa
| | | | | | - Jacob Lage
- Wheat Breeding, KWS UK Ltd, Thriplow, United Kingdom
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13
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Joukhadar R, Li Y, Thistlethwaite R, Forrest KL, Tibbits JF, Trethowan R, Hayden MJ. Optimising desired gain indices to maximise selection response. FRONTIERS IN PLANT SCIENCE 2024; 15:1337388. [PMID: 38978519 PMCID: PMC11228337 DOI: 10.3389/fpls.2024.1337388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 05/23/2024] [Indexed: 07/10/2024]
Abstract
Introduction In plant breeding, we often aim to improve multiple traits at once. However, without knowing the economic value of each trait, it is hard to decide which traits to focus on. This is where "desired gain selection indices" come in handy, which can yield optimal gains in each trait based on the breeder's prioritisation of desired improvements when economic weights are not available. However, they lack the ability to maximise the selection response and determine the correlation between the index and net genetic merit. Methods Here, we report the development of an iterative desired gain selection index method that optimises the sampling of the desired gain values to achieve a targeted or a user-specified selection response for multiple traits. This targeted selection response can be constrained or unconstrained for either a subset or all the studied traits. Results We tested the method using genomic estimated breeding values (GEBVs) for seven traits in a bread wheat (Triticum aestivum) reference breeding population comprising 3,331 lines and achieved prediction accuracies ranging between 0.29 and 0.47 across the seven traits. The indices were validated using 3,005 double haploid lines that were derived from crosses between parents selected from the reference population. We tested three user-specified response scenarios: a constrained equal weight (INDEX1), a constrained yield dominant weight (INDEX2), and an unconstrained weight (INDEX3). Our method achieved an equivalent response to the user-specified selection response when constraining a set of traits, and this response was much better than the response of the traditional desired gain selection indices method without iteration. Interestingly, when using unconstrained weight, our iterative method maximised the selection response and shifted the average GEBVs of the selection candidates towards the desired direction. Discussion Our results show that the method is an optimal choice not only when economic weights are unavailable, but also when constraining the selection response is an unfavourable option.
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Affiliation(s)
- Reem Joukhadar
- Agriculture Victoria, Centre for AgriBioscience, AgriBio, Bundoora, VIC, Australia
| | - Yongjun Li
- Agriculture Victoria, Centre for AgriBioscience, AgriBio, Bundoora, VIC, Australia
| | - Rebecca Thistlethwaite
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Narrabri, NSW, Australia
| | - Kerrie L. Forrest
- Agriculture Victoria, Centre for AgriBioscience, AgriBio, Bundoora, VIC, Australia
| | - Josquin F. Tibbits
- Agriculture Victoria, Centre for AgriBioscience, AgriBio, Bundoora, VIC, Australia
| | - Richard Trethowan
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Narrabri, NSW, Australia
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Cobbitty, NSW, Australia
| | - Matthew J. Hayden
- Agriculture Victoria, Centre for AgriBioscience, AgriBio, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
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14
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Schierenbeck M, Alqudah AM, Thabet SG, Avogadro EG, Dietz JI, Simón MR, Börner A. Natural allelic variation confers diversity in the regulation of flag leaf traits in wheat. Sci Rep 2024; 14:13316. [PMID: 38858489 PMCID: PMC11164900 DOI: 10.1038/s41598-024-64161-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 06/05/2024] [Indexed: 06/12/2024] Open
Abstract
Flag leaf (FL) dimension has been reported as a key ecophysiological aspect for boosting grain yield in wheat. A worldwide winter wheat panel consisting of 261 accessions was tested to examine the phenotypical variation and identify quantitative trait nucleotides (QTNs) with candidate genes influencing FL morphology. To this end, four FL traits were evaluated during the early milk stage under two growing seasons at the Leibniz Institute of Plant Genetics and Crop Plant Research. The results showed that all leaf traits (Flag leaf length, width, area, and length/width ratio) were significantly influenced by the environments, genotypes, and environments × genotypes interactions. Then, a genome-wide association analysis was performed using 17,093 SNPs that showed 10 novel QTNs that potentially play a role in modulating FL morphology in at least two environments. Further analysis revealed 8 high-confidence candidate genes likely involved in these traits and showing high expression values from flag leaf expansion until its senescence and also during grain development. An important QTN (wsnp_RFL_Contig2177_1500201) was associated with FL width and located inside TraesCS3B02G047300 at chromosome 3B. This gene encodes a major facilitator, sugar transporter-like, and showed the highest expression values among the candidate genes reported, suggesting their positive role in controlling flag leaf and potentially being involved in photosynthetic assimilation. Our study suggests that the detection of novel marker-trait associations and the subsequent elucidation of the genetic mechanism influencing FL morphology would be of interest for improving plant architecture, light capture, and photosynthetic efficiency during grain development.
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Affiliation(s)
- Matías Schierenbeck
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, 06466, Seeland, Germany.
- Faculty of Agricultural Sciences and Forestry, National University of La Plata, La Plata, Argentina.
- CONICET CCT La Plata, La Plata, Argentina.
| | - Ahmad Mohammad Alqudah
- Biological Science Program, Department of Biological and Environmental Sciences, College of Art and Science, Qatar University, Doha, Qatar.
| | - Samar Gamal Thabet
- Department of Botany, Faculty of Science, Fayoum University, Fayoum, Egypt
| | - Evangelina Gabriela Avogadro
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
| | - Juan Ignacio Dietz
- CONICET CCT La Plata, La Plata, Argentina
- EEA INTA Bordenave, Ruta 76 km 36, Bordenave, Argentina
| | - María Rosa Simón
- Faculty of Agricultural Sciences and Forestry, National University of La Plata, La Plata, Argentina
- CONICET CCT La Plata, La Plata, Argentina
| | - Andreas Börner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
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15
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Vasistha NK, Sharma V, Singh S, Kaur R, Kumar A, Ravat VK, Kumar R, Gupta PK. Meta-QTL analysis and identification of candidate genes for multiple-traits associated with spot blotch resistance in bread wheat. Sci Rep 2024; 14:13083. [PMID: 38844568 PMCID: PMC11156910 DOI: 10.1038/s41598-024-63924-w] [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: 01/04/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024] Open
Abstract
In bread wheat, a literature search gave 228 QTLs for six traits, including resistance against spot blotch and the following five other related traits: (i) stay green; (ii) flag leaf senescence; (iii) green leaf area duration; (iv) green leaf area of the main stem; and (v) black point resistance. These QTLs were used for metaQTL (MQTL) analysis. For this purpose, a consensus map with 72,788 markers was prepared; 69 of the above 228 QTLs, which were suitable for MQTL analysis, were projected on the consensus map. This exercise resulted in the identification of 16 meta-QTLs (MQTLs) located on 11 chromosomes, with the PVE ranging from 5.4% (MQTL7) to 21.8% (MQTL5), and the confidence intervals ranging from 1.5 to 20.7 cM (except five MQTLs with a range of 36.1-57.8 cM). The number of QTLs associated with individual MQTLs ranged from a maximum of 17 in MQTL3 to 8 each in MQTL5 and MQTL8 and 5 each in MQTL7 and MQTL14. The 16 MQTLs, included 12 multi-trait MQTLs; one of the MQTL also overlapped a genomic region carrying the major spot blotch resistance gene Sb1. Of the total 16 MQTLs, 12 MQTLs were also validated through marker-trait associations that were available from earlier genome-wide association studies. The genomic regions associated with MQTLs were also used for the identification of candidate genes (CGs) and led to the identification of 516 CGs encoding 508 proteins; 411 of these proteins are known to be associated with resistance against several biotic stresses. In silico expression analysis of CGs using transcriptome data allowed the identification of 71 differentially expressed CGs, which were examined for further possible studies. The findings of the present study should facilitate fine-mapping and cloning of genes, enabling Marker Assisted Selection.
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Affiliation(s)
- Neeraj Kumar Vasistha
- Department of Genetics and Plant Breeding, Rajiv Gandhi University, Rono Hills, Itanagar, India
- Department of Genetics-Plant Breeding and Biotechnology, Dr K. S. Gill, Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, India
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | - Vaishali Sharma
- Department of Genetics-Plant Breeding and Biotechnology, Dr K. S. Gill, Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, India
| | - Sahadev Singh
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
- Meerut Institute of Technology, NH-58 Baral Partapur Bypass Road, Meerut, India
| | - Ramandeep Kaur
- Department of Genetics-Plant Breeding and Biotechnology, Dr K. S. Gill, Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, India
| | - Anuj Kumar
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | - Vikas Kumar Ravat
- Department of Plant Pathology, Rajiv Gandhi University, Rono Hills, Itanagar, India
| | - Rahul Kumar
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | - Pushpendra K Gupta
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India.
- Murdoch's Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia.
- Borlaug Institute for South Asia (BISA), National Agricultural Science Complex (NASC), Dev Prakash Shastri (DPS) Marg, New Delhi, India.
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Zhou L, Chang G, Shen C, Teng W, He X, Zhao X, Jing Y, Huang Z, Tong Y. Functional divergences of natural variations of TaNAM-A1 in controlling leaf senescence during wheat grain filling. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1242-1260. [PMID: 38656698 DOI: 10.1111/jipb.13658] [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: 06/05/2023] [Accepted: 03/13/2024] [Indexed: 04/26/2024]
Abstract
Leaf senescence is an essential physiological process related to grain yield potential and nutritional quality. Green leaf duration (GLD) after anthesis directly reflects the leaf senescence process and exhibits large genotypic differences in common wheat; however, the underlying gene regulatory mechanism is still lacking. Here, we identified TaNAM-A1 as the causal gene of the major loci qGLD-6A for GLD during grain filling by map-based cloning. Transgenic assays and TILLING mutant analyses demonstrated that TaNAM-A1 played a critical role in regulating leaf senescence, and also affected spike length and grain size. Furthermore, the functional divergences among the three haplotypes of TaNAM-A1 were systematically evaluated. Wheat varieties with TaNAM-A1d (containing two mutations in the coding DNA sequence of TaNAM-A1) exhibited a longer GLD and superior yield-related traits compared to those with the wild type TaNAM-A1a. All three haplotypes were functional in activating the expression of genes involved in macromolecule degradation and mineral nutrient remobilization, with TaNAM-A1a showing the strongest activity and TaNAM-A1d the weakest. TaNAM-A1 also modulated the expression of the senescence-related transcription factors TaNAC-S-7A and TaNAC016-3A. TaNAC016-3A enhanced the transcriptional activation ability of TaNAM-A1a by protein-protein interaction, thereby promoting the senescence process. Our study offers new insights into the fine-tuning of the leaf functional period and grain yield formation for wheat breeding under various geographical climatic conditions.
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Affiliation(s)
- Longxi Zhou
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guowei Chang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chuncai Shen
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wan Teng
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xue He
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xueqiang Zhao
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanfu Jing
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Sciences, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhixiong Huang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Sciences, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiping Tong
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Sciences, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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17
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Xu X, Li G, Bai G, Bian R, Bernardo A, Kolmer J, Carver BF, Wolabu TW, Wu Y. Characterization of Quantitative Trait Loci for Leaf Rust Resistance in the Uzbekistani Wheat Landrace Teremai Bugdai. PHYTOPATHOLOGY 2024; 114:1373-1379. [PMID: 38281142 DOI: 10.1094/phyto-09-23-0320-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Leaf rust, caused by Puccinia triticina, is a major cause of wheat yield losses globally, and novel leaf rust resistance genes are needed to enhance wheat leaf rust resistance. Teremai Bugdai is a landrace from Uzebekistan that is highly resistant to many races of P. triticina in the United States. To unravel leaf rust resistance loci in Teremai Bugdai, a recombinant inbred line (RIL) population of Teremai Bugdai × TAM 110 was evaluated for response to P. triticina race Pt54-1 (TNBGJ) and genotyped using single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing (GBS). Quantitative trait loci (QTL) analysis using 5,130 high-quality GBS-SNPs revealed three QTLs, QLr-Stars-2DS, QLr-Stars-6BL, and QLr.Stars-7BL, for leaf rust resistance in two experiments. QLr-Stars-2DS, which is either a new Lr2 allele or a new resistance locus, was delimited to an ∼19.47-Mb interval between 46.4 and 65.9 Mb on 2DS and explained 31.3 and 33.2% of the phenotypic variance in the two experiments. QLr-Stars-6BL was mapped in an ∼84.0-kb interval between 719.48 and 719.56 Mb on 6BL, accounting for 33 to 36.8% of the phenotypic variance in two experiments. QLr.Stars-7BL was placed in a 350-kb interval between 762.41 and 762.76 Mb on 7BL and explained 4.4 to 5.3% of the phenotypic variance. Nine GBS-SNPs flanking these QTLs were converted to kompetitive allele specific PCR (KASP) markers, and these markers can be used to facilitate their introgression into locally adapted wheat lines.
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Affiliation(s)
- Xiangyang Xu
- U.S. Department of Agriculture-Agricultural Research Service, Peanut and Small Grains Research Unit, Stillwater, OK 74075
| | - Genqiao Li
- U.S. Department of Agriculture-Agricultural Research Service, Peanut and Small Grains Research Unit, Stillwater, OK 74075
| | - Guihua Bai
- U.S. Department of Agriculture-Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506
| | - Ruolin Bian
- Department of Agronomy, Kansas State University, Manhattan, KS 66506
| | - Amy Bernardo
- U.S. Department of Agriculture-Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506
| | - Jim Kolmer
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108
| | - Brett F Carver
- Department of Plant and Soil Science, Oklahoma State University, Stillwater, OK 74075
| | - Tezera W Wolabu
- Department of Plant and Soil Science, Oklahoma State University, Stillwater, OK 74075
| | - Yanqi Wu
- Department of Plant and Soil Science, Oklahoma State University, Stillwater, OK 74075
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18
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Li Y, Wang M, Hu X, Chen X. Identification of a Locus for High-Temperature Adult-Plant Resistance to Stripe Rust in the Wheat Yr8 Near-Isogenic Line Through Mutagenesis and Molecular Mapping. PLANT DISEASE 2024; 108:1261-1269. [PMID: 37938905 DOI: 10.1094/pdis-10-23-2037-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Aegilops species are wheat relatives that harbor valuable disease resistance genes for wheat breeding. The wheat Yr8 near-isogenic line AvSYr8NIL has long been believed to carry only Yr8 for race-specific all-stage resistance to stripe rust, caused by Puccinia striiformis f. sp. tritici, derived from Aegilops comosa. However, AvSYr8NIL has been found to have high-temperature adult-plant (HTAP) resistance in our field and greenhouse tests. To confirm both HTAP and Yr8 resistance, seeds from AvSYr8NIL were treated with ethyl methanesulfonate to generate mutant lines. The mutant lines with only Yr8 (M641) and only HTAP resistance (M488) were crossed with the susceptible recurrent parent Avocet S (AvS). The F1 and F4 lines of AvS/M641 were phenotyped with Yr8-avirulent races in the seedling stage at the low-temperature (4 to 20°C) profile, while the F1, F2, F4, and F5 lines of AvS/M488 were phenotyped with Yr8-virulent races in the adult-plant stage at the high-temperature (10 to 30°C) profile. Both Yr8 and the HTAP resistance gene (YrM488) were recessive. The F4 populations of AvS/M641 and AvS/M488 were genotyped using polymorphic Kompetitive allele-specific PCR markers converted from single-nucleotide polymorphisms. Yr8 was mapped to a 0.66-cM fragment, and YrM488 was mapped to a 1.22-cM interval on chromosome 2D. The physical distance between the two resistance genes was estimated to be more than 500 Mb, indicating their distinct loci. The mutant lines with separated resistance genes would be useful in enhancing our understanding of different types of resistance and in further studying the interactions between wheat and the stripe rust pathogen.
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Affiliation(s)
- Yuxiang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, U.S.A
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, U.S.A
| | - Xiaoping Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, U.S.A
- U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164, U.S.A
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19
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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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20
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Jighly A, Thayalakumaran T, Kant S, Panozzo J, Aggarwal R, Hessel D, Forrest KL, Technow F, Totir R, Goddard M, Pryce J, Hayden MJ, Munkvold J, O'Leary GJ. Statistical sampling of missing environmental variables improves biophysical genomic prediction in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:108. [PMID: 38637355 DOI: 10.1007/s00122-024-04613-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 03/27/2024] [Indexed: 04/20/2024]
Abstract
KEY MESSAGE The integration of genomic prediction with crop growth models enabled the estimation of missing environmental variables which improved the prediction accuracy of grain yield. Since the invention of whole-genome prediction (WGP) more than two decades ago, breeding programmes have established extensive reference populations that are cultivated under diverse environmental conditions. The introduction of the CGM-WGP model, which integrates crop growth models (CGM) with WGP, has expanded the applications of WGP to the prediction of unphenotyped traits in untested environments, including future climates. However, CGMs require multiple seasonal environmental records, unlike WGP, which makes CGM-WGP less accurate when applied to historical reference populations that lack crucial environmental inputs. Here, we investigated the ability of CGM-WGP to approximate missing environmental variables to improve prediction accuracy. Two environmental variables in a wheat CGM, initial soil water content (InitlSoilWCont) and initial nitrate profile, were sampled from different normal distributions separately or jointly in each iteration within the CGM-WGP algorithm. Our results showed that sampling InitlSoilWCont alone gave the best results and improved the prediction accuracy of grain number by 0.07, yield by 0.06 and protein content by 0.03. When using the sampled InitlSoilWCont values as an input for the traditional CGM, the average narrow-sense heritability of the genotype-specific parameters (GSPs) improved by 0.05, with GNSlope, PreAnthRes, and VernSen showing the greatest improvements. Moreover, the root mean square of errors for grain number and yield was reduced by about 7% for CGM and 31% for CGM-WGP when using the sampled InitlSoilWCont values. Our results demonstrate the advantage of sampling missing environmental variables in CGM-WGP to improve prediction accuracy and increase the size of the reference population by enabling the utilisation of historical data that are missing environmental records.
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Affiliation(s)
- Abdulqader Jighly
- AgriBio, Centre for AgriBiosciences, Agriculture Victoria, Bundoora, VIC, 3083, Australia.
- SuSTATability Statistical Solutions, Melbourne, VIC, 3081, Australia.
| | - Thabo Thayalakumaran
- AgriBio, Centre for AgriBiosciences, Agriculture Victoria, Bundoora, VIC, 3083, Australia
| | - Surya Kant
- Grains Innovation Park, Agriculture Victoria, Horsham, VIC, 3400, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Joe Panozzo
- Grains Innovation Park, Agriculture Victoria, Horsham, VIC, 3400, Australia
- Centre for Agricultural Innovation, The University of Melbourne, Parkville, VIC, 3010, Australia
| | | | | | - Kerrie L Forrest
- AgriBio, Centre for AgriBiosciences, Agriculture Victoria, Bundoora, VIC, 3083, Australia
| | | | | | - Mike Goddard
- AgriBio, Centre for AgriBiosciences, Agriculture Victoria, Bundoora, VIC, 3083, Australia
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Jennie Pryce
- AgriBio, Centre for AgriBiosciences, Agriculture Victoria, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Matthew J Hayden
- AgriBio, Centre for AgriBiosciences, Agriculture Victoria, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | | | - Garry J O'Leary
- Grains Innovation Park, Agriculture Victoria, Horsham, VIC, 3400, Australia
- Centre for Agricultural Innovation, The University of Melbourne, Parkville, VIC, 3010, Australia
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21
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Golan G, Weiner J, Zhao Y, Schnurbusch T. Agroecological genetics of biomass allocation in wheat uncovers genotype interactions with canopy shade and plant size. THE NEW PHYTOLOGIST 2024; 242:107-120. [PMID: 38326944 DOI: 10.1111/nph.19576] [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: 09/09/2023] [Accepted: 01/21/2024] [Indexed: 02/09/2024]
Abstract
How plants distribute biomass among organs influences resource acquisition, reproduction and plant-plant interactions, and is essential in understanding plant ecology, evolution, and yield production in agriculture. However, the genetic mechanisms regulating allocation responses to the environment are largely unknown. We studied recombinant lines of wheat (Triticum spp.) grown as single plants under sunlight and simulated canopy shade to investigate genotype-by-environment interactions in biomass allocation to the leaves, stems, spikes, and grains. Size-corrected mass fractions and allometric slopes were employed to dissect allocation responses to light limitation and plant size. Size adjustments revealed light-responsive alleles associated with adaptation to the crop environment. Combined with an allometric approach, we demonstrated that polymorphism in the DELLA protein is associated with the response to shade and size. While a gibberellin-sensitive allelic effect on stem allocation was amplified when plants were shaded, size-dependent effects of this allele drive allocation to reproduction, suggesting that the ontogenetic trajectory of the plant affects the consequences of shade responses for allocation. Our approach provides a basis for exploring the genetic determinants underlying investment strategies in the face of different resource constraints and will be useful in predicting social behaviours of individuals in a crop community.
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Affiliation(s)
- Guy Golan
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, 06466, Seeland, Germany
| | - Jacob Weiner
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871, Frederiksberg, Denmark
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, 06466, Seeland, Germany
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, 06466, Seeland, Germany
- Martin Luther University Halle-Wittenberg, Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, 06120, Halle, Germany
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22
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Hong MJ, Ko CS, Kim DY. Genome-Wide Association Study to Identify Marker-Trait Associations for Seed Color in Colored Wheat ( Triticum aestivum L.). Int J Mol Sci 2024; 25:3600. [PMID: 38612412 PMCID: PMC11011601 DOI: 10.3390/ijms25073600] [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: 02/29/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024] Open
Abstract
This study conducted phenotypic evaluations on a wheat F3 population derived from 155 F2 plants. Traits related to seed color, including chlorophyll a, chlorophyll b, carotenoid, anthocyanin, L*, a*, and b*, were assessed, revealing highly significant correlations among various traits. Genotyping using 81,587 SNP markers resulted in 3969 high-quality markers, revealing a genome-wide distribution with varying densities across chromosomes. A genome-wide association study using fixed and random model circulating probability unification (FarmCPU) and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) identified 11 significant marker-trait associations (MTAs) associated with L*, a*, and b*, and chromosomal distribution patterns revealed predominant locations on chromosomes 2A, 2B, and 4B. A comprehensive annotation uncovered 69 genes within the genomic vicinity of each MTA, providing potential functional insights. Gene expression analysis during seed development identified greater than 2-fold increases or decreases in expression in colored wheat for 16 of 69 genes. Among these, eight genes, including transcription factors and genes related to flavonoid and ubiquitination pathways, exhibited distinct expression patterns during seed development, providing further approaches for exploring seed coloration. This comprehensive exploration expands our understanding of the genetic basis of seed color and paves the way for informed discussions on the molecular intricacies contributing to this phenotypic trait.
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Affiliation(s)
- Min Jeong Hong
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu, Jeongeup 56212, Republic of Korea; (M.J.H.); (C.S.K.)
| | - Chan Seop Ko
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu, Jeongeup 56212, Republic of Korea; (M.J.H.); (C.S.K.)
| | - Dae Yeon Kim
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, 54 Daehak-ro, Yesan-eup 32439, Republic of Korea
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23
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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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24
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Berraies S, Ruan Y, Knox R, DePauw R, Bokore F, Cuthbert R, Blackwell B, Henriquez MA, Konkin D, Yu B, Pozniak C, Meyer B. Genetic mapping of deoxynivalenol and fusarium damaged kernel resistance in an adapted durum wheat population. BMC PLANT BIOLOGY 2024; 24:183. [PMID: 38475749 DOI: 10.1186/s12870-023-04708-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 12/26/2023] [Indexed: 03/14/2024]
Abstract
BACKGROUND Fusarium head blight (FHB) infection results in Fusarium damaged kernels (FDK) and deoxynivalenol (DON) contamination that are downgrading factors at the Canadian elevators. Durum wheat (Triticum turgidum L. var. durum Desf.) is particularly susceptible to FHB and most of the adapted Canadian durum wheat cultivars are susceptible to moderately susceptible to this disease. However, the durum line DT696 is less susceptible to FHB than commercially grown cultivars. Little is known about genetic variation for durum wheat ability to resist FDK infection and DON accumulation. This study was undertaken to map genetic loci conferring resistance to DON and FDK resistance using a SNP high-density genetic map of a DT707/DT696 DH population and to identify SNP markers useful in marker-assisted breeding. One hundred twenty lines were grown in corn spawn inoculated nurseries near Morden, MB in 2015, 2016 and 2017 and the harvested seeds were evaluated for DON. The genetic map of the population was used in quantitative trait locus analysis performed with MapQTL.6® software. RESULTS Four DON accumulation resistance QTL detected in two of the three years were identified on chromosomes 1 A, 5 A (2 loci) and 7 A and two FDK resistance QTL were identified on chromosomes 5 and 7 A in single environments. Although not declared significant due to marginal LOD values, the QTL for FDK on the 5 and 7 A were showing in other years suggesting their effects were real. DT696 contributed the favourable alleles for low DON and FDK on all the chromosomes. Although no resistance loci contributed by DT707, transgressive segregant lines were identified resulting in greater resistance than DT696. Breeder-friendly KASP markers were developed for two of the DON and FDK QTL detected on chromosomes 5 and 7 A. Markers flanking each QTL were physically mapped against the durum wheat reference sequence and candidate genes which might be involved in FDK and DON resistance were identified within the QTL intervals. CONCLUSIONS The DH lines harboring the desired resistance QTL will serve as useful resources in breeding for FDK and DON resistance in durum wheat. Furthermore, breeder-friendly KASP markers developed during this study will be useful for the selection of durum wheat varieties with low FDK and DON levels in durum wheat breeding programs.
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Affiliation(s)
- Samia Berraies
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada.
| | - Yuefeng Ruan
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada.
| | - Ron Knox
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada
| | - Ron DePauw
- Agriculture and Agri-Food Canada (Retired), Ottawa, Canada
- Advancing Wheat Technologies, Calgary, AB, T3H 1P3, Canada
| | - Firdissa Bokore
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada
| | - Richard Cuthbert
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada
| | - Barbara Blackwell
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
| | - Maria Antonia Henriquez
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - David Konkin
- National Research Council Canada, Aquatic and Crop Resource Development, Saskatoon, SK, S7N 0W9, Canada
| | - Bianyun Yu
- National Research Council Canada, Aquatic and Crop Resource Development, Saskatoon, SK, S7N 0W9, Canada
| | - Curtis Pozniak
- Crop Development Centre, Department of Plant Science, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Brad Meyer
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada
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25
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Edae EA, Kosgey Z, Bajgain P, Ndung'u KC, Gemechu A, Bhavani S, Anderson JA, Rouse MN. The genetics of Ug99 stem rust resistance in spring wheat variety 'Linkert'. FRONTIERS IN PLANT SCIENCE 2024; 15:1343148. [PMID: 38516672 PMCID: PMC10954791 DOI: 10.3389/fpls.2024.1343148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/12/2024] [Indexed: 03/23/2024]
Abstract
Wheat stem rust caused by Puccinia graminis f. sp. tritici (Pgt) threatens wheat production worldwide. The objective of this study was to characterize wheat stem rust resistance in 'Linkert', a variety with adult plant resistance effective to emerging wheat stem rust pathogen strain Ug99. Two doubled haploid (DH) populations and one recombinant inbred line (RIL) population were developed with 'Linkert' as a stem rust resistant parent. Hard red spring wheat variety 'Forefront' and genetic stock 'LMPG' were used as stem rust susceptible parents of the DH populations. Breeding line 'MN07098-6' was used as a susceptible parent of the RIL population. Both DH and RIL populations with their parents were evaluated both at the seedling stage and in the field against Pgt races. Genotyping data of the DH populations were generated using the wheat iSelect 90k SNP assay. The RIL population was genotyped by genotyping-by-sequencing. We found QTL consistently associated with wheat stem rust resistance on chromosome 2BS for the Linkert/Forefront DH population and the Linkert/MN07098-6 RIL population both in Ethiopia and Kenya. Additional reliable QTL were detected on chromosomes 5BL (125.91 cM) and 4AL (Sr7a) for the Linkert/LMPG population in Ethiopia and Kenya. Different QTL identified in the populations reflect the importance of examining the genetics of resistance in populations derived from adapted germplasm (Forefront and MN07098-6) in addition to a genetic stock (LMPG). The associated markers in this study could be used to track and select for the identified QTL in wheat breeding programs.
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Affiliation(s)
- Erena A. Edae
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Zennah Kosgey
- Kenya Agricultural and Livestock Research Organization (KALRO), Food Crops Research Centre, Njoro, Kenya
| | - Prabin Bajgain
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
| | - Kimani C. Ndung'u
- Kenya Agricultural and Livestock Research Organization (KALRO), Food Crops Research Centre, Njoro, Kenya
| | - Ashenafi Gemechu
- Ethiopian Institute of Agriculture, Debre Zeit Agricultural Research Center, Bishoftu, Ethiopia
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - James A. Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
| | - Matthew N. Rouse
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, Saint Paul, MN, United States
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26
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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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27
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Hiraoka Y, Ferrante SP, Wu GA, Federici CT, Roose ML. Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives. PLANTS (BASEL, SWITZERLAND) 2024; 13:691. [PMID: 38475537 DOI: 10.3390/plants13050691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/13/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
Rapid advancements in technologies provide various tools to analyze fruit crop genomes to better understand genetic diversity and relationships and aid in breeding. Genome-wide single nucleotide polymorphism (SNP) genotyping arrays offer highly multiplexed assays at a relatively low cost per data point. We report the development and validation of 1.4M SNP Axiom® Citrus HD Genotyping Array (Citrus 15AX 1 and Citrus 15AX 2) and 58K SNP Axiom® Citrus Genotyping Arrays for Citrus and close relatives. SNPs represented were chosen from a citrus variant discovery panel consisting of 41 diverse whole-genome re-sequenced accessions of Citrus and close relatives, including eight progenitor citrus species. SNPs chosen mainly target putative genic regions of the genome and are accurately called in both Citrus and its closely related genera while providing good coverage of the nuclear and chloroplast genomes. Reproducibility of the arrays was nearly 100%, with a large majority of the SNPs classified as the most stringent class of markers, "PolyHighResolution" (PHR) polymorphisms. Concordance between SNP calls in sequence data and array data average 98%. Phylogenies generated with array data were similar to those with comparable sequence data and little affected by 3 to 5% genotyping error. Both arrays are publicly available.
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Affiliation(s)
- Yoko Hiraoka
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Sergio Pietro Ferrante
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Guohong Albert Wu
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Claire T Federici
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Mikeal L Roose
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
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28
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Zeng D, Ford B, Doležel J, Karafiátová M, Hayden MJ, Rathjen TM, George TS, Brown LK, Ryan PR, Pettolino FA, Mathesius U, Delhaize E. A conditional mutation in a wheat (Triticum aestivum L.) gene regulating root morphology. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:48. [PMID: 38345612 PMCID: PMC10861616 DOI: 10.1007/s00122-024-04555-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/12/2024] [Indexed: 02/15/2024]
Abstract
KEY MESSAGE Characterisation and genetic mapping of a key gene defining root morphology in bread wheat. Root morphology is central to plants for the efficient uptake up of soil water and mineral nutrients. Here we describe a conditional mutant of hexaploid wheat (Triticum aestivum L.) that when grown in soil with high Ca2+ develops a larger rhizosheath accompanied with shorter roots than the wild type. In wheat, rhizosheath size is a reliable surrogate for root hair length and this was verified in the mutant which possessed longer root hairs than the wild type when grown in high Ca2+ soil. We named the mutant Stumpy and showed it to be due to a single semi-dominant mutation. The short root phenotype at high Ca2+ was due to reduced cellular elongation which might also explain the long root hair phenotype. Analysis of root cell walls showed that the polysaccharide composition of Stumpy roots is remodelled when grown at non-permissive (high) Ca2+ concentrations. The mutation mapped to chromosome 7B and sequencing of the 7B chromosomes in both wild type and Stumpy identified a candidate gene underlying the Stumpy mutation. As part of the process to determine whether the candidate gene was causative, we identified wheat lines in a Cadenza TILLING population with large rhizosheaths but accompanied with normal root length. This finding illustrates the potential of manipulating the gene to disconnect root length from root hair length as a means of developing wheat lines with improved efficiency of nutrient and water uptake. The Stumpy mutant will be valuable for understanding the mechanisms that regulate root morphology in wheat.
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Affiliation(s)
- Deying Zeng
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, 610101, China
| | - Brett Ford
- Grains Research and Development Corporation, Barton, ACT, 2600, Australia
- CSIRO Agriculture & Food, PO Box 1700, Canberra, ACT, 2601, Australia
| | - Jaroslav Doležel
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
| | - Miroslava Karafiátová
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
| | - Mathew J Hayden
- Department of Jobs, Precincts and Regions, Agriculture Victoria Research, AgriBio, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Tina M Rathjen
- CSIRO Agriculture & Food, PO Box 1700, Canberra, ACT, 2601, Australia
| | | | - Lawrie K Brown
- James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Peter R Ryan
- CSIRO Agriculture & Food, PO Box 1700, Canberra, ACT, 2601, Australia
| | | | - Ulrike Mathesius
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Emmanuel Delhaize
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia.
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29
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Deng P, Du X, Wang Y, Yang X, Cheng X, Huang C, Li T, Li T, Chen C, Zhao J, Wang C, Liu X, Tian Z, Ji W. GenoBaits®WheatplusEE: a targeted capture sequencing panel for quick and accurate identification of wheat-Thinopyrum derivatives. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:36. [PMID: 38291310 DOI: 10.1007/s00122-023-04538-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 12/27/2023] [Indexed: 02/01/2024]
Abstract
KEY MESSAGE A total of 90,000 capture probes derived from wheat and Thinopyrum elongatum were integrated into one chip, which served as an economical genotype for explorating Thinopyrumspecies and their derivatives. Thinopyrum species play a crucial role as a source of new genetic variations for enhancing wheat traits, including resistance to both abiotic and biotic factors. Accurate identification of exogenous chromosome(s) or chromosome segments or genes is essential following the introduction of alien genetic material into wheat, but this task remains challenging. This study aimed to develop a high-resolution wheat-Thinopyrum elongatum array, named GenoBaits®WheatplusEE, to trace alien genetic information by genotyping using a target sequencing system. This GenoBaits®WheatplusEE array included 90,000 capture probes derived from two species and integrated into one chip, with 10,000 and 80,000 originating from wheat and Th. elongatum, respectively. The capture probes were strategically positioned in genes and evenly distributed across the genome, facilitating the development of a roadmap for identifying each alien gene. The array was applied to the high-throughput identification of the alien chromosomes or segments in Thinopyrum and distantly related species and their derivatives. Our results demonstrated that the GenoBaits®WheatplusEE array could be used for direct identification of the breakpoint of alien segments, determine copy number of alien chromosomes, and reveal variations in wheat chromosomes by a single round of target sequencing of the sample. Additionally, we could efficiently and cost-effectively genotype, supporting the exploration of subgenome composition, phylogenetic relationships, and polymorphisms in essential genes (e.g., Fhb7 gene) among Thinopyrum species and their derivatives. We hope that GenoBaits®WheatplusEE will become a widely adopted tool for exporting wild germplasm for wheat improvement in the future.
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Affiliation(s)
- Pingchuan Deng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xin Du
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yanzhen Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, Shanxi, China
| | - Xiaoying Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiaofang Cheng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chenxi Huang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Tingting Li
- College of Bioengineering, Yangling Vocational Technical College, Yangling, 712100, Shaanxi, China
| | - Tingdong Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chunhuan Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jixin Zhao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Changyou Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xinlun Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zengrong Tian
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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30
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Ahmed MIY, Kamal NM, Gorafi YSA, Abdalla MGA, Tahir ISA, Tsujimoto H. Heat Stress-Tolerant Quantitative Trait Loci Identified Using Backcrossed Recombinant Inbred Lines Derived from Intra-Specifically Diverse Aegilops tauschii Accessions. PLANTS (BASEL, SWITZERLAND) 2024; 13:347. [PMID: 38337879 PMCID: PMC10856904 DOI: 10.3390/plants13030347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
In the face of climate change, bringing more useful alleles and genes from wild relatives of wheat is crucial to develop climate-resilient varieties. We used two populations of backcrossed recombinant inbred lines (BIL1 and BIL2), developed by crossing and backcrossing two intra-specifically diverse Aegilops tauschii accessions from lineage 1 and lineage 2, respectively, with the common wheat cultivar 'Norin 61'. This study aimed to identify quantitative trait loci (QTLs) associated with heat stress (HS) tolerance. The two BILs were evaluated under heat stress environments in Sudan for phenology, plant height (PH), grain yield (GY), biomass (BIO), harvest index (HI), and thousand-kernel weight (TKW). Grain yield was significantly correlated with BIO and TKW under HS; therefore, the stress tolerance index (STI) was calculated for these traits as well as for GY. A total of 16 heat-tolerant lines were identified based on GY and STI-GY. The QTL analysis performed using inclusive composite interval mapping identified a total of 40 QTLs in BIL1 and 153 QTLs in BIL2 across all environments. We detected 39 QTLs associated with GY-STI, BIO-STI, and TKW-STI in both populations (14 in BIL1 and 25 in BIL2). The QTLs associated with STI were detected on chromosomes 1A, 3A, 5A, 2B, 4B, and all the D-subgenomes. We found that QTLs were detected only under HS for GY on chromosome 5A, TKW on 3B and 5B, PH on 3B and 4B, and grain filling duration on 2B. The higher number of QTLs identified in BIL2 for heat stress tolerance suggests the importance of assessing the effects of intraspecific variation of Ae. tauschii in wheat breeding as it could modulate the heat stress responses/adaptation. Our study provides useful genetic resources for uncovering heat-tolerant QTLs for wheat improvement for heat stress environments.
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Affiliation(s)
- Monir Idres Yahya Ahmed
- United Graduate School of Agricultural Sciences, Tottori University, Tottori 680-8550, Japan;
| | - Nasrein Mohamed Kamal
- Arid Land Research Center, Tottori University, Tottori 680-0001, Japan; (N.M.K.); (I.S.A.T.)
- Agricultural Research Corporation (ARC), Wad-Medani P.O. Box 126, Sudan; (Y.S.A.G.); (M.G.A.A.)
| | - Yasir Serag Alnor Gorafi
- Agricultural Research Corporation (ARC), Wad-Medani P.O. Box 126, Sudan; (Y.S.A.G.); (M.G.A.A.)
- International Platform for Dryland Research and Education, Tottori University, Tottori 680-0001, Japan
| | | | - Izzat Sidahmed Ali Tahir
- Arid Land Research Center, Tottori University, Tottori 680-0001, Japan; (N.M.K.); (I.S.A.T.)
- Agricultural Research Corporation (ARC), Wad-Medani P.O. Box 126, Sudan; (Y.S.A.G.); (M.G.A.A.)
| | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, Tottori 680-0001, Japan; (N.M.K.); (I.S.A.T.)
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31
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Zhang H, Li Y, Liu W, Sun Y, Tang J, Che J, Yang S, Wang X, Zhang R. Genetic Analysis of Adaptive Traits in Spring Wheat in Northeast China. Life (Basel) 2024; 14:168. [PMID: 38398677 PMCID: PMC10890535 DOI: 10.3390/life14020168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/13/2024] [Accepted: 01/17/2024] [Indexed: 02/25/2024] Open
Abstract
The dissection of the genetic architecture and the detection of the loci for adaptive traits are important for marker-assisted selection (MAS) for breeding. A spring wheat diversity panel with 251 cultivars, mainly from China, was obtained to conduct a genome-wide association study (GWAS) to detect the new loci, including the heading date (HD), maturating date (MD), plant height (PH), and lodging resistance (LR). In total, 41 loci existing in all 21 chromosomes, except for 4A and 6B, were identified, and each explained 4.3-18.9% of the phenotypic variations existing in two or more environments. Of these, 13 loci are overlapped with the known genes or quantitative trait loci (QTLs), whereas the other 28 are likely to be novel. The 1A locus (296.9-297.7 Mb) is a multi-effect locus for LR and PH, whereas the locus on chromosome 6D (464.5-471.0 Mb) affects both the HD and MD. Furthermore, four candidate genes for adaptive traits were identified, involved in cell division, signal transduction, and plant development. Additionally, two competitive, allele-specific PCR (KASP) markers, Kasp_2D_PH for PH and Kasp_6D_HD for HD, were developed and validated in another 162 spring wheat accessions. Our study uncovered the genetic basis of adaptive traits and provided the associated SNPs and varieties with more favorable alleles for wheat MAS breeding.
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Affiliation(s)
- Hongji Zhang
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (W.L.); (Y.S.); (J.T.); (S.Y.); (X.W.)
| | - Yuyao Li
- Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China;
| | - Wenlin Liu
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (W.L.); (Y.S.); (J.T.); (S.Y.); (X.W.)
| | - Yan Sun
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (W.L.); (Y.S.); (J.T.); (S.Y.); (X.W.)
| | - Jingquan Tang
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (W.L.); (Y.S.); (J.T.); (S.Y.); (X.W.)
| | - Jingyu Che
- Keshan Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar 161600, China;
| | - Shuping Yang
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (W.L.); (Y.S.); (J.T.); (S.Y.); (X.W.)
| | - Xiangyu Wang
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (W.L.); (Y.S.); (J.T.); (S.Y.); (X.W.)
| | - Rui Zhang
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China;
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Sharma JS, Che M, Fetch T, McCallum BD, Xu SS, Hiebert CW. Identification of Sr67, a new gene for stem rust resistance in KU168-2 located close to the Sr13 locus in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:30. [PMID: 38265482 PMCID: PMC10808535 DOI: 10.1007/s00122-023-04530-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/14/2023] [Indexed: 01/25/2024]
Abstract
KEY MESSAGE Sr67 is a new stem rust resistance gene that represents a new resource for breeding stem rust resistant wheat cultivars Re-appearance of stem rust disease, caused by the fungal pathogen Puccinia graminis f. sp. tritici (Pgt), in different parts of Europe emphasized the need to develop wheat varieties with effective resistance to local Pgt populations and exotic threats. A Kyoto University wheat (Triticum aestivum L.) accession KU168-2 was reported to carry good resistance to leaf and stem rust. To identify the genomic region associated with the KU168-2 stem rust resistance, a genetic study was conducted using a doubled haploid (DH) population from the cross RL6071 × KU168-2. The DH population was phenotyped with three Pgt races (TTKSK, TPMKC, and QTHSF) and genotyped using the Illumina 90 K wheat SNP array. Linkage mapping showed the resistance to all three Pgt races was conferred by a single stem rust resistance (Sr) gene on chromosome arm 6AL, associated with Sr13. Presently, four Sr13 resistance alleles have been reported. Sr13 allele-specific KASP and STARP markers, and sequencing markers all showed null alleles in KU168-2. KU168-2 showed a unique combination of seedling infection types for five Pgt races (TTKSK, QTHSF, RCRSF, TMRTF, and TPMKC) compared to Sr13 alleles. The phenotypic uniqueness of the stem rust resistance gene in KU168-2 and null alleles for Sr13 allele-specific markers showed the resistance was conferred by a new gene, designated Sr67. Since Sr13 is less effective in hexaploid background, Sr67 will be a good source of stem rust resistance in bread wheat breeding programs.
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Affiliation(s)
- Jyoti Saini Sharma
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB, R6M 1Y5, Canada
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Mingzhe Che
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Thomas Fetch
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Brent D McCallum
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Steven S Xu
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, USDA-ARS, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Colin W Hiebert
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB, R6M 1Y5, Canada.
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Sowadan O, Xu S, Li Y, Muleke EM, Sitoe HM, Dang X, Jiang J, Dong H, Hong D. Genome-Wide Association Analysis Unravels New Quantitative Trait Loci (QTLs) for Eight Lodging Resistance Constituent Traits in Rice ( Oryza sativa L.). Genes (Basel) 2024; 15:105. [PMID: 38254994 PMCID: PMC10815206 DOI: 10.3390/genes15010105] [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: 12/14/2023] [Revised: 01/13/2024] [Accepted: 01/14/2024] [Indexed: 01/24/2024] Open
Abstract
Lodging poses a significant challenge to rice yield, prompting the need to identify elite alleles for lodging resistance traits to improve cultivated rice varieties. In this study, a natural population of 518 rice accessions was examined to identify elite alleles associated with plant height (PH), stem diameter (SD), stem anti-thrust (AT/S), and various internode lengths (first (FirINL), second (SecINL), third (ThirINL), fourth (ForINL), and fifth (FifINL) internode lengths). A total of 262 SSR markers linked to these traits were uncovered through association mapping in two environmental conditions. Phenotypic evaluations revealed striking differences among cultivars, and genetic diversity assessments showed polymorphisms across the accessions. Favorable alleles were identified for PH, SD, AT/S, and one to five internode lengths, with specific alleles displaying considerable effects. Noteworthy alleles include RM6811-160 bp on chromosome 6 (which reduces PH) and RM161-145 bp on chromosome 5 (which increases SD). The study identified a total of 42 novel QTLs. Specifically, seven QTLs were identified for PH, four for SD, five for AT/S, five for FirINL, six for SecINL, five for ThirINL, six for ForINL, and four for FifINL. QTLs qAT/S-2, qPH2.1, qForINL2.1, and qFifINL exhibited the most significant phenotypic variance (PVE) of 3.99% for the stem lodging trait. AT/S, PH, ForINL, and FifINL had additive effects of 5.31 kPa, 5.42 cm, 4.27 cm, and 4.27 cm, respectively, offering insights into eight distinct cross-combinations for enhancing each trait. This research suggests the potential for crossbreeding superior parents based on stacked alleles, promising improved rice cultivars with enhanced lodging resistance to meet market demands.
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Affiliation(s)
- Ognigamal Sowadan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (O.S.); (S.X.); (Y.L.); (E.M.M.); (H.M.S.); (H.D.)
| | - Shanbin Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (O.S.); (S.X.); (Y.L.); (E.M.M.); (H.M.S.); (H.D.)
| | - Yulong Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (O.S.); (S.X.); (Y.L.); (E.M.M.); (H.M.S.); (H.D.)
- Institute of Crop Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Everlyne Mmbone Muleke
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (O.S.); (S.X.); (Y.L.); (E.M.M.); (H.M.S.); (H.D.)
- Department of Agriculture and Land Use Management, School of Agriculture, Veterinary Sciences and Technology, Masinde Muliro University of Science and Technology, Kakamega P.O. Box 190-50100, Kenya
| | - Hélder Manuel Sitoe
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (O.S.); (S.X.); (Y.L.); (E.M.M.); (H.M.S.); (H.D.)
- Faculty of Agronomy and Biological Sciences, Púngue University, P.O. Box 323, Manica 2202, Mozambique
| | - Xiaojing Dang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China; (X.D.); (J.J.)
| | - Jianhua Jiang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China; (X.D.); (J.J.)
| | - Hui Dong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (O.S.); (S.X.); (Y.L.); (E.M.M.); (H.M.S.); (H.D.)
| | - Delin Hong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (O.S.); (S.X.); (Y.L.); (E.M.M.); (H.M.S.); (H.D.)
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Marone D, Laidò G, Saccomanno A, Petruzzino G, Giaretta Azevedo CV, De Vita P, Mastrangelo AM, Gadaleta A, Ammar K, Bassi FM, Wang M, Chen X, Rubiales D, Matny O, Steffenson BJ, Pecchioni N. Genome-wide association study of common resistance to rust species in tetraploid wheat. FRONTIERS IN PLANT SCIENCE 2024; 14:1290643. [PMID: 38235202 PMCID: PMC10792004 DOI: 10.3389/fpls.2023.1290643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
Rusts of the genus Puccinia are wheat pathogens. Stem (black; Sr), leaf (brown; Lr), and stripe (yellow; Yr) rust, caused by Puccinia graminis f. sp. tritici (Pgt), Puccinia triticina (Pt), and Puccinia striiformis f. sp. tritici (Pst), can occur singularly or in mixed infections and pose a threat to wheat production globally in terms of the wide dispersal of their urediniospores. The development of durable resistant cultivars is the most sustainable method for controlling them. Many resistance genes have been identified, characterized, genetically mapped, and cloned; several quantitative trait loci (QTLs) for resistance have also been described. However, few studies have considered resistance to all three rust pathogens in a given germplasm. A genome-wide association study (GWAS) was carried out to identify loci associated with resistance to the three rusts in a collection of 230 inbred lines of tetraploid wheat (128 of which were Triticum turgidum ssp. durum) genotyped with SNPs. The wheat panel was phenotyped in the field and subjected to growth chamber experiments across different countries (USA, Mexico, Morocco, Italy, and Spain); then, a mixed linear model (MLM) GWAS was performed. In total, 9, 34, and 5 QTLs were identified in the A and B genomes for resistance to Pgt, Pt, and Pst, respectively, at both the seedling and adult plant stages. Only one QTL on chromosome 4A was found to be effective against all three rusts at the seedling stage. Six QTLs conferring resistance to two rust species at the adult plant stage were mapped: three on chromosome 1B and one each on 5B, 7A, and 7B. Fifteen QTLs conferring seedling resistance to two rusts were mapped: five on chromosome 2B, three on 7B, two each on 5B and 6A, and one each on 1B, 2A, and 7A. Most of the QTLs identified were specific for a single rust species or race of a species. Candidate genes were identified within the confidence intervals of a QTL conferring resistance against at least two rust species by using the annotations of the durum (cv. 'Svevo') and wild emmer wheat ('Zavitan') reference genomes. The 22 identified loci conferring resistance to two or three rust species may be useful for breeding new and potentially durable resistant wheat cultivars.
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Affiliation(s)
- Daniela Marone
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Giovanni Laidò
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Antonietta Saccomanno
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Reggio Emilia, Italy
| | - Giuseppe Petruzzino
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Cleber V. Giaretta Azevedo
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Pasquale De Vita
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Anna Maria Mastrangelo
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Agata Gadaleta
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti (Di.S.S.P.A.), Università di Bari “Aldo Moro”, Bari, Italy
| | - Karim Ammar
- International Maize and Wheat Improvement Centre (CIMMYT), Ciudad de México, Mexico
| | - Filippo M. Bassi
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
- Wheat Health, Genetics, and Quality Research Unit, United States Department of Agriculture - Agriculture Research Service (USDA-ARS), Pullman, WA, United States
| | - Diego Rubiales
- Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (CSIC), Córdoba, Spain
| | - Oadi Matny
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Nicola Pecchioni
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Reggio Emilia, Italy
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Yang J, Wang J. Genome-Wide Association Study of Preharvest Sprouting in Wheat. Methods Mol Biol 2024; 2830:121-129. [PMID: 38977573 DOI: 10.1007/978-1-0716-3965-8_11] [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] [Indexed: 07/10/2024]
Abstract
Genome-wide association study (GWAS) is widely used to characterize genes or quantitative trait loci (QTLs) associated with preharvest sprouting and seed dormancy. GWAS can identify both previously discovered and novel QTLs across diverse genetic panels. The high-throughput SNP arrays or next-generation sequencing technologies have facilitated the identification of numerous genetic markers, thereby significantly enhancing the resolution of GWAS. Although various methods have been developed, the fundamental principles underlying these techniques remain constant. Here, we provide a basic technological flow to perform seed dormancy assay, followed by GWAS using population structure control, and compared it with previous identified QTLs and genes.
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Affiliation(s)
- Jian Yang
- Institute of Wheat, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
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Norman M, Chen C, Miah H, Patpour M, Sørensen C, Hovmøller M, Forrest K, Kumar S, Prasad P, Gangwar OP, Bhardwaj S, Bariana H, Periyannan S, Bansal U. Sr65: a widely effective gene for stem rust resistance in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 137:1. [PMID: 38071267 DOI: 10.1007/s00122-023-04507-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023]
Abstract
KEY MESSAGE Sr65 in chromosome 1A of Indian wheat landrace Hango-2 is a potentially useful all-stage resistance gene that currently protects wheat from stem rust in Australia, India, Africa and Europe. Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), threatened global wheat production with the appearance of widely virulent races that included TTKSK and TTRTF. Indian landrace Hango-2 showed resistance to Pgt races in India and Australia. Screening of a Hango-2/Avocet 'S' (AvS) recombinant inbred line population identified two stem rust resistance genes, a novel gene (temporarily named as SrH2) from Hango-2 and Sr26 from AvS. A mapping population segregating for SrH2 alone was developed from two recombinant lines. SrH2 was mapped on the short arm of chromosome 1A, where it was flanked by KASP markers KASP_7944 (proximal) and KASP_12147 (distal). SrH2 was delimited to an interval of 1.8-2.3 Mb on chromosome arm 1AS. The failure to detect candidate genes through MutRenSeq and comparative genomic analysis with the pan-genome dataset indicated the necessity to generate a Hango-2 specific assembly for detecting the gene sequence linked with SrH2 resistance. MutRenSeq however enabled identification of SrH2-linked KASP marker sunCS_265. Markers KASP_12147 and sunCS_265 showed 92% and 85% polymorphism among an Australian cereal cultivar diversity panel and can be used for marker-assisted selection of SrH2 in breeding programs. The effectiveness of SrH2 against Pgt races from Europe, Africa, India, and Australia makes it a valuable resource for breeding stem rust-resistant wheat cultivars. Since no wheat-derived gene was previously located in chromosome arm 1AS, SrH2 represents a new locus and named as SR65.
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Affiliation(s)
- Michael Norman
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Chunhong Chen
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Hanif Miah
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
| | - Mehran Patpour
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Chris Sørensen
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Mogens Hovmøller
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Kerrie Forrest
- Agriculture Victoria, Department of Energy, Environment and Climate Action, AgriBio, Centre for AgriBioscience, 5 Ring Rd., Bundoora, VIC, 3083, Australia
| | - Subodh Kumar
- Indian Council of Agricultural Research - Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Pramod Prasad
- Indian Council of Agricultural Research - Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Om Prakash Gangwar
- Indian Council of Agricultural Research - Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Subhash Bhardwaj
- Indian Council of Agricultural Research - Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Harbans Bariana
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
- School of Science, Western Sydney University, Bourke Road, Richmond, NSW, 2753, Australia
| | - Sambasivam Periyannan
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, ACT, 2601, Australia.
- School of Agriculture and Environmental Science, Centre for Crop Health, University of Southern Queensland, West Street, Toowoomba, QLD, 4350, Australia.
| | - Urmil Bansal
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia.
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Fradgley NS, Bentley AR, Gardner KA, Swarbreck SM, Kerton M. Maintenance of UK bread baking quality: Trends in wheat quality traits over 50 years of breeding and potential for future application of genomic-assisted selection. THE PLANT GENOME 2023; 16:e20326. [PMID: 37057385 DOI: 10.1002/tpg2.20326] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/22/2023] [Accepted: 02/28/2023] [Indexed: 06/19/2023]
Abstract
Improved selection of wheat varieties with high end-use quality contributes to sustainable food systems by ensuring productive crops are suitable for human consumption end-uses. Here, we investigated the genetic control and genomic prediction of milling and baking quality traits in a panel of 379 historic and elite, high-quality UK bread wheat (Triticum eastivum L.) varieties and breeding lines. Analysis of the panel showed that genetic diversity has not declined over recent decades of selective breeding while phenotypic analysis found a clear trend of increased loaf baking quality of modern milling wheats despite declining grain protein content. Genome-wide association analysis identified 24 quantitative trait loci (QTL) across all quality traits, many of which had pleiotropic effects. Changes in the frequency of positive alleles of QTL over recent decades reflected trends in trait variation and reveal where progress has historically been made for improved baking quality traits. It also demonstrates opportunities for marker-assisted selection for traits such as Hagberg falling number and specific weight that do not appear to have been improved by recent decades of phenotypic selection. We demonstrate that applying genomic prediction in a commercial wheat breeding program for expensive late-stage loaf baking quality traits outperforms phenotypic selection based on early-stage predictive quality traits. Finally, trait-assisted genomic prediction combining both phenotypic and genomic selection enabled slightly higher prediction accuracy, but genomic prediction alone was the most cost-effective selection strategy considering genotyping and phenotyping costs per sample.
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Affiliation(s)
- Nick S Fradgley
- Genetics and Pre-Breeding Department, National Institute of Agricultural Botany (NIAB), 93 Lawrence Weaver Road, Cambridge, UK
| | - Alison R Bentley
- Genetics and Pre-Breeding Department, National Institute of Agricultural Botany (NIAB), 93 Lawrence Weaver Road, Cambridge, UK
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz, México
| | - Keith A Gardner
- Genetics and Pre-Breeding Department, National Institute of Agricultural Botany (NIAB), 93 Lawrence Weaver Road, Cambridge, UK
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz, México
| | - Stéphanie M Swarbreck
- Genetics and Pre-Breeding Department, National Institute of Agricultural Botany (NIAB), 93 Lawrence Weaver Road, Cambridge, UK
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Ahmed MIY, Gorafi YSA, Kamal NM, Balla MY, Tahir ISA, Zheng L, Kawakami N, Tsujimoto H. Mining Aegilops tauschii genetic diversity in the background of bread wheat revealed a novel QTL for seed dormancy. FRONTIERS IN PLANT SCIENCE 2023; 14:1270925. [PMID: 38107013 PMCID: PMC10723804 DOI: 10.3389/fpls.2023.1270925] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/14/2023] [Indexed: 12/19/2023]
Abstract
Due to the low genetic diversity in the current wheat germplasm, gene mining from wild relatives is essential to develop new wheat cultivars that are more resilient to the changing climate. Aegilops tauschii, the D-genome donor of bread wheat, is a great gene source for wheat breeding; however, identifying suitable genes from Ae. tauschii is challenging due to the different morphology and the wide intra-specific variation within the species. In this study, we developed a platform for the systematic evaluation of Ae. tauschii traits in the background of the hexaploid wheat cultivar 'Norin 61' and thus for the identification of QTLs and genes. To validate our platform, we analyzed the seed dormancy trait that confers resistance to preharvest sprouting. We used a multiple synthetic derivative (MSD) population containing a genetic diversity of 43 Ae. tauschii accessions representing the full range of the species. Our results showed that only nine accessions in the population provided seed dormancy, and KU-2039 from Afghanistan had the highest level of seed dormancy. Therefore, 166 backcross inbred lines (BILs) were developed by crossing the synthetic wheat derived from KU-2039 with 'Norin 61' as the recurrent parent. The QTL mapping revealed one novel QTL, Qsd.alrc.5D, associated with dormancy explaining 41.7% of the phenotypic variation and other five unstable QTLs, two of which have already been reported. The Qsd.alrc.5D, identified for the first time within the natural variation of wheat, would be a valuable contribution to breeding after appropriate validation. The proposed platform that used the MSD population derived from the diverse Ae. tauschii gene pool and recombinant inbred lines proved to be a valuable platform for mining new and important QTLs or alleles, such as the novel seed dormancy QTL identified here. Likewise, such a platform harboring genetic diversity from wheat wild relatives could be a useful source for mining agronomically important traits, especially in the era of climate change and the narrow genetic diversity within the current wheat germplasm.
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Affiliation(s)
| | - Yasir Serag Alnor Gorafi
- International Platform for Dryland Research and Education, Tottori University, Tottori, Japan
- Gezira Research Station, Agricultural Research Corporation (ARC), Wad-Medani, Sudan
| | - Nasrein Mohamed Kamal
- Gezira Research Station, Agricultural Research Corporation (ARC), Wad-Medani, Sudan
- Arid Land Research Center, Tottori University, Tottori, Japan
| | - Mohammed Yousif Balla
- Gezira Research Station, Agricultural Research Corporation (ARC), Wad-Medani, Sudan
- Arid Land Research Center, Tottori University, Tottori, Japan
| | - Izzat Sidahmed Ali Tahir
- Gezira Research Station, Agricultural Research Corporation (ARC), Wad-Medani, Sudan
- Arid Land Research Center, Tottori University, Tottori, Japan
| | - Lipeng Zheng
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Naoto Kawakami
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
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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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Sharma D, Kumari A, Sharma P, Singh A, Sharma A, Mir ZA, Kumar U, Jan S, Parthiban M, Mir RR, Bhati P, Pradhan AK, Yadav A, Mishra DC, Budhlakoti N, Yadav MC, Gaikwad KB, Singh AK, Singh GP, Kumar S. Meta-QTL analysis in wheat: progress, challenges and opportunities. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:247. [PMID: 37975911 DOI: 10.1007/s00122-023-04490-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023]
Abstract
Wheat, an important cereal crop globally, faces major challenges due to increasing global population and changing climates. The production and productivity are challenged by several biotic and abiotic stresses. There is also a pressing demand to enhance grain yield and quality/nutrition to ensure global food and nutritional security. To address these multifaceted concerns, researchers have conducted numerous meta-QTL (MQTL) studies in wheat, resulting in the identification of candidate genes that govern these complex quantitative traits. MQTL analysis has successfully unraveled the complex genetic architecture of polygenic quantitative traits in wheat. Candidate genes associated with stress adaptation have been pinpointed for abiotic and biotic traits, facilitating targeted breeding efforts to enhance stress tolerance. Furthermore, high-confidence candidate genes (CGs) and flanking markers to MQTLs will help in marker-assisted breeding programs aimed at enhancing stress tolerance, yield, quality and nutrition. Functional analysis of these CGs can enhance our understanding of intricate trait-related genetics. The discovery of orthologous MQTLs shared between wheat and other crops sheds light on common evolutionary pathways governing these traits. Breeders can leverage the most promising MQTLs and CGs associated with multiple traits to develop superior next-generation wheat cultivars with improved trait performance. This review provides a comprehensive overview of MQTL analysis in wheat, highlighting progress, challenges, validation methods and future opportunities in wheat genetics and breeding, contributing to global food security and sustainable agriculture.
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Affiliation(s)
- Divya Sharma
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Anita Kumari
- Department of Botany, University of Delhi, Delhi, India
| | - Priya Sharma
- Department of Botany, University of Delhi, Delhi, India
| | - Anupma Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Anshu Sharma
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Zahoor Ahmad Mir
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Uttam Kumar
- Borlaug Institute for South Asia (BISA), Ludhiana, India
| | - Sofora Jan
- Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Srinagar, Kashmir, India
| | - M Parthiban
- Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Srinagar, Kashmir, India
| | - Reyazul Rouf Mir
- Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Srinagar, Kashmir, India
| | - Pradeep Bhati
- Borlaug Institute for South Asia (BISA), Ludhiana, India
| | - Anjan Kumar Pradhan
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Aakash Yadav
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | | | - Neeraj Budhlakoti
- ICAR- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mahesh C Yadav
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Kiran B Gaikwad
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Amit Kumar Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | | | - Sundeep Kumar
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India.
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Kaur R, Vasistha NK, Ravat VK, Mishra VK, Sharma S, Joshi AK, Dhariwal R. Genome-Wide Association Study Reveals Novel Powdery Mildew Resistance Loci in Bread Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:3864. [PMID: 38005757 PMCID: PMC10675159 DOI: 10.3390/plants12223864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023]
Abstract
Powdery mildew (PM), caused by the fungal pathogen Blumeria graminis f. sp. tritici (Bgt), significantly threatens global bread wheat production. Although the use of resistant cultivars is an effective strategy for managing PM, currently available wheat cultivars lack sufficient levels of resistance. To tackle this challenge, we conducted a comprehensive genome-wide association study (GWAS) using a diverse panel of 286 bread wheat genotypes. Over three consecutive years (2020-2021, 2021-2022, and 2022-2023), these genotypes were extensively evaluated for PM severity under field conditions following inoculation with virulent Bgt isolates. The panel was previously genotyped using the Illumina 90K Infinium iSelect assay to obtain genome-wide single-nucleotide polymorphism (SNP) marker coverage. By applying FarmCPU, a multilocus mixed model, we identified a total of 113 marker-trait associations (MTAs) located on chromosomes 1A, 1B, 2B, 3A, 3B, 4A, 4B, 5A, 5B, 6B, 7A, and 7B at a significance level of p ≤ 0.001. Notably, four novel MTAs on chromosome 6B were consistently detected in 2020-2021 and 2021-2022. Furthermore, within the confidence intervals of the identified SNPs, we identified 96 candidate genes belonging to different proteins including 12 disease resistance/host-pathogen interaction-related protein families. Among these, protein kinases, leucine-rich repeats, and zinc finger proteins were of particular interest due to their potential roles in PM resistance. These identified loci can serve as targets for breeding programs aimed at developing disease-resistant wheat cultivars.
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Affiliation(s)
- Ramandeep Kaur
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Sigh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour 173101, India
| | - Neeraj Kumar Vasistha
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Sigh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour 173101, India
- Department of Genetics and Plant Breeding, Rajiv Gandhi University, Rono Hills, Itanagar 791112, India
| | - Vikas Kumar Ravat
- Department of Plant Pathology, Rajiv Gandhi University, Rono Hills, Itanagar 791112, India
| | - Vinod Kumar Mishra
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Sandeep Sharma
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Arun Kumar Joshi
- Borlaug Institute for South Asia (BISA), NASC Complex, DPS Marg, New Delhi 110012, India
- International Maize and Wheat Improvement Center (CIMMYT) Regional Office, NASC Complex, DPS Marg, New Delhi 110012, India
| | - Raman Dhariwal
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, 5403 1 Avenue South, Lethbridge, AB T1J 4B1, Canada
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Xu YF, Ma FF, Zhang JP, Liu H, Li LH, An DG. Unraveling the genetic basis of grain number-related traits in a wheat-Agropyron cristatum introgressed line through high-resolution linkage mapping. BMC PLANT BIOLOGY 2023; 23:563. [PMID: 37964231 PMCID: PMC10647127 DOI: 10.1186/s12870-023-04547-7] [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: 06/26/2023] [Accepted: 10/19/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND Grain number per spike (GNS) is a pivotal determinant of grain yield in wheat. Pubing 3228 (PB3228), a wheat-Agropyron cristatum germplasm, exhibits a notably higher GNS. RESULTS In this study, we developed a recombinant inbred line (RIL) population derived from PB3228/Gao8901 (PG-RIL) and constructed a high-density genetic map comprising 101,136 loci, spanning 4357.3 cM using the Wheat 660 K SNP array. The genetic map demonstrated high collinearity with the wheat assembly IWGSC RefSeq v1.0. Traits related to grain number and spikelet number per spike were evaluated in seven environments for quantitative trait locus (QTL) analysis. Five environmentally stable QTLs were detected in at least three environments. Among these, two major QTLs, QGns-4A.2 and QGns-1A.1, associated with GNS, exhibited positive alleles contributed by PB3228. Further, the conditional QTL analysis revealed a predominant contribution of PB3228 to the GNS QTLs, with both grain number per spikelet (GNSL) and spikelet number per spike (SNS) contributing to the overall GNS trait. Four kompetitive allele-specific PCR (KASP) markers that linked to QGns-4A.2 and QGns-1A.1 were developed and found to be effective in verifying the QTL effect within a diversity panel. Compared to previous studies, QGns-4A.2 exhibited stability across different trials, while QGns-1A.1 represents a novel QTL. The results from unconditional and conditional QTL analyses are valuable for dissecting the genetic contribution of the component traits to GNS at the individual QTL level and for understanding the genetic basis of the superior grain number character in PB3228. The KASP markers can be utilized in marker-assisted selection for enhancing GNS. CONCLUSIONS Five environmentally stable QTLs related to grain number and spikelet number per spike were identified. PB3228 contributed to the majority of the QTLs associated with GNS.
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Affiliation(s)
- Yun-Feng Xu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
| | - Fei-Fei Ma
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
| | - Jin-Peng Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hong Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
| | - Li-Hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Diao-Guo An
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China.
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Rabieyan E, Darvishzadeh R, Mohammadi R, Gul A, Rasheed A, Akhar FK, Abdi H, Alipour H. Genetic diversity, linkage disequilibrium, and population structure of tetraploid wheat landraces originating from Europe and Asia. BMC Genomics 2023; 24:682. [PMID: 37964224 PMCID: PMC10644499 DOI: 10.1186/s12864-023-09768-6] [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: 06/11/2023] [Accepted: 10/26/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND Durum wheat is one of the most important crops, especially in the Mediterranean region. Insight into the genetic diversity of germplasm can improve the breeding program management in various traits. This study was done using single nucleotide polymorphisms (SNP) markers to characterize the genetic distinctiveness and differentiation of tetraploid wheat landraces collected from nine European and Asian countries. A sum of 23,334 polymorphic SNPs was detected in 126 tetraploid wheat landraces in relation to the reference genome. RESULTS The number of identified SNPs was 11,613 and 11,721 in A and B genomes, respectively. The highest and lowest diversity was on 6B and 6 A chromosomes, respectively. Structure analysis classified the landraces into two distinct subpopulations (K = 2). Evaluating the principal coordinate analysis (PCoA) and weighted pair-group method using arithmetic averages (WPGMA) clustering results demonstrated that landraces (99.2%) are categorized into one of the two chief subpopulations. Therefore, the grouping pattern did not clearly show the presence of a clear pattern of relationships between genetic diversity and their geographical derivation. Part of this result could be due to the historical exchange between different germplasms. Although the result did not separate landraces based on their region of origin, the landraces collected from Iran were classified into the same group and cluster. Analysis of molecular variance (AMOVA) also confirmed the results of population structure. Finally, Durum wheat landraces in some countries, including Turkey, Russia, Ukraine, and Afghanistan, were highly diverse, while others, including Iran and China, were low-diversity. CONCLUSION The recent study concluded that the 126 tetraploid wheat genotypes and their GBS-SNP markers are very appropriate for quantitative trait loci (QTLs) mapping and genome-wide association studies (GWAS). The core collection comprises two distinct subpopulations. Subpopulation II genotypes are the most diverse genotypes, and if they possess desired traits, they may be used in future breeding programs. The degree of diversity in the landraces of countries can provide the ground for the improvement of new cultivars with international cooperation. linkage disequilibrium (LD) hotspot distribution across the genome was investigated, which provides useful information about the genomic regions that contain intriguing genes.
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Affiliation(s)
- Ehsan Rabieyan
- Department of Agronomy and Plant Breeding, University of Tehran, Karaj, Iran
| | - Reza Darvishzadeh
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Reza Mohammadi
- Dryland Agricultural Research Institute (DARI), AREEO, Sararood branch, Iran
| | - Alvina Gul
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Awais Rasheed
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT), c/o CAAS, Beijing, 100081, China
- Department of Plant Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Fatemeh Keykha Akhar
- Department of Plant Biotechnology, College of Agriculture, Jahrom University, Jahrom, Iran
| | - Hossein Abdi
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Hadi Alipour
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran.
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Pundir S, Singh R, Singh VK, Sharma S, Balyan HS, Gupta PK, Sharma S. Mapping of QTLs and meta-QTLs for Heterodera avenae Woll. resistance in common wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2023; 23:529. [PMID: 37904124 PMCID: PMC10617160 DOI: 10.1186/s12870-023-04526-y] [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: 02/03/2023] [Accepted: 10/14/2023] [Indexed: 11/01/2023]
Abstract
BACKGROUND In hexaploid wheat, quantitative trait loci (QTL) and meta-QTL (MQTL) analyses were conducted to identify genomic regions controlling resistance to cereal cyst nematode (CCN), Heterodera avenae. A mapping population comprising 149 RILs derived from the cross HUW 468 × C 306 was used for composite interval mapping (CIM) and inclusive composite interval mapping (ICIM). RESULTS Eight main effect QTLs on three chromosomes (1B, 2A and 3A) were identified using two repeat experiments. One of these QTLs was co-localized with a previously reported wheat gene Cre5 for resistance to CCN. Seven important digenic epistatic interactions (PVE = 5% or more) were also identified, each involving one main effect QTL and another novel E-QTL. Using QTLs earlier reported in literature, two meta-QTLs were also identified, which were also used for identification of 57 candidate genes (CGs). Out of these, 29 CGs have high expression in roots and encoded the following proteins having a role in resistance to plant parasitic nematodes (PPNs): (i) NB-ARC,P-loop containing NTP hydrolase, (ii) Protein Kinase, (iii) serine-threonine/tyrosine-PK, (iv) protein with leucine-rich repeat, (v) virus X resistance protein-like, (vi) zinc finger protein, (vii) RING/FYVE/PHD-type, (viii) glycosyl transferase, family 8 (GT8), (ix) rubisco protein with small subunit domain, (x) protein with SANT/Myb domain and (xi) a protein with a homeobox. CONCLUSION Identification and selection of resistance loci with additive and epistatic effect along with two MQTL and associated CGs, identified in the present study may prove useful for understanding the molecular basis of resistance against H. avenae in wheat and for marker-assisted selection (MAS) for breeding CCN resistant wheat cultivars.
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Affiliation(s)
- Saksham Pundir
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, Uttar Pradesh, 250 004, India
- Department of Botany, Chaudhary Charan Singh University (CCSU), Meerut, Uttar Pradesh, 250 004, India
| | - Rakhi Singh
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, Uttar Pradesh, 250 004, India
| | - Vikas Kumar Singh
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, Uttar Pradesh, 250 004, India
| | - Shiveta Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, Uttar Pradesh, 250 004, India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, Uttar Pradesh, 250 004, India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, Uttar Pradesh, 250 004, India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, Uttar Pradesh, 250 004, India.
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Muqaddasi QH, Muqaddasi RK, Ebmeyer E, Korzun V, Argillier O, Mirdita V, Reif JC, Ganal MW, Röder MS. Genetic control and prospects of predictive breeding for European winter wheat's Zeleny sedimentation values and Hagberg-Perten falling number. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:229. [PMID: 37874400 PMCID: PMC10598174 DOI: 10.1007/s00122-023-04450-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/16/2023] [Indexed: 10/25/2023]
Abstract
KEY MESSAGE Sedimentation values and falling number in the last decades have helped maintain high baking quality despite rigorous selection for grain yield in wheat. Allelic combinations of major loci sustained the bread-making quality while improving grain yield. Glu-D1, Pinb-D1, and non-gluten proteins are associated with sedimentation values and falling number in European wheat. Zeleny sedimentation values (ZSV) and Hagberg-Perten falling number (HFN) are among the most important parameters that help determine the baking quality classes of wheat and, thus, influence the monetary benefits for growers. We used a published data set of 372 European wheat varieties evaluated in replicated field trials in multiple environments. ZSV and HFN traits hold a wide and significant genotypic variation and high broad-sense heritability. The genetic correlations revealed positive and significant associations of ZSV and HFN with each other, grain protein content (GPC) and grain hardness; however, they were all significantly negatively correlated with grain yield. Besides, GPC appeared to be the major predictor for ZSV and HFN. Our genome-wide association analyses based on high-quality SSR, SNP, and candidate gene markers revealed a strong quantitative genetic nature of ZSV and HFN by explaining their total genotypic variance as 41.49% and 38.06%, respectively. The association of known Glutenin (Glu-1) and Puroindoline (Pin-1) with ZSV provided positive analytic proof of our studies. We report novel candidate loci associated with globulins and albumins-the non-gluten monomeric proteins in wheat. In addition, predictive breeding analyses for ZSV and HFN suggest using genomic selection in the early stages of breeding programs with an average prediction accuracy of 81 and 59%, respectively.
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Affiliation(s)
- Quddoos H Muqaddasi
- European Wheat Breeding Center, BASF Agricultural Solutions GmbH, Am Schwabeplan 8, 06466, Stadt Seeland OT Gatersleben, Germany.
- KWS SAAT SE & Co. KGaA, Einbeck, 37574, Germany.
| | - Roop Kamal Muqaddasi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Stadt Seeland OT Gatersleben, Germany
| | | | | | | | - Vilson Mirdita
- European Wheat Breeding Center, BASF Agricultural Solutions GmbH, Am Schwabeplan 8, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Martin W Ganal
- TraitGenetics GmbH, Am Schwabeplan 1B, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Marion S Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Stadt Seeland OT Gatersleben, Germany
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Alomari DZ, Schierenbeck M, Alqudah AM, Alqahtani MD, Wagner S, Rolletschek H, Borisjuk L, Röder MS. Wheat Grains as a Sustainable Source of Protein for Health. Nutrients 2023; 15:4398. [PMID: 37892473 PMCID: PMC10609835 DOI: 10.3390/nu15204398] [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: 09/10/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Protein deficiency is recognized among the major global health issues with an underestimation of its importance. Genetic biofortification is a cost-effective and sustainable strategy to overcome global protein malnutrition. This study was designed to focus on protein-dense grains of wheat (Triticum aestivum L.) and identify the genes governing grain protein content (GPC) that improve end-use quality and in turn human health. Genome-wide association was applied using the 90k iSELECT Infinium and 35k Affymetrix arrays with GPC quantified by using a proteomic-based technique in 369 wheat genotypes over three field-year trials. The results showed significant natural variation among bread wheat genotypes that led to detecting 54 significant quantitative trait nucleotides (QTNs) surpassing the false discovery rate (FDR) threshold. These QTNs showed contrasting effects on GPC ranging from -0.50 to +0.54% that can be used for protein content improvement. Further bioinformatics analyses reported that these QTNs are genomically linked with 35 candidate genes showing high expression during grain development. The putative candidate genes have functions in the binding, remobilization, or transport of protein. For instance, the promising QTN AX-94727470 on chromosome 6B increases GPC by +0.47% and is physically located inside the gene TraesCS6B02G384500 annotated as Trehalose 6-phosphate phosphatase (T6P), which can be employed to improve grain protein quality. Our findings are valuable for the enhancement of protein content and end-use quality in one of the major daily food resources that ultimately improve human nutrition.
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Affiliation(s)
- Dalia Z. Alomari
- Department of Clinical Nutrition and Dietetics, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan
| | - Matías Schierenbeck
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, OT Gatersleben, D-06466 Seeland, Germany; (S.W.); (H.R.); (L.B.); (M.S.R.)
- CONICET CCT La Plata, La Plata 1900, Buenos Aires, Argentina
| | - Ahmad M. Alqudah
- Biological Science Program, Department of Biological and Environmental Sciences, College of Art and Science, Qatar University, Doha P.O. Box 2713, Qatar;
| | - Mashael Daghash Alqahtani
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia;
| | - Steffen Wagner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, OT Gatersleben, D-06466 Seeland, Germany; (S.W.); (H.R.); (L.B.); (M.S.R.)
| | - Hardy Rolletschek
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, OT Gatersleben, D-06466 Seeland, Germany; (S.W.); (H.R.); (L.B.); (M.S.R.)
| | - Ljudmilla Borisjuk
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, OT Gatersleben, D-06466 Seeland, Germany; (S.W.); (H.R.); (L.B.); (M.S.R.)
| | - Marion S. Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, OT Gatersleben, D-06466 Seeland, Germany; (S.W.); (H.R.); (L.B.); (M.S.R.)
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Li H, Zhang P, Luo M, Hoque M, Chakraborty S, Brooks B, Li J, Singh S, Forest K, Binney A, Zhang L, Mather D, Ayliffe M. Introgression of the bread wheat D genome encoded Lr34/Yr18/Sr57/Pm38/Ltn1 adult plant resistance gene into Triticum turgidum (durum wheat). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:226. [PMID: 37847385 PMCID: PMC10581953 DOI: 10.1007/s00122-023-04466-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 09/18/2023] [Indexed: 10/18/2023]
Abstract
KEY MESSAGE Lack of function of a D-genome adult plant resistance gene upon introgression into durum wheat. The wheat Lr34/Yr18/Sr57/Pm38/Ltn1 adult plant resistance gene (Lr34), located on chromosome arm 7DS, provides broad spectrum, partial, adult plant resistance to leaf rust, stripe rust, stem rust and powdery mildew. It has been used extensively in hexaploid bread wheat (AABBDD) and conferred durable resistance for many decades. These same diseases also occur on cultivated tetraploid durum wheat and emmer wheat but transfer of D genome sequences to those subspecies is restricted due to very limited intergenomic recombination. Herein we have introgressed the Lr34 gene into chromosome 7A of durum wheat. Durum chromosome substitution line Langdon 7D(7A) was crossed to Cappelli ph1c, a mutant derivative of durum cultivar Cappelli homozygous for a deletion of the chromosome pairing locus Ph1. Screening of BC1F2 plants and their progeny by KASP and PCR markers, 90 K SNP genotyping and cytology identified 7A chromosomes containing small chromosome 7D fragments encoding Lr34. However, in contrast to previous transgenesis experiments in durum wheat, resistance to wheat stripe rust was not observed in either Cappelli/Langdon 7D(7A) or Bansi durum plants carrying this Lr34 encoding segment due to low levels of Lr34 gene expression. KEY MESSAGE
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Affiliation(s)
- Hongyu Li
- CSIRO Agriculture and Food, Clunies Ross Street, GPO Box 1700, Canberra, ACT, 2601, Australia
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Peng Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Ming Luo
- CSIRO Agriculture and Food, Clunies Ross Street, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Mohammad Hoque
- CSIRO Agriculture and Food, Clunies Ross Street, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Soma Chakraborty
- CSIRO Agriculture and Food, Clunies Ross Street, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Brenton Brooks
- CSIRO Agriculture and Food, Clunies Ross Street, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Jianbo Li
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Smriti Singh
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Kerrie Forest
- Agriculture Victoria, Department of Energy, Environment and Climate Action, AgriBio Centre for AgriBioscience, 5 Ring Rd, Bundoora, VIC, 3083, Australia
| | - Allan Binney
- School of Agriculture, Food & Wine, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Lianquan Zhang
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Diane Mather
- School of Agriculture, Food & Wine, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Michael Ayliffe
- CSIRO Agriculture and Food, Clunies Ross Street, GPO Box 1700, Canberra, ACT, 2601, Australia.
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Jin Y, Wang Y, Liu J, Wang F, Qiu X, Liu P. Genome-wide linkage mapping of root system architecture-related traits in common wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1274392. [PMID: 37900737 PMCID: PMC10612324 DOI: 10.3389/fpls.2023.1274392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 09/22/2023] [Indexed: 10/31/2023]
Abstract
Identifying loci for root system architecture (RSA) traits and developing available markers are crucial for wheat breeding. In this study, RSA-related traits, including total root length (TRL), total root area (TRA), and number of root tips (NRT), were evaluated in the Doumai/Shi4185 recombinant inbred line (RIL) population under hydroponics. In addition, both the RILs and parents were genotyped using the wheat 90K single-nucleotide polymorphism (SNP) array. In total, two quantitative trait loci (QTLs) each for TRL (QTRL.caas-4A.1 and QTRL.caas-4A.2), TRA (QTRA.caas-4A and QTRA.caas-4D), and NRT (QNRT.caas-5B and QNRT.caas-5D) were identified and each explaining 5.94%-9.47%, 6.85%-7.10%, and 5.91%-10.16% phenotypic variances, respectively. Among these, QTRL.caas-4A.1 and QTRA.caas-4A overlapped with previous reports, while QTRL.caas-4A.2, QTRA.caas-4D, QNRT.caas-5B, and QNRT.caas-5D were novel. The favorable alleles of QTRL.caas-4A.1, QTRA.caas-4A, and QTRA.caas-5B were contributed by Doumai, whereas the favorable alleles of QTRL.caas-4A.2, QTRA.caas-4D, and QTRA.caas-5D originated from Shi 4185. Additionally, two competitive allele-specific PCR (KASP) markers, Kasp_4A_RL (QTRA.caas-4A) and Kasp_5D_RT (QNRT.caas-5D), were developed and validated in 165 wheat accessions. This study provides new loci and available KASP markers, accelerating wheat breeding for higher yields.
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Affiliation(s)
- Yirong Jin
- Wheat Research Institute, Dezhou Academy of Agricultural Sciences, Dezhou, China
| | - Yamei Wang
- School of Agriculture, Sun Yat-sen University, Shenzhen, China
| | - Jindong Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fuyan Wang
- Wheat Research Institute, Dezhou Academy of Agricultural Sciences, Dezhou, China
| | - Xiaodong Qiu
- Department of Science and Technology of Shandong Province, Jinan, China
| | - Peng Liu
- Wheat Research Institute, Dezhou Academy of Agricultural Sciences, Dezhou, China
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Haile JK, Sertse D, N’Diaye A, Klymiuk V, Wiebe K, Ruan Y, Chawla HS, Henriquez MA, Wang L, Kutcher HR, Steiner B, Buerstmayr H, Pozniak CJ. Multi-locus genome-wide association studies reveal the genetic architecture of Fusarium head blight resistance in durum wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1182548. [PMID: 37900749 PMCID: PMC10601657 DOI: 10.3389/fpls.2023.1182548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 09/18/2023] [Indexed: 10/31/2023]
Abstract
Durum wheat is more susceptible to Fusarium head blight (FHB) than other types or classes of wheat. The disease is one of the most devastating in wheat; it reduces yield and end-use quality and contaminates the grain with fungal mycotoxins such as deoxynivalenol (DON). A panel of 265 Canadian and European durum wheat cultivars, as well as breeding and experimental lines, were tested in artificially inoculated field environments (2019-2022, inclusive) and two greenhouse trials (2019 and 2020). The trials were assessed for FHB severity and incidence, visual rating index, Fusarium-damaged kernels, DON accumulation, anthesis or heading date, maturity date, and plant height. In addition, yellow pigment and protein content were analyzed for the 2020 field season. To capture loci underlying FHB resistance and related traits, GWAS was performed using single-locus and several multi-locus models, employing 13,504 SNPs. Thirty-one QTL significantly associated with one or more FHB-related traits were identified, of which nine were consistent across environments and associated with multiple FHB-related traits. Although many of the QTL were identified in regions previously reported to affect FHB, the QTL QFhb-3B.2, associated with FHB severity, incidence, and DON accumulation, appears to be novel. We developed KASP markers for six FHB-associated QTL that were consistently detected across multiple environments and validated them on the Global Durum Panel (GDP). Analysis of allelic diversity and the frequencies of these revealed that the lines in the GDP harbor between zero and six resistance alleles. This study provides a comprehensive assessment of the genetic basis of FHB resistance and DON accumulation in durum wheat. Accessions with multiple favorable alleles were identified and will be useful genetic resources to improve FHB resistance in durum breeding programs through marker-assisted recurrent selection and gene stacking.
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Affiliation(s)
- Jemanesh K. Haile
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Demissew Sertse
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
| | - Amidou N’Diaye
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Valentyna Klymiuk
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Krystalee Wiebe
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yuefeng Ruan
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Harmeet S. Chawla
- Department of Plant Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Maria-Antonia Henriquez
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Lipu Wang
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Hadley R. Kutcher
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Barbara Steiner
- Department of Agrobiotechnology, Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences Vienna, Tulln, Austria
| | - Hermann Buerstmayr
- Department of Agrobiotechnology, Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences Vienna, Tulln, Austria
| | - Curtis J. Pozniak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
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Kim S, Kim DS, Moyle H, Heo S. ShinyCore: An R/Shiny program for establishing core collection based on single nucleotide polymorphism data. PLANT METHODS 2023; 19:106. [PMID: 37821997 PMCID: PMC10566191 DOI: 10.1186/s13007-023-01084-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/28/2023] [Indexed: 10/13/2023]
Abstract
BACKGROUND Managing and investigating all available genetic resources are challenging. As an alternative, breeders and researchers use core collection-a representative subset of the entire collection. A good core is characterized by high genetic diversity and low repetitiveness. Among the several available software, GenoCore uses a coverage criterion that does not require computationally expensive distance-based metrics. RESULTS ShinyCore is a new method to select a core collection through two phases. The first phase uses the coverage criterion to quickly attain a fixed coverage, and the second phase uses a newly devised score (referred to as the rarity score) to further enhance diversity. It can attain a fixed coverage faster than a currently available algorithm devised for the coverage criterion, so it will benefit users who have big data. ShinyCore attains the minimum coverage specified by a user faster than GenoCore, and it then seeks to add entries with the rarest allele for each marker. Therefore, measures of genetic diversity and distance can be improved. CONCLUSION Although GenoCore is a fast algorithm, its implementation is difficult for those unfamiliar with R, ShinyCore can be easily implemented in Shiny with RStudio and an interactive web applet is available for those who are not familiar with programming languages.
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Affiliation(s)
- Steven Kim
- Department of Mathematics and Statistics, California State University, Monterey Bay, Seaside, USA
| | - Dong Sub Kim
- Department of Horticulture, Kongju National University, Yesan, Korea
| | - Hana Moyle
- Department of Mathematics and Statistics, California State University, Monterey Bay, Seaside, USA
- Department of Marine Science, California State University, Monterey Bay, Seaside, USA
| | - Seong Heo
- Department of Horticulture, Kongju National University, Yesan, Korea.
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