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Radecka-Janusik M, Piechota U, Piaskowska D, Słowacki P, Bartosiak S, Czembor P. Haplotype-based association mapping of genomic regions associated with Zymoseptoria tritici resistance using 217 diverse wheat genotypes. BMC PLANT BIOLOGY 2024; 24:682. [PMID: 39020304 PMCID: PMC11256644 DOI: 10.1186/s12870-024-05400-1] [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: 07/29/2023] [Accepted: 07/09/2024] [Indexed: 07/19/2024]
Abstract
BACKGROUND Septoria tritici blotch (STB) is considered to be one of the most destructive foliar wheat diseases and is caused by Zymoseptoria tritici. The yield losses are severe and in Northwestern Europe can reach up to 50%. The efficacy of fungicides is diminishing due to changes in the genetic structure of the pathogen. Therefore, resistance breeding is the most effective strategy of disease management. Recently, genome-wide association studies (GWAS) have become more popular due to their robustness in dissecting complex traits, including STB resistance in wheat. This was made possible by the use of large mapping populations and new sequencing technologies. High-resolution mapping benefits from historical recombination and greater allele numbers in GWAS. RESULTS In our study, 217 wheat genotypes of diverse origin were phenotyped against five Z. tritici isolates (IPO323, IPO88004, IPO92004, IPO86036 and St1-03) and genotyped on the DArTseq platform. In polytunnel tests two disease parameters were evaluated: the percentage of leaf area covered by necrotic lesions (NEC) and the percentage of leaf area covered by lesions bearing pycnidia (PYC). The disease escape parameters heading date (Hd) and plant height (Ht) were also measured. Pearson's correlation showed a positive effect between disease parameters, providing additional information. The Structure analysis indicated four subpopulations which included from 28 (subpopulation 2) to 79 genotypes (subpopulation 3). All of the subpopulations showed a relatively high degree of admixture, which ranged from 60% of genotypes with less than 80% of proportions of the genome attributed to assigned subpopulation for group 2 to 85% for group 4. Haplotype-based GWAS analysis allowed us to identify 27 haploblocks (HBs) significantly associated with analysed traits with a p-value above the genome-wide significance threshold (5%, which was -log10(p) > 3.64) and spread across the wheat genome. The explained phenotypic variation of identified significant HBs ranged from 0.2% to 21.5%. The results of the analysis showed that four haplotypes (HTs) associated with disease parameters cause a reduction in the level of leaf coverage by necrosis and pycnidia, namely: Chr3A_HB98_HT2, Chr5B_HB47_HT1, Chr7B_HB36_HT1 and Chr5D_HB10_HT3. CONCLUSIONS GWAS analysis enabled us to identify four significant chromosomal regions associated with a reduction in STB disease parameters. The list of valuable HBs and wheat varieties possessing them provides promising material for further molecular analysis of resistance loci and development of breeding programmes.
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Affiliation(s)
- Magdalena Radecka-Janusik
- Plant Breeding and Acclimatization Institute - National Research Institute, Radzików, Błonie, 05-870, Poland
| | - Urszula Piechota
- Plant Breeding and Acclimatization Institute - National Research Institute, Radzików, Błonie, 05-870, Poland
| | - Dominika Piaskowska
- Plant Breeding and Acclimatization Institute - National Research Institute, Radzików, Błonie, 05-870, Poland
| | - Piotr Słowacki
- Plant Breeding and Acclimatization Institute - National Research Institute, Radzików, Błonie, 05-870, Poland
| | - Sławomir Bartosiak
- Plant Breeding and Acclimatization Institute - National Research Institute, Radzików, Błonie, 05-870, Poland
| | - Paweł Czembor
- Plant Breeding and Acclimatization Institute - National Research Institute, Radzików, Błonie, 05-870, Poland.
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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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Alemu A, Åstrand J, Montesinos-López OA, Isidro Y Sánchez J, Fernández-Gónzalez J, Tadesse W, Vetukuri RR, Carlsson AS, Ceplitis A, Crossa J, Ortiz R, Chawade A. Genomic selection in plant breeding: Key factors shaping two decades of progress. MOLECULAR PLANT 2024; 17:552-578. [PMID: 38475993 DOI: 10.1016/j.molp.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/22/2024] [Accepted: 03/08/2024] [Indexed: 03/14/2024]
Abstract
Genomic selection, the application of genomic prediction (GP) models to select candidate individuals, has significantly advanced in the past two decades, effectively accelerating genetic gains in plant breeding. This article provides a holistic overview of key factors that have influenced GP in plant breeding during this period. We delved into the pivotal roles of training population size and genetic diversity, and their relationship with the breeding population, in determining GP accuracy. Special emphasis was placed on optimizing training population size. We explored its benefits and the associated diminishing returns beyond an optimum size. This was done while considering the balance between resource allocation and maximizing prediction accuracy through current optimization algorithms. The density and distribution of single-nucleotide polymorphisms, level of linkage disequilibrium, genetic complexity, trait heritability, statistical machine-learning methods, and non-additive effects are the other vital factors. Using wheat, maize, and potato as examples, we summarize the effect of these factors on the accuracy of GP for various traits. The search for high accuracy in GP-theoretically reaching one when using the Pearson's correlation as a metric-is an active research area as yet far from optimal for various traits. We hypothesize that with ultra-high sizes of genotypic and phenotypic datasets, effective training population optimization methods and support from other omics approaches (transcriptomics, metabolomics and proteomics) coupled with deep-learning algorithms could overcome the boundaries of current limitations to achieve the highest possible prediction accuracy, making genomic selection an effective tool in plant breeding.
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Affiliation(s)
- Admas Alemu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
| | - Johanna Åstrand
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden; Lantmännen Lantbruk, Svalöv, Sweden
| | | | - Julio Isidro Y Sánchez
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo-UPM, 28223 Madrid, Spain
| | - Javier Fernández-Gónzalez
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo-UPM, 28223 Madrid, Spain
| | - Wuletaw Tadesse
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Ramesh R Vetukuri
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Anders S Carlsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - José Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Km 45, Carretera México-Veracruz, Texcoco, México 52640, Mexico
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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Salami M, Heidari B, Alizadeh B, Batley J, Wang J, Tan XL, Dadkhodaie A, Richards C. Dissection of quantitative trait nucleotides and candidate genes associated with agronomic and yield-related traits under drought stress in rapeseed varieties: integration of genome-wide association study and transcriptomic analysis. FRONTIERS IN PLANT SCIENCE 2024; 15:1342359. [PMID: 38567131 PMCID: PMC10985355 DOI: 10.3389/fpls.2024.1342359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/26/2024] [Indexed: 04/04/2024]
Abstract
Introduction An important strategy to combat yield loss challenge is the development of varieties with increased tolerance to drought to maintain production. Improvement of crop yield under drought stress is critical to global food security. Methods In this study, we performed multiomics analysis in a collection of 119 diverse rapeseed (Brassica napus L.) varieties to dissect the genetic control of agronomic traits in two watering regimes [well-watered (WW) and drought stress (DS)] for 3 years. In the DS treatment, irrigation continued till the 50% pod development stage, whereas in the WW condition, it was performed throughout the whole growing season. Results The results of the genome-wide association study (GWAS) using 52,157 single-nucleotide polymorphisms (SNPs) revealed 1,281 SNPs associated with traits. Six stable SNPs showed sequence variation for flowering time between the two irrigation conditions across years. Three novel SNPs on chromosome C04 for plant weight were located within drought tolerance-related gene ABCG16, and their pleiotropically effects on seed weight per plant and seed yield were characterized. We identified the C02 peak as a novel signal for flowering time, harboring 52.77% of the associated SNPs. The 288-kbps LD decay distance analysis revealed 2,232 candidate genes (CGs) associated with traits. The CGs BIG1-D, CAND1, DRG3, PUP10, and PUP21 were involved in phytohormone signaling and pollen development with significant effects on seed number, seed weight, and grain yield in drought conditions. By integrating GWAS and RNA-seq, 215 promising CGs were associated with developmental process, reproductive processes, cell wall organization, and response to stress. GWAS and differentially expressed genes (DEGs) of leaf and seed in the yield contrasting accessions identified BIG1-D, CAND1, and DRG3 genes for yield variation. Discussion The results of our study provide insights into the genetic control of drought tolerance and the improvement of marker-assisted selection (MAS) for breeding high-yield and drought-tolerant varieties.
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Affiliation(s)
- Maryam Salami
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Bahram Heidari
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Bahram Alizadeh
- Oil Crops Research Department, Seed and Plant Improvement Institute, Agricultural Research Education and Extension, Organization, (AREEO), Karaj, Iran
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Jin Wang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xiao-Li Tan
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Ali Dadkhodaie
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Christopher Richards
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Laboratory for Genetic Resources Preservation, Fort Collins, CO, United States
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Wang H, Bai Y, Biligetu B. Effects of SNP marker density and training population size on prediction accuracy in alfalfa (Medicago sativa L.) genomic selection. THE PLANT GENOME 2024; 17:e20431. [PMID: 38263612 DOI: 10.1002/tpg2.20431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 11/29/2023] [Accepted: 01/04/2024] [Indexed: 01/25/2024]
Abstract
Effects of individual single-nucleotide polymorphism (SNP) markers and the size of "training" and "test" populations affect prediction accuracy in genomic selection (GS). This study evaluated 11 subsets of 4932 SNPs using six genetic additive methods to understand marker density in GS prediction in alfalfa (Medicago sativa L.). In the GS methods, the effect of "training" to "test" population size was also evaluated. Fourteen alfalfa populations sampled from long-term grazing sites were genotyped using genotyping by sequencing for the identification of SNPs. These populations were also phenotyped for six agromorphological and three nutritive traits from 2018 to 2020. The accuracy of GS prediction improved across six GS methods when the ratio of "training" to "test" population size increased. However, the prediction accuracy of the six GS methods reduced to a range of -0.27 to 0.11 when random, uninformative SNPs were used. In this study, five Bayesian methods and ridge-regression best linear unbiased prediction (rrBLUP) method had similar GS accuracies for "training" sets, but rrBLUP tended to outperform Bayesian methods in independent "test" sets when SNP subsets with high mean-squared-estimated-marker effect were used. These findings can enhance the application of GS in alfalfa genetic improvement.
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Affiliation(s)
- Hu Wang
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yuguang Bai
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Bill Biligetu
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Lin M, Islamov B, Aleliūnas A, Armonienė R, Gorash A, Meigas E, Ingver A, Tamm I, Kollist H, Strazdiņa V, Bleidere M, Brazauskas G, Lillemo M. Genome-wide association analysis identifies a consistent QTL for powdery mildew resistance on chromosome 3A in Nordic and Baltic spring wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:25. [PMID: 38240841 PMCID: PMC10799116 DOI: 10.1007/s00122-023-04529-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/14/2023] [Indexed: 01/22/2024]
Abstract
KEY MESSAGE QPm.NOBAL-3A is an important QTL providing robust adult plant powdery mildew resistance in Nordic and Baltic spring wheat, aiding sustainable crop protection and breeding. Powdery mildew, caused by the biotrophic fungal pathogen Blumeria graminis f. sp. tritici, poses a significant threat to bread wheat (Triticum aestivum L.), one of the world's most crucial cereal crops. Enhancing cultivar resistance against this devastating disease requires a comprehensive understanding of the genetic basis of powdery mildew resistance. In this study, we performed a genome-wide association study (GWAS) using extensive field trial data from multiple environments across Estonia, Latvia, Lithuania, and Norway. The study involved a diverse panel of recent wheat cultivars and breeding lines sourced from the Baltic region and Norway. We identified a major quantitative trait locus (QTL) on chromosome 3A, designated as QPm.NOBAL-3A, which consistently conferred high resistance to powdery mildew across various environments and countries. Furthermore, the consistency of the QTL haplotype effect was validated using an independent Norwegian spring wheat panel. Subsequent greenhouse seedling inoculations with 15 representative powdery mildew isolates on a subset of the GWAS panel indicated that this QTL provides adult plant resistance and is likely of race non-specific nature. Moreover, we developed and validated KASP markers for QPm.NOBAL-3A tailored for use in breeding. These findings provide a critical foundation for marker-assisted selection in breeding programs aimed at pyramiding resistance QTL/genes to achieve durable and broad-spectrum resistance against powdery mildew.
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Affiliation(s)
- Min Lin
- Department of Plant Sciences, Norwegian University of Life Sciences, Post Box 5003, NO-1432, ÅS, Norway
| | - Bulat Islamov
- Centre of Estonian Rural Research and Knowledge, J. Aamisepa 1, Jõgeva Alevik, 48309, Jõgeva Maakond, Estonia
| | - Andrius Aleliūnas
- Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, 58344, Akademija, Lithuania
| | - Rita Armonienė
- Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, 58344, Akademija, Lithuania
| | - Andrii Gorash
- Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, 58344, Akademija, Lithuania
| | - Egon Meigas
- Institute of Bioengineering, University of Tartu, Nooruse 1, 50411, Tartu, Estonia
| | - Anne Ingver
- Centre of Estonian Rural Research and Knowledge, J. Aamisepa 1, Jõgeva Alevik, 48309, Jõgeva Maakond, Estonia
| | - Ilmar Tamm
- Centre of Estonian Rural Research and Knowledge, J. Aamisepa 1, Jõgeva Alevik, 48309, Jõgeva Maakond, Estonia
| | - Hannes Kollist
- Institute of Bioengineering, University of Tartu, Nooruse 1, 50411, Tartu, Estonia
| | - Vija Strazdiņa
- Institute of Agricultural Resources and Economics, Zinatnes Iela 2, Cesis County, 4126, Latvia
| | - Māra Bleidere
- Institute of Agricultural Resources and Economics, Zinatnes Iela 2, Cesis County, 4126, Latvia
| | - Gintaras Brazauskas
- Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, 58344, Akademija, Lithuania
| | - Morten Lillemo
- Department of Plant Sciences, Norwegian University of Life Sciences, Post Box 5003, NO-1432, ÅS, Norway.
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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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Zakieh M, Alemu A, Henriksson T, Pareek N, Singh PK, Chawade A. Exploring GWAS and genomic prediction to improve Septoria tritici blotch resistance in wheat. Sci Rep 2023; 13:15651. [PMID: 37730954 PMCID: PMC10511425 DOI: 10.1038/s41598-023-42856-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: 07/13/2023] [Accepted: 09/15/2023] [Indexed: 09/22/2023] Open
Abstract
Septoria tritici blotch (STB) is a destructive foliar diseases threatening wheat grain yield. Wheat breeding for STB disease resistance has been identified as the most sustainable and environment-friendly approach. In this work, a panel of 316 winter wheat breeding lines from a commercial breeding program were evaluated for STB resistance at the seedling stage under controlled conditions followed by genome-wide association study (GWAS) and genomic prediction (GP). The study revealed a significant genotypic variation for STB seedling resistance, while disease severity scores exhibited a normal frequency distribution. Moreover, we calculated a broad-sense heritability of 0.62 for the trait. Nine single- and multi-locus GWAS models identified 24 marker-trait associations grouped into 20 quantitative trait loci (QTLs) for STB seedling-stage resistance. The seven QTLs located on chromosomes 1B, 2A, 2B, 5B (two), 7A, and 7D are reported for the first time and could potentially be novel. The GP cross-validation analysis in the RR-BLUP model estimated the genomic-estimated breeding values (GEBVs) of STB resistance with a prediction accuracy of 0.49. Meanwhile, the GWAS assisted wRR-BLUP model improved the accuracy to 0.58. The identified QTLs can be used for marker-assisted backcrossing against STB in winter wheat. Moreover, the higher prediction accuracy recorded from the GWAS-assisted GP analysis implies its power to successfully select superior candidate lines based on their GEBVs for STB resistance.
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Affiliation(s)
- Mustafa Zakieh
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 23422, Lomma, Sweden
| | - Admas Alemu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 23422, Lomma, Sweden
| | | | - Nidhi Pareek
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305801, India
| | - Pawan K Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 23422, Lomma, Sweden.
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Taranto F, Esposito S, Fania F, Sica R, Marzario S, Logozzo G, Gioia T, De Vita P. Breeding effects on durum wheat traits detected using GWAS and haplotype block analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1206517. [PMID: 37794940 PMCID: PMC10546023 DOI: 10.3389/fpls.2023.1206517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 08/08/2023] [Indexed: 10/06/2023]
Abstract
Introduction The recent boosting of genomic data in durum wheat (Triticum turgidum subsp. durum) offers the opportunity to better understand the effects of breeding on the genetic structures that regulate the expression of traits of agronomic interest. Furthermore, the identification of DNA markers useful for marker-assisted selection could also improve the reliability of technical protocols used for variety protection and registration. Methods Within this motivation context, 123 durum wheat accessions, classified into three groups: landraces (LR), ancient (OC) and modern cultivars (MC), were evaluated in two locations, for 34 agronomic traits, including UPOV descriptors, to assess the impact of changes that occurred during modern breeding. Results The association mapping analysis, performed with 4,241 SNP markers and six multi-locus-GWAS models, revealed 28 reliable Quantitative Trait Nucleotides (QTNs) related to plant morphology and kernel-related traits. Some important genes controlling flowering time and plant height were in linkage disequilibrium (LD) decay with QTNs identified in this study. A strong association for yellow berry was found on chromosome 6A (Q.Yb-6A) in a region containing the nadh-ubiquinone oxidoreductase subunit, a gene involved in starch metabolism. The Q.Kcp-2A harbored the PPO locus, with the associated marker (Ku_c13700_1196) in LD decay with Ppo-A1 and Ppo-A2. Interestingly, the Q.FGSGls-2B.1, identified by RAC875_c34512_685 for flag leaf glaucosity, mapped less than 1 Mb from the Epistatic inhibitors of glaucousness (Iw1), thus representing a good candidate for supporting the morphological DUS traits also with molecular markers. LD haplotype block approach revealed a higher diversity, richness and length of haploblocks in MC than OC and LR (580 in LR, 585 in OC and 612 in MC), suggesting a possible effect exerted by breeding programs on genomic regions associated with the agronomic traits. Discussion Our findings pave new ways to support the phenotypic characterization necessary for variety registration by using a panel of cost-effectiveness SNP markers associated also to the UPOV descriptors. Moreover, the panel of associated SNPs might represent a reservoir of favourable alleles to use in durum wheat breeding and genetics.
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Affiliation(s)
- F. Taranto
- Italian National Council of Research (CNR), Institute of Biosciences and Bioresources (IBBR), Bari, Italy
| | - S. Esposito
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
| | - F. Fania
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
- Department of Agriculture, Food, Natural Resources, and Engineering (DAFNE) - University of Foggia, Foggia, Italy
| | - R. Sica
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - S. Marzario
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - G. Logozzo
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - T. Gioia
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - P. De Vita
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
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10
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Semagn K, Henriquez MA, Iqbal M, Brûlé-Babel AL, Strenzke K, Ciechanowska I, Navabi A, N’Diaye A, Pozniak C, Spaner D. Identification of Fusarium head blight sources of resistance and associated QTLs in historical and modern Canadian spring wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1190358. [PMID: 37680355 PMCID: PMC10482112 DOI: 10.3389/fpls.2023.1190358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/18/2023] [Indexed: 09/09/2023]
Abstract
Fusarium head blight (FHB) is one the most globally destructive fungal diseases in wheat and other small grains, causing a reduction in grain yield by 10-70%. The present study was conducted in a panel of historical and modern Canadian spring wheat (Triticum aestivum L.) varieties and lines to identify new sources of FHB resistance and map associated quantitative trait loci (QTLs). We evaluated 249 varieties and lines for reaction to disease incidence, severity, and visual rating index (VRI) in seven environments by artificially spraying a mixture of four Fusarium graminearum isolates. A subset of 198 them were genotyped with the Wheat 90K iSelect single nucleotide polymorphisms (SNPs) array. Genome-wide association mapping performed on the overall best linear unbiased estimators (BLUE) computed from all seven environments and the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v2.0 physical map of 26,449 polymorphic SNPs out of the 90K identified sixteen FHB resistance QTLs that individually accounted for 5.7-10.2% of the phenotypic variance. The positions of two of the FHB resistance QTLs overlapped with plant height and flowering time QTLs. Four of the QTLs (QFhb.dms-3B.1, QFhb.dms-5A.5, QFhb.dms-5A.7, and QFhb.dms-6A.4) were simultaneously associated with disease incidence, severity, and VRI, which accounted for 27.0-33.2% of the total phenotypic variance in the combined environments. Three of the QTLs (QFhb.dms-2A.2, QFhb.dms-2D.2, and QFhb.dms-5B.8) were associated with both incidence and VRI and accounted for 20.5-22.1% of the total phenotypic variance. In comparison with the VRI of the checks, we identified four highly resistant and thirty-three moderately resistant lines and varieties. The new FHB sources of resistance and the physical map of the associated QTLs would provide wheat breeders valuable information towards their efforts in developing improved varieties in western Canada.
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Affiliation(s)
- Kassa Semagn
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, Canada
| | - Maria Antonia Henriquez
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Muhammad Iqbal
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, Canada
| | | | - Klaus Strenzke
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, Canada
| | - Izabela Ciechanowska
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, Canada
| | - Alireza Navabi
- Department of Plant Agriculture, Crop Science Building, University of Guelph, Guelph, ON, Canada
| | - Amidou N’Diaye
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Dean Spaner
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, Canada
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11
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Wang B, Meng T, Xiao B, Yu T, Yue T, Jin Y, Ma P. Fighting wheat powdery mildew: from genes to fields. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:196. [PMID: 37606731 DOI: 10.1007/s00122-023-04445-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/07/2023] [Indexed: 08/23/2023]
Abstract
KEY MESSAGE Host resistance conferred by Pm genes provides an effective strategy to control powdery mildew. The study of Pm genes helps modern breeding develop toward more intelligent and customized. Powdery mildew of wheat is one of the most destructive diseases seriously threatening the crop yield and quality worldwide. The genetic research on powdery mildew (Pm) resistance has entered a new era. Many Pm genes from wheat and its wild and domesticated relatives have been mined and cloned. Meanwhile, modern breeding strategies based on high-throughput sequencing and genome editing are emerging and developing toward more intelligent and customized. This review highlights mining and cloning of Pm genes, molecular mechanism studies on the resistance and avirulence genes, and prospects for genomic-assisted breeding for powdery mildew resistance in wheat.
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Affiliation(s)
- Bo Wang
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Ting Meng
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Bei Xiao
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Tianying Yu
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Tingyan Yue
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Yuli Jin
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Pengtao Ma
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China.
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12
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Ababa G. Biology, taxonomy, genetics, and management of Zymoseptoria tritici: the causal agent of wheat leaf blotch. Mycology 2023; 14:292-315. [PMID: 38187886 PMCID: PMC10769150 DOI: 10.1080/21501203.2023.2241492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/22/2023] [Indexed: 01/09/2024] Open
Abstract
Septoria tritici blotch or Septoria leaf blotch has been used for long time, but leaf blotch is a correct disease name. Moreover, Lb resistant gene is the correct name, but, not Stb gene. It has sexual and asexual parts on the mycelia, known as heterothallic fungi. Its pathogenic diversity ranged from 40% to 93% and has produced a wide variety of AvrLb6 haplotypes. M. graminicola has a plasmogamy and karyogamy sexual process. The pathogen can use macropycnidiospores, micropycnidiospores, and pycnidia vegetative growths for infection and overwintering. Synthetic M3, Kavkaz-K4500, Synthetic 6×, and TE9111 wheat genotypes have horizontal resistance. Avirulence (Avr) genes in Z. tritici and their matching wheat (R) genes indicate gene for gene mechanisms of resistance. Twenty-two R genes (vertical resistance) have been identified. In both horizontal and vertical resistance, different Lb genes have been broken down due to new Z.tritici virulent gene and currently Lb19 resistant gene is being recommended. Mixing of resistant and susceptible cultivars is also the most effective management strategy. Moreover, different cultural practices and biological control have been proposed. Lastly, different fungicides are also available. However, in developing countries cultivar mixture, isolates diversity, biological control, and epidemic studies have been greatly missed.
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Affiliation(s)
- Girma Ababa
- Department of Plant Protection (Plant Pathology), Holetta Agricultural Research Center (HARC), Ethiopian Institute of Agricultural Research (EIAR), Holetta, Addis Ababa, Ethiopia
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13
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Li X, Wang J, Su M, Zhang M, Hu Y, Du J, Zhou H, Yang X, Zhang X, Jia H, Gao Z, Ye Z. Multiple-statistical genome-wide association analysis and genomic prediction of fruit aroma and agronomic traits in peaches. HORTICULTURE RESEARCH 2023; 10:uhad117. [PMID: 37577398 PMCID: PMC10419450 DOI: 10.1093/hr/uhad117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 05/21/2023] [Indexed: 08/15/2023]
Abstract
'Chinese Cling' is an important founder in peach breeding history due to the pleasant flavor. Genome-wide association studies (GWAS) combined with genomic selection are promising tools in fruit tree breeding, as there is a considerable time lapse between crossing and release of a cultivar. In this study, 242 peaches from Shanghai germplasm were genotyped with 145 456 single-nucleotide polymorphisms (SNPs). The six agronomic traits of fruit flesh color, fruit shape, fruit hairiness, flower type, pollen sterility, and soluble solids content, along with 14 key volatile odor compounds (VOCs), were recorded for multiple-statistical GWAS. Except the reported candidate genes, six novel genes were identified as associated with these traits. Thirty-nine significant SNPs were associated with eight VOCs. The putative candidate genes were confirmed for VOCs by RNA-seq, including three genes in the biosynthesis pathway found to be associated with linalool, soluble solids content, and cis-3-hexenyl acetate. Multiple-trait genomic prediction enhanced the predictive ability for γ-decalactone to 0.7415 compared with the single-trait model value of 0.1017. One PTS1-SSR marker was designed to predict the linalool content, and the favorable genotype 187/187 was confirmed, mainly existing in the 'Shanghai Shuimi' landrace. Overall, our findings will be helpful in determining peach accessions with the ideal phenotype and show the potential of multiple-trait genomic prediction to improve accuracy for highly correlated genetic traits. The diagnostic marker will be valuable for the breeder to bridge the gap between quantitative trait loci and marker-assisted selection for developing strong-aroma cultivars.
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Affiliation(s)
- Xiongwei Li
- Peach Research Department of Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Jiabo Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Southwest Minzu University, Ministry of Education), Chengdu, Sichuan 610041, China
| | - Mingshen Su
- Peach Research Department of Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Minghao Zhang
- Peach Research Department of Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Yang Hu
- Peach Research Department of Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Jihong Du
- Peach Research Department of Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Huijuan Zhou
- Peach Research Department of Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Xiaofeng Yang
- Peach Group of Shanghai Runzhuang Agricultural Science and Technology Institute, Shanghai 201415, China
| | - Xianan Zhang
- Peach Research Department of Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Huijuan Jia
- Department of Horticulture, Key Laboratory for Horticultural Plant Growth, Development and Quality Improvement of State Agriculture Ministry, Zhejiang Unihversity, Hangzhou 310058, China
| | - Zhongshan Gao
- Department of Horticulture, Key Laboratory for Horticultural Plant Growth, Development and Quality Improvement of State Agriculture Ministry, Zhejiang Unihversity, Hangzhou 310058, China
| | - Zhengwen Ye
- Peach Research Department of Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
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14
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Mourad AM, Hamdy RM, Esmail SM. Novel genomic regions on chromosome 5B controlling wheat powdery mildew seedling resistance under Egyptian conditions. FRONTIERS IN PLANT SCIENCE 2023; 14:1160657. [PMID: 37235018 PMCID: PMC10208068 DOI: 10.3389/fpls.2023.1160657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/27/2023] [Indexed: 05/28/2023]
Abstract
Wheat powdery mildew (PM) causes significant yield losses worldwide. None of the Egyptian wheat cultivars was detected to be highly resistant to such a severe disease. Therefore, a diverse spring wheat panel was evaluated for PM seedling resistance using different Bgt conidiospores collected from Egyptian fields in two growing seasons. The evaluation was done in two separate experiments. Highly significant differences were found between the two experiments suggesting the presence of different isolates populations. Highly significant differences were found among the tested genotypes confirming the ability to improve PM resistance using the recent panel. Genome-wide association study (GWAS) was done for each experiment separately and a total of 71 significant markers located within 36 gene models were identified. The majority of these markers are located on chromosome 5B. Haplotype block analysis identified seven blocks containing the significant markers on chromosome 5B. Five gene models were identified on the short arm of the chromosome. Gene enrichment analysis identified five and seven pathways based on the biological process and molecular functions respectively for the detected gene models. All these pathways are associated with disease resistance in wheat. The genomic regions on 5B seem to be novel regions that are associated with PM resistance under Egyptian conditions. Selection of superior genotypes was done and Grecian genotypes seem to be a good source for improving PM resistance under Egyptian conditions.
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Affiliation(s)
- Amira M.I. Mourad
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, OT Gatersleben, Germany
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Rania M. Hamdy
- Food Science and Technology Department, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Samar M. Esmail
- Wheat Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
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15
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Alemu A, Batista L, Singh PK, Ceplitis A, Chawade A. Haplotype-tagged SNPs improve genomic prediction accuracy for Fusarium head blight resistance and yield-related traits in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:92. [PMID: 37009920 PMCID: PMC10068637 DOI: 10.1007/s00122-023-04352-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
Linkage disequilibrium (LD)-based haplotyping with subsequent SNP tagging improved the genomic prediction accuracy up to 0.07 and 0.092 for Fusarium head blight resistance and spike width, respectively, across six different models. Genomic prediction is a powerful tool to enhance genetic gain in plant breeding. However, the method is accompanied by various complications leading to low prediction accuracy. One of the major challenges arises from the complex dimensionality of marker data. To overcome this issue, we applied two pre-selection methods for SNP markers viz. LD-based haplotype-tagging and GWAS-based trait-linked marker identification. Six different models were tested with preselected SNPs to predict the genomic estimated breeding values (GEBVs) of four traits measured in 419 winter wheat genotypes. Ten different sets of haplotype-tagged SNPs were selected by adjusting the level of LD thresholds. In addition, various sets of trait-linked SNPs were identified with different scenarios from the training-test combined and only from the training populations. The BRR and RR-BLUP models developed from haplotype-tagged SNPs had a higher prediction accuracy for FHB and SPW by 0.07 and 0.092, respectively, compared to the corresponding models developed without marker pre-selection. The highest prediction accuracy for SPW and FHB was achieved with tagged SNPs pruned at weak LD thresholds (r2 < 0.5), while stringent LD was required for spike length (SPL) and flag leaf area (FLA). Trait-linked SNPs identified only from training populations failed to improve the prediction accuracy of the four studied traits. Pre-selection of SNPs via LD-based haplotype-tagging could play a vital role in optimizing genomic selection and reducing genotyping costs. Furthermore, the method could pave the way for developing low-cost genotyping methods through customized genotyping platforms targeting key SNP markers tagged to essential haplotype blocks.
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Affiliation(s)
- Admas Alemu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Pawan K Singh
- International Maize and Wheat Improvement Center, Texcoco, Mexico
| | | | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
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16
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Mulugeta B, Tesfaye K, Ortiz R, Johansson E, Hailesilassie T, Hammenhag C, Hailu F, Geleta M. Marker-trait association analyses revealed major novel QTLs for grain yield and related traits in durum wheat. FRONTIERS IN PLANT SCIENCE 2023; 13:1009244. [PMID: 36777537 PMCID: PMC9909559 DOI: 10.3389/fpls.2022.1009244] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
The growing global demand for wheat for food is rising due to the influence of population growth and climate change. The dissection of complex traits by employing a genome-wide association study (GWAS) allows the identification of DNA markers associated with complex traits to improve the productivity of crops. We used GWAS with 10,045 single nucleotide polymorphism (SNP) markers to search for genomic regions associated with grain yield and related traits based on diverse panels of Ethiopian durum wheat. In Ethiopia, multi-environment trials of the genotypes were carried out at five locations. The genotyping was conducted using the 25k Illumina Wheat SNP array to explore population structure, linkage disequilibrium (LD), and marker-trait associations (MTAs). For GWAS, the multi-locus Fixed and Random Model Circulating Probability Unification (FarmCPU) model was applied. Broad-sense heritability estimates were high, ranging from 0.63 (for grain yield) to 0.97 (for thousand-kernel weight). The population structure based on principal component analysis, and model-based cluster analysis revealed two genetically distinct clusters with limited admixtures. The LD among SNPs declined within the range of 2.02-10.04 Mbp with an average of 4.28 Mbp. The GWAS scan based on the mean performance of the genotypes across the environments identified 44 significant MTAs across the chromosomes. Twenty-six of these MTAs are novel, whereas the remaining 18 were previously reported and confirmed in this study. We also identified candidate genes for the novel loci potentially regulating the traits. Hence, this study highlights the significance of the Ethiopian durum wheat gene pool for improving durum wheat globally. Furthermore, a breeding strategy focusing on accumulating favorable alleles at these loci could improve durum wheat production in the East African highlands and elsewhere.
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Affiliation(s)
- Behailu Mulugeta
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
- Sinana Agricultural Research Center, Oromia Agricultural Research Institute, Bale-Robe, Ethiopia
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Director General, Bio and Emerging Technology Institute (BETin), Addis Ababa, Ethiopia
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Eva Johansson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Faris Hailu
- Department of Biology and Biotechnology, Wollo University, Dessie, Ethiopia
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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17
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Sehgal D, Dhakate P, Ambreen H, Shaik KHB, Rathan ND, Anusha NM, Deshmukh R, Vikram P. Wheat Omics: Advancements and Opportunities. PLANTS (BASEL, SWITZERLAND) 2023; 12:426. [PMID: 36771512 PMCID: PMC9919419 DOI: 10.3390/plants12030426] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/07/2022] [Accepted: 12/14/2022] [Indexed: 06/18/2023]
Abstract
Plant omics, which includes genomics, transcriptomics, metabolomics and proteomics, has played a remarkable role in the discovery of new genes and biomolecules that can be deployed for crop improvement. In wheat, great insights have been gleaned from the utilization of diverse omics approaches for both qualitative and quantitative traits. Especially, a combination of omics approaches has led to significant advances in gene discovery and pathway investigations and in deciphering the essential components of stress responses and yields. Recently, a Wheat Omics database has been developed for wheat which could be used by scientists for further accelerating functional genomics studies. In this review, we have discussed various omics technologies and platforms that have been used in wheat to enhance the understanding of the stress biology of the crop and the molecular mechanisms underlying stress tolerance.
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Affiliation(s)
- Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco 56237, Mexico
- Syngenta, Jealott’s Hill International Research Centre, Bracknell, Berkshire RG42 6EY, UK
| | - Priyanka Dhakate
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110076, India
| | - Heena Ambreen
- School of Life Sciences, University of Sussex, Brighton BN1 9RH, UK
| | - Khasim Hussain Baji Shaik
- Faculty of Agriculture Sciences, Georg-August-Universität, Wilhelmsplatz 1, 37073 Göttingen, Germany
| | - Nagenahalli Dharmegowda Rathan
- Indian Agricultural Research Institute (ICAR-IARI), New Delhi 110012, India
- Corteva Agriscience, Hyderabad 502336, Telangana, India
| | | | - Rupesh Deshmukh
- Department of Biotechnology, Central University of Haryana, Mahendragarh 123031, Haryana, India
| | - Prashant Vikram
- Bioseed Research India Ltd., Hyderabad 5023324, Telangana, India
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18
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Singh J, Chhabra B, Raza A, Yang SH, Sandhu KS. Important wheat diseases in the US and their management in the 21st century. FRONTIERS IN PLANT SCIENCE 2023; 13:1010191. [PMID: 36714765 PMCID: PMC9877539 DOI: 10.3389/fpls.2022.1010191] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 11/28/2022] [Indexed: 05/27/2023]
Abstract
Wheat is a crop of historical significance, as it marks the turning point of human civilization 10,000 years ago with its domestication. Due to the rapid increase in population, wheat production needs to be increased by 50% by 2050 and this growth will be mainly based on yield increases, as there is strong competition for scarce productive arable land from other sectors. This increasing demand can be further achieved using sustainable approaches including integrated disease pest management, adaption to warmer climates, less use of water resources and increased frequency of abiotic stress tolerances. Out of 200 diseases of wheat, 50 cause economic losses and are widely distributed. Each year, about 20% of wheat is lost due to diseases. Some major wheat diseases are rusts, smut, tan spot, spot blotch, fusarium head blight, common root rot, septoria blotch, powdery mildew, blast, and several viral, nematode, and bacterial diseases. These diseases badly impact the yield and cause mortality of the plants. This review focuses on important diseases of the wheat present in the United States, with comprehensive information of causal organism, economic damage, symptoms and host range, favorable conditions, and disease management strategies. Furthermore, major genetic and breeding efforts to control and manage these diseases are discussed. A detailed description of all the QTLs, genes reported and cloned for these diseases are provided in this review. This study will be of utmost importance to wheat breeding programs throughout the world to breed for resistance under changing environmental conditions.
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Affiliation(s)
- Jagdeep Singh
- Department of Crop, Soil & Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Bhavit Chhabra
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, United States
| | - Ali Raza
- College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Seung Hwan Yang
- Department of Integrative Biotechnology, Chonnam National University, Yeosu, Republic of Korea
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19
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Yang N, Ovenden B, Baxter B, McDonald MC, Solomon PS, Milgate A. Multi-stage resistance to Zymoseptoria tritici revealed by GWAS in an Australian bread wheat diversity panel. FRONTIERS IN PLANT SCIENCE 2022; 13:990915. [PMID: 36352863 PMCID: PMC9637935 DOI: 10.3389/fpls.2022.990915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Septoria tritici blotch (STB) has been ranked the third most important wheat disease in the world, threatening a large area of wheat production. Although major genes play an important role in the protection against Zymoseptoria tritici infection, the lifespan of their resistance unfortunately is very short in modern wheat production systems. Combinations of quantitative resistance with minor effects, therefore, are believed to have prolonged and more durable resistance to Z. tritici. In this study, new quantitative trait loci (QTLs) were identified that are responsible for seedling-stage resistance and adult-plant stage resistance (APR). More importantly was the characterisation of a previously unidentified QTL that can provide resistance during different stages of plant growth or multi-stage resistance (MSR). At the seedling stage, we discovered a new isolate-specific QTL, QSt.wai.1A.1. At the adult-plant stage, the new QTL QStb.wai.6A.2 provided stable and consistent APR in multiple sites and years, while the QTL QStb.wai.7A.2 was highlighted to have MSR. The stacking of multiple favourable MSR alleles was found to improve resistance to Z. tritici by up to 40%.
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Affiliation(s)
- Nannan Yang
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Ben Ovenden
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Brad Baxter
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Megan C. McDonald
- University of Birmingham, School of Biosciences, Birmingham, West Midlands, United Kingdom
| | - Peter S. Solomon
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Andrew Milgate
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
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20
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Enyew M, Feyissa T, Carlsson AS, Tesfaye K, Hammenhag C, Seyoum A, Geleta M. Genome-wide analyses using multi-locus models revealed marker-trait associations for major agronomic traits in Sorghum bicolor. FRONTIERS IN PLANT SCIENCE 2022; 13:999692. [PMID: 36275578 PMCID: PMC9585286 DOI: 10.3389/fpls.2022.999692] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/14/2022] [Indexed: 06/01/2023]
Abstract
Globally, sorghum is the fifth most important cereal crop, and it is a major crop in Ethiopia, where it has a high genetic diversity. The country's sorghum gene pool contributes significantly to sorghum improvement worldwide. This study aimed to identify genomic regions and candidate genes associated with major agronomic traits in sorghum by using its genetic resources in Ethiopia for a genome-wide association study (GWAS). Phenotypic data of days to flowering (DTF), plant height (PH), panicle length (PALH), panicle width (PAWD), panicle weight (PAWT), and grain yield (GY) were collected from a GWAS panel comprising 324 sorghum accessions grown in three environments. SeqSNP, a targeted genotyping method, was used to genotype the panel using 5,000 gene-based single nucleotide polymorphism (SNP) markers. For marker-trait association (MTA) analyses, fixed and random model circulating probability unification (FarmCPU), and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) models were used. In all traits, high phenotypic variation was observed, with broad-sense heritability ranging from 0.32 (for GY) to 0.90 (for PALH). A population structure, principal component analysis, and kinship analysis revealed that the accessions could be divided into two groups. In total, 54 MTAs were identified, 11 of which were detected by both BLINK and farmCPU. MTAs identified for each trait ranged from five (PAWT and GY) to fourteen (PH) representing both novel and previously identified quantitative trait loci (QTLs). Three SNPs were associated with more than one trait, including a SNP within the Sobic.004G189200 gene that was associated with PH and PAWT. Major effect SNP loci, Sbi2393610 (PVE = 23.3%), Sbi10438246 (PVE = 35.2%), Sbi17789352 (PVE = 11.9%) and Sbi30169733 (PVE = 18.9%) on chromosomes 1, 3, 5 and 9 that showed strong association signals for PAWD, DTF, GY and PALH, respectively, were major findings of this study. The SNP markers and candidate genes identified in this study provide insights into the genetic control of grain yield and related agronomic traits, and once validated, the markers could be used in genomics-led breeding.
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Affiliation(s)
- Muluken Enyew
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Tileye Feyissa
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Anders S. Carlsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Biotechnology Institute, Addis Ababa, Ethiopia
| | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Amare Seyoum
- National Sorghum Research Program, Crop Research Department, Melkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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21
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Roitsch T, Himanen K, Chawade A, Jaakola L, Nehe A, Alexandersson E. Functional phenomics for improved climate resilience in Nordic agriculture. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5111-5127. [PMID: 35727101 PMCID: PMC9440434 DOI: 10.1093/jxb/erac246] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 06/06/2022] [Indexed: 05/26/2023]
Abstract
The five Nordic countries span the most northern region for field cultivation in the world. This presents challenges per se, with short growing seasons, long days, and a need for frost tolerance. Climate change has additionally increased risks for micro-droughts and water logging, as well as pathogens and pests expanding northwards. Thus, Nordic agriculture demands crops that are adapted to the specific Nordic growth conditions and future climate scenarios. A focus on crop varieties and traits important to Nordic agriculture, including the unique resource of nutritious wild crops, can meet these needs. In fact, with a future longer growing season due to climate change, the region could contribute proportionally more to global agricultural production. This also applies to other northern regions, including the Arctic. To address current growth conditions, mitigate impacts of climate change, and meet market demands, the adaptive capacity of crops that both perform well in northern latitudes and are more climate resilient has to be increased, and better crop management systems need to be built. This requires functional phenomics approaches that integrate versatile high-throughput phenotyping, physiology, and bioinformatics. This review stresses key target traits, the opportunities of latitudinal studies, and infrastructure needs for phenotyping to support Nordic agriculture.
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Affiliation(s)
- Thomas Roitsch
- Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
- Department of Adaptive Biotechnologies, Global Change Research Institute, Czech Academy of Sciences, Brno, Czechia
| | - Kristiina Himanen
- National Plant Phenotyping Infrastructure, HiLIFE, University of Helsinki, Finland
- Organismal and Evolutionary Biology Research Program, Viikki Plant Science Centre, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Laura Jaakola
- Climate laboratory Holt, Department of Arctic and Marine Biology, UiT the Arctic University of Norway, Tromsø, Norway
- NIBIO, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Ajit Nehe
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
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22
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Mapping and Validation of qHD7b: Major Heading-Date QTL Functions Mainly under Long-Day Conditions. PLANTS 2022; 11:plants11172288. [PMID: 36079670 PMCID: PMC9459803 DOI: 10.3390/plants11172288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/16/2022] [Accepted: 08/30/2022] [Indexed: 11/23/2022]
Abstract
Heading date (HD) is one of the agronomic traits that influence maturity, regional adaptability, and grain yield. The present study was a follow-up of a previous quantitative trait loci (QTL) mapping study conducted on three populations, which uncovered a total of 62 QTLs associated with 10 agronomic traits. Two of the QTLs for HD on chromosome 7 (qHD7a and qHD7b) had a common flanking marker (RM3670) that may be due to tight linkage, and/or weakness of the statistical method. The objectives of the present study were to map QTLs associated with HD in a set of 76 chromosome segment substitution lines (CSSLs), fine map and validate one of the QTLs (qHD7b) using 2997 BC5F2:3 plants, and identify candidate genes using sequencing and expression analysis. Using the CSSLs genotyped with 120 markers and evaluated under two short-day and two long-day growing conditions, we uncovered a total of fourteen QTLs (qHD2a, qHD4a, qHD4b, qHD5a, qHD6a, qHD6b, qHD7b, qHD7c, qHD8a, qHD10a, qHD10b, qHD11a, qHD12a, and qHD12b). However, only qHD6a and qHD7b were consistently detected in all four environments. The phenotypic variance explained by qHD6a and qHD7b varied from 10.1% to 36.1% (mean 23.1%) and from 8.1% to 32.8% (mean 20.5%), respectively. One of the CSSL lines (CSSL52), which harbored a segment from the early heading XieqingzaoB (XQZB) parent at the qHD7b locus, was then used to develop a BC5F2:3 population for fine mapping and validation. Using a backcross population evaluated for four seasons under different day lengths and temperatures, the qHD7b interval was delimited to a 912.7-kb region, which is located between RM5436 and RM5499. Sequencing and expression analysis revealed a total of 29 candidate genes, of which Ghd7 (Os07g0261200) is a well-known gene that affects heading date, plant height, and grain yield in rice. The ghd7 mutants generated through CRISPR/Cas9 gene editing exhibited early heading. Taken together, the results from both the previous and present study revealed a consistent QTL for heading date on chromosome 7, which coincided not only with the physical position of a known gene, but also with two major effect QTLs that controlled the stigma exertion rate and the number of spikelets in rice. The results provide contributions to the broader adaptability of marker-assisted breeding to develop high-yield rice varieties.
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Semagn K, Crossa J, Cuevas J, Iqbal M, Ciechanowska I, Henriquez MA, Randhawa H, Beres BL, Aboukhaddour R, McCallum BD, Brûlé-Babel AL, N'Diaye A, Pozniak C, Spaner D. Comparison of single-trait and multi-trait genomic predictions on agronomic and disease resistance traits in spring wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2747-2767. [PMID: 35737008 DOI: 10.1007/s00122-022-04147-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
This study performed comprehensive analyses on the predictive abilities of single-trait and two multi-trait models in three populations. Our results demonstrated the superiority of multi-traits over single-trait models across seven agronomic and four to seven disease resistance traits of different genetic architecture. The predictive ability of multi-trait and single-trait prediction models has not been investigated on diverse traits evaluated under organic and conventional management systems. Here, we compared the predictive abilities of 25% of a testing set that has not been evaluated for a single trait (ST), not evaluated for multi-traits (MT1), and evaluated for some traits but not others (MT2) in three spring wheat populations genotyped either with the wheat 90K single nucleotide polymorphisms array or DArTseq. Analyses were performed on seven agronomic traits evaluated under conventional and organic management systems, four to seven disease resistance traits, and all agronomic and disease resistance traits simultaneously. The average prediction accuracies of the ST, MT1, and MT2 models varied from 0.03 to 0.78 (mean 0.41), from 0.05 to 0.82 (mean 0.47), and from 0.05 to 0.92 (mean 0.67), respectively. The predictive ability of the MT2 model was significantly greater than the ST model in all traits and populations except common bunt with the MT1 model being intermediate between them. The MT2 model increased prediction accuracies over the ST and MT1 models in all traits by 9.0-82.4% (mean 37.3%) and 2.9-82.5% (mean 25.7%), respectively, except common bunt that showed up to 7.7% smaller accuracies in two populations. A joint analysis of all agronomic and disease resistance traits further improved accuracies within the MT1 and MT2 models on average by 21.4% and 17.4%, respectively, as compared to either the agronomic or disease resistance traits, demonstrating the high potential of the multi-traits models in improving prediction accuracies.
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Affiliation(s)
- Kassa Semagn
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | - José Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico
| | | | - Muhammad Iqbal
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Izabela Ciechanowska
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Maria Antonia Henriquez
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Harpinder Randhawa
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - Brian L Beres
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - Reem Aboukhaddour
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - Brent D McCallum
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Anita L Brûlé-Babel
- Department of Plant Science, University of Manitoba, 66 Dafoe Road, Winnipeg, MB, R3T 2N2, Canada
| | - Amidou N'Diaye
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Dean Spaner
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
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Muvunyi BP, Zou W, Zhan J, He S, Ye G. Multi-Trait Genomic Prediction Models Enhance the Predictive Ability of Grain Trace Elements in Rice. Front Genet 2022; 13:883853. [PMID: 35812754 PMCID: PMC9257107 DOI: 10.3389/fgene.2022.883853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/05/2022] [Indexed: 11/13/2022] Open
Abstract
Multi-trait (MT) genomic prediction models enable breeders to save phenotyping resources and increase the prediction accuracy of unobserved target traits by exploiting available information from non-target or auxiliary traits. Our study evaluated different MT models using 250 rice accessions from Asian countries genotyped and phenotyped for grain content of zinc (Zn), iron (Fe), copper (Cu), manganese (Mn), and cadmium (Cd). The predictive performance of MT models compared to a traditional single trait (ST) model was assessed by 1) applying different cross-validation strategies (CV1, CV2, and CV3) inferring varied phenotyping patterns and budgets; 2) accounting for local epistatic effects along with the main additive effect in MT models; and 3) using a selective marker panel composed of trait-associated SNPs in MT models. MT models were not statistically significantly (p < 0.05) superior to ST model under CV1, where no phenotypic information was available for the accessions in the test set. After including phenotypes from auxiliary traits in both training and test sets (MT-CV2) or simply in the test set (MT-CV3), MT models significantly (p < 0.05) outperformed ST model for all the traits. The highest increases in the predictive ability of MT models relative to ST models were 11.1% (Mn), 11.5 (Cd), 33.3% (Fe), 95.2% (Cu) and 126% (Zn). Accounting for the local epistatic effects using a haplotype-based model further improved the predictive ability of MT models by 4.6% (Cu), 3.8% (Zn), and 3.5% (Cd) relative to MT models with only additive effects. The predictive ability of the haplotype-based model was not improved after optimizing the marker panel by only considering the markers associated with the traits. This study first assessed the local epistatic effects and marker optimization strategies in the MT genomic prediction framework and then illustrated the power of the MT model in predicting trace element traits in rice for the effective use of genetic resources to improve the nutritional quality of rice grain.
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Affiliation(s)
- Blaise Pascal Muvunyi
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wenli Zou
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Junhui Zhan
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Sang He
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- *Correspondence: Sang He, ; Guoyou Ye,
| | - Guoyou Ye
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Philippines
- *Correspondence: Sang He, ; Guoyou Ye,
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25
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Juliana P, He X, Poland J, Roy KK, Malaker PK, Mishra VK, Chand R, Shrestha S, Kumar U, Roy C, Gahtyari NC, Joshi AK, Singh RP, Singh PK. Genomic selection for spot blotch in bread wheat breeding panels, full-sibs and half-sibs and index-based selection for spot blotch, heading and plant height. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1965-1983. [PMID: 35416483 PMCID: PMC9205839 DOI: 10.1007/s00122-022-04087-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
KEY MESSAGE Genomic selection is a promising tool to select for spot blotch resistance and index-based selection can simultaneously select for spot blotch resistance, heading and plant height. A major biotic stress challenging bread wheat production in regions characterized by humid and warm weather is spot blotch caused by the fungus Bipolaris sorokiniana. Since genomic selection (GS) is a promising selection tool, we evaluated its potential for spot blotch in seven breeding panels comprising 6736 advanced lines from the International Maize and Wheat Improvement Center. Our results indicated moderately high mean genomic prediction accuracies of 0.53 and 0.40 within and across breeding panels, respectively which were on average 177.6% and 60.4% higher than the mean accuracies from fixed effects models using selected spot blotch loci. Genomic prediction was also evaluated in full-sibs and half-sibs panels and sibs were predicted with the highest mean accuracy (0.63) from a composite training population with random full-sibs and half-sibs. The mean accuracies when full-sibs were predicted from other full-sibs within families and when full-sibs panels were predicted from other half-sibs panels were 0.47 and 0.44, respectively. Comparison of GS with phenotypic selection (PS) of the top 10% of resistant lines suggested that GS could be an ideal tool to discard susceptible lines, as greater than 90% of the susceptible lines discarded by PS were also discarded by GS. We have also reported the evaluation of selection indices to simultaneously select non-late and non-tall genotypes with low spot blotch phenotypic values and genomic-estimated breeding values. Overall, this study demonstrates the potential of integrating GS and index-based selection for improving spot blotch resistance in bread wheat.
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Affiliation(s)
- Philomin Juliana
- Borlaug Institute for South Asia (BISA), Ludhiana, Punjab, India
| | - Xinyao He
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico
| | - Jesse Poland
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Krishna K Roy
- Bangladesh Wheat and Maize Research Institute, Nashipur, Dinajpur, 5200, Bangladesh
| | - Paritosh K Malaker
- Bangladesh Wheat and Maize Research Institute, Nashipur, Dinajpur, 5200, Bangladesh
| | - Vinod K Mishra
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Ramesh Chand
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Sandesh Shrestha
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Uttam Kumar
- Borlaug Institute for South Asia (BISA), Ludhiana, Punjab, India
| | - Chandan Roy
- Department of Plant Breeding and Genetics, Bihar Agricultural University, Sabour, Bihar, 813210, India
| | - Navin C Gahtyari
- ICAR-Vivekanand Parvatiya Krishi Anushandhan Sansthan, Almora, Uttarakhand, 263601, India
| | - Arun K Joshi
- Borlaug Institute for South Asia (BISA), Ludhiana, Punjab, India
- CIMMYT-India, NASC Complex, DPS Marg, New Delhi, India
| | - Ravi P Singh
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico.
| | - Pawan K Singh
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico.
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Genomic Predictions for Common Bunt, FHB, Stripe Rust, Leaf Rust, and Leaf Spotting Resistance in Spring Wheat. Genes (Basel) 2022; 13:genes13040565. [PMID: 35456370 PMCID: PMC9032109 DOI: 10.3390/genes13040565] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/15/2022] [Accepted: 03/21/2022] [Indexed: 02/04/2023] Open
Abstract
Some studies have investigated the potential of genomic selection (GS) on stripe rust, leaf rust, Fusarium head blight (FHB), and leaf spot in wheat, but none of them have assessed the effect of the reaction norm model that incorporated GE interactions. In addition, the prediction accuracy on common bunt has not previously been studied. Here, we investigated within-population prediction accuracies using the baseline M1 model and two reaction norm models (M2 and M3) with three random cross-validation (CV1, CV2, and CV0) schemes. Three Canadian spring wheat populations were evaluated in up to eight field environments and genotyped with 3158, 5732, and 23,795 polymorphic markers. The M3 model that incorporated GE interactions reduced residual variance by an average of 10.2% as compared with the main effect M2 model and increased prediction accuracies on average by 2–6%. In some traits, the M3 model increased prediction accuracies up to 54% as compared with the M2 model. The average prediction accuracies of the M3 model with CV1, CV2, and CV0 schemes varied from 0.02 to 0.48, from 0.25 to 0.84, and from 0.14 to 0.87, respectively. In both CV2 and CV0 schemes, stripe rust in all three populations, common bunt and leaf rust in two populations, as well as FHB severity, FHB index, and leaf spot in one population had high to very high (0.54–0.87) prediction accuracies. This is the first comprehensive genomic selection study on five major diseases in spring wheat.
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Alemu A, Brantestam AK, Chawade A. Unraveling the Genetic Basis of Key Agronomic Traits of Wrinkled Vining Pea ( Pisum sativum L.) for Sustainable Production. FRONTIERS IN PLANT SCIENCE 2022; 13:844450. [PMID: 35360298 PMCID: PMC8964273 DOI: 10.3389/fpls.2022.844450] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Estimating the allelic variation and exploring the genetic basis of quantitatively inherited complex traits are the two foremost breeding scenarios for sustainable crop production. The current study utilized 188 wrinkled vining pea genotypes comprising historical varieties and breeding lines to evaluate the existing genetic diversity and to detect molecular markers associated with traits relevant to vining pea production, such as wrinkled vining pea yield (YTM100), plant height (PH), earliness (ERL), adult plant resistance to downy mildew (DM), pod length (PDL), numbers of pods per plant (PDP), number of peas per pod (PPD), and percent of small wrinkled vining peas (PSP). Marker-trait associations (MTAs) were conducted using 6902 quality single nucleotide polymorphism (SNP) markers generated from the diversity arrays technology sequencing (DArTseq) and Genotyping-by-sequencing (GBS) sequencing methods. The best linear unbiased prediction (BLUP) values were estimated from the two-decades-long (1999-2020) unbalanced phenotypic data sets recorded from two private breeding programs, the Findus and the Birds eye, now owned by Nomad Foods. Analysis of variance revealed a highly significant variation between genotypes and genotype-by-environment interactions for the ten traits. The genetic diversity and population structure analyses estimated an intermediate level of genetic variation with two optimal sub-groups within the current panel. A total of 48 significant (P < 0.0001) MTAs were identified for eight different traits, including five for wrinkled vining pea yield on chr2LG1, chr4LG4, chr7LG7, and scaffolds (two), and six for adult plant resistance to downy mildew on chr1LG6, chr3LG5 (two), chr6LG2, and chr7LG7 (two). We reported several novel MTAs for different crucial traits with agronomic importance in wrinkled vining pea production for the first time, and these candidate markers could be easily validated and integrated into the active breeding programs for marker-assisted selection.
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Affiliation(s)
- Admas Alemu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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28
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Saini DK, Chahal A, Pal N, Srivastava P, Gupta PK. Meta-analysis reveals consensus genomic regions associated with multiple disease resistance in wheat ( Triticum aestivum L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:11. [PMID: 37309411 PMCID: PMC10248701 DOI: 10.1007/s11032-022-01282-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
In wheat, meta-QTLs (MQTLs) and candidate genes (CGs) were identified for multiple disease resistance (MDR). For this purpose, information was collected from 58 studies for mapping QTLs for resistance to one or more of the five diseases. As many as 493 QTLs were available from these studies, which were distributed in five diseases as follows: septoria tritici blotch (STB) 126 QTLs; septoria nodorum blotch (SNB), 103 QTLs; fusarium head blight (FHB), 184 QTLs; karnal bunt (KB), 66 QTLs; and loose smut (LS), 14 QTLs. Of these 493 QTLs, only 291 QTLs could be projected onto a consensus genetic map, giving 63 MQTLs. The CI of the MQTLs ranged from 0.04 to 15.31 cM with an average of 3.09 cM per MQTL. This is a ~ 4.39 fold reduction from the CI of QTLs, which ranged from 0 to 197.6 cM, with a mean of 13.57 cM. Of 63 MQTLs, 60 were anchored to the reference physical map of wheat (the physical interval of these MQTLs ranged from 0.30 to 726.01 Mb with an average of 74.09 Mb). Thirty-eight (38) of these MQTLs were verified using marker-trait associations (MTAs) derived from genome-wide association studies. As many as 874 CGs were also identified which were further investigated for differential expression using data from five transcriptome studies, resulting in 194 differentially expressed candidate genes (DECGs). Among the DECGs, 85 genes had functions previously reported to be associated with disease resistance. These results should prove useful for fine mapping and cloning of MDR genes and marker-assisted breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01282-z.
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Affiliation(s)
- Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab-141004 India
| | - Amneek Chahal
- College of Agriculture, Punjab Agricultural University, Ludhiana, Punjab-141004 India
| | - Neeraj Pal
- Department of Molecular Biology and Genetic Engineering, G. B. Pant, University of Agriculture and Technology, Pantnagar, Uttrakhand-263145 India
| | - Puja Srivastava
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab-141004 India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
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Gangurde SS, Xavier A, Naik YD, Jha UC, Rangari SK, Kumar R, Reddy MSS, Channale S, Elango D, Mir RR, Zwart R, Laxuman C, Sudini HK, Pandey MK, Punnuri S, Mendu V, Reddy UK, Guo B, Gangarao NVPR, Sharma VK, Wang X, Zhao C, Thudi M. Two decades of association mapping: Insights on disease resistance in major crops. FRONTIERS IN PLANT SCIENCE 2022; 13:1064059. [PMID: 37082513 PMCID: PMC10112529 DOI: 10.3389/fpls.2022.1064059] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/10/2022] [Indexed: 05/03/2023]
Abstract
Climate change across the globe has an impact on the occurrence, prevalence, and severity of plant diseases. About 30% of yield losses in major crops are due to plant diseases; emerging diseases are likely to worsen the sustainable production in the coming years. Plant diseases have led to increased hunger and mass migration of human populations in the past, thus a serious threat to global food security. Equipping the modern varieties/hybrids with enhanced genetic resistance is the most economic, sustainable and environmentally friendly solution. Plant geneticists have done tremendous work in identifying stable resistance in primary genepools and many times other than primary genepools to breed resistant varieties in different major crops. Over the last two decades, the availability of crop and pathogen genomes due to advances in next generation sequencing technologies improved our understanding of trait genetics using different approaches. Genome-wide association studies have been effectively used to identify candidate genes and map loci associated with different diseases in crop plants. In this review, we highlight successful examples for the discovery of resistance genes to many important diseases. In addition, major developments in association studies, statistical models and bioinformatic tools that improve the power, resolution and the efficiency of identifying marker-trait associations. Overall this review provides comprehensive insights into the two decades of advances in GWAS studies and discusses the challenges and opportunities this research area provides for breeding resistant varieties.
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Affiliation(s)
- Sunil S. Gangurde
- Crop Genetics and Breeding Research, United States Department of Agriculture (USDA) - Agriculture Research Service (ARS), Tifton, GA, United States
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Alencar Xavier
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | | | - Uday Chand Jha
- Indian Council of Agricultural Research (ICAR), Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh, India
| | | | - Raj Kumar
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
| | - M. S. Sai Reddy
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
| | - Sonal Channale
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
| | - Dinakaran Elango
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Reyazul Rouf Mir
- Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST), Sopore, India
| | - Rebecca Zwart
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
| | - C. Laxuman
- Zonal Agricultural Research Station (ZARS), Kalaburagi, University of Agricultural Sciences, Raichur, Karnataka, India
| | - Hari Kishan Sudini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Manish K. Pandey
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Somashekhar Punnuri
- College of Agriculture, Family Sciences and Technology, Dr. Fort Valley State University, Fort Valley, GA, United States
| | - Venugopal Mendu
- Department of Plant Science and Plant Pathology, Montana State University, Bozeman, MT, United States
| | - Umesh K. Reddy
- Department of Biology, West Virginia State University, West Virginia, WV, United States
| | - Baozhu Guo
- Crop Genetics and Breeding Research, United States Department of Agriculture (USDA) - Agriculture Research Service (ARS), Tifton, GA, United States
| | | | - Vinay K. Sharma
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
| | - Xingjun Wang
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences (SAAS), Jinan, China
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences (SAAS), Jinan, China
- *Correspondence: Mahendar Thudi, ; Chuanzhi Zhao,
| | - Mahendar Thudi
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences (SAAS), Jinan, China
- *Correspondence: Mahendar Thudi, ; Chuanzhi Zhao,
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