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Visioni A, Basile B, Amri A, Sanchez-Garcia M, Corrado G. Advancing the Conservation and Utilization of Barley Genetic Resources: Insights into Germplasm Management and Breeding for Sustainable Agriculture. Plants (Basel) 2023; 12:3186. [PMID: 37765350 PMCID: PMC10535687 DOI: 10.3390/plants12183186] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023]
Abstract
Barley is a very important crop particularly in marginal dry areas, where it often serves as the most viable option for farmers. Additionally, barley carries great significance in the Western world, serving not only as a fundamental crop for animal feed and malting but also as a nutritious food source. The broad adaptability of barley and its ability to withstand various biotic and abiotic stresses often make this species the sole cereal that can be cultivated in arid regions. The collection and utilization of barley genetic resources are crucial for identifying valuable traits to enhance productivity and mitigate the adverse effects of climate change. This review aims to provide an overview of the management and exploitation of barley genetic resources. Furthermore, the review explores the relationship between gene banks and participatory breeding, offering insights into the diversity and utilization of barley genetic resources through some examples such as the initiatives undertaken by ICARDA. Finally, this contribution highlights the importance of these resources for boosting barley productivity, addressing climate change impacts, and meeting the growing food demands in a rapidly changing agriculture. The understanding and utilizing the rich genetic diversity of barley can contribute to sustainable agriculture and ensure the success of this vital crop for future generations globally.
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Affiliation(s)
- Andrea Visioni
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat 10100, Morocco; (A.A.); (M.S.-G.)
| | - Boris Basile
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy;
| | - Ahmed Amri
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat 10100, Morocco; (A.A.); (M.S.-G.)
| | - Miguel Sanchez-Garcia
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat 10100, Morocco; (A.A.); (M.S.-G.)
| | - Giandomenico Corrado
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy;
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Romano G, Del Coco L, Milano F, Durante M, Palombieri S, Sestili F, Visioni A, Jilal A, Fanizzi FP, Laddomada B. Phytochemical Profiling and Untargeted Metabolite Fingerprinting of the MEDWHEALTH Wheat, Barley and Lentil Wholemeal Flours. Foods 2022; 11:foods11244070. [PMID: 36553812 PMCID: PMC9777840 DOI: 10.3390/foods11244070] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/10/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
An important research target is improving the health benefits of traditional Mediterranean, durum wheat-based foods using innovative raw materials. In this study, we characterised wholemeal flours obtained from a traditional durum wheat cv. Svevo, two innovative durum wheat varieties (Svevo-High Amylose and Faridur), the naked barley cv. Chifaa and the elite lentil line 6002/ILWL118/1-1, evaluating them for targeted phytochemicals, untargeted metabolomics fingerprints and antioxidant capacity. To this aim, individual phenolic acids, flavonoids, tocochromanols and carotenoids were identified and quantified through HPLC-DAD, and the antioxidant capacities of both the extracts and whole meals were detected by ABTS assays. An untargeted metabolomics fingerprinting of the samples was conducted through NMR spectroscopy. Results showed that the innovative materials improved phytochemical profiles and antioxidant capacity compared to Svevo. In particular, Svevo-HA and Faridur had higher contents of ferulic and sinapic acids, β-tocotrienol and lutein. Moreover, Chifaa is a rich source of phenolic acids, β-tocopherols, lutein and zeaxanthin whereas lentil of flavonoids (i.e., catechin and procyanidin B2). The NMR profiles of Svevo-HA and Faridur showed a significant reduction of sugar content, malate and tryptophan compared to that of Svevo. Finally, substantial differences characterised the lentil profiles, especially for citrate, trigonelline and phenolic resonances of secondary metabolites, such as catechin-like compounds. Overall, these results support the potential of the above innovative materials to renew the health value of traditional Mediterranean durum wheat-based products.
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Affiliation(s)
- Giuseppe Romano
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), via Monteroni, 73100 Lecce, Italy
| | - Laura Del Coco
- Department of Biological and Environmental Sciences and Technologies (Di.S.Te.B.A.), University of Salento, via Monteroni, 73100 Lecce, Italy
| | - Francesco Milano
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), via Monteroni, 73100 Lecce, Italy
| | - Miriana Durante
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), via Monteroni, 73100 Lecce, Italy
| | - Samuela Palombieri
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy
| | - Francesco Sestili
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy
| | - Andrea Visioni
- International Center for Agricultural Research in the Dry Areas (ICARDA), Biodiversity and Crop Improvement Program, Rabat P.O. Box 6299, Morocco
| | - Abderrazek Jilal
- National Institute for Agricultural Research Morocco (INRAM), Rabat P.O. Box 415, Morocco
| | - Francesco Paolo Fanizzi
- Department of Biological and Environmental Sciences and Technologies (Di.S.Te.B.A.), University of Salento, via Monteroni, 73100 Lecce, Italy
- Correspondence: (F.P.F.); (B.L.); Tel.: +39-08-3229-9265 (F.P.F.); +39-08-3242-2613 (B.L.)
| | - Barbara Laddomada
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), via Monteroni, 73100 Lecce, Italy
- Correspondence: (F.P.F.); (B.L.); Tel.: +39-08-3229-9265 (F.P.F.); +39-08-3242-2613 (B.L.)
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Bouhlal O, Visioni A, Verma RPS, Kandil M, Gyawali S, Capettini F, Sanchez-Garcia M. CGIAR Barley Breeding Toolbox: A diversity panel to facilitate breeding and genomic research in the developing world. Front Plant Sci 2022; 13:1034322. [PMID: 36452106 PMCID: PMC9702823 DOI: 10.3389/fpls.2022.1034322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/19/2022] [Indexed: 06/17/2023]
Abstract
Breeding programs in developing countries still cannot afford the new genotyping technologies, hindering their research. We aimed to assemble an Association Mapping panel to serve as CGIAR Barley Breeding Toolbox (CBBT), especially for the Developing World. The germplasm had to be representative of the one grown in the Developing World; with high genetic variability and be of public domain. For it, we genotyped with the Infinium iSelect 50K chip, a Global Barley Panel (GBP) of 530 genotypes representing a wide range of row-types, end-uses, growth habits, geographical origins and environments. 40,342 markers were polymorphic with an average polymorphism information content of 0.35 and 66% of them exceeding 0.25. The analysis of the population structure identified 8 subpopulations mostly linked to geographical origin, four of them with significant ICARDA origin. The 16 allele combinations at 4 major flowering genes (HvVRN-H3, HvPPD-H1, HvVRN-H1 and HvCEN) explained 11.07% genetic variation and were linked to the geographic origins of the lines. ICARDA material showed the widest diversity as revealed by the highest number of polymorphic loci (99.76% of all polymorphic SNPs in GBP), number of private alleles and the fact that ICARDA lines were present in all 8 subpopulations and carried all 16 allelic combinations. Due to their genetic diversity and their representativity of the germplasm adapted to the Developing World, ICARDA-derived lines and cultivated landraces were pre-selected to form the CBBT. Using the Mean of Transformed Kinships method, we assembled a panel capturing most of the allelic diversity in the GBP. The CBBT (N=250) preserves good balance between row-types and good representation of both phenology allelic combinations and subpopulations of the GBP. The CBBT and its genotypic data is available to researchers worldwide as a collaborative tool to underpin the genetic mechanisms of traits of interest for barley cultivation.
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Affiliation(s)
- Outmane Bouhlal
- Biodiversity and Crop Improvement Program (BCIP), International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
- Team of Anthropogenetics and Biotechnologies, Faculty of Sciences, Chouaib Doukkali University, El-Jadida, Morocco
| | - Andrea Visioni
- Biodiversity and Crop Improvement Program (BCIP), International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | | | - Mostafa Kandil
- Team of Anthropogenetics and Biotechnologies, Faculty of Sciences, Chouaib Doukkali University, El-Jadida, Morocco
| | | | | | - Miguel Sanchez-Garcia
- Biodiversity and Crop Improvement Program (BCIP), International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
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Puglisi D, Visioni A, Ozkan H, Kara İ, Lo Piero AR, Rachdad FE, Tondelli A, Valè G, Cattivelli L, Fricano A. High accuracy of genome-enabled prediction of belowground and physiological traits in barley seedlings. G3 Genes|Genomes|Genetics 2022; 12:6517783. [PMID: 35099521 PMCID: PMC8895982 DOI: 10.1093/g3journal/jkac022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/21/2022] [Indexed: 11/24/2022]
Abstract
In plants, the study of belowground traits is gaining momentum due to their importance on yield formation and the uptake of water and nutrients. In several cereal crops, seminal root number and seminal root angle are proxy traits of the root system architecture at the mature stages, which in turn contributes to modulating the uptake of water and nutrients. Along with seminal root number and seminal root angle, experimental evidence indicates that the transpiration rate response to evaporative demand or vapor pressure deficit is a key physiological trait that might be targeted to cope with drought tolerance as the reduction of the water flux to leaves for limiting transpiration rate at high levels of vapor pressure deficit allows to better manage soil moisture. In the present study, we examined the phenotypic diversity of seminal root number, seminal root angle, and transpiration rate at the seedling stage in a panel of 8-way Multiparent Advanced Generation Inter-Crosses lines of winter barley and correlated these traits with grain yield measured in different site-by-season combinations. Second, phenotypic and genotypic data of the Multiparent Advanced Generation Inter-Crosses population were combined to fit and cross-validate different genomic prediction models for these belowground and physiological traits. Genomic prediction models for seminal root number were fitted using threshold and log-normal models, considering these data as ordinal discrete variable and as count data, respectively, while for seminal root angle and transpiration rate, genomic prediction was implemented using models based on extended genomic best linear unbiased predictors. The results presented in this study show that genome-enabled prediction models of seminal root number, seminal root angle, and transpiration rate data have high predictive ability and that the best models investigated in the present study include first-order additive × additive epistatic interaction effects. Our analyses indicate that beyond grain yield, genomic prediction models might be used to predict belowground and physiological traits and pave the way to practical applications for barley improvement.
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Affiliation(s)
- Damiano Puglisi
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), Università di Catania , 95123 Catania, Italy
| | - Andrea Visioni
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas , 6299 Rabat, Morocco
| | - Hakan Ozkan
- Faculty of Agriculture, Department of Field Crops, University of Cukurova , 01330 Adana, Turkey
| | - İbrahim Kara
- Bahri Dagdas International Agricultural Research Institute , Km Karatay/Konya 42020, Turkey
| | - Angela Roberta Lo Piero
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), Università di Catania , 95123 Catania, Italy
| | - Fatima Ezzahra Rachdad
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas , 6299 Rabat, Morocco
- Faculty of Sciences Ben M’sik, Department of Biology, Environment and Ecology Laboratory, Hassan II University of Casablanca , 7955 Casablanca, Morocco
| | - Alessandro Tondelli
- Council for Agricultural Research and Economics—Research Centre for Genomics and Bioinformatics , 29017 Fiorenzuola d’Arda (PC), Italy
| | - Giampiero Valè
- DiSIT, Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale , 13100 Vercelli, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics—Research Centre for Genomics and Bioinformatics , 29017 Fiorenzuola d’Arda (PC), Italy
| | - Agostino Fricano
- Council for Agricultural Research and Economics—Research Centre for Genomics and Bioinformatics , 29017 Fiorenzuola d’Arda (PC), Italy
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Bouhlal O, Affricot JR, Puglisi D, El-Baouchi A, El Otmani F, Kandil M, Hafidi A, Keser M, Sanchez-Garcia M, Visioni A. Malting Quality of ICARDA Elite Winter Barley (Hordeum vulgare L.) Germplasm Grown in Moroccan Middle Atlas. Journal of the American Society of Brewing Chemists 2021. [DOI: 10.1080/03610470.2021.1978036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Outmane Bouhlal
- Biodiversity and Crop Improvement Program (BICP), International Centre for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
- Team of Anthropogenetics and Biotechnologies, Faculty of Sciences, Chouaib Doukkali University, El-Jadida, Morocco
| | - Jean Raymond Affricot
- Biodiversity and Crop Improvement Program (BICP), International Centre for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
- Food Sciences Laboratory, Department of Biology, Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakech, Morocco
| | - Damiano Puglisi
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Adil El-Baouchi
- African Integrated Plant and Soil Research Group (AiPlaS), AgroBioSciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Fatima El Otmani
- Microbiology, Health and Environment Research Team, Department of Biology, Faculty of Sciences, Chouaib Doukkali University, El Jadida, Morocco
| | - Mostafa Kandil
- Team of Anthropogenetics and Biotechnologies, Faculty of Sciences, Chouaib Doukkali University, El-Jadida, Morocco
| | - Abdellatif Hafidi
- Food Sciences Laboratory, Department of Biology, Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakech, Morocco
| | - Mesut Keser
- Biodiversity and Crop Improvement Program (BICP), International Centre for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Miguel Sanchez-Garcia
- Biodiversity and Crop Improvement Program (BICP), International Centre for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Andrea Visioni
- Biodiversity and Crop Improvement Program (BICP), International Centre for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
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Puglisi D, Delbono S, Visioni A, Ozkan H, Kara İ, Casas AM, Igartua E, Valè G, Piero ARL, Cattivelli L, Tondelli A, Fricano A. Genomic Prediction of Grain Yield in a Barley MAGIC Population Modeling Genotype per Environment Interaction. Front Plant Sci 2021; 12:664148. [PMID: 34108982 PMCID: PMC8183822 DOI: 10.3389/fpls.2021.664148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
Multi-parent Advanced Generation Inter-crosses (MAGIC) lines have mosaic genomes that are generated shuffling the genetic material of the founder parents following pre-defined crossing schemes. In cereal crops, these experimental populations have been extensively used to investigate the genetic bases of several traits and dissect the genetic bases of epistasis. In plants, genomic prediction models are usually fitted using either diverse panels of mostly unrelated accessions or individuals of biparental families and several empirical analyses have been conducted to evaluate the predictive ability of models fitted to these populations using different traits. In this paper, we constructed, genotyped and evaluated a barley MAGIC population of 352 individuals developed with a diverse set of eight founder parents showing contrasting phenotypes for grain yield. We combined phenotypic and genotypic information of this MAGIC population to fit several genomic prediction models which were cross-validated to conduct empirical analyses aimed at examining the predictive ability of these models varying the sizes of training populations. Moreover, several methods to optimize the composition of the training population were also applied to this MAGIC population and cross-validated to estimate the resulting predictive ability. Finally, extensive phenotypic data generated in field trials organized across an ample range of water regimes and climatic conditions in the Mediterranean were used to fit and cross-validate multi-environment genomic prediction models including G×E interaction, using both genomic best linear unbiased prediction and reproducing kernel Hilbert space along with a non-linear Gaussian Kernel. Overall, our empirical analyses showed that genomic prediction models trained with a limited number of MAGIC lines can be used to predict grain yield with values of predictive ability that vary from 0.25 to 0.60 and that beyond QTL mapping and analysis of epistatic effects, MAGIC population might be used to successfully fit genomic prediction models. We concluded that for grain yield, the single-environment genomic prediction models examined in this study are equivalent in terms of predictive ability while, in general, multi-environment models that explicitly split marker effects in main and environmental-specific effects outperform simpler multi-environment models.
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Affiliation(s)
- Damiano Puglisi
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), Università di Catania, Catania, Italy
| | - Stefano Delbono
- Council for Agricultural Research and Economics–Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Andrea Visioni
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas, Avenue Hafiane Cherkaoui, Rabat, Morocco
| | - Hakan Ozkan
- Department of Field Crops, Faculty of Agriculture, University of Cukurova, Adana, Turkey
| | - İbrahim Kara
- Bahri Dagdas International Agricultural Research Institute, Konya, Turkey
| | - Ana M. Casas
- Aula Dei Experimental Station (EEAD-CSIC), Spanish Research Council, Zaragoza, Spain
| | - Ernesto Igartua
- Aula Dei Experimental Station (EEAD-CSIC), Spanish Research Council, Zaragoza, Spain
| | - Giampiero Valè
- DiSIT, Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Vercelli, Italy
| | - Angela Roberta Lo Piero
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), Università di Catania, Catania, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics–Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Alessandro Tondelli
- Council for Agricultural Research and Economics–Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Agostino Fricano
- Council for Agricultural Research and Economics–Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
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Visioni A, Rehman S, Viash SS, Singh SP, Vishwakarma R, Gyawali S, Al-Abdallat AM, Verma RPS. Genome Wide Association Mapping of Spot Blotch Resistance at Seedling and Adult Plant Stages in Barley. Front Plant Sci 2020; 11:642. [PMID: 32670303 PMCID: PMC7326046 DOI: 10.3389/fpls.2020.00642] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 04/24/2020] [Indexed: 05/05/2023]
Abstract
Barley spot blotch (SB) caused by Cochliobolus sativus is one of the major constrains to barley production in warmer regions worldwide. The study was undertaken to identify and estimate effects of loci underlying quantitative resistance to SB at the seedling and adult plant stages. A panel of 261 high input (HI-AM) barley genotypes consisting of released cultivars, advanced breeding lines, and landraces, was screened for resistance to SB. The seedling resistance screening was conducted using two virulent isolates from Morocco (ICSB3 and SB54) while the adult plant stage resistance was evaluated at two hot spot locations, Faizabad and Varanasi, in India under artificial inoculation using a mixture of prevalent virulent isolates. The HI-AM panel was genotyped using DArT-Seq high-throughput genotyping platform. Genome wide association mapping (GWAM) was conducted using 13,182 PAV and 6,311 SNP markers, for seedling and adult plant resistance. Both GLM and MLM model were employed in TASSEL (v 5.0) using principal component analysis and Kinship Matrix as covariates. Final disease rating and Area Under Disease Progress Curve (AUDPC) were used for the evaluation of adult stage plant resistance. The GWAM analysis indicated 23 QTL at the seedling stage (14 for isolate ICSB3 and 9 for isolate SB54), while 15 QTL were detected at the adult plant stage resistance (6 at Faizabad and 9 at Varanasi) and 5 for AUDPC based resistance at Varanasi. Common QTL at seedling and adult plant stages were found across all barley chromosomes. Seedling stage QTL explained together 73.24% of the variance for seedling resistance to isolate ICSB3 and 49.26% for isolate SB54, whereas, QTL for adult plant stage resistance explained together 38.32%, 44.09% and 26.42% of the variance at Faizabad and Varanasi and AUDPC at Varanasi, respectively. Several QTL identified in this study were also reported in previous studies using bi-parental and association mapping populations, corroborating our results. The promising QTL detected at both stages, once validated, can be used for marker assisted selection (MAS) in SB resistance barley breeding program.
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Affiliation(s)
- Andrea Visioni
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
- *Correspondence: Andrea Visioni,
| | - Sajid Rehman
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
| | - Shyam Saran Viash
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Shiw Pratap Singh
- Department of Plant Pathology, Narendra Dev University of Agriculture and Technology, Faizabad, India
| | - Ram Vishwakarma
- Department of Plant Pathology, Narendra Dev University of Agriculture and Technology, Faizabad, India
| | - Sanjaya Gyawali
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
- Vegetable Seed Pathology Department, Washington State University, Northwest Washington Research and Extension Center, Mount Vernon, WA, United States
| | - Ayed M. Al-Abdallat
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
- Department of Horticulture and Crop Science, Faculty of Agriculture, The University of Jordan, Amman, Jordan
| | - Ramesh Pal Singh Verma
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
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Visioni A, Gyawali S, Selvakumar R, Gangwar OP, Shekhawat PS, Bhardwaj SC, Al-Abdallat AM, Kehel Z, Verma RPS. Genome Wide Association Mapping of Seedling and Adult Plant Resistance to Barley Stripe Rust ( Puccinia striiformis f. sp. hordei) in India. Front Plant Sci 2018; 9:520. [PMID: 29740461 PMCID: PMC5928535 DOI: 10.3389/fpls.2018.00520] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 04/04/2018] [Indexed: 05/08/2023]
Abstract
Barley stripe rust is caused by Puccinia striiformis f.sp. hordei, (Psh), occurs worldwide, and is a major disease in South Asia. The aim of this work was to identify and estimate effects of loci underlying quantitative resistance to rust at seedling and adult plant stages. HI-AM panel of 261 barley genotypes consisting of released cultivars from North and South America, Europe, Australia, advanced breeding lines, and local landraces from ICARDA barley program were screened at seedling and adult plant stages for resistance to Psh. Seedling resistance was evaluated with the five prevalent Psh races in India. Screening for the adult plant stage resistance was also performed in two different locations by inoculating with a mixture of the five races used for seedling screeing. The panel was genotyped using DaRT-Seq high-throughput genotyping platform. The genome-wide association mapping (GWAM) showed a total of 45 QTL located across the seven barley chromosomes for seedling resistance to the five races and 18 QTL for adult plant stage resistance. Common QTL for different races at seedling stage were found on all chromosomes except on chromosome 1H. Four common QTL associated with seedling and adult plant stage resistance were found on chromosomes 2, 5, and 6H. Moreover, one of the QTL located on the long arm of chromosome 5H showed stable effects across environments for adult plant stage resistance. Several QTL identified in this study were also reported before in bi-parental and association mapping populations studies validating current GWAM. However 15 new QTL were found at adult plant stage on all chromosomes except the 4H, explaining up to 36.79% of the variance. The promising QTL detected at both stages, once validated, can be used for MAS in Psh resistance breeding program globally.
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Affiliation(s)
- Andrea Visioni
- Biodiversity and Integrated Gene Management, International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
- *Correspondence: Andrea Visioni
| | - Sanjaya Gyawali
- Biodiversity and Integrated Gene Management, International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada
| | - Rajan Selvakumar
- Indian Institute of Wheat and Barley Research, Indian Council of Agricultural Research, Karnal, India
| | - Om P. Gangwar
- Indian Institute of Wheat and Barley Research, Indian Council of Agricultural Research, Karnal, India
| | | | - Subhash C. Bhardwaj
- Indian Institute of Wheat and Barley Research, Indian Council of Agricultural Research, Karnal, India
| | - Ayed M. Al-Abdallat
- Biodiversity and Integrated Gene Management, International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
- Department of Horticulture and Crop Science, Faculty of Agriculture, The University of Jordan, Amman, Jordan
| | - Zakaria Kehel
- Biodiversity and Integrated Gene Management, International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
| | - Ramesh P. S. Verma
- Biodiversity and Integrated Gene Management, International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
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Visioni A, Tondelli A, Francia E, Pswarayi A, Malosetti M, Russell J, Thomas W, Waugh R, Pecchioni N, Romagosa I, Comadran J. Genome-wide association mapping of frost tolerance in barley (Hordeum vulgare L.). BMC Genomics 2013; 14:424. [PMID: 23802597 PMCID: PMC3701572 DOI: 10.1186/1471-2164-14-424] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 06/12/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Frost tolerance is a key trait with economic and agronomic importance in barley because it is a major component of winter hardiness, and therefore limits the geographical distribution of the crop and the effective transfer of quality traits between spring and winter crop types. Three main frost tolerance QTL (Fr-H1, Fr-H2 and Fr-H3) have been identified from bi-parental genetic mapping but it can be argued that those mapping populations only capture a portion of the genetic diversity of the species. A genetically broad dataset consisting of 184 genotypes, representative of the barley gene pool cultivated in the Mediterranean basin over an extended time period, was genotyped with 1536 SNP markers. Frost tolerance phenotype scores were collected from two trial sites, Foradada (Spain) and Fiorenzuola (Italy) and combined with the genotypic data in genome wide association analyses (GWAS) using Eigenstrat and kinship approaches to account for population structure. RESULTS GWAS analyses identified twelve and seven positive SNP associations at Foradada and Fiorenzuola, respectively, using Eigenstrat and six and four, respectively, using kinship. Linkage disequilibrium analyses of the significant SNP associations showed they are genetically independent. In the kinship analysis, two of the significant SNP associations were tightly linked to the Fr-H2 and HvBmy loci on chromosomes 5H and 4HL, respectively. The other significant kinship associations were located in genomic regions that have not previously been associated with cold stress. CONCLUSIONS Haplotype analysis revealed that most of the significant SNP loci are fixed in the winter or facultative types, while they are freely segregating within the un-adapted spring barley genepool. Although there is a major interest in detecting new variation to improve frost tolerance of available winter and facultative types, from a GWAS perspective, working within the un-adapted spring germplasm pool is an attractive alternative strategy which would minimize statistical issues, simplify the interpretation of the data and identify phenology independent genetic determinants of frost tolerance.
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Affiliation(s)
- Andrea Visioni
- Centre UdL-IRTA, Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida, Lleida, Spain
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