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Szabo-Hever A, Singh G, Haugrud ARP, Running KLD, Seneviratne S, Zhang Z, Shi G, Bassi FM, Maccaferri M, Cattivelli L, Tuberosa R, Friesen TL, Liu Z, Xu SS, Faris JD. Association Mapping of Resistance to Tan Spot in the Global Durum Panel. Phytopathology 2023; 113:1967-1978. [PMID: 37199466 DOI: 10.1094/phyto-02-23-0043-r] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Tan spot, caused by the necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr), is an important disease of durum and common wheat worldwide. Compared with common wheat, less is known about the genetics and molecular basis of tan spot resistance in durum wheat. We evaluated 510 durum lines from the Global Durum Wheat Panel (GDP) for sensitivity to the necrotrophic effectors (NEs) Ptr ToxA and Ptr ToxB and for reaction to Ptr isolates representing races 1 to 5. Overall, susceptible durum lines were most prevalent in South Asia, the Middle East, and North Africa. Genome-wide association analysis showed that the resistance locus Tsr7 was significantly associated with tan spot caused by races 2 and 3, but not races 1, 4, or 5. The NE sensitivity genes Tsc1 and Tsc2 were associated with susceptibility to Ptr ToxC- and Ptr ToxB-producing isolates, respectively, but Tsn1 was not associated with tan spot caused by Ptr ToxA-producing isolates, which further validates that the Tsn1-Ptr ToxA interaction does not play a significant role in tan spot development in durum. A unique locus on chromosome arm 2AS was associated with tan spot caused by race 4, a race once considered avirulent. A novel trait characterized by expanding chlorosis leading to increased disease severity caused by the Ptr ToxB-producing race 5 isolate DW5 was identified, and this trait was governed by a locus on chromosome 5B. We recommend that durum breeders select resistance alleles at the Tsr7, Tsc1, Tsc2, and the chromosome 2AS loci to obtain broad resistance to tan spot.
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Affiliation(s)
- Agnes Szabo-Hever
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102
| | - Gurminder Singh
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102
| | - Amanda R Peters Haugrud
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102
| | | | - Sudeshi Seneviratne
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102
| | - Zengcui Zhang
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102
| | - Gongjun Shi
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102
| | - Filippo M Bassi
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat Institutes, Rabat 10101, Morocco
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna 40127, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics-Research Center for Genomics and Bioinformatics, Fiorenzuola d'Arda 29017, Italy
| | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, Bologna 40127, Italy
| | - Timothy L Friesen
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102
| | - Steven S Xu
- U.S. Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA 94710
| | - Justin D Faris
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102
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Marone D, Mazzucotelli E, Matny O, Desiderio F, Sciara G, Maccaferri M, Marcotuli I, Gadaleta A, Steffenson B, Mastrangelo AM. QTL Mapping of Stem Rust Resistance in Populations of Durum Wheat. Genes (Basel) 2022; 13:genes13101793. [PMID: 36292678 PMCID: PMC9601996 DOI: 10.3390/genes13101793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
Stem rinfectionust, caused by the fungus Puccinia graminis f. sp. tritici (Pgt), is one of the most devastating fungal diseases of durum and common wheat worldwide. The identification of sources of resistance and the validation of QTLs identified through genome-wide association studies is of paramount importance for reducing the losses caused by this disease to wheat grain yield and quality. Four segregating populations whose parents showed contrasting reactions to some Pgt races were assessed in the present study, and 14 QTLs were identified on chromosomes 3A, 4A, 6A, and 6B, with some regions in common between different segregating populations. Several QTLs were mapped to chromosomal regions coincident with previously mapped stem rust resistance loci; however, their reaction to different Pgt races suggest that novel genes or alleles could be present on chromosomes 3A and 6B. Putative candidate genes with a disease-related functional annotation have been identified in the QTL regions based on information available from the reference genome of durum cv. ‘Svevo’.
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Affiliation(s)
- Daniela Marone
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia, Italy
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinfomatics, 29017 Fiorenzuola d’Arda, Italy
| | - Oadi Matny
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Francesca Desiderio
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinfomatics, 29017 Fiorenzuola d’Arda, Italy
| | - Giuseppe Sciara
- Department of Agricultural Sciences, University of Bologna, 40127 Bologna, Italy
| | - Marco Maccaferri
- Department of Agricultural Sciences, University of Bologna, 40127 Bologna, Italy
| | - Ilaria Marcotuli
- Research Unit of “Genetics and Plant Biotechnology”, Department of Agricultural & Environmental Science, University of Bari, 70126 Bari, Italy
| | - Agata Gadaleta
- Research Unit of “Genetics and Plant Biotechnology”, Department of Agricultural & Environmental Science, University of Bari, 70126 Bari, Italy
| | - Brian Steffenson
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Anna Maria Mastrangelo
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia, Italy
- Correspondence: ; Tel.: +39-088-171-4911
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3
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Cowger C, Bulli P, Chen F, Lillemo M, Maccaferri M. Editorial: Advances in breeding for wheat disease resistance. Front Plant Sci 2022; 13:1034506. [PMID: 36186052 PMCID: PMC9523782 DOI: 10.3389/fpls.2022.1034506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Christina Cowger
- United States Department of Agriculture, Plant Science Research Unit, Raleigh, NC, United States
| | - Peter Bulli
- School of Agricultural and Food Sciences, Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya
| | - Feng Chen
- National Key Laboratory of Wheat and Corn Crop Science/Agronomy College, Centro de Investigation y Mejoramiento de Maiz y Trigo-China Wheat and Maize Joint Research Center, Henan Agricultural University, Zhengzhou, China
| | - Morten Lillemo
- Department of Plant Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
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4
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Mahboubi M, Talebi R, Mehrabi R, Mohammad Naji A, Maccaferri M, Kema GHJ. Genetic analysis of novel resistance sources and genome-wide association mapping identified novel QTLs for resistance to Zymoseptoria tritici, the causal agent of septoria tritici blotch in wheat. J Appl Genet 2022; 63:429-445. [PMID: 35482212 DOI: 10.1007/s13353-022-00696-x] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 04/11/2022] [Accepted: 04/20/2022] [Indexed: 11/29/2022]
Abstract
Septoria tritici blotch (STB) caused by Zymoseptoria tritici is one of the most important foliar diseases of wheat causing significant yield losses worldwide. In this study, a panel of bread wheat genotypes comprised 185 globally diverse genotypes were tested against 10 Z. tritici isolates at the seedling stage. Genome-wide association study (GWAS) using high-throughput DArTseq markers was performed and further gene expression analysis of significant markers trait association (MTAs) associated with resistance to STB was analyzed. Disease severity level showed significant differences among wheat genotypes for resistance to different Z. tritici isolates. We found novel landrace genotypes that showed highly resistance spectra to all tested isolates. GWAS analysis resulted in 19 quantitative trait loci (QTLs) for resistance to STB that were located on 14 chromosomes. Overall, 14 QTLs were overlapped with previously known QTLs or resistance genes, as well as five potentially novel QTLs on chromosomes 1A, 4A, 5B, 5D, and 6D. Identified novel resistance sources and also novel QTLs for resistance to different Z. tritici isolates can be used for gene pyramiding and development of durable resistance cultivars in future wheat breeding programs.
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Affiliation(s)
- Mozghan Mahboubi
- Department of Agronomy and Plant Breeding, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
| | - Reza Talebi
- Department of Agronomy and Plant Breeding, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran. .,Keygene N.V, P.O. Box 216, 6700 AE, Wageningen, Netherlands.
| | - Rahim Mehrabi
- Keygene N.V, P.O. Box 216, 6700 AE, Wageningen, Netherlands. .,Department of Biotechnology, College of Agriculture, Isfahan University of Technology, POBox 8415683111, Isfahan, Iran.
| | - Amir Mohammad Naji
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahed University, Tehran, Iran
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Gert H J Kema
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, The Netherlands
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Arriagada O, Gadaleta A, Marcotuli I, Maccaferri M, Campana M, Reveco S, Alfaro C, Matus I, Schwember AR. A comprehensive meta-QTL analysis for yield-related traits of durum wheat ( Triticum turgidum L. var. durum) grown under different water regimes. Front Plant Sci 2022; 13:984269. [PMID: 36147234 PMCID: PMC9486101 DOI: 10.3389/fpls.2022.984269] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/18/2022] [Indexed: 05/13/2023]
Abstract
Abiotic stress strongly affects yield-related traits in durum wheat, in particular drought is one of the main environmental factors that have effect on grain yield and plant architecture. In order to obtain new genotypes well adapted to stress conditions, the highest number of desirable traits needs to be combined in the same genotype. In this context, hundreds of quantitative trait loci (QTL) have been identified for yield-related traits in different genetic backgrounds and environments. Meta-QTL (MQTL) analysis is a useful approach to combine data sets and for creating consensus positions for the QTL detected in independent studies for the reliability of their location and effects. MQTL analysis is a useful method to dissect the genetic architecture of complex traits, which provide an extensive allelic coverage, a higher mapping resolution and allow the identification of putative molecular markers useful for marker-assisted selection (MAS). In the present study, a complete and comprehensive MQTL analysis was carried out to identify genomic regions associated with grain-yield related traits in durum wheat under different water regimes. A total of 724 QTL on all 14 chromosomes (genomes A and B) were collected for the 19 yield-related traits selected, of which 468 were reported under rainfed conditions, and 256 under irrigated conditions. Out of the 590 QTL projected on the consensus map, 421 were grouped into 76 MQTL associated with yield components under both irrigated and rainfed conditions, 12 genomic regions containing stable MQTL on all chromosomes except 1A, 4A, 5A, and 6B. Candidate genes associated to MQTL were identified and an in-silico expression analysis was carried out for 15 genes selected among those that were differentially expressed under drought. These results can be used to increase durum wheat grain yields under different water regimes and to obtain new genotypes adapted to climate change.
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Affiliation(s)
- Osvin Arriagada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Agata Gadaleta
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, Bari, Italy
| | - Ilaria Marcotuli
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, Bari, Italy
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Matteo Campana
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Samantha Reveco
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Christian Alfaro
- Centro Regional Rayentue, Instituto de Investigaciones Agropecuarias (INIA), Rengo, Chile
| | - Iván Matus
- Centro Regional Quilamapu, Instituto de Investigaciones Agropecuarias (INIA), Chillán, Chile
| | - Andrés R. Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
- *Correspondence: Andrés R. Schwember,
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Zendonadi Dos Santos N, Piepho HP, Condorelli GE, Licieri Groli E, Newcomb M, Ward R, Tuberosa R, Maccaferri M, Fiorani F, Rascher U, Muller O. High-throughput field phenotyping reveals genetic variation in photosynthetic traits in durum wheat under drought. Plant Cell Environ 2021; 44:2858-2878. [PMID: 34189744 DOI: 10.1111/pce.14136] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 04/14/2021] [Accepted: 06/13/2021] [Indexed: 06/13/2023]
Abstract
Chlorophyll fluorescence (ChlF) is a powerful non-invasive technique for probing photosynthesis. Although proposed as a method for drought tolerance screening, ChlF has not yet been fully adopted in physiological breeding, mainly due to limitations in high-throughput field phenotyping capabilities. The light-induced fluorescence transient (LIFT) sensor has recently been shown to reliably provide active ChlF data for rapid and remote characterisation of plant photosynthetic performance. We used the LIFT sensor to quantify photosynthesis traits across time in a large panel of durum wheat genotypes subjected to a progressive drought in replicated field trials over two growing seasons. The photosynthetic performance was measured at the canopy level by means of the operating efficiency of Photosystem II ( Fq'/Fm' ) and the kinetics of electron transport measured by reoxidation rates ( Fr1' and Fr2' ). Short- and long-term changes in ChlF traits were found in response to soil water availability and due to interactions with weather fluctuations. In mild drought, Fq'/Fm' and Fr2' were little affected, while Fr1' was consistently accelerated in water-limited compared to well-watered plants, increasingly so with rising vapour pressure deficit. This high-throughput approach allowed assessment of the native genetic diversity in ChlF traits while considering the diurnal dynamics of photosynthesis.
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Affiliation(s)
| | - Hans-Peter Piepho
- Biostatistics Unit, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | | | - Eder Licieri Groli
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Maria Newcomb
- Maricopa Agricultural Center, University of Arizona, Maricopa, Arizona, USA
| | - Richard Ward
- Maricopa Agricultural Center, University of Arizona, Maricopa, Arizona, USA
| | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Fabio Fiorani
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Uwe Rascher
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Onno Muller
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
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7
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Ober ES, Alahmad S, Cockram J, Forestan C, Hickey LT, Kant J, Maccaferri M, Marr E, Milner M, Pinto F, Rambla C, Reynolds M, Salvi S, Sciara G, Snowdon RJ, Thomelin P, Tuberosa R, Uauy C, Voss-Fels KP, Wallington E, Watt M. Wheat root systems as a breeding target for climate resilience. Theor Appl Genet 2021; 134:1645-1662. [PMID: 33900415 PMCID: PMC8206059 DOI: 10.1007/s00122-021-03819-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/18/2021] [Indexed: 05/08/2023]
Abstract
In the coming decades, larger genetic gains in yield will be necessary to meet projected demand, and this must be achieved despite the destabilizing impacts of climate change on crop production. The root systems of crops capture the water and nutrients needed to support crop growth, and improved root systems tailored to the challenges of specific agricultural environments could improve climate resiliency. Each component of root initiation, growth and development is controlled genetically and responds to the environment, which translates to a complex quantitative system to navigate for the breeder, but also a world of opportunity given the right tools. In this review, we argue that it is important to know more about the 'hidden half' of crop plants and hypothesize that crop improvement could be further enhanced using approaches that directly target selection for root system architecture. To explore these issues, we focus predominantly on bread wheat (Triticum aestivum L.), a staple crop that plays a major role in underpinning global food security. We review the tools available for root phenotyping under controlled and field conditions and the use of these platforms alongside modern genetics and genomics resources to dissect the genetic architecture controlling the wheat root system. To contextualize these advances for applied wheat breeding, we explore questions surrounding which root system architectures should be selected for, which agricultural environments and genetic trait configurations of breeding populations are these best suited to, and how might direct selection for these root ideotypes be implemented in practice.
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Affiliation(s)
- Eric S Ober
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.
| | - Samir Alahmad
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - James Cockram
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Cristian Forestan
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127, Bologna, Italy
| | - Lee T Hickey
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Josefine Kant
- Forschungszentrum Jülich, IBG-2, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127, Bologna, Italy
| | - Emily Marr
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | | | - Francisco Pinto
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Estado de Mexico, Mexico
| | - Charlotte Rambla
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Matthew Reynolds
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Estado de Mexico, Mexico
| | - Silvio Salvi
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127, Bologna, Italy
| | - Giuseppe Sciara
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127, Bologna, Italy
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | | | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127, Bologna, Italy
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Kai P Voss-Fels
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | | | - Michelle Watt
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
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Di Tinco R, Bertani G, Pisciotta A, Bertoni L, Pignatti E, Maccaferri M, Salvarani C, Carnevale G. Role of mesenchymal stem cells isolated from dental pulp (hDPSCS) in immunomodulation processes mediated by programmed death-ligand 1 (PD-L1) and interleukin 6 (IL-6). Cytotherapy 2021. [DOI: 10.1016/s1465324921003480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Bányai J, Maccaferri M, Láng L, Mayer M, Tóth V, Cséplő M, Pál M, Mészáros K, Vida G. Abiotic Stress Response of Near-Isogenic Spring Durum Wheat Lines under Different Sowing Densities. Int J Mol Sci 2021; 22:2053. [PMID: 33669605 PMCID: PMC7923076 DOI: 10.3390/ijms22042053] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/02/2021] [Accepted: 02/07/2021] [Indexed: 11/29/2022] Open
Abstract
A detailed study was made of changes in the plant development, morphology, physiology and yield biology of near-isogenic lines of spring durum wheat sown in the field with different plant densities in two consecutive years (2013-2014). An analysis was made of the drought tolerance of isogenic lines selected for yield QTLs (QYld.idw-2B and QYld.idw-3B), and the presence of QTL effects was examined in spring sowings. Comparisons were made of the traits of the isogenic pairs QYld.idw-3B++ and QYld.idw-3B-- both within and between the pairs. Changes in the polyamine content, antioxidant enzyme activity, chlorophyll content of the flag leaf and the normalized difference vegetation index (NDVI) of the plot were monitored in response to drought stress, and the relationship between these components and the yield was analyzed. In the case of moderate stress, differences between the NIL++ and NIL-- pairs appeared in the early dough stage, indicating that the QYld.idw-3B++ QTL region was able to maintain photosynthetic activity for a longer period, resulting in greater grain number and grain weight at the end of the growing period. The chlorophyll content of the flag leaf in phenophases Z77 and Z83 was significantly correlated with the grain number and grain weight of the main spike. The grain yield was greatly influenced by the treatment, while the genotype had a significant effect on the thousand-kernel weight and on the grain number and grain weight of the main spike. When the lines were compared in the non-irrigated treatment, significantly more grains and significantly higher grain weight were observed in the main spike in NIL++ lines, confirming the theory that the higher yields of the QYld.idw-3B++ lines when sown in spring and exposed to drought stress could be attributed to the positive effect of the "Kofa" QTL on chromosome 3B.
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Affiliation(s)
- Judit Bányai
- Centre for Agricultural Research, Agricultural Institute, ELKH, 2462 Martonvásár, Hungary; (L.L.); (M.M.); (V.T.); (M.C.); (M.P.); (K.M.); (G.V.)
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, 40126 Bologna, Italy;
| | - László Láng
- Centre for Agricultural Research, Agricultural Institute, ELKH, 2462 Martonvásár, Hungary; (L.L.); (M.M.); (V.T.); (M.C.); (M.P.); (K.M.); (G.V.)
| | - Marianna Mayer
- Centre for Agricultural Research, Agricultural Institute, ELKH, 2462 Martonvásár, Hungary; (L.L.); (M.M.); (V.T.); (M.C.); (M.P.); (K.M.); (G.V.)
| | - Viola Tóth
- Centre for Agricultural Research, Agricultural Institute, ELKH, 2462 Martonvásár, Hungary; (L.L.); (M.M.); (V.T.); (M.C.); (M.P.); (K.M.); (G.V.)
| | - Mónika Cséplő
- Centre for Agricultural Research, Agricultural Institute, ELKH, 2462 Martonvásár, Hungary; (L.L.); (M.M.); (V.T.); (M.C.); (M.P.); (K.M.); (G.V.)
| | - Magda Pál
- Centre for Agricultural Research, Agricultural Institute, ELKH, 2462 Martonvásár, Hungary; (L.L.); (M.M.); (V.T.); (M.C.); (M.P.); (K.M.); (G.V.)
| | - Klára Mészáros
- Centre for Agricultural Research, Agricultural Institute, ELKH, 2462 Martonvásár, Hungary; (L.L.); (M.M.); (V.T.); (M.C.); (M.P.); (K.M.); (G.V.)
| | - Gyula Vida
- Centre for Agricultural Research, Agricultural Institute, ELKH, 2462 Martonvásár, Hungary; (L.L.); (M.M.); (V.T.); (M.C.); (M.P.); (K.M.); (G.V.)
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10
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Alemu A, Feyissa T, Maccaferri M, Sciara G, Tuberosa R, Ammar K, Badebo A, Acevedo M, Letta T, Abeyo B. Genome-wide association analysis unveils novel QTLs for seminal root system architecture traits in Ethiopian durum wheat. BMC Genomics 2021; 22:20. [PMID: 33407083 PMCID: PMC7789649 DOI: 10.1186/s12864-020-07320-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetic improvement of root system architecture is essential to improve water and nutrient use efficiency of crops or to boost their productivity under stress or non-optimal soil conditions. One hundred ninety-two Ethiopian durum wheat accessions comprising 167 historical landraces and 25 modern cultivars were assembled for GWAS analysis to identify QTLs for root system architecture (RSA) traits and genotyped with a high-density 90 K wheat SNP array by Illumina. RESULTS Using a non-roll, paper-based root phenotyping platform, a total of 2880 seedlings and 14,947 seminal roots were measured at the three-leaf stage to collect data for total root length (TRL), total root number (TRN), root growth angle (RGA), average root length (ARL), bulk root dry weight (RDW), individual root dry weight (IRW), bulk shoot dry weight (SDW), presence of six seminal roots per seedling (RT6) and root shoot ratio (RSR). Analysis of variance revealed highly significant differences between accessions for all RSA traits. Four major (- log10P ≥ 4) and 34 nominal (- log10P ≥ 3) QTLs were identified and grouped in 16 RSA QTL clusters across chromosomes. A higher number of significant RSA QTL were identified on chromosome 4B particularly for root vigor traits (root length, number and/or weight). CONCLUSIONS After projecting the identified QTLs on to a high-density tetraploid consensus map along with previously reported RSA QTL in both durum and bread wheat, fourteen nominal QTLs were found to be novel and could potentially be used to tailor RSA in elite lines. The major RGA QTLs on chromosome 6AL detected in the current study and reported in previous studies is a good candidate for cloning the causative underlining sequence and identifying the beneficial haplotypes able to positively affect yield under water- or nutrient-limited conditions.
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Affiliation(s)
- Admas Alemu
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia. .,Department of Biology, Debre Tabor University, Debra Tabor, Ethiopia.
| | - Tileye Feyissa
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Giuseppe Sciara
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Karim Ammar
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Ayele Badebo
- International Maize and Wheat Improvement Center (CIMMYT), Addis Ababa, Ethiopia
| | - Maricelis Acevedo
- International Programs, College of Agriculture and Life Sciences, Cornell University, New York City, NY, USA
| | - Tesfaye Letta
- Oromia Agricultural Research Institute, Addis Ababa, Ethiopia
| | - Bekele Abeyo
- International Maize and Wheat Improvement Center (CIMMYT), Addis Ababa, Ethiopia
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11
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Cutignano A, Mamone G, Boscaino F, Ceriotti A, Maccaferri M, Picariello G. Monitoring changes of lipid composition in durum wheat during grain development. J Cereal Sci 2021. [DOI: 10.1016/j.jcs.2020.103131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Hao C, Jiao C, Hou J, Li T, Liu H, Wang Y, Zheng J, Liu H, Bi Z, Xu F, Zhao J, Ma L, Wang Y, Majeed U, Liu X, Appels R, Maccaferri M, Tuberosa R, Lu H, Zhang X. Resequencing of 145 Landmark Cultivars Reveals Asymmetric Sub-genome Selection and Strong Founder Genotype Effects on Wheat Breeding in China. Mol Plant 2020; 13:1733-1751. [PMID: 32896642 DOI: 10.1016/j.molp.2020.09.001] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/19/2020] [Accepted: 09/02/2020] [Indexed: 05/18/2023]
Abstract
Controlled pedigrees and the multi-decade timescale of national crop plant breeding programs offer a unique experimental context for examining how selection affects plant genomes. More than 3000 wheat cultivars have been registered, released, and documented since 1949 in China. In this study, a set of 145 elite cultivars selected from historical points of wheat breeding in China were re-sequenced. A total of 43.75 Tb of sequence data were generated with an average read depth of 17.94× for each cultivar, and more than 60.92 million SNPs and 2.54 million InDels were captured, based on the Chinese Spring RefSeq genome v1.0. Seventy years of breeder-driven selection led to dramatic changes in grain yield and related phenotypes, with distinct genomic regions and phenotypes targeted by different breeders across the decades. There are very clear instances illustrating how introduced Italian and other foreign germplasm was integrated into Chinese wheat programs and reshaped the genomic landscape of local modern cultivars. Importantly, the resequencing data also highlighted significant asymmetric breeding selection among the three sub-genomes: this was evident in both the collinear blocks for homeologous chromosomes and among sets of three homeologous genes. Accumulation of more newly assembled genes in newer cultivars implied the potential value of these genes in breeding. Conserved and extended sharing of linkage disequilibrium (LD) blocks was highlighted among pedigree-related cultivars, in which fewer haplotype differences were detected. Fixation or replacement of haplotypes from founder genotypes after generations of breeding was related to their breeding value. Based on the haplotype frequency changes in LD blocks of pedigree-related cultivars, we propose a strategy for evaluating the breeding value of any given line on the basis of the accumulation (pyramiding) of beneficial haplotypes. Collectively, our study demonstrates the influence of "founder genotypes" on the output of breeding efforts over many decades and also suggests that founder genotype perspectives are in fact more dynamic when applied in the context of modern genomics-informed breeding.
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Affiliation(s)
- Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chengzhi Jiao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Novogene Bioinformatics Institute, Beijing 100083, China
| | - Jian Hou
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongxia Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuquan Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jun Zheng
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hong Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhihong Bi
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Fengfeng Xu
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Jing Zhao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lin Ma
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yamei Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Uzma Majeed
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xu Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Hongfeng Lu
- Novogene Bioinformatics Institute, Beijing 100083, China.
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Gupta P, Kabbaj H, El Hassouni K, Maccaferri M, Sanchez-Garcia M, Tuberosa R, Bassi FM. Genomic Regions Associated with the Control of Flowering Time in Durum Wheat. Plants (Basel) 2020; 9:plants9121628. [PMID: 33255147 PMCID: PMC7759329 DOI: 10.3390/plants9121628] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 01/17/2023]
Abstract
Flowering time is a critical stage for crop development as it regulates the ability of plants to adapt to an environment. To understand the genetic control of flowering time, a genome-wide association study (GWAS) was conducted to identify the genomic regions associated with the control of this trait in durum wheat (Triticum durum Desf.). A total of 96 landraces and 288 modern lines were evaluated for days to heading, growing degree days, and accumulated day length at flowering across 13 environments spread across Morocco, Lebanon, Mauritania, and Senegal. These environments were grouped into four pheno-environments based on temperature, day length, and other climatic variables. Genotyping with a 35K Axiom array generated 7652 polymorphic single nucleotide polymorphisms (SNPs) in addition to 3 KASP markers associated with known flowering genes. In total, 32 significant QTLs were identified in both landraces and modern lines. Some QTLs had a strong association with already known regulatory photoperiod genes, Ppd-A and Ppd-B, and vernalization genes Vrn-A1 and VrnA7. However, these loci explained only 5% to 20% of variance for days to heading. Seven QTLs overlapped between the two germplasm groups in which Q.ICD.Eps-03 and Q.ICD.Vrn-15 consistently affected flowering time in all the pheno-environments, while Q.ICD.Eps-09 and Q.ICD.Ppd-10 were significant only in two pheno-environments and the combined analysis across all environments. These results help clarify the genetic mechanism controlling flowering time in durum wheat and show some clear distinctions to what is known for common wheat (Triticum aestivum L.).
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Affiliation(s)
- Priyanka Gupta
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127 Bologna, Italy; (P.G.); (M.M.); (R.T.)
- International Center for Agricultural Research in the Dry Areas (ICARDA), 10000 Rabat, Morocco; (H.K.); (K.E.H.); (M.S.-G.)
| | - Hafssa Kabbaj
- International Center for Agricultural Research in the Dry Areas (ICARDA), 10000 Rabat, Morocco; (H.K.); (K.E.H.); (M.S.-G.)
| | - Khaoula El Hassouni
- International Center for Agricultural Research in the Dry Areas (ICARDA), 10000 Rabat, Morocco; (H.K.); (K.E.H.); (M.S.-G.)
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127 Bologna, Italy; (P.G.); (M.M.); (R.T.)
| | - Miguel Sanchez-Garcia
- International Center for Agricultural Research in the Dry Areas (ICARDA), 10000 Rabat, Morocco; (H.K.); (K.E.H.); (M.S.-G.)
| | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127 Bologna, Italy; (P.G.); (M.M.); (R.T.)
| | - Filippo Maria Bassi
- International Center for Agricultural Research in the Dry Areas (ICARDA), 10000 Rabat, Morocco; (H.K.); (K.E.H.); (M.S.-G.)
- Correspondence: ; Tel.: +212-614-402-717
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14
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Alemu A, Feyissa T, Tuberosa R, Maccaferri M, Sciara G, Letta T, Abeyo B. Genome-wide association mapping for grain shape and color traits in Ethiopian durum wheat (Triticum turgidum ssp. durum). ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.cj.2020.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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15
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Anuarbek S, Abugalieva S, Pecchioni N, Laidò G, Maccaferri M, Tuberosa R, Turuspekov Y. Quantitative trait loci for agronomic traits in tetraploid wheat for enhancing grain yield in Kazakhstan environments. PLoS One 2020; 15:e0234863. [PMID: 32574201 PMCID: PMC7310741 DOI: 10.1371/journal.pone.0234863] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/03/2020] [Indexed: 12/02/2022] Open
Abstract
Durum wheat (Triticum turgidum L. ssp. durum) is one of the top crops in Kazakhstan, where it is cultivated in different ecological niches, mainly at higher latitudes in the steppe zone of the northern region. Therefore, local breeding programs for durum wheat are primarily focused on selection for high productivity in Northern Kazakhstan based on the introduction of promising foreign germplasm and the adoption of marker-assisted selection. In this study, a world tetraploid wheat collection consisted of 184 primitive and domesticated accessions, which were previously genotyped using 16,425 polymorphic SNP markers, was field-tested in Northern and South-eastern Kazakhstan. The field tests have allowed the identification of 80 durum wheat promising lines in Northern Kazakhstan in comparison with a local standard cultivar. Also, GGE (Genotype and Genotype by Environment) biplot analyses for yield performance revealed that accessions of T. dicoccum, T. carthlicum, and T. turanicum also have potential to improve durum wheat yield in the region. The genome-wide association study (GWAS) has allowed the identification of 83 MTAs (marker-trait associations) for heading date, seed maturation time, plant height, spike length, number of fertile spikes, number of kernels per spike, and thousand kernel weight. The comparison of the 83 identified MTAs with those previously reported in GWAS for durum wheat suggests that 38 MTAs are presumably novel, while the co-localization of a large number of MTAs with those previously published confirms the validity of the results of this study. The MTAs reported herewith will provide the opportunity to implement marker-assisted selection in ongoing durum wheat breeding projects targeting higher productivity in the region.
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Affiliation(s)
- Shynar Anuarbek
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Saule Abugalieva
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- Kazakh National Agrarian University, Almaty, Kazakhstan
| | - Nicola Pecchioni
- Research Centre for Cereal and Industrial Crops, CREA, Foggia, Italy
| | - Giovanni Laidò
- Research Centre for Cereal and Industrial Crops, CREA, Foggia, Italy
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Yerlan Turuspekov
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- al-Farabi Kazakh National University, Almaty, Kazakhstan
- * E-mail:
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16
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Mazzucotelli E, Sciara G, Mastrangelo AM, Desiderio F, Xu SS, Faris J, Hayden MJ, Tricker PJ, Ozkan H, Echenique V, Steffenson BJ, Knox R, Niane AA, Udupa SM, Longin FCH, Marone D, Petruzzino G, Corneti S, Ormanbekova D, Pozniak C, Roncallo PF, Mather D, Able JA, Amri A, Braun H, Ammar K, Baum M, Cattivelli L, Maccaferri M, Tuberosa R, Bassi FM. The Global Durum Wheat Panel (GDP): An International Platform to Identify and Exchange Beneficial Alleles. Front Plant Sci 2020; 11:569905. [PMID: 33408724 PMCID: PMC7779600 DOI: 10.3389/fpls.2020.569905] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 11/24/2020] [Indexed: 05/04/2023]
Abstract
Representative, broad and diverse collections are a primary resource to dissect genetic diversity and meet pre-breeding and breeding goals through the identification of beneficial alleles for target traits. From 2,500 tetraploid wheat accessions obtained through an international collaborative effort, a Global Durum wheat Panel (GDP) of 1,011 genotypes was assembled that captured 94-97% of the original diversity. The GDP consists of a wide representation of Triticum turgidum ssp. durum modern germplasm and landraces, along with a selection of emmer and primitive tetraploid wheats to maximize diversity. GDP accessions were genotyped using the wheat iSelect 90K SNP array. Among modern durum accessions, breeding programs from Italy, France and Central Asia provided the highest level of genetic diversity, with only a moderate decrease in genetic diversity observed across nearly 50 years of breeding (1970-2018). Further, the breeding programs from Europe had the largest sets of unique alleles. LD was lower in the landraces (0.4 Mbp) than in modern germplasm (1.8 Mbp) at r 2 = 0.5. ADMIXTURE analysis of modern germplasm defined a minimum of 13 distinct genetic clusters (k), which could be traced to the breeding program of origin. Chromosome regions putatively subjected to strong selection pressure were identified from fixation index (F st ) and diversity reduction index (DRI) metrics in pairwise comparisons among decades of release and breeding programs. Clusters of putative selection sweeps (PSW) were identified as co-localized with major loci controlling phenology (Ppd and Vrn), plant height (Rht) and quality (gliadins and glutenins), underlining the role of the corresponding genes as driving elements in modern breeding. Public seed availability and deep genetic characterization of the GDP make this collection a unique and ideal resource to identify and map useful genetic diversity at loci of interest to any breeding program.
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Affiliation(s)
- Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Giuseppe Sciara
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Anna M. Mastrangelo
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, Foggia, Italy
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, Bergamo, Italy
| | - Francesca Desiderio
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Steven S. Xu
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, Fargo, ND, United States
| | - Justin Faris
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, Fargo, ND, United States
| | - Matthew J. Hayden
- Agriculture Victoria, Agribio, Centre for AgriBiosciences, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Penny J. Tricker
- School of Agriculture, Food and Wine, Faculty of Sciences, Waite Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Hakan Ozkan
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Turkey
| | - Viviana Echenique
- Centro de Recursos Naturales Renovables de la Zona Semiárida, Departamento de Agronomía, Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas, Bahía Blanca, Argentina
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Ron Knox
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Abdoul A. Niane
- International Center for Agricultural Research in the Dry Areas, Beirut, Lebanon
| | - Sripada M. Udupa
- International Center for Agricultural Research in the Dry Areas, Beirut, Lebanon
| | | | - Daniela Marone
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, Foggia, Italy
| | - Giuseppe Petruzzino
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, Foggia, Italy
| | - Simona Corneti
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Danara Ormanbekova
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Curtis Pozniak
- Plant Sciences and Crop Development Center, University of Saskatchewan, Saskatoon, SK, Canada
| | - Pablo F. Roncallo
- Centro de Recursos Naturales Renovables de la Zona Semiárida, Departamento de Agronomía, Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas, Bahía Blanca, Argentina
| | - Diane Mather
- School of Agriculture, Food and Wine, Faculty of Sciences, Waite Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Jason A. Able
- School of Agriculture, Food and Wine, Faculty of Sciences, Waite Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Ahmed Amri
- International Center for Agricultural Research in the Dry Areas, Beirut, Lebanon
| | - Hans Braun
- Plant Sciences and Crop Development Center, University of Saskatchewan, Saskatoon, SK, Canada
| | - Karim Ammar
- International Maize and Wheat Improvement Center, Texcoco de Mora, Mexico
| | - Michael Baum
- International Center for Agricultural Research in the Dry Areas, Beirut, Lebanon
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Filippo M. Bassi
- International Center for Agricultural Research in the Dry Areas, Beirut, Lebanon
- *Correspondence: Filippo M. Bassi,
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Montesinos-López OA, Montesinos-López A, Tuberosa R, Maccaferri M, Sciara G, Ammar K, Crossa J. Multi-Trait, Multi-Environment Genomic Prediction of Durum Wheat With Genomic Best Linear Unbiased Predictor and Deep Learning Methods. Front Plant Sci 2019; 10:1311. [PMID: 31787990 PMCID: PMC6856087 DOI: 10.3389/fpls.2019.01311] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/20/2019] [Indexed: 05/23/2023]
Abstract
Although durum wheat (Triticum turgidum var. durum Desf.) is a minor cereal crop representing just 5-7% of the world's total wheat crop, it is a staple food in Mediterranean countries, where it is used to produce pasta, couscous, bulgur and bread. In this paper, we cover multi-trait prediction of grain yield (GY), days to heading (DH) and plant height (PH) of 270 durum wheat lines that were evaluated in 43 environments (country-location-year combinations) across a broad range of water regimes in the Mediterranean Basin and other locations. Multi-trait prediction analyses were performed by implementing a multi-trait deep learning model (MTDL) with a feed-forward network topology and a rectified linear unit activation function with a grid search approach for the selection of hyper-parameters. The results of the multi-trait deep learning method were also compared with univariate predictions of the genomic best linear unbiased predictor (GBLUP) method and the univariate counterpart of the multi-trait deep learning method (UDL). All models were implemented with and without the genotype × environment interaction term. We found that the best predictions were observed without the genotype × environment interaction term in the UDL and MTDL methods. However, under the GBLUP method, the best predictions were observed when the genotype × environment interaction term was taken into account. We also found that in general the best predictions were observed under the GBLUP model; however, the predictions of the MTDL were very similar to those of the GBLUP model. This result provides more evidence that the GBLUP model is a powerful approach for genomic prediction, but also that the deep learning method is a practical approach for predicting univariate and multivariate traits in the context of genomic selection.
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Affiliation(s)
| | - Abelardo Montesinos-López
- Departamento de Matemáticas, Centro Universitario de Ciencias Exactas e Ingenierías (CUCEI), Universidad de Guadalajara, Guadalajara, Mexico
| | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Giuseppe Sciara
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Karim Ammar
- Global Wheat Breeding Program, International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
| | - José Crossa
- Global Wheat Breeding Program, International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
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18
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Colasuonno P, Marcotuli I, Blanco A, Maccaferri M, Condorelli GE, Tuberosa R, Parada R, de Camargo AC, Schwember AR, Gadaleta A. Carotenoid Pigment Content in Durum Wheat ( Triticum turgidum L. var durum): An Overview of Quantitative Trait Loci and Candidate Genes. Front Plant Sci 2019; 10:1347. [PMID: 31787991 PMCID: PMC6853866 DOI: 10.3389/fpls.2019.01347] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/27/2019] [Indexed: 05/21/2023]
Abstract
Carotenoid pigment content is an important quality trait as it confers a natural bright yellow color to pasta preferred by consumers (whiteness vs. yellowness) and nutrients, such as provitamin A and antioxidants, essential for human diet. The main goal of the present review is to summarize the knowledge about the genetic regulation of the accumulation of pigment content in durum wheat grain and describe the genetic improvements obtained by using breeding approaches in the last two decades. Although carotenoid pigment content is a quantitative character regulated by various genes with additive effects, its high heritability has facilitated the durum breeding progress for this quality trait. Mapping research for yellow index and yellow pigment content has identified quantitative trait loci (QTL) on all wheat chromosomes. The major QTL, accounting for up to 60%, were mapped on 7L homoeologous chromosome arms, and they are explained by allelic variations of the phytoene synthase (PSY) genes. Minor QTL were detected on all chromosomes and associated to significant molecular markers, indicating the complexity of the trait. Despite there being currently a better knowledge of the mechanisms controlling carotenoid content and composition, there are gaps that require further investigation and bridging to better understand the genetic architecture of this important trait. The development and the utilization of molecular markers in marker-assisted selection (MAS) programs for improving grain quality have been reviewed and discussed.
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Affiliation(s)
- Pasqualina Colasuonno
- Department of Agricultural and Environmental Science (DISAAT), University of Bari “Aldo Moro”, Bari, Italy
| | - Ilaria Marcotuli
- Department of Agricultural and Environmental Science (DISAAT), University of Bari “Aldo Moro”, Bari, Italy
| | - Antonio Blanco
- Department of Agricultural and Environmental Science (DISAAT), University of Bari “Aldo Moro”, Bari, Italy
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | | | - Roberto Tuberosa
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Roberto Parada
- Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Adriano Costa de Camargo
- Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Andrés R. Schwember
- Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Agata Gadaleta
- Department of Agricultural and Environmental Science (DISAAT), University of Bari “Aldo Moro”, Bari, Italy
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Vendramin V, Ormanbekova D, Scalabrin S, Scaglione D, Maccaferri M, Martelli P, Salvi S, Jurman I, Casadio R, Cattonaro F, Tuberosa R, Massi A, Morgante M. Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm. BMC Genomics 2019; 20:278. [PMID: 30971220 PMCID: PMC6456968 DOI: 10.1186/s12864-019-5645-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 03/25/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The tetraploid durum wheat (Triticum turgidum L. ssp. durum Desf. Husnot) is an important crop which provides the raw material for pasta production and a valuable source of genetic diversity for breeding hexaploid wheat (Triticum aestivum L.). Future breeding efforts to enhance yield potential and climate resilience will increasingly rely on genomics-based approaches to identify and select beneficial alleles. A deeper characterisation of the molecular and functional diversity of the durum wheat transcriptome will be instrumental to more effectively harness its genetic diversity. RESULTS We report on the de novo transcriptome assembly of durum wheat cultivar 'Svevo'. The transcriptome of four tissues/organs (shoots and roots at the seedling stage, reproductive organs and developing grains) was assembled de novo, yielding 180,108 contigs, with a N50 length of 1121 bp and mean contig length of 883 bp. Alignment against the transcriptome of nine plant species identified 43% of transcripts with homology to at least one reference transcriptome. The functional annotation was completed by means of a combination of complementary software. The presence of differential expression between the A- and B-homoeolog copies of the durum wheat tetraploid genome was ascertained by phase reconstruction of polymorphic sites based on the T. urartu transcripts and inferring homoeolog-specific sequences. We observed greater expression divergence between A and B homoeologs in grains rather than in leaves and roots. The transcriptomes of 13 durum wheat cultivars spanning the breeding period from 1969 to 2005 were analysed for SNP diversity, leading to 95,358 non-rare, hemi-SNPs shared among two or more cultivars and 33,747 locus-specific (diploid inheritance) SNPs. CONCLUSIONS Our study updates and expands the de novo transcriptome reference assembly available for durum wheat. Out of 180,108 assembled transcripts, 13,636 were specific to the Svevo cultivar as compared to the only other reference transcriptome available for durum, thus contributing to the identification of the tetraploid wheat pan-transcriptome. Additionally, the analysis of 13 historically relevant hallmark varieties produced a SNP dataset that could successfully validate the genotyping in tetraploid wheat and provide a valuable resource for genomics-assisted breeding of both tetraploid and hexaploid wheats.
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Affiliation(s)
- Vera Vendramin
- IGA Technology Services, via J. Linussio 51, 33100, Udine, Italy.
| | - Danara Ormanbekova
- Department of Agricultural and Food Sciences DISTAL, University of Bologna, Viale G. Fanin 44, 40127, Bologna, Italy
| | - Simone Scalabrin
- IGA Technology Services, via J. Linussio 51, 33100, Udine, Italy
| | - Davide Scaglione
- IGA Technology Services, via J. Linussio 51, 33100, Udine, Italy
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences DISTAL, University of Bologna, Viale G. Fanin 44, 40127, Bologna, Italy
| | - Pierluigi Martelli
- Biocomputing Group, University of Bologna, via San Giacomo 9/2, 40126, Bologna, Italy
| | - Silvio Salvi
- Department of Agricultural and Food Sciences DISTAL, University of Bologna, Viale G. Fanin 44, 40127, Bologna, Italy
| | - Irena Jurman
- Istituto di Genomica Applicata, via J. Linussio 51, 33100, Udine, Italy
| | - Rita Casadio
- Biocomputing Group, University of Bologna, via San Giacomo 9/2, 40126, Bologna, Italy
| | | | - Roberto Tuberosa
- Department of Agricultural and Food Sciences DISTAL, University of Bologna, Viale G. Fanin 44, 40127, Bologna, Italy
| | - Andrea Massi
- Società produttori Sementi Bologna, Via Macero 1, 40050, Argelato, BO, Italy
| | - Michele Morgante
- Istituto di Genomica Applicata, via J. Linussio 51, 33100, Udine, Italy.,Department od Agricultural, Food, Environmental and Animal Research - DI4A, University of Udine, via delle Scienze 206, 33100, Udine, Italy
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20
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Steiner B, Michel S, Maccaferri M, Lemmens M, Tuberosa R, Buerstmayr H. Exploring and exploiting the genetic variation of Fusarium head blight resistance for genomic-assisted breeding in the elite durum wheat gene pool. Theor Appl Genet 2019; 132:969-988. [PMID: 30506523 PMCID: PMC6449325 DOI: 10.1007/s00122-018-3253-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/27/2018] [Indexed: 05/09/2023]
Abstract
KEY MESSAGE Genomic selection had a higher selection response for FHB resistance than phenotypic selection, while association mapping identified major QTL on chromosome 3B unaffected by plant height and flowering date. Fusarium head blight (FHB) is one of the most destructive diseases of durum wheat. Hence, minimizing losses in yield, quality and avoiding contamination with mycotoxins are of pivotal importance, as durum wheat is mostly used for human consumption. While growing resistant varieties is the most promising approach for controlling this fungal disease, FHB resistance breeding in durum wheat is hampered by the limited variation in the elite gene pool and difficulties in efficiently combining the numerous small-effect resistance quantitative trait loci (QTL) in the same line. We evaluated an international collection of 228 genotyped durum wheat cultivars for FHB resistance over 3 years to investigate the genetic architecture and potential of genomic-assisted breeding for FHB resistance in durum wheat. Plant height was strongly positively correlated with FHB resistance and led to co-localization of plant height and resistance QTL. Nevertheless, a major QTL on chromosome 3B independent of plant height was identified in the same chromosomal interval as reported for the prominent hexaploid resistance QTL Fhb1, though haplotype analysis highlighted the distinctiveness of both QTL. Comparison between phenotypic and genomic selection for FHB resistance revealed a superior prediction ability of the former. However, simulated selection experiments resulted in higher selection responses when using genomic breeding values for early generation selection. An earlier identification of the most promising lines and crossing parents was feasible with a genomic selection index, which suggested a much faster short-term population improvement than previously possible in durum wheat, complementing long-term strategies with exotic resistance donors.
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Affiliation(s)
- Barbara Steiner
- Department of Agrobiotechnology (IFA-Tulln), Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
| | - Sebastian Michel
- Department of Agrobiotechnology (IFA-Tulln), Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430, Tulln, Austria.
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, 40127, Bologna, Italy
| | - Marc Lemmens
- Department of Agrobiotechnology (IFA-Tulln), Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
| | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, 40127, Bologna, Italy
| | - Hermann Buerstmayr
- Department of Agrobiotechnology (IFA-Tulln), Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
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21
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Condorelli GE, Maccaferri M, Newcomb M, Andrade-Sanchez P, White JW, French AN, Sciara G, Ward R, Tuberosa R. Comparative Aerial and Ground Based High Throughput Phenotyping for the Genetic Dissection of NDVI as a Proxy for Drought Adaptive Traits in Durum Wheat. Front Plant Sci 2018; 9:893. [PMID: 29997645 PMCID: PMC6028805 DOI: 10.3389/fpls.2018.00893] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/07/2018] [Indexed: 05/04/2023]
Abstract
High-throughput phenotyping platforms (HTPPs) provide novel opportunities to more effectively dissect the genetic basis of drought-adaptive traits. This genome-wide association study (GWAS) compares the results obtained with two Unmanned Aerial Vehicles (UAVs) and a ground-based platform used to measure Normalized Difference Vegetation Index (NDVI) in a panel of 248 elite durum wheat (Triticum turgidum L. ssp. durum Desf.) accessions at different growth stages and water regimes. Our results suggest increased ability of aerial over ground-based platforms to detect quantitative trait loci (QTL) for NDVI, particularly under terminal drought stress, with 22 and 16 single QTLs detected, respectively, and accounting for 89.6 vs. 64.7% phenotypic variance based on multiple QTL models. Additionally, the durum panel was investigated for leaf chlorophyll content (SPAD), leaf rolling and dry biomass under terminal drought stress. In total, 46 significant QTLs affected NDVI across platforms, 22 of which showed concomitant effects on leaf greenness, 2 on leaf rolling and 10 on biomass. Among 9 QTL hotspots on chromosomes 1A, 1B, 2B, 4B, 5B, 6B, and 7B that influenced NDVI and other drought-adaptive traits, 8 showed per se effects unrelated to phenology.
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Affiliation(s)
| | - Marco Maccaferri
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Maria Newcomb
- Maricopa Agricultural Center, University of Arizona, Tucson, AZ, United States
| | | | - Jeffrey W. White
- US Arid Land Agricultural Research Center, USDA-ARS, Maricopa, AZ, United States
| | - Andrew N. French
- US Arid Land Agricultural Research Center, USDA-ARS, Maricopa, AZ, United States
| | - Giuseppe Sciara
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Rick Ward
- Maricopa Agricultural Center, University of Arizona, Tucson, AZ, United States
| | - Roberto Tuberosa
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
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22
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Ponti G, Maccaferri M, Manfredini M, Cotugno M, Pellacani G, Conti A, Micali S, Mandrioli M, Tomasi A. Seminal cell-free DNA molecular profile as a novel diagnostic and prognostic prostate cancer biomarkers. Med Hypotheses 2018; 114:69. [DOI: 10.1016/j.mehy.2018.02.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 02/25/2018] [Indexed: 10/17/2022]
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23
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Avni R, Nave M, Barad O, Baruch K, Twardziok SO, Gundlach H, Hale I, Mascher M, Spannagl M, Wiebe K, Jordan KW, Golan G, Deek J, Ben-Zvi B, Ben-Zvi G, Himmelbach A, MacLachlan RP, Sharpe AG, Fritz A, Ben-David R, Budak H, Fahima T, Korol A, Faris JD, Hernandez A, Mikel MA, Levy AA, Steffenson B, Maccaferri M, Tuberosa R, Cattivelli L, Faccioli P, Ceriotti A, Kashkush K, Pourkheirandish M, Komatsuda T, Eilam T, Sela H, Sharon A, Ohad N, Chamovitz DA, Mayer KFX, Stein N, Ronen G, Peleg Z, Pozniak CJ, Akhunov ED, Distelfeld A. Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science 2018; 357:93-97. [PMID: 28684525 DOI: 10.1126/science.aan0032] [Citation(s) in RCA: 465] [Impact Index Per Article: 77.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/08/2017] [Indexed: 01/07/2023]
Abstract
Wheat (Triticum spp.) is one of the founder crops that likely drove the Neolithic transition to sedentary agrarian societies in the Fertile Crescent more than 10,000 years ago. Identifying genetic modifications underlying wheat's domestication requires knowledge about the genome of its allo-tetraploid progenitor, wild emmer (T. turgidum ssp. dicoccoides). We report a 10.1-gigabase assembly of the 14 chromosomes of wild tetraploid wheat, as well as analyses of gene content, genome architecture, and genetic diversity. With this fully assembled polyploid wheat genome, we identified the causal mutations in Brittle Rachis 1 (TtBtr1) genes controlling shattering, a key domestication trait. A study of genomic diversity among wild and domesticated accessions revealed genomic regions bearing the signature of selection under domestication. This reference assembly will serve as a resource for accelerating the genome-assisted improvement of modern wheat varieties.
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Affiliation(s)
- Raz Avni
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Moran Nave
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | | | | | - Sven O Twardziok
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Neuherberg, Germany
| | - Heidrun Gundlach
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Neuherberg, Germany
| | - Iago Hale
- University of New Hampshire, Durham, NH, USA
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, Germany. .,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Manuel Spannagl
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Neuherberg, Germany
| | | | | | - Guy Golan
- The Hebrew University of Jerusalem, Rehovot, Israel
| | - Jasline Deek
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Batsheva Ben-Zvi
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | | | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, Germany
| | | | - Andrew G Sharpe
- University of Saskatchewan, Saskatoon, Canada.,Global Institute for Food Security, Saskatoon, SK, Canada
| | | | - Roi Ben-David
- Agricultural Research Organization (ARO), Bet Dagan, Israel
| | | | | | | | - Justin D Faris
- U.S. Department of Agriculture (USDA)-Agricultural Research Service, Fargo, ND, USA
| | | | | | | | | | | | | | - Luigi Cattivelli
- Council of Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Primetta Faccioli
- Council of Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Aldo Ceriotti
- CNR-National Research Council, Institute of Agricultural Biology and Biotechnology, Milano, Italy
| | | | | | - Takao Komatsuda
- National Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Tamar Eilam
- The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv, Israel
| | - Hanan Sela
- The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv, Israel
| | - Amir Sharon
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.,The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv, Israel
| | - Nir Ohad
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Daniel A Chamovitz
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Klaus F X Mayer
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Neuherberg, Germany.,School of Life Sciences Weihenstephan, Technical University of Munich, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, Germany
| | | | - Zvi Peleg
- The Hebrew University of Jerusalem, Rehovot, Israel
| | | | | | - Assaf Distelfeld
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.,The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv, Israel
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24
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Condorelli GE, Maccaferri M, Newcomb M, Andrade-Sanchez P, White JW, French AN, Sciara G, Ward R, Tuberosa R. Corrigendum: Comparative Aerial and Ground Based High Throughput Phenotyping for the Genetic Dissection of NDVI as a Proxy for Drought Adaptive Traits in Durum Wheat. Front Plant Sci 2018; 9:1885. [PMID: 30613202 PMCID: PMC6312001 DOI: 10.3389/fpls.2018.01885] [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] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 05/13/2023]
Abstract
[This corrects the article DOI: 10.3389/fpls.2018.00893.].
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Affiliation(s)
| | - Marco Maccaferri
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
- *Correspondence: Marco Maccaferri
| | - Maria Newcomb
- Maricopa Agricultural Center, University of Arizona, Tucson, AZ, United States
| | | | - Jeffrey W. White
- US Arid Land Agricultural Research Center, USDA-ARS, Maricopa, AZ, United States
| | - Andrew N. French
- US Arid Land Agricultural Research Center, USDA-ARS, Maricopa, AZ, United States
| | - Giuseppe Sciara
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Rick Ward
- Maricopa Agricultural Center, University of Arizona, Tucson, AZ, United States
| | - Roberto Tuberosa
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
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25
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Liu W, Maccaferri M, Chen X, Laghetti G, Pignone D, Pumphrey M, Tuberosa R. Genome-wide association mapping reveals a rich genetic architecture of stripe rust resistance loci in emmer wheat (Triticum turgidum ssp. dicoccum). Theor Appl Genet 2017; 130:2249-2270. [PMID: 28770301 PMCID: PMC5641275 DOI: 10.1007/s00122-017-2957-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/26/2017] [Indexed: 05/05/2023]
Abstract
KEY MESSAGE SNP-based genome scanning in worldwide domesticated emmer germplasm showed high genetic diversity, rapid linkage disequilibrium decay and 51 loci for stripe rust resistance, a large proportion of which were novel. Cultivated emmer wheat (Triticum turgidum ssp. dicoccum), one of the oldest domesticated crops in the world, is a potentially rich reservoir of variation for improvement of resistance/tolerance to biotic and abiotic stresses in wheat. Resistance to stripe rust (Puccinia striiformis f. sp. tritici) in emmer wheat has been under-investigated. Here, we employed genome-wide association (GWAS) mapping with a mixed linear model to dissect effective stripe rust resistance loci in a worldwide collection of 176 cultivated emmer wheat accessions. Adult plants were tested in six environments and seedlings were evaluated with five races from the United States and one from Italy under greenhouse conditions. Five accessions were resistant across all experiments. The panel was genotyped with the wheat 90,000 Illumina iSelect single nucleotide polymorphism (SNP) array and 5106 polymorphic SNP markers with mapped positions were obtained. A high level of genetic diversity and fast linkage disequilibrium decay were observed. In total, we identified 14 loci associated with field resistance in multiple environments. Thirty-seven loci were significantly associated with all-stage (seedling) resistance and six of them were effective against multiple races. Of the 51 total loci, 29 were mapped distantly from previously reported stripe rust resistance genes or quantitative trait loci and represent newly discovered resistance loci. Our results suggest that GWAS is an effective method for characterizing genes in cultivated emmer wheat and confirm that emmer wheat is a rich source of stripe rust resistance loci that can be used for wheat improvement.
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Affiliation(s)
- Weizhen Liu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | - Marco Maccaferri
- Department of Agricultural Sciences, University of Bologna, 40127, Bologna, Italy
| | - Xianming Chen
- Wheat Health, Genetics, and Quality Research Unit, USDA-ARS, Pullman, WA, 99164-6430, USA
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Gaetano Laghetti
- CNR-Institute of Biosciences and Bioresources, 072006, Bari, Italy
| | - Domenico Pignone
- CNR-Institute of Biosciences and Bioresources, 072006, Bari, Italy
| | - Michael Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA.
| | - Roberto Tuberosa
- Department of Agricultural Sciences, University of Bologna, 40127, Bologna, Italy
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26
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Arena S, D'Ambrosio C, Vitale M, Mazzeo F, Mamone G, Di Stasio L, Maccaferri M, Curci PL, Sonnante G, Zambrano N, Scaloni A. Differential representation of albumins and globulins during grain development in durum wheat and its possible functional consequences. J Proteomics 2017; 162:86-98. [DOI: 10.1016/j.jprot.2017.05.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/21/2017] [Accepted: 05/01/2017] [Indexed: 01/03/2023]
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27
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Liu W, Maccaferri M, Rynearson S, Letta T, Zegeye H, Tuberosa R, Chen X, Pumphrey M. Novel Sources of Stripe Rust Resistance Identified by Genome-Wide Association Mapping in Ethiopian Durum Wheat ( Triticum turgidum ssp. durum). Front Plant Sci 2017; 8:774. [PMID: 28553306 PMCID: PMC5427679 DOI: 10.3389/fpls.2017.00774] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 04/25/2017] [Indexed: 05/22/2023]
Abstract
Stripe rust of wheat, caused by Puccinia striiformis f. sp. tritici (Pst), is a global concern for wheat production, and has been increasingly destructive in Ethiopia, as well as in the United States and in many other countries. As Ethiopia has a long history of stripe rust epidemics, its native wheat germplasm harbors potentially valuable resistance loci. Moreover, the Ethiopian germplasm has been historically underutilized in breeding of modern wheat worldwide and thus the resistance alleles from the Ethiopian germplasm represent potentially novel sources. The objective of this study was to identify loci conferring resistance to predominant Pst races in Ethiopia and the United States. Using a high-density 90 K wheat single nucleotide polymorphism array, a genome-wide association analysis (GWAS) was conducted on 182 durum wheat landrace accessions and contemporary varieties originating from Ethiopia. Landraces were detected to be more resistant at the seedling stage while cultivars were more resistant at the adult-plant stages. GWAS identified 68 loci associated with seedling resistance to one or more races. Six loci on chromosome arms 1AS, 1BS, 3AS, 4BL, and 5BL were associated with resistance against at least two races at the seedling stage, and five loci were previously undocumented. GWAS analysis of field resistance reactions identified 12 loci associated with resistance on chromosomes 1A, 1B, 2BS, 3BL, 4AL, 4B and 5AL, which were detected in at least two of six field screening nurseries at the adult-plant stage. Comparison with previously mapped resistance loci indicates that six of the 12 resistance loci are newly documented. This study reports effective sources of resistance to contemporary races in Ethiopia and the United States and reveals that Ethiopian durum wheat landraces are abundant in novel Pst resistance loci that may be transferred into adapted cultivars to provide resistance against Pst.
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Affiliation(s)
- Weizhen Liu
- Department of Crop and Soil Sciences, Washington State University, PullmanWA, USA
| | - Marco Maccaferri
- Department of Agricultural Sciences, University of BolognaBologna, Italy
| | - Sheri Rynearson
- Department of Crop and Soil Sciences, Washington State University, PullmanWA, USA
| | - Tesfaye Letta
- Sinana Agricultural Research CenterBale-Robe, Ethiopia
| | | | - Roberto Tuberosa
- Department of Agricultural Sciences, University of BolognaBologna, Italy
| | - Xianming Chen
- Wheat Health, Genetics, and Quality Research Unit, Agricultural Research Service (USDA), PullmanWA, USA
- Department of Plant Pathology, Washington State University, PullmanWA, USA
| | - Michael Pumphrey
- Department of Crop and Soil Sciences, Washington State University, PullmanWA, USA
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Liu W, Maccaferri M, Bulli P, Rynearson S, Tuberosa R, Chen X, Pumphrey M. Genome-wide association mapping for seedling and field resistance to Puccinia striiformis f. sp. tritici in elite durum wheat. Theor Appl Genet 2017; 130:649-667. [PMID: 28039515 DOI: 10.1007/s00122-016-2841-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 12/13/2016] [Indexed: 05/06/2023]
Abstract
Genome-wide association analysis in tetraploid wheat revealed novel and diverse loci for seedling and field resistance to stripe rust in elite spring durum wheat accessions from worldwide. Improving resistance to stripe rust, caused by Puccinia striiformis f. sp. tritici, is a major objective for wheat breeding. To identify effective stripe rust resistance loci, a genome-wide association study (GWAS) was conducted using 232 elite durum wheat (Triticum turgidum ssp. durum) lines from worldwide breeding programs. Genotyping with the 90 K iSelect wheat single nucleotide polymorphism (SNP) array resulted in 11,635 markers distributed across the genome. Response to stripe rust infection at the seedling stage revealed resistant and susceptible accessions present in rather balanced frequencies for the six tested races, with a higher frequency of susceptible responses to United States races as compared to Italian races (61.1 vs. 43.1% of susceptible accessions). Resistance at the seedling stage only partially explained adult plant resistance, which was found to be more frequent with 67.7% of accessions resistant across six nurseries in the United States. GWAS identified 82 loci associated with seedling stripe rust resistance, five of which were significant at the false discovery rate adjusted P value <0.1 and 11 loci were detected for the field response at the adult plant stages in at least two environments. Notably, Yrdurum-1BS.1 showed the largest effect for both seedling and field resistance, and is therefore considered as a major locus for resistance in tetraploid wheat. Our GWAS study is the first of its kind for stripe rust resistance in tetraploid wheat and provides an overview of resistance in elite germplasm and reports new loci that can be used in breeding resistant cultivars.
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Affiliation(s)
- Weizhen Liu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA.
| | - Marco Maccaferri
- Department of Agricultural Sciences, University of Bologna, 40127, Bologna, Italy
| | - Peter Bulli
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | - Sheri Rynearson
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | - Roberto Tuberosa
- Department of Agricultural Sciences, University of Bologna, 40127, Bologna, Italy
| | - Xianming Chen
- Wheat Health, Genetics, and Quality Research Unit, USDA-ARS, Pullman, WA, 99164-6430, USA
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Michael Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA.
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Ponti G, Maccaferri M, Depenni R, Mandrioli M, Pellacani G, Manfredini M, Ozben T, Ruini C, Iattoni E, Cerioli D, Cascinu S, Tomasi A. Quantification of circulating cell-free DNA by fluorimetry (Qubit) and spectrophotometry (NanoDrop) in patients with malignant melanoma and prostate cancer. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw341.09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Maccaferri M, Pierini V, Di Giacomo D, Zucchini P, Forghieri F, Bonacorsi G, Paolini A, Quadrelli C, Giacobbi F, Fontana F, Cappelli G, Potenza L, Marasca R, Luppi M, Mecucci C. The importance of cytogenetic and molecular analyses in eosinophilia-associated myeloproliferative neoplasms: an unusual case with normal karyotype and TNIP1- PDGFRB rearrangement and overview ofPDGFRBpartner genes. Leuk Lymphoma 2016; 58:489-493. [DOI: 10.1080/10428194.2016.1197396] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Salvi S, Giuliani S, Ricciolini C, Carraro N, Maccaferri M, Presterl T, Ouzunova M, Tuberosa R. Two major quantitative trait loci controlling the number of seminal roots in maize co-map with the root developmental genes rtcs and rum1. J Exp Bot 2016; 67:1149-59. [PMID: 26880748 PMCID: PMC4753855 DOI: 10.1093/jxb/erw011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The genetic dissection of root architecture and functions allows for a more effective and informed design of novel root ideotypes and paves the way to evaluate their effects on crop resilience to a number of abiotic stresses. In maize, limited attention has been devoted to the genetic analysis of root architecture diversity at the early stage. The difference in embryonic (including seminal and primary) root architecture between the maize reference line B73 (which mostly develops three seminal roots) and the landrace Gaspé Flint (with virtually no seminal roots) was genetically dissected using a collection of introgression lines grown in paper rolls and pots. Quantitative trait locus (QTL) analysis identified three QTLs controlling seminal root number (SRN) on chromosome bins 1.02, 3.07, and 8.04-8.05, which collectively explained 66% of the phenotypic variation. In all three cases, Gaspé Flint contributed the allele for lower SRN. Primary root dry weight was negatively correlated with SRN (r= -0.52), and QTLs for primary root size co-mapped with SRN QTLs, suggesting a pleiotropic effect of SRN QTLs on the primary root, most probably caused by competition for seed resources. Interestingly, two out of three SRN QTLs co-mapped with the only two known maize genes (rtcs and rum1) affecting the number of seminal roots. The strong additive effect of the three QTLs and the development of near isogenic lines for each QTL in the elite B73 background provide unique opportunities to characterize functionally the genes involved in root development and to evaluate how root architecture affects seedling establishment, early development, and eventually yield in maize.
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Affiliation(s)
- Silvio Salvi
- DipSA University of Bologna, viale Fanin 44, 40127 Bologna, Italy
| | - Silvia Giuliani
- DipSA University of Bologna, viale Fanin 44, 40127 Bologna, Italy
| | | | - Nicola Carraro
- DipSA University of Bologna, viale Fanin 44, 40127 Bologna, Italy
| | - Marco Maccaferri
- DipSA University of Bologna, viale Fanin 44, 40127 Bologna, Italy
| | | | | | - Roberto Tuberosa
- DipSA University of Bologna, viale Fanin 44, 40127 Bologna, Italy
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Milner SG, Maccaferri M, Huang BE, Mantovani P, Massi A, Frascaroli E, Tuberosa R, Salvi S. A multiparental cross population for mapping QTL for agronomic traits in durum wheat (Triticum turgidum ssp. durum). Plant Biotechnol J 2016; 14:735-48. [PMID: 26132599 DOI: 10.1111/pbi.12424] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 04/08/2015] [Accepted: 04/29/2015] [Indexed: 05/02/2023]
Abstract
Multiparental cross designs for mapping quantitative trait loci (QTL) provide an efficient alternative to biparental populations because of their broader genetic basis and potentially higher mapping resolution. We describe the development and deployment of a recombinant inbred line (RIL) population in durum wheat (Triticum turgidum ssp. durum) obtained by crossing four elite cultivars. A linkage map spanning 2664 cM and including 7594 single nucleotide polymorphisms (SNPs) was produced by genotyping 338 RILs. QTL analysis was carried out by both interval mapping on founder haplotype probabilities and SNP bi-allelic tests for heading date and maturity date, plant height and grain yield from four field experiments. Sixteen QTL were identified across environments and detection methods, including two yield QTL on chromosomes 2BL and 7AS, with the former mapped independently from the photoperiod response gene Ppd-B1, while the latter overlapped with the vernalization locus VRN-A3. Additionally, 21 QTL with environment-specific effects were found. Our results indicated a prevalence of environment-specific QTL with relatively small effect on the control of grain yield. For all traits, functionally different QTL alleles in terms of direction and size of genetic effect were distributed among parents. We showed that QTL results based on founder haplotypes closely matched functional alleles at known heading date loci. Despite the four founders, only 2.1 different functional haplotypes were estimated per QTL, on average. This durum wheat population provides a mapping resource for detailed genetic dissection of agronomic traits in an elite background typical of breeding programmes.
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Affiliation(s)
- Sara Giulia Milner
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Marco Maccaferri
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Bevan Emma Huang
- Digital Productivity Flagship and Agriculture Flagship, CSIRO, St Lucia, Qld, Australia
| | - Paola Mantovani
- Società Produttori Sementi Bologna, Argelato, Bologna, Italy
| | - Andrea Massi
- Società Produttori Sementi Bologna, Argelato, Bologna, Italy
| | | | - Roberto Tuberosa
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Silvio Salvi
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
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Maccaferri M, El-Feki W, Nazemi G, Salvi S, Canè MA, Colalongo MC, Stefanelli S, Tuberosa R. Prioritizing quantitative trait loci for root system architecture in tetraploid wheat. J Exp Bot 2016; 67:1161-78. [PMID: 26880749 PMCID: PMC4753857 DOI: 10.1093/jxb/erw039] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Optimization of root system architecture (RSA) traits is an important objective for modern wheat breeding. Linkage and association mapping for RSA in two recombinant inbred line populations and one association mapping panel of 183 elite durum wheat (Triticum turgidum L. var. durum Desf.) accessions evaluated as seedlings grown on filter paper/polycarbonate screening plates revealed 20 clusters of quantitative trait loci (QTLs) for root length and number, as well as 30 QTLs for root growth angle (RGA). Divergent RGA phenotypes observed by seminal root screening were validated by root phenotyping of field-grown adult plants. QTLs were mapped on a high-density tetraploid consensus map based on transcript-associated Illumina 90K single nucleotide polymorphisms (SNPs) developed for bread and durum wheat, thus allowing for an accurate cross-referencing of RSA QTLs between durum and bread wheat. Among the main QTL clusters for root length and number highlighted in this study, 15 overlapped with QTLs for multiple RSA traits reported in bread wheat, while out of 30 QTLs for RGA, only six showed co-location with previously reported QTLs in wheat. Based on their relative additive effects/significance, allelic distribution in the association mapping panel, and co-location with QTLs for grain weight and grain yield, the RSA QTLs have been prioritized in terms of breeding value. Three major QTL clusters for root length and number (RSA_QTL_cluster_5#, RSA_QTL_cluster_6#, and RSA_QTL_cluster_12#) and nine RGA QTL clusters (QRGA.ubo-2A.1, QRGA.ubo-2A.3, QRGA.ubo-2B.2/2B.3, QRGA.ubo-4B.4, QRGA.ubo-6A.1, QRGA.ubo-6A.2, QRGA.ubo-7A.1, QRGA.ubo-7A.2, and QRGA.ubo-7B) appear particularly valuable for further characterization towards a possible implementation of breeding applications in marker-assisted selection and/or cloning of the causal genes underlying the QTLs.
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Affiliation(s)
- Marco Maccaferri
- Department of Agricultural Sciences (DipSA), University of Bologna, 40127 Bologna, Italy
| | - Walid El-Feki
- Department of Agricultural Sciences (DipSA), University of Bologna, 40127 Bologna, Italy Department of Crop Sciences, Faculty of Agriculture, Alexandria University, 23714 Alexandria, Egypt
| | - Ghasemali Nazemi
- Department of Agricultural Sciences (DipSA), University of Bologna, 40127 Bologna, Italy Department of Agriculture, Hajiabad Branch, Islamic Azad University, 21100 Hajiabad, Iran
| | - Silvio Salvi
- Department of Agricultural Sciences (DipSA), University of Bologna, 40127 Bologna, Italy
| | - Maria Angela Canè
- Department of Agricultural Sciences (DipSA), University of Bologna, 40127 Bologna, Italy
| | - Maria Chiara Colalongo
- Department of Agricultural Sciences (DipSA), University of Bologna, 40127 Bologna, Italy
| | - Sandra Stefanelli
- Department of Agricultural Sciences (DipSA), University of Bologna, 40127 Bologna, Italy
| | - Roberto Tuberosa
- Department of Agricultural Sciences (DipSA), University of Bologna, 40127 Bologna, Italy
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Maccaferri M, Ricci A, Salvi S, Milner SG, Noli E, Martelli PL, Casadio R, Akhunov E, Scalabrin S, Vendramin V, Ammar K, Blanco A, Desiderio F, Distelfeld A, Dubcovsky J, Fahima T, Faris J, Korol A, Massi A, Mastrangelo AM, Morgante M, Pozniak C, N'Diaye A, Xu S, Tuberosa R. A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding. Plant Biotechnol J 2015; 13:648-63. [PMID: 25424506 DOI: 10.1111/pbi.12288] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 09/26/2014] [Accepted: 10/03/2014] [Indexed: 05/20/2023]
Abstract
Consensus linkage maps are important tools in crop genomics. We have assembled a high-density tetraploid wheat consensus map by integrating 13 data sets from independent biparental populations involving durum wheat cultivars (Triticum turgidum ssp. durum), cultivated emmer (T. turgidum ssp. dicoccum) and their ancestor (wild emmer, T. turgidum ssp. dicoccoides). The consensus map harboured 30 144 markers (including 26 626 SNPs and 791 SSRs) half of which were present in at least two component maps. The final map spanned 2631 cM of all 14 durum wheat chromosomes and, differently from the individual component maps, all markers fell within the 14 linkage groups. Marker density per genetic distance unit peaked at centromeric regions, likely due to a combination of low recombination rate in the centromeric regions and even gene distribution along the chromosomes. Comparisons with bread wheat indicated fewer regions with recombination suppression, making this consensus map valuable for mapping in the A and B genomes of both durum and bread wheat. Sequence similarity analysis allowed us to relate mapped gene-derived SNPs to chromosome-specific transcripts. Dense patterns of homeologous relationships have been established between the A- and B-genome maps and between nonsyntenic homeologous chromosome regions as well, the latter tracing to ancient translocation events. The gene-based homeologous relationships are valuable to infer the map location of homeologs of target loci/QTLs. Because most SNP and SSR markers were previously mapped in bread wheat, this consensus map will facilitate a more effective integration and exploitation of genes and QTL for wheat breeding purposes.
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Affiliation(s)
- Marco Maccaferri
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Andrea Ricci
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Silvio Salvi
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Sara Giulia Milner
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Enrico Noli
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | | | - Rita Casadio
- Biocomputing Group, University of Bologna, Bologna, Italy
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Simone Scalabrin
- Istituto di Genomica Applicata, Udine, Italy
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
| | - Vera Vendramin
- Istituto di Genomica Applicata, Udine, Italy
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
| | | | - Antonio Blanco
- Dipartimento di Biologia e Chimica Agro-forestale ed ambientale, Università di Bari, Aldo Moro, Bari, Italy
| | - Francesca Desiderio
- Consiglio per la ricerca e la sperimentazione in agricoltura, Genomics Research Centre, Fiorenzuola d'Arda, Italy
| | - Assaf Distelfeld
- Faculty of Life Sciences, Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Tzion Fahima
- Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Science and Science Education, University of Haifa, Haifa, Israel
| | - Justin Faris
- USDA-ARS Cereal Crops Research Unit, Fargo, ND, USA
| | - Abraham Korol
- Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Science and Science Education, University of Haifa, Haifa, Israel
| | - Andrea Massi
- Società Produttori Sementi Bologna (PSB), Argelato, Italy
| | - Anna Maria Mastrangelo
- Consiglio per la ricerca e la sperimentazione in agricoltura, Cereal Research Centre, Foggia, Italy
| | - Michele Morgante
- Istituto di Genomica Applicata, Udine, Italy
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Amidou N'Diaye
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Steven Xu
- USDA-ARS Cereal Crops Research Unit, Fargo, ND, USA
| | - Roberto Tuberosa
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
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Maccaferri M, Zhang J, Bulli P, Abate Z, Chao S, Cantu D, Bossolini E, Chen X, Pumphrey M, Dubcovsky J. A genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in a worldwide collection of hexaploid spring wheat (Triticum aestivum L.). G3 (Bethesda) 2015; 5:449-65. [PMID: 25609748 PMCID: PMC4349098 DOI: 10.1534/g3.114.014563] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 01/17/2015] [Indexed: 02/01/2023]
Abstract
New races of Puccinia striiformis f. sp. tritici (Pst), the causal pathogen of wheat stripe rust, show high virulence to previously deployed resistance genes and are responsible for large yield losses worldwide. To identify new sources of resistance we performed a genome-wide association study (GWAS) using a worldwide collection of 1000 spring wheat accessions. Adult plants were evaluated under field conditions in six environments in the western United States, and seedlings were tested with four Pst races. A single-nucleotide polymorphism (SNP) Infinium 9K-assay provided 4585 SNPs suitable for GWAS. High correlations among environments and high heritabilities were observed for stripe rust infection type and severity. Greater levels of Pst resistance were observed in a subpopulation from Southern Asia than in other groups. GWAS identified 97 loci that were significant for at least three environments, including 10 with an experiment-wise adjusted Bonferroni probability < 0.10. These 10 quantitative trait loci (QTL) explained 15% of the phenotypic variation in infection type, a percentage that increased to 45% when all QTL were considered. Three of these 10 QTL were mapped far from previously identified Pst resistance genes and QTL, and likely represent new resistance loci. The other seven QTL mapped close to known resistance genes and allelism tests will be required to test their relationships. In summary, this study provides an integrated view of stripe rust resistance resources in spring wheat and identifies new resistance loci that will be useful to diversify the current set of resistance genes deployed to control this devastating disease.
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Affiliation(s)
- Marco Maccaferri
- Department of Plant Sciences, University of California, Davis, California 95616 Department of Agricultural Sciences (DipSA), University of Bologna, Bologna 40127, Italy
| | - Junli Zhang
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Peter Bulli
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420
| | - Zewdie Abate
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Shiaoman Chao
- USDA-ARS, 1605 Albrecht Blvd, Fargo, North Dakota 58105
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, California 95616
| | - Eligio Bossolini
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Xianming Chen
- USDA-ARS, Wheat Genetics, Quality Physiology, and Disease Research Unit, and Department of Plant Pathology, Washington State University, Pullman, Washington 99164
| | - Michael Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, California 95616 Howard Hughes Medical Institute, Chevy Chase, Maryland 20815
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Maccaferri M, Cane' MA, Sanguineti MC, Salvi S, Colalongo MC, Massi A, Clarke F, Knox R, Pozniak CJ, Clarke JM, Fahima T, Dubcovsky J, Xu S, Ammar K, Karsai I, Vida G, Tuberosa R. A consensus framework map of durum wheat (Triticum durum Desf.) suitable for linkage disequilibrium analysis and genome-wide association mapping. BMC Genomics 2014; 15:873. [PMID: 25293821 PMCID: PMC4287192 DOI: 10.1186/1471-2164-15-873] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [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: 05/25/2014] [Accepted: 09/23/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Durum wheat (Triticum durum Desf.) is a tetraploid cereal grown in the medium to low-precipitation areas of the Mediterranean Basin, North America and South-West Asia. Genomics applications in durum wheat have the potential to boost exploitation of genetic resources and to advance understanding of the genetics of important complex traits (e.g. resilience to environmental and biotic stresses). A dense and accurate consensus map specific for T. durum will greatly facilitate genetic mapping, functional genomics and marker-assisted improvement. RESULTS High quality genotypic data from six core recombinant inbred line populations were used to obtain a consensus framework map of 598 simple sequence repeats (SSR) and Diversity Array Technology® (DArT) anchor markers (common across populations). Interpolation of unique markers from 14 maps allowed us to position a total of 2,575 markers in a consensus map of 2,463 cM. The T. durum A and B genomes were covered in their near totality based on the reference SSR hexaploid wheat map. The consensus locus order compared to those of the single component maps showed good correspondence, (average Spearman's rank correlation rho ρ value of 0.96). Differences in marker order and local recombination rate were observed between the durum and hexaploid wheat consensus maps. The consensus map was used to carry out a whole-genome search for genetic differentiation signatures and association to heading date in a panel of 183 accessions adapted to the Mediterranean areas. Linkage disequilibrium was found to decay below the r2 threshold=0.3 within 2.20 cM, on average. Strong molecular differentiations among sub-populations were mapped to 87 chromosome regions. A genome-wide association scan for heading date from 27 field trials in the Mediterranean Basin and in Mexico yielded 50 chromosome regions with evidences of association in multiple environments. CONCLUSIONS The consensus map presented here was used as a reference for genetic diversity and mapping analyses in T. durum, providing nearly complete genome coverage and even marker density. Markers previously mapped in hexaploid wheat constitute a strong link between the two species. The consensus map provides the basis for high-density single nucleotide polymorphic (SNP) marker implementation in durum wheat.
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Affiliation(s)
- Marco Maccaferri
- Department of Agricultural Sciences (DipSA), Viale Fanin 44, University of Bologna, 40127 Bologna, Italy.
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Wang S, Wong D, Forrest K, Allen A, Chao S, Huang BE, Maccaferri M, Salvi S, Milner SG, Cattivelli L, Mastrangelo AM, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, Lillemo M, Mather D, Appels R, Dolferus R, Brown-Guedira G, Korol A, Akhunova AR, Feuillet C, Salse J, Morgante M, Pozniak C, Luo MC, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards KJ, Hayden M, Akhunov E. Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array. Plant Biotechnol J 2014; 12:787-796. [PMID: 24646323 DOI: 10.1111/pbi.12183/pdf] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 01/29/2014] [Accepted: 02/05/2014] [Indexed: 05/29/2023]
Abstract
High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker-trait associations in mapping experiments. We developed a genotyping array including about 90,000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence-absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.
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Affiliation(s)
- Shichen Wang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
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Wang S, Wong D, Forrest K, Allen A, Chao S, Huang BE, Maccaferri M, Salvi S, Milner SG, Cattivelli L, Mastrangelo AM, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, Lillemo M, Mather D, Appels R, Dolferus R, Brown‐Guedira G, Korol A, Akhunova AR, Feuillet C, Salse J, Morgante M, Pozniak C, Luo M, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards KJ, Hayden M, Akhunov E. Characterization of polyploid wheat genomic diversity using a high‐density 90 000 single nucleotide polymorphism array. Plant Biotechnol J 2014; 12:787-96. [PMID: 24646323 PMCID: PMC4265271 DOI: 10.1111/pbi.12183] [Citation(s) in RCA: 1067] [Impact Index Per Article: 106.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 01/29/2014] [Accepted: 02/05/2014] [Indexed: 05/18/2023]
Affiliation(s)
- Shichen Wang
- Department of Plant Pathology Kansas State University Manhattan KS USA
| | - Debbie Wong
- Department of Environment and Primary Industry AgriBioSciences La Trobe R&D Park Bundoora Vic. Australia
| | - Kerrie Forrest
- Department of Environment and Primary Industry AgriBioSciences La Trobe R&D Park Bundoora Vic. Australia
| | - Alexandra Allen
- School of Biological Sciences University of Bristol Bristol UK
| | - Shiaoman Chao
- US Department of Agriculture–Agricultural Research Service Biosciences Research Laboratory Fargo ND USA
| | - Bevan E. Huang
- Commonwealth Scientific and Industrial Research Organization Computational Informatics and Food Futures National Research Flagship Dutton Park Qld Australia
| | - Marco Maccaferri
- Department of Agricultural Sciences University of Bologna Bologna Italy
| | - Silvio Salvi
- Department of Agricultural Sciences University of Bologna Bologna Italy
| | - Sara G. Milner
- Department of Agricultural Sciences University of Bologna Bologna Italy
| | - Luigi Cattivelli
- Consiglio per la Ricerca e la sperimentazione in Agricoltura Genomics Research Centre Fiorenzuola d'arda Italy
| | - Anna M. Mastrangelo
- Consiglio per la Ricerca e la sperimentazione in Agricoltura Cereal Research Centre Foggia Italy
| | - Alex Whan
- Commonwealth Scientific and Industrial Research Organization Plant Industry and Food Futures National Research Flagship Canberra ACT Australia
| | - Stuart Stephen
- Commonwealth Scientific and Industrial Research Organization Plant Industry and Food Futures National Research Flagship Canberra ACT Australia
| | - Gary Barker
- School of Biological Sciences University of Bristol Bristol UK
| | | | | | - Morten Lillemo
- Department of Plant Sciences Norwegian University of Life Sciences Ås Norway
| | - Diane Mather
- Waite Research Institute School of Agriculture, Food and Wine University of Adelaide Urrbrae SA Australia
| | | | - Rudy Dolferus
- Commonwealth Scientific and Industrial Research Organization Plant Industry and Food Futures National Research Flagship Canberra ACT Australia
| | - Gina Brown‐Guedira
- US Department of Agriculture–Agricultural Research Service Eastern Regional Small Grains Genotyping Laboratory Raleigh NC USA
| | - Abraham Korol
- Department of Evolutionary and Environmental Biology and Institute of Evolution University of Haifa Mount Carmel Haifa Israel
| | - Alina R. Akhunova
- K‐State Integrated Genomics Facility Kansas State University Manhattan KS USA
| | - Catherine Feuillet
- INRA – Université Blaise Pascal, UMR 1095 Genetics Diversity and Ecophysiology of Cereals Clermont‐Ferrand France
| | - Jerome Salse
- INRA – Université Blaise Pascal, UMR 1095 Genetics Diversity and Ecophysiology of Cereals Clermont‐Ferrand France
| | - Michele Morgante
- Department of Crop and Environmental Sciences University of Udine Via delle Scienze Udine Italy
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences University of Saskatchewan Saskatoon SK Canada
| | - Ming‐Cheng Luo
- Department of Plant Sciences University of California Davis CA USA
| | - Jan Dvorak
- Department of Plant Sciences University of California Davis CA USA
| | - Matthew Morell
- Commonwealth Scientific and Industrial Research Organization Plant Industry and Food Futures National Research Flagship Canberra ACT Australia
| | - Jorge Dubcovsky
- Department of Plant Sciences University of California Davis CA USA
- Howard Hughes Medical Institute Chevy Chase MD USA
| | | | - Roberto Tuberosa
- Department of Agricultural Sciences University of Bologna Bologna Italy
| | | | | | - Colin Cavanagh
- Commonwealth Scientific and Industrial Research Organization Plant Industry and Food Futures National Research Flagship Canberra ACT Australia
| | | | - Matthew Hayden
- Department of Environment and Primary Industry AgriBioSciences La Trobe R&D Park Bundoora Vic. Australia
| | - Eduard Akhunov
- Department of Plant Pathology Kansas State University Manhattan KS USA
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Canè MA, Maccaferri M, Nazemi G, Salvi S, Francia R, Colalongo C, Tuberosa R. Association mapping for root architectural traits in durum wheat seedlings as related to agronomic performance. Mol Breed 2014; 34:1629-1645. [PMID: 25506257 PMCID: PMC4257993 DOI: 10.1007/s11032-014-0177-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 10/08/2014] [Indexed: 05/18/2023]
Abstract
Association mapping provides useful insights on the genetic architecture of quantitative traits across a large number of unrelated genotypes, which in turn allows an informed choice of the lines to be crossed for a more accurate characterization of major QTLs in a biparental genetic background. In this study, seedlings of 183 durum wheat elite accessions were evaluated in order to identify QTLs for root system architecture (RSA). The QTLs identified were compared with QTLs detected for grain yield and its component traits, plant height and peduncle length measured in a previous study where the same accessions were evaluated in 15 field trials with a broad range of soil moisture availability and productivity (Maccaferri et al. in J Exp Bot 62:409-438, 2011). The following RSA features were investigated in seedlings at the four-leaf stage: seminal root angle, primary root length, total root length, average root length, root number and shoot length. Highly significant differences among accessions were detected for all traits. The highest repeatability (h2 = 0.72) was observed for seminal root angle. Out of the 48 QTLs detected for RSA, 15 overlapped with QTLs for agronomic traits and/or grain yield in two or more environments. The congruency of the effects of RSA traits and agronomic traits was evaluated. Seminal root angle and root number appear the most promising traits for further studies on the adaptive role of RSA plasticity on field performance in environments differing for water availability. Our results provide novel insights on the genetic control of RSA and its implications on field performance of durum wheat.
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Affiliation(s)
- Maria Angela Canè
- Department of Agricultural Sciences (DipSA), University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Marco Maccaferri
- Department of Agricultural Sciences (DipSA), University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Ghasemali Nazemi
- Department of Agricultural Sciences (DipSA), University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
- Department of Plant Production, I.A.U. Haji abad Branch, Haji abad, Iran
| | - Silvio Salvi
- Department of Agricultural Sciences (DipSA), University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Rossella Francia
- Department of Agricultural Sciences (DipSA), University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Chiara Colalongo
- Department of Agricultural Sciences (DipSA), University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Roberto Tuberosa
- Department of Agricultural Sciences (DipSA), University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
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40
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Pont C, Murat F, Guizard S, Flores R, Foucrier S, Bidet Y, Quraishi UM, Alaux M, Doležel J, Fahima T, Budak H, Keller B, Salvi S, Maccaferri M, Steinbach D, Feuillet C, Quesneville H, Salse J. Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo- and neoduplicated subgenomes. Plant J 2013; 76:1030-1044. [PMID: 24164652 DOI: 10.1111/tpj.12366] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 10/01/2013] [Accepted: 10/08/2013] [Indexed: 05/27/2023]
Abstract
Bread wheat derives from a grass ancestor structured in seven protochromosomes followed by a paleotetraploidization to reach a 12 chromosomes intermediate and a neohexaploidization (involving subgenomes A, B and D) event that finally shaped the 21 modern chromosomes. Insights into wheat syntenome in sequencing conserved orthologous set (COS) genes unravelled differences in genomic structure (such as gene conservation and diversity) and genetical landscape (such as recombination pattern) between ancestral as well as recent duplicated blocks. Contrasted evolutionary plasticity is observed where the B subgenome appears more sensitive (i.e. plastic) in contrast to A as dominant (i.e. stable) in response to the neotetraploidization and D subgenome as supra-dominant (i.e. pivotal) in response to the neohexaploidization event. Finally, the wheat syntenome, delivered through a public web interface PlantSyntenyViewer at http://urgi.versailles.inra.fr/synteny-wheat, can be considered as a guide for accelerated dissection of major agronomical traits in wheat.
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Affiliation(s)
- Caroline Pont
- INRA/UBP UMR 1095, Centre de Clermont Ferrand-Theix, 5 Chemin de Beaulieu, 63100, Clermont Ferrand, France
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41
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van Poecke RMP, Maccaferri M, Tang J, Truong HT, Janssen A, van Orsouw NJ, Salvi S, Sanguineti MC, Tuberosa R, van der Vossen EAG. Sequence-based SNP genotyping in durum wheat. Plant Biotechnol J 2013; 11:809-17. [PMID: 23639032 DOI: 10.1111/pbi.12072] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 03/08/2013] [Accepted: 03/15/2013] [Indexed: 05/10/2023]
Abstract
Marker development for marker-assisted selection in plant breeding is increasingly based on next-generation sequencing (NGS). However, marker development in crops with highly repetitive, complex genomes is still challenging. Here we applied sequence-based genotyping (SBG), which couples AFLP®-based complexity reduction to NGS, for de novo single nucleotide polymorphisms (SNP) marker discovery in and genotyping of a biparental durum wheat population. We identified 9983 putative SNPs in 6372 contigs between the two parents and used these SNPs for genotyping 91 recombinant inbred lines (RILs). Excluding redundant information from multiple SNPs per contig, 2606 (41%) markers were used for integration in a pre-existing framework map, resulting in the integration of 2365 markers over 2607 cM. Of the 2606 markers available for mapping, 91% were integrated in the pre-existing map, containing 708 SSRs, DArT markers, and SNPs from CRoPS technology, with a map-size increase of 492 cM (23%). These results demonstrate the high quality of the discovered SNP markers. With this methodology, it was possible to saturate the map at a final marker density of 0.8 cM/marker. Looking at the binned marker distribution (Figure 2), 63 of the 268 10-cM bins contained only SBG markers, showing that these markers are filling in gaps in the framework map. As to the markers that could not be used for mapping, the main reason was the low sequencing coverage used for genotyping. We conclude that SBG is a valuable tool for efficient, high-throughput and high-quality marker discovery and genotyping for complex genomes such as that of durum wheat.
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Letta T, Maccaferri M, Badebo A, Ammar K, Ricci A, Crossa J, Tuberosa R. Searching for novel sources of field resistance to Ug99 and Ethiopian stem rust races in durum wheat via association mapping. Theor Appl Genet 2013; 126:1237-56. [PMID: 23429902 DOI: 10.1007/s00122-013-2050-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 01/19/2013] [Indexed: 05/20/2023]
Abstract
Puccinia graminis f. sp. tritici, the causative agent of stem rust in wheat, is a devastating disease of durum wheat. While more than 50 stem rust resistance (Sr) loci have been identified in wheat, only a few of them have remained effective against Ug99 (TTKSK race) and other durum-specific Ethiopian races. An association mapping (AM) approach based on 183 diverse durum wheat accessions was utilized to identify resistance loci for stem rust response in Ethiopia over four field-evaluation seasons and artificial inoculation with Ug99 and a mixture of durum-specific races. The panel was profiled with simple sequence repeat, Diversity Arrays Technology and sequence-tagged site markers (1,253 in total). The resistance turned out to be oligogenic, with twelve QTL-tagging markers that were significant (P < 0.05) across three or four seasons. R (2) values ranged from 1.1 to 11.3 %.Twenty-four additional single-marker/QTL regions were found to be significant over two seasons. The AM results confirmed the role of Sr13, previously described in bi-parental mapping studies, and the role of chromosome regions putatively harbouring Sr9, Sr14, Sr17 and Sr28. Three minor QTLs were coincident with those reported in hexaploid wheat and five overlapped with those recently reported in the Sebatel × Kristal durum mapping population. Thirteen single-marker/QTL regions were located in chromosome regions where no Sr genes/QTLs have been previously reported. The allelic variation identified in this study is readily available and can be exploited for marker-assisted selection, thus providing additional opportunities for a more durable stem rust resistance under field conditions.
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Affiliation(s)
- Tesfaye Letta
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127, Bologna, Italy
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Terracciano I, Maccaferri M, Bassi F, Mantovani P, Sanguineti MC, Salvi S, Simková H, Doležel J, Massi A, Ammar K, Kolmer J, Tuberosa R. Development of COS-SNP and HRM markers for high-throughput and reliable haplotype-based detection of Lr14a in durum wheat (Triticum durum Desf.). Theor Appl Genet 2013; 126:1077-101. [PMID: 23292293 DOI: 10.1007/s00122-012-2038-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 12/17/2012] [Indexed: 05/09/2023]
Abstract
Leaf rust (Puccinia triticina Eriks. & Henn.) is a major disease affecting durum wheat production. The Lr14a-resistant gene present in the durum wheat cv. Creso and its derivative cv. Colosseo is one of the best characterized leaf-rust resistance sources deployed in durum wheat breeding. Lr14a has been mapped close to the simple sequence repeat markers gwm146, gwm344 and wmc10 in the distal portion of the chromosome arm 7BL, a gene-dense region. The objectives of this study were: (1) to enrich the Lr14a region with single nucleotide polymorphisms (SNPs) and high-resolution melting (HRM)-based markers developed from conserved ortholog set (COS) genes and from sequenced Diversity Array Technology (DArT(®)) markers; (2) to further investigate the gene content and colinearity of this region with the Brachypodium and rice genomes. Ten new COS-SNP and five HRM markers were mapped within an 8.0 cM interval spanning Lr14a. Two HRM markers pinpointed the locus in an interval of <1.0 cM and eight COS-SNPs were mapped 2.1-4.1 cM distal to Lr14a. Each marker was tested for its capacity to predict the state of Lr14a alleles (in particular, Lr14-Creso associated to resistance) in a panel of durum wheat elite germplasm including 164 accessions. Two of the most informative markers were converted into KASPar(®) markers. Single assay markers ubw14 and wPt-4038-HRM designed for agarose gel electrophoresis/KASPar(®) assays and high-resolution melting analysis, respectively, as well as the double-marker combinations ubw14/ubw18, ubw14/ubw35 and wPt-4038-HRM-ubw35 will be useful for germplasm haplotyping and for molecular-assisted breeding.
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Affiliation(s)
- Irma Terracciano
- Department of Agricultural Sciences (DipSA), University of Bologna, Viale Fanin 44, Bologna 40127, Italy
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Maccaferri M, Ratti C, Rubies-Autonell C, Vallega V, Demontis A, Stefanelli S, Tuberosa R, Sanguineti MC. Resistance to Soil-borne cereal mosaic virus in durum wheat is controlled by a major QTL on chromosome arm 2BS and minor loci. Theor Appl Genet 2011; 123:527-44. [PMID: 21594676 DOI: 10.1007/s00122-011-1605-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Accepted: 04/26/2011] [Indexed: 05/15/2023]
Abstract
Soil-borne cereal mosaic (SBCM) is a viral disease, which seriously affects hexaploid as well as tetraploid wheat crops in Europe. In durum wheat (Triticum durum Desf.), the elite germplasm is characterized by a wide range of responses to SBCMV, from susceptibility to almost complete resistance. In this study, the genetic analysis of SBCMV resistance was carried out using a population of 181 durum wheat recombinant inbred lines (RILs) obtained from Meridiano (resistant) × Claudio (moderately susceptible), which were profiled with SSR and DArT markers. The RILs were characterized for SBCMV response in the field under severe and uniform SBCMV infection during 2007 and 2008. A wide range of disease reactions (as estimated by symptom severity and DAS-ELISA) was observed. A large portion of the variability for SBCMV response was explained by a major QTL (QSbm.ubo-2BS) located in the distal telomeric region of chromosome 2BS near the marker triplet Xbarc35-Xwmc661-Xgwm210, with R(2) values ranging from 51.6 to 91.6%. The favorable allele was contributed by Meridiano. Several QTLs with minor effects on SBCMV response were also detected. Consistently with the observed transgressive segregation, the resistance alleles at minor QTLs were contributed by both parents. The presence and effects of QSbm.ubo-2BS were validated through association mapping in a panel of 111 elite durum wheat accessions.
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Affiliation(s)
- Marco Maccaferri
- Department of Agroenvironmental Science and Technology, University of Bologna, Viale G. Fanin 44, 40127 Bologna, Italy
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Trebbi D, Maccaferri M, de Heer P, Sørensen A, Giuliani S, Salvi S, Sanguineti MC, Massi A, van der Vossen EAG, Tuberosa R. High-throughput SNP discovery and genotyping in durum wheat (Triticum durum Desf.). Theor Appl Genet 2011; 123:555-69. [PMID: 21611761 DOI: 10.1007/s00122-011-1607-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2011] [Accepted: 04/26/2011] [Indexed: 05/07/2023]
Abstract
We describe the application of complexity reduction of polymorphic sequences (CRoPS(®)) technology for the discovery of SNP markers in tetraploid durum wheat (Triticum durum Desf.). A next-generation sequencing experiment was carried out on reduced representation libraries obtained from four durum cultivars. SNP validation and minor allele frequency (MAF) estimate were carried out on a panel of 12 cultivars, and the feasibility of genotyping these SNPs in segregating populations was tested using the Illumina Golden Gate (GG) technology. A total of 2,659 SNPs were identified on 1,206 consensus sequences. Among the 768 SNPs that were chosen irrespective of their genomic repetitiveness level and assayed on the Illumina BeadExpress genotyping system, 275 (35.8%) SNPs matched the expected genotypes observed in the SNP discovery phase. MAF data indicated that the overall SNP informativeness was high: a total of 196 (71.3%) SNPs had MAF >0.2, of which 76 (27.6%) showed MAF >0.4. Of these SNPs, 157 were mapped in one of two mapping populations (Meridiano × Claudio and Colosseo × Lloyd) and integrated into a common genetic map. Despite the relatively low genotyping efficiency of the GG assay, the validated CRoPS-derived SNPs showed valuable features for genomics and breeding applications such as a uniform distribution across the wheat genome, a prevailing single-locus codominant nature and a high polymorphism. Here, we report a new set of 275 highly robust genome-wide Triticum SNPs that are readily available for breeding purposes.
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Affiliation(s)
- Daniele Trebbi
- Keygene NV, Applied Research, Agro Business Park 90, 6708, PW, Wageningen, The Netherlands.
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Maccaferri M, Sanguineti MC, Demontis A, El-Ahmed A, Garcia del Moral L, Maalouf F, Nachit M, Nserallah N, Ouabbou H, Rhouma S, Royo C, Villegas D, Tuberosa R. Association mapping in durum wheat grown across a broad range of water regimes. J Exp Bot 2011; 62:409-38. [PMID: 21041372 DOI: 10.1093/jxb/erq287] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Association mapping was used to dissect the genetic basis of drought-adaptive traits and grain yield (GY) in a collection of 189 elite durum wheat accessions evaluated in 15 environments highly different for water availability during the crop cycle (from 146 to 711 mm) and GY (from 9.9 to 67.3 q ha(-1)). For highly heritable traits (e.g. heading date, kernel weight, etc.) several significant experiment-wise marker-trait associations were detected across five or more (up to 13 for kernel weight) environments, with R(2) values ranging from ca. 5 to 10%. As to GY, significant associations (R(2) from 2.5 to 4.2%) were mostly detected in one environment only (56 markers), while decreasing rapidly from two to five environments (from 20 to three markers, respectively) and with only one marker (Xbarc197 on chr. 5A) found significant in six environments (ranging from low- to high-yielding). These results are probably due to the complex genetic basis of GY and its interaction with environmental conditions. The number of markers significantly affecting GY decreased considerably under drought conditions, suggesting a limited effectiveness of association mapping to identify loci for GY under low-moisture conditions, most likely because different genotypes can attain similar phenotypes via different morpho-physiological traits and corresponding gene networks. Our study confirmed the role of major loci for phenology previously described in biparental mapping populations, highlighted a novel set of loci for drought-adaptive traits, and provided information on the agronomic value of the alleles at such loci across a broad range of soil moisture conditions.
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Affiliation(s)
- Marco Maccaferri
- Department of Agroenvironmental Sciences and Technology, University of Bologna, I-40127 Bologna, Italy
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47
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Graziani M, Maccaferri M, Tuberosa R, Feuillet C, Salse J, Demontis A. Fine mapping approaches of two major QTLs for yield in durum wheat. J Biotechnol 2010. [DOI: 10.1016/j.jbiotec.2010.09.783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Mantovani P, Maccaferri M, Tuberosa R, Kolmer J. Virulence Phenotypes and Molecular Genotypes in Collections of Puccinia triticina from Italy. Plant Dis 2010; 94:420-424. [PMID: 30754518 DOI: 10.1094/pdis-94-4-0420] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Twenty-four isolates of Puccinia triticina from Italy were characterized for virulence to seedlings of 22 common wheat Thatcher isolines, each with a different leaf rust resistance gene, and for molecular genotypes at 15 simple sequence repeat (SSR) loci. The isolates were compared to a set of 13 previously characterized P. triticina isolates from either durum or common wheat. Clustering based on virulence phenotypes and SSR genotypes grouped the Italian P. triticina isolates into three groups. In the first group, the isolates had virulence phenotypes and SSR genotypes that were similar to the isolates collected from durum wheat. Isolates in the second group were unique because they had virulence similar to the isolates from common wheat but were distinct for SSR genotypes compared to the isolates from durum wheat and from common wheat. Isolates in the third group had virulence phenotypes and SSR genotypes closely related to the isolates from common wheat. The isolates were grouped based on the known or assumed host of origin, virulence phenotype, and SSR genotypes. Measures of FST and RST for SSR genotypes, and ΦST for virulence phenotype were significant, which indicated differentiation among the three groups of isolates. Virulence phenotypes and molecular genotypes were highly correlated with r = 0.74.
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Affiliation(s)
- Paola Mantovani
- Department of Agroenvironmental Sciences and Technology, Viale Fanin 44, 40127, Bologna, Italy
| | - Marco Maccaferri
- Department of Agroenvironmental Sciences and Technology, Viale Fanin 44, 40127, Bologna, Italy
| | - Roberto Tuberosa
- Department of Agroenvironmental Sciences and Technology, Viale Fanin 44, 40127, Bologna, Italy
| | - James Kolmer
- Cereal Disease Laboratory, Agricultural Research Service, U.S. Department of Agriculture, 1551 Lindig Avenue, St. Paul, MN 55108, USA
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Maccaferri M, Mantovani P, Tuberosa R, Deambrogio E, Giuliani S, Demontis A, Massi A, Sanguineti MC. A major QTL for durable leaf rust resistance widely exploited in durum wheat breeding programs maps on the distal region of chromosome arm 7BL. Theor Appl Genet 2008; 117:1225-40. [PMID: 18712342 DOI: 10.1007/s00122-008-0857-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2008] [Accepted: 07/28/2008] [Indexed: 05/02/2023]
Abstract
A recombinant inbred line (RIL) population and a set of advanced lines from multiple crosses were used to investigate the leaf rust (Puccinia triticina Eriks.) resistance carried by the durum wheat cultivar Creso and its derivatives (Colosseo and Plinio). One hundred seventy-six RILs from the cross Colosseo x Lloyd were tested under artificial rust inoculation in the field. The response at the seedling stage was also investigated. A major QTL (QLr.ubo-7B.2) for leaf rust resistance controlling both the seedling and the adult open field based-response was mapped on 7BL, with the favourable allele inherited from Colosseo. QLr.ubo-7B.2 showed R2 and LOD peak values for the area under disease progress curve (AUDPC) equal to 72.9% and 44.5, respectively. The presence and location of QLr.ubo-7B.2 was validated by a linkage disequilibrium-based test using two-year field data of 62 advanced lines from 21 crosses with Creso, Colosseo or Plinio as resistance donors. QLr.ubo-7B.2 maps in a gene-dense region (7BL10-0.78-1.00) carrying several genes/QTLs in wheat and barley for resistance to rusts and other fungal diseases.
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Affiliation(s)
- M Maccaferri
- Department of Agroenvironmental Science and Technology, University of Bologna, Viale G. Fanin 44, 40127, Bologna, Italy
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Mantovani P, van der Linden G, Maccaferri M, Sanguineti MC, Tuberosa R. Nucleotide-binding site (NBS) profiling of genetic diversity in durum wheat. Genome 2007; 49:1473-80. [PMID: 17426762 DOI: 10.1139/g06-100] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Molecular markers are effective tools to investigate genetic diversity for resistance to pathogens. NBS (nucleotide-binding site) profiling is a PCR (polymerase chain reaction)-based approach to studying genetic variability that specifically targets chromosome regions containing R-genes and R-gene analogues. We used NBS profiling to measure genetic diversity among 58 accessions of durum wheat. Mean polymorphism rates detected using MseI and AluI as restriction enzymes were 34% and 22%, respectively. Mean number of polymorphisms per enzyme-primer combination was equal to 23.8 +/- 5.9, ranging from 13 to 31 polymorphic bands. In total, 96 markers over 190 indicated a good capacity to discriminate between accessions (the polymorphic index content ranging from 0.30 to 0.50). The results obtained with NBS profiling were compared with simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) data of the same set of accessions. The genetic distances computed with 190 NBS profiling markers were in close agreement with those obtained with AFLP and SSR markers (r = 0.73 and 0.76, respectively). Our results indicate that NBS profiling provides an effective means to investigate genetic diversity in durum wheat.
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Affiliation(s)
- Paola Mantovani
- Department of Agroenvironmental Sciences and Technology, Viale Fanin 44, 40127 Bologna, Italy
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