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Mastrangelo AM, Roncallo P, Matny O, Čegan R, Steffenson B, Echenique V, Šafář J, Battaglia R, Barabaschi D, Cattivelli L, Özkan H, Mazzucotelli E. A new wild emmer wheat panel allows to map new loci associated with resistance to stem rust at seedling stage. Plant Genome 2023:e20413. [PMID: 38087443 DOI: 10.1002/tpg2.20413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/26/2023] [Accepted: 10/18/2023] [Indexed: 01/21/2024]
Abstract
Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a major wheat disease worldwide. A collection of 283 wild emmer wheat [Triticum turgidum L. subsp. dicoccoides (Körn. ex Asch. & Graebn.) Thell] accessions, representative of the entire Fertile Crescent region where wild emmer naturally occurs, was assembled, genotyped, and characterized for population structure, genetic diversity, and rate of linkage disequilibrium (LD) decay. Then, the collection was employed for mapping Pgt resistance genes, as a proof of concept of the effectiveness of genome-wide association studies in wild emmer. The collection was evaluated in controlled conditions for reaction to six common Pgt pathotypes (TPMKC, TTTTF, JRCQC, TRTTF, TTKSK/Ug99, and TKTTF). Most resistant accessions originated from the Southern Levant wild emmer lineage, with some showing a resistance reaction toward three to six tested races. Association analysis was conducted considering a 12K polymorphic single-nucleotide polymorphisms dataset, kinship relatedness between accessions, and population structure. Eleven significant marker-trait associations (MTA) were identified across the genome, which explained from 17% to up to 49% of phenotypic variance with an average 1.5 additive effect (based on the 1-9 scoring scale). The identified loci were either effective against single or multiple races. Some MTAs colocalized with known Pgt resistance genes, while others represent novel resistance loci useful for durum and bread wheat prebreeding. Candidate genes with an annotated function related to plant response to pathogens were identified at the regions linked to the resistance and defined according to the estimated small LD (about 126 kb), as typical of wild species.
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Affiliation(s)
- Anna Maria Mastrangelo
- Research Centre for Cereal and Industrial Crops, Council for Agricultural Research and Economics (CREA), Foggia, Italy
| | - Pablo Roncallo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Departamento de Agronomía, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Oadi Matny
- Department of Plant Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Radim Čegan
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Brian Steffenson
- Department of Plant Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Viviana Echenique
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Departamento de Agronomía, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Jan Šafář
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
| | - Raffaella Battaglia
- Research Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics (CREA), Fiorenzuola d'Arda, Italy
| | - Delfina Barabaschi
- Research Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics (CREA), Fiorenzuola d'Arda, Italy
| | - Luigi Cattivelli
- Research Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics (CREA), Fiorenzuola d'Arda, Italy
| | - Hakan Özkan
- Faculty of Agriculture, Department of Field Crops, University of Çukurova, Adana, Turkey
| | - Elisabetta Mazzucotelli
- Research Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics (CREA), Fiorenzuola d'Arda, Italy
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Valladares García AP, Desiderio F, Simeone R, Ravaglia S, Ciorba R, Fricano A, Guerra D, Blanco A, Cattivelli L, Mazzucotelli E. QTL mapping for kernel-related traits in a durum wheat x T. dicoccum segregating population. Front Plant Sci 2023; 14:1253385. [PMID: 37849841 PMCID: PMC10577384 DOI: 10.3389/fpls.2023.1253385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/28/2023] [Indexed: 10/19/2023]
Abstract
Durum wheat breeding relies on grain yield improvement to meet its upcoming demand while coping with climate change. Kernel size and shape are the determinants of thousand kernel weight (TKW), which is a key component of grain yield, and the understanding of the genetic control behind these traits supports the progress in yield potential. The present study aimed to dissect the genetic network responsible for kernel size components (length, width, perimeter, and area) and kernel shape traits (width-to-length ratio and formcoefficient) as well as their relationships with kernel weight, plant height, and heading date in durum wheat. Quantitative Trait Locus (QTL) mapping was performed on a segregating population of 110 recombinant inbred lines, derived from a cross between the domesticated emmer wheat accession MG5323 and the durum wheat cv. Latino, evaluated in four different environments. A total of 24 QTLs stable across environments were found and further grouped in nine clusters on chromosomes 2A, 2B, 3A, 3B, 4B, 6B, and 7A. Among them, a QTL cluster on chromosome 4B was associated with kernel size traits and TKW, where the parental MG5323 contributed the favorable alleles, highlighting its potential to improve durum wheat germplasm. The physical positions of the clusters, defined by the projection on the T. durum reference genome, overlapped with already known genes (i.e., BIG GRAIN PROTEIN 1 on chromosome 4B). These results might provide genome-based guidance for the efficient exploitation of emmer wheat diversity in wheat breeding, possibly through yield-related molecular markers.
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Affiliation(s)
- Ana Paola Valladares García
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, Valencia, Spain
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Francesca Desiderio
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Rosanna Simeone
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Bari, Italy
| | | | - Roberto Ciorba
- Council for Agricultural Research and Economics (CREA) - Research Centre for Olive, Fruit and Citrus Crops, Rome, Italy
| | - Agostino Fricano
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Davide Guerra
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Antonio Blanco
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Bari, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
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Mazzucotelli E, Mastrangelo AM. Coping with Fungal Diseases in Crops: New Advances in Genomics, Breeding and Management. Genes (Basel) 2023; 14:1758. [PMID: 37761898 PMCID: PMC10531414 DOI: 10.3390/genes14091758] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 07/10/2023] [Indexed: 09/29/2023] Open
Abstract
This Special Issue comprises a collection of eight peer-reviewed articles centered around the plant-pathogen interaction with the aim of proposing strategies that enhance plant resistance to pathogens and limit the damage to crop production, utilizing a multidisciplinary approach [...].
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Affiliation(s)
- Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinfomatics, 29017 Fiorenzuola d’Arda, Italy;
| | - Anna Maria Mastrangelo
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia, Italy
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4
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Strejčková B, Mazzucotelli E, Čegan R, Milec Z, Brus J, Çakır E, Mastrangelo AM, Özkan H, Šafář J. Wild emmer wheat, the progenitor of modern bread wheat, exhibits great diversity in the VERNALIZATION1 gene. Front Plant Sci 2023; 13:1106164. [PMID: 36684759 PMCID: PMC9853909 DOI: 10.3389/fpls.2022.1106164] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Wild emmer wheat is an excellent reservoir of genetic variability that can be utilized to improve cultivated wheat to address the challenges of the expanding world population and climate change. Bearing this in mind, we have collected a panel of 263 wild emmer wheat (WEW) genotypes across the Fertile Crescent. The genotypes were grown in different locations and phenotyped for heading date. Genome-wide association mapping (GWAS) was carried out, and 16 SNPs were associated with the heading date. As the flowering time is controlled by photoperiod and vernalization, we sequenced the VRN1 gene, the most important of the vernalization response genes, to discover new alleles. Unlike most earlier attempts, which characterized known VRN1 alleles according to a partial promoter or intron sequences, we obtained full-length sequences of VRN-A1 and VRN-B1 genes in a panel of 95 wild emmer wheat from the Fertile Crescent and uncovered a significant sequence variation. Phylogenetic analysis of VRN-A1 and VRN-B1 haplotypes revealed their evolutionary relationships and geographic distribution in the Fertile Crescent region. The newly described alleles represent an attractive resource for durum and bread wheat improvement programs.
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Affiliation(s)
- Beáta Strejčková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics (CREA) Research Centre for Genomics and Bioinformatics via San Protaso 302, Fiorenzuola d’Arda, Italy
| | - Radim Čegan
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, ;Czechia
| | - Zbyněk Milec
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Jan Brus
- Department of Geoinformatics, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Esra Çakır
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Anna Maria Mastrangelo
- Council for Agricultural Research and Economics (CREA) Research Centre for Cereal and Industrial Crops, Foggia, Italy
| | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Jan Šafář
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
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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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6
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Mores A, Borrelli GM, Laidò G, Petruzzino G, Pecchioni N, Amoroso LGM, Desiderio F, Mazzucotelli E, Mastrangelo AM, Marone D. Genomic Approaches to Identify Molecular Bases of Crop Resistance to Diseases and to Develop Future Breeding Strategies. Int J Mol Sci 2021; 22:5423. [PMID: 34063853 PMCID: PMC8196592 DOI: 10.3390/ijms22115423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/30/2021] [Accepted: 05/15/2021] [Indexed: 12/16/2022] Open
Abstract
Plant diseases are responsible for substantial crop losses each year and affect food security and agricultural sustainability. The improvement of crop resistance to pathogens through breeding represents an environmentally sound method for managing disease and minimizing these losses. The challenge is to breed varieties with a stable and broad-spectrum resistance. Different approaches, from markers to recent genomic and 'post-genomic era' technologies, will be reviewed in order to contribute to a better understanding of the complexity of host-pathogen interactions and genes, including those with small phenotypic effects and mechanisms that underlie resistance. An efficient combination of these approaches is herein proposed as the basis to develop a successful breeding strategy to obtain resistant crop varieties that yield higher in increasing disease scenarios.
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Affiliation(s)
- Antonia Mores
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Grazia Maria Borrelli
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Giovanni Laidò
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Giuseppe Petruzzino
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Nicola Pecchioni
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | | | - Francesca Desiderio
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (F.D.); (E.M.)
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (F.D.); (E.M.)
| | - Anna Maria Mastrangelo
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Daniela Marone
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
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7
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Desiderio F, Bourras S, Mazzucotelli E, Rubiales D, Keller B, Cattivelli L, Valè G. Characterization of the Resistance to Powdery Mildew and Leaf Rust Carried by the Bread Wheat Cultivar Victo. Int J Mol Sci 2021; 22:ijms22063109. [PMID: 33803699 PMCID: PMC8003046 DOI: 10.3390/ijms22063109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/02/2021] [Accepted: 03/12/2021] [Indexed: 11/28/2022] Open
Abstract
Leaf rust and powdery mildew are two important foliar diseases in wheat. A recombinant inbred line (RIL) population, obtained by crossing two bread wheat cultivars (‘Victo’ and ‘Spada’), was evaluated for resistance to the two pathogens at seedling stage. Upon developing a genetic map of 8726 SNP loci, linkage analysis identified three resistance Quantitative Trait Loci (QTLs), with ‘Victo’ contributing the resistant alleles to all loci. One major QTL (QPm.gb-7A) was detected in response to Blumeria graminis on chromosome 7A, which explained 90% of phenotypic variation (PV). The co-positional relationship with known powdery mildew (Pm) resistance loci suggested that a new source of resistance was identified in T. aestivum. Two QTLs were detected in response to Puccinia triticina: a major gene on chromosome 5D (QLr.gb-5D), explaining a total PV of about 59%, and a minor QTL on chromosome 2B (QLr.gb-2B). A positional relationship was observed between the QLr.gb-5D with the known Lr1 gene, but polymorphisms were found between the cloned Lr1 and the corresponding ‘Victo’ allele, suggesting that QLr.gb-5D could represent a new functional Lr1 allele. Lastly, upon anchoring the QTL on the T. aestivum reference genome, candidate genes were hypothesized on the basis of gene annotation and in silico gene expression analysis.
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Affiliation(s)
- Francesca Desiderio
- CREA Research Centre for Genomics and Bioinformatics, 29017 Fiorenzuola d’Arda, Italy; (E.M.); (L.C.)
- Correspondence: ; Tel.: +39-0523-983758
| | - Salim Bourras
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland; (S.B.); (B.K.)
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75651 Uppsala, Sweden
| | - Elisabetta Mazzucotelli
- CREA Research Centre for Genomics and Bioinformatics, 29017 Fiorenzuola d’Arda, Italy; (E.M.); (L.C.)
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, 14004 Córdoba, Spain;
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland; (S.B.); (B.K.)
| | - Luigi Cattivelli
- CREA Research Centre for Genomics and Bioinformatics, 29017 Fiorenzuola d’Arda, Italy; (E.M.); (L.C.)
| | - Giampiero Valè
- DiSIT—Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, 13100 Vercelli, Italy;
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Nigro D, Fortunato S, Giove SL, Mazzucotelli E, Gadaleta A. Functional Validation of Glutamine synthetase and Glutamate synthase Genes in Durum Wheat near Isogenic Lines with QTL for High GPC. Int J Mol Sci 2020; 21:ijms21239253. [PMID: 33291583 PMCID: PMC7730160 DOI: 10.3390/ijms21239253] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 10/25/2020] [Revised: 11/25/2020] [Accepted: 12/02/2020] [Indexed: 11/16/2022] Open
Abstract
Durum wheat (Triticum turgidum L. ssp. durum) is a minor crop grown on about 17 million hectares of land worldwide. Several grain characteristics determine semolina's high end-use quality, such as grain protein content (GPC) which is directly related to the final products' nutritional and technological values. GPC improvement could be pursued by considering a candidate gene approach. The glutamine synthetase (GS)/glutamate synthase (GOGAT) cycle represents a bottleneck in the first step of nitrogen assimilation. QTL for GPC have been located on all chromosomes, and several major ones have been reported on 2A and 2B chromosomes, where GS2 and Fd-GOGAT genes have been mapped. A useful and efficient method to validate a putative QTL is the constitution of near-isogenic lines (NILs) by using the marker found to be associated to that QTL. Here, we present the development of two distinct sets of heterogeneous inbred family (HIF)- based NILs segregating for GS2 and Fd-GOGAT genes obtained from heterozygous lines at those loci, as well as their genotypic and phenotypic characterizations. The results allow the validation of the previously identified GPC QTL on 2A and 2B chromosomes, along with the role of these key genes in GPC control.
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Affiliation(s)
- Domenica Nigro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70126 Bari, Italy
- Correspondence: (D.N.); (A.G.); Tel.: +39-0805442997(D.N.); +39-0805442995 (A.G.)
| | | | - Stefania Lucia Giove
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, 70126 Bari, Italy;
| | | | - Agata Gadaleta
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, 70126 Bari, Italy;
- Correspondence: (D.N.); (A.G.); Tel.: +39-0805442997(D.N.); +39-0805442995 (A.G.)
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9
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Alahmad S, Kang Y, Dinglasan E, Mazzucotelli E, Voss-Fels KP, Able JA, Christopher J, Bassi FM, Hickey LT. Adaptive Traits to Improve Durum Wheat Yield in Drought and Crown Rot Environments. Int J Mol Sci 2020; 21:ijms21155260. [PMID: 32722187 PMCID: PMC7432628 DOI: 10.3390/ijms21155260] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 06/26/2020] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 02/07/2023] Open
Abstract
Durum wheat (Triticum turgidum L. ssp. durum) production can experience significant yield losses due to crown rot (CR) disease. Losses are usually exacerbated when disease infection coincides with terminal drought. Durum wheat is very susceptible to CR, and resistant germplasm is not currently available in elite breeding pools. We hypothesize that deploying physiological traits for drought adaptation, such as optimal root system architecture to reduce water stress, might minimize losses due to CR infection. This study evaluated a subset of lines from a nested association mapping population for stay-green traits, CR incidence and yield in field experiments as well as root traits under controlled conditions. Weekly measurements of normalized difference vegetative index (NDVI) in the field were used to model canopy senescence and to determine stay-green traits for each genotype. Genome-wide association studies using DArTseq molecular markers identified quantitative trait loci (QTLs) on chromosome 6B (qCR-6B) associated with CR tolerance and stay-green. We explored the value of qCR-6B and a major QTL for root angle QTL qSRA-6A using yield datasets from six rainfed environments, including two environments with high CR disease pressure. In the absence of CR, the favorable allele for qSRA-6A provided an average yield advantage of 0.57 t·ha−1, whereas in the presence of CR, the combination of favorable alleles for both qSRA-6A and qCR-6B resulted in a yield advantage of 0.90 t·ha−1. Results of this study highlight the value of combining above- and belowground physiological traits to enhance yield potential. We anticipate that these insights will assist breeders to design improved durum varieties that mitigate production losses due to water deficit and CR.
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Affiliation(s)
- Samir Alahmad
- Centre for Crop Science, The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Brisbane, QLD 4072, Australia; (Y.K.); (E.D.); (K.P.V.-F.)
- Correspondence: (S.A.); (L.T.H.)
| | - Yichen Kang
- Centre for Crop Science, The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Brisbane, QLD 4072, Australia; (Y.K.); (E.D.); (K.P.V.-F.)
| | - Eric Dinglasan
- Centre for Crop Science, The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Brisbane, QLD 4072, Australia; (Y.K.); (E.D.); (K.P.V.-F.)
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics (CREA)—Research Centre for Genomics and Bioinformatics, 29017 Fiorenzuola d’Arda (PC), Italy;
| | - Kai P. Voss-Fels
- Centre for Crop Science, The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Brisbane, QLD 4072, Australia; (Y.K.); (E.D.); (K.P.V.-F.)
| | - Jason A. Able
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Urrbrae, SA 5064, Australia;
| | - Jack Christopher
- Centre for Crop Science, The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Leslie Research Facility, Toowoomba, QLD 4350, Australia;
| | - Filippo M. Bassi
- International Center for the Agricultural Research in the Dry Areas, Rabat 10000, Morocco;
| | - Lee T. Hickey
- Centre for Crop Science, The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Brisbane, QLD 4072, Australia; (Y.K.); (E.D.); (K.P.V.-F.)
- Correspondence: (S.A.); (L.T.H.)
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10
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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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11
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Bertazzon N, Bagnaresi P, Forte V, Mazzucotelli E, Filippin L, Guerra D, Zechini A, Cattivelli L, Angelini E. Grapevine comparative early transcriptomic profiling suggests that Flavescence dorée phytoplasma represses plant responses induced by vector feeding in susceptible varieties. BMC Genomics 2019; 20:526. [PMID: 31242866 PMCID: PMC6595628 DOI: 10.1186/s12864-019-5908-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 02/26/2019] [Accepted: 06/17/2019] [Indexed: 01/18/2023] Open
Abstract
Background Flavescence dorée is the most serious grapevine yellows disease in Europe. It is caused by phytoplasmas which are transmitted from grapevine to grapevine by the leafhopper Scaphoideus titanus. Differences in susceptibility among grapevine varieties suggest the existence of specific genetic features associated with resistance to the phytoplasma and/or possibly with its vector. In this work, RNA-Seq was used to compare early transcriptional changes occurring during the three-trophic interaction between the phytoplasma, its vector and the grapevine, represented by two different cultivars, one very susceptible to the disease and the other scarcely susceptible. Results The comparative analysis of the constitutive transcriptomic profiles suggests the existence of passive defense strategies against the insect and/or the phytoplasma in the scarcely-susceptible cultivar. Moreover, the attack by the infective vector on the scarcely-susceptible variety prompted immediate and substantial transcriptomic changes that led to the rapid erection of further active defenses. On the other hand, in the most susceptible variety the response was delayed and mainly consisted of the induction of phytoalexin synthesis. Surprisingly, the jasmonic acid- and ethylene-mediated defense reactions, activated by the susceptible cultivar following FD-free insect feeding, were not detected in the presence of the phytoplasma-infected vector. Conclusions The comparison of the transcriptomic response in two grapevine varieties with different levels of susceptibility to Flavescence dorèe highlighted both passive and active defense mechanisms against the vector and/or the pathogen in the scarcely-susceptible variety, as well as the capacity of the phytoplasmas to repress the defense reaction against the insect in the susceptible variety. Electronic supplementary material The online version of this article (10.1186/s12864-019-5908-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nadia Bertazzon
- CREA Research Centre for Viticulture and Enology, 31015, Conegliano (TV), Italy.
| | - Paolo Bagnaresi
- CREA Research Centre for Genomics and Bioinformatics, 29017, Fiorenzuola d'Arda (PC), Italy
| | - Vally Forte
- CREA Research Centre for Viticulture and Enology, 31015, Conegliano (TV), Italy
| | | | - Luisa Filippin
- CREA Research Centre for Viticulture and Enology, 31015, Conegliano (TV), Italy
| | - Davide Guerra
- CREA Research Centre for Genomics and Bioinformatics, 29017, Fiorenzuola d'Arda (PC), Italy
| | - Antonella Zechini
- CREA Research Centre for Genomics and Bioinformatics, 29017, Fiorenzuola d'Arda (PC), Italy
| | - Luigi Cattivelli
- CREA Research Centre for Genomics and Bioinformatics, 29017, Fiorenzuola d'Arda (PC), Italy
| | - Elisa Angelini
- CREA Research Centre for Viticulture and Enology, 31015, Conegliano (TV), Italy
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12
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Desiderio F, Zarei L, Licciardello S, Cheghamirza K, Farshadfar E, Virzi N, Sciacca F, Bagnaresi P, Battaglia R, Guerra D, Palumbo M, Cattivelli L, Mazzucotelli E. Genomic Regions From an Iranian Landrace Increase Kernel Size in Durum Wheat. Front Plant Sci 2019; 10:448. [PMID: 31057571 PMCID: PMC6482228 DOI: 10.3389/fpls.2019.00448] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/25/2019] [Indexed: 05/27/2023]
Abstract
Kernel size and shape are important parameters determining the wheat profitability, being main determinants of yield and its technological quality. In this study, a segregating population of 118 recombinant inbred lines, derived from a cross between the Iranian durum landrace accession "Iran_249" and the Iranian durum cultivar "Zardak", was used to investigate durum wheat kernel morphology factors and their relationships with kernel weight, and to map the corresponding QTLs. A high density genetic map, based on wheat 90k iSelect Infinium SNP assay, comprising 6,195 markers, was developed and used to perform the QTL analysis for kernel length and width, traits related to kernel shape and weight, and heading date, using phenotypic data from three environments. Overall, a total of 31 different QTLs and 9 QTL interactions for kernel size, and 21 different QTLs and 5 QTL interactions for kernel shape were identified. The landrace Iran_249 contributed the allele with positive effect for most of the QTLs related to kernel length and kernel weight suggesting that the landrace might have considerable potential toward enhancing the existing gene pool for grain shape and size traits and for further yield improvement in wheat. The correlation among traits and co-localization of corresponding QTLs permitted to define 11 clusters suggesting causal relationships between simplest kernel size trait, like kernel length and width, and more complex secondary trait, like kernel shape and weight related traits. Lastly, the recent release of the T. durum reference genome sequence allowed to define the physical interval of our QTL/clusters and to hypothesize novel candidate genes inspecting the gene content of the genomic regions associated to target traits.
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Affiliation(s)
- Francesca Desiderio
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Leila Zarei
- Department of Agronomy and Plant Breeding, Razi University, Kermanshah, Iran
| | - Stefania Licciardello
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, Acireale, Italy
| | | | | | - Nino Virzi
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, Acireale, Italy
| | - Fabiola Sciacca
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, Acireale, Italy
| | - Paolo Bagnaresi
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Raffaella Battaglia
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Davide Guerra
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Massimo Palumbo
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, Acireale, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
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13
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Alahmad S, El Hassouni K, Bassi FM, Dinglasan E, Youssef C, Quarry G, Aksoy A, Mazzucotelli E, Juhász A, Able JA, Christopher J, Voss-Fels KP, Hickey LT. A Major Root Architecture QTL Responding to Water Limitation in Durum Wheat. Front Plant Sci 2019; 10:436. [PMID: 31024600 PMCID: PMC6468307 DOI: 10.3389/fpls.2019.00436] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/22/2019] [Indexed: 05/21/2023]
Abstract
The optimal root system architecture (RSA) of a crop is context dependent and critical for efficient resource capture in the soil. Narrow root growth angle promoting deeper root growth is often associated with improved access to water and nutrients in deep soils during terminal drought. RSA, therefore is a drought-adaptive trait that could minimize yield losses in regions with limited rainfall. Here, GWAS for seminal root angle (SRA) identified seven marker-trait associations clustered on chromosome 6A, representing a major quantitative trait locus (qSRA-6A) which also displayed high levels of pairwise LD (r 2 = 0.67). Subsequent haplotype analysis revealed significant differences between major groups. Candidate gene analysis revealed loci related to gravitropism, polar growth and hormonal signaling. No differences were observed for root biomass between lines carrying hap1 and hap2 for qSRA-6A, highlighting the opportunity to perform marker-assisted selection for the qSRA-6A locus and directly select for wide or narrow RSA, without influencing root biomass. Our study revealed that the genetic predisposition for deep rooting was best expressed under water-limitation, yet the root system displayed plasticity producing root growth in response to water availability in upper soil layers. We discuss the potential to deploy root architectural traits in cultivars to enhance yield stability in environments that experience limited rainfall.
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Affiliation(s)
- Samir Alahmad
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Khaoula El Hassouni
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
- International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
| | - Filippo M. Bassi
- International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
| | - Eric Dinglasan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Chvan Youssef
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Georgia Quarry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Alpaslan Aksoy
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | | | - Angéla Juhász
- School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Jason A. Able
- School of Agriculture, Food & Wine, Waite Research Institute, The University of Adelaide, Urrbrae, SA, Australia
| | - Jack Christopher
- Leslie Research Facility, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Kai P. Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Lee T. Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
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14
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Saccomanno A, Matny O, Marone D, Laidò G, Petruzzino G, Mazzucotelli E, Desiderio F, Blanco A, Gadaleta A, Pecchioni N, De Vita P, Steffenson B, Mastrangelo AM. Genetic Mapping of Loci for Resistance to Stem Rust in a Tetraploid Wheat Collection. Int J Mol Sci 2018; 19:E3907. [PMID: 30563213 PMCID: PMC6321032 DOI: 10.3390/ijms19123907] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 11/07/2018] [Revised: 12/04/2018] [Accepted: 12/04/2018] [Indexed: 01/31/2023] Open
Abstract
Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a major biotic constraint to wheat production worldwide. Disease resistant cultivars are a sustainable means for the efficient control of this disease. To identify quantitative trait loci (QTLs) conferring resistance to stem rust at the seedling stage, an association mapping panel consisting of 230 tetraploid wheat accessions were evaluated for reaction to five Pgt races under greenhouse conditions. A high level of phenotypic variation was observed in the panel in response to all of the races, allowing for genome-wide association mapping of resistance QTLs in wild, landrace, and cultivated tetraploid wheats. Twenty-two resistance QTLs were identified, which were characterized by at least two marker-trait associations. Most of the identified resistance loci were coincident with previously identified rust resistance genes/QTLs; however, six regions detected on chromosomes 1B, 5A, 5B, 6B, and 7B may be novel. Availability of the reference genome sequence of wild emmer wheat accession Zavitan facilitated the search for candidate resistance genes in the regions where QTLs were identified, and many of them were annotated as NOD (nucleotide binding oligomerization domain)-like receptor (NLR) genes or genes related to broad spectrum resistance.
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Affiliation(s)
- Antonietta Saccomanno
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia (FG), Italy.
| | - Oadi Matny
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA.
| | - Daniela Marone
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia (FG), Italy.
| | - Giovanni Laidò
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia (FG), Italy.
| | - Giuseppe Petruzzino
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia (FG), Italy.
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinfomatics, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Francesca Desiderio
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinfomatics, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Antonio Blanco
- Department of Agricultural & Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, 70126 Bari, Italy.
| | - Agata Gadaleta
- Department of Agricultural & Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, 70126 Bari, Italy.
| | - Nicola Pecchioni
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia (FG), Italy.
| | - Pasquale De Vita
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia (FG), 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, 24126 Bergamo (BG), Italy.
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15
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Borrelli GM, Mazzucotelli E, Marone D, Crosatti C, Michelotti V, Valè G, Mastrangelo AM. Regulation and Evolution of NLR Genes: A Close Interconnection for Plant Immunity. Int J Mol Sci 2018; 19:E1662. [PMID: 29867062 PMCID: PMC6032283 DOI: 10.3390/ijms19061662] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [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: 05/04/2018] [Revised: 06/01/2018] [Accepted: 06/02/2018] [Indexed: 12/12/2022] Open
Abstract
NLR (NOD-like receptor) genes belong to one of the largest gene families in plants. Their role in plants' resistance to pathogens has been clearly described for many members of this gene family, and dysregulation or overexpression of some of these genes has been shown to induce an autoimmunity state that strongly affects plant growth and yield. For this reason, these genes have to be tightly regulated in their expression and activity, and several regulatory mechanisms are described here that tune their gene expression and protein levels. This gene family is subjected to rapid evolution, and to maintain diversity at NLRs, a plethora of genetic mechanisms have been identified as sources of variation. Interestingly, regulation of gene expression and evolution of this gene family are two strictly interconnected aspects. Indeed, some examples have been reported in which mechanisms of gene expression regulation have roles in promotion of the evolution of this gene family. Moreover, co-evolution of the NLR gene family and other gene families devoted to their control has been recently demonstrated, as in the case of miRNAs.
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Affiliation(s)
- Grazia M Borrelli
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 673, km 25.2, 71122 Foggia, Italy.
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Daniela Marone
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 673, km 25.2, 71122 Foggia, Italy.
| | - Cristina Crosatti
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Vania Michelotti
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Giampiero Valè
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, Italy.
| | - Anna M Mastrangelo
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, via Stezzano 24, 24126 Bergamo, Italy.
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16
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Mazzucotelli E, Trono D. Cloning, expression analysis, and functional characterization of two secretory phospholipases A2 in durum wheat (Triticum durum Desf.). Plant Sci 2015; 241:295-306. [PMID: 26706080 DOI: 10.1016/j.plantsci.2015.10.009] [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] [Received: 09/07/2015] [Revised: 10/16/2015] [Accepted: 10/17/2015] [Indexed: 06/05/2023]
Abstract
We previously isolated four cDNAs in durum wheat, TdsPLA2I, TdsPLA2II, TdsPLA2III and TdsPLA2IV, that encode proteins with homology to plant secretory phospholipases A2 (sPLA2s) (Verlotta et al., Int. J. Mol. Sci., 14, 2013, 5146-5169). In this study, we have further characterized TdsPLA2II and TdsPLA2III sequences that, on the basis of our previous findings, might encode sPLA2 isoforms with different features. Functional analysis revealed that, similarly to other known sPLA2s, TdsPLA2II and TdsPLA2III have an optimum at pH 9.0, require Ca(2+), are heat stable, and are inhibited by the disulfide-bond-reducing agent dithiothreitol. However, differences emerged between these TdsPLA2 isoforms. Transcript analysis revealed that the TdsPLA2III gene is highly up-regulated under different environmental stresses; conversely, the TdsPLA2II gene is expressed at constant levels under almost all of the stress conditions examined. Moreover, TdsPLA2II is saturated at micromolar substrate and Ca(2+) concentrations, whereas TdsPLA2III requires millimolar concentrations to reach maximal activity. This suggests that TdsPLA2II normally functions under optimal conditions in vivo, whereas TdsPLA2III is only partially activated, depending on the specific phospholipid and Ca(2+) levels. Altogether these data lead to the hypothesis that in vivo TdsPLA2II and TdsPLA2III are differently regulated at both molecular and biochemical level and that TdsPLA2III plays a major role in durum wheat response to adverse environmental conditions.
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MESH Headings
- Amino Acid Sequence
- Cloning, Molecular
- DNA, Complementary/genetics
- DNA, Complementary/metabolism
- DNA, Plant/genetics
- DNA, Plant/metabolism
- Gene Expression Regulation, Plant
- Molecular Sequence Data
- Phospholipases A2, Secretory/genetics
- Phospholipases A2, Secretory/metabolism
- Phylogeny
- Plant Proteins/genetics
- Plant Proteins/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Sequence Alignment
- Triticum/enzymology
- Triticum/genetics
- Triticum/metabolism
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Affiliation(s)
- Elisabetta Mazzucotelli
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per la Genomica Vegetale, Via San Protaso 302, 29017 Fiorenzuola d'Arda, Italy
| | - Daniela Trono
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per la Cerealicoltura, S.S. 673, Km 25,200, 71122 Foggia, Italy.
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17
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Guerra D, Crosatti C, Khoshro HH, Mastrangelo AM, Mica E, Mazzucotelli E. Post-transcriptional and post-translational regulations of drought and heat response in plants: a spider's web of mechanisms. Front Plant Sci 2015; 6:57. [PMID: 25717333 PMCID: PMC4324062 DOI: 10.3389/fpls.2015.00057] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/22/2015] [Indexed: 05/14/2023]
Abstract
Drought and heat tolerance are complex quantitative traits. Moreover, the adaptive significance of some stress-related traits is more related to plant survival than to agronomic performance. A web of regulatory mechanisms fine-tunes the expression of stress-related traits and integrates both environmental and developmental signals. Both post-transcriptional and post-translational modifications contribute substantially to this network with a pivotal regulatory function of the transcriptional changes related to cellular and plant stress response. Alternative splicing and RNA-mediated silencing control the amount of specific transcripts, while ubiquitin and SUMO modify activity, sub-cellular localization and half-life of proteins. Interactions across these modification mechanisms ensure temporally and spatially appropriate patterns of downstream-gene expression. For key molecular components of these regulatory mechanisms, natural genetic diversity exists among genotypes with different behavior in terms of stress tolerance, with effects upon the expression of adaptive morphological and/or physiological target traits.
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Affiliation(s)
- Davide Guerra
- Genomics Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Fiorenzuola d’Arda, Piacenza, Italy
| | - Cristina Crosatti
- Genomics Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Fiorenzuola d’Arda, Piacenza, Italy
| | - Hamid H. Khoshro
- Department of Agronomy and Plant Breeding, Ilam University, Ilam, Iran
| | - Anna M. Mastrangelo
- Cereal Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Foggia, Italy
| | - Erica Mica
- Genomics Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Fiorenzuola d’Arda, Piacenza, Italy
| | - Elisabetta Mazzucotelli
- Genomics Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Fiorenzuola d’Arda, Piacenza, Italy
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Crosatti C, Rizza F, Badeck FW, Mazzucotelli E, Cattivelli L. Harden the chloroplast to protect the plant. Physiol Plant 2013; 147:55-63. [PMID: 22938043 DOI: 10.1111/j.1399-3054.2012.01689.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Revised: 06/23/2012] [Accepted: 07/03/2012] [Indexed: 05/04/2023]
Abstract
The chloroplast is the central switch of the plant's response to cold and light stress. The ability of many plant species to develop a cold tolerant phenotype is dependent on the presence of light and photosynthetic activity during low-temperature growth. Light exposure at low temperature stimulates an over-reduction of the plastoquinone pool as well as the accumulation of reactive oxygen species, and both metabolic conditions generate a retrograde signal controlling nuclear gene expression. At the same time the chloroplast is the target of many cold acclimation processes which are the results of the chloroplast-nucleus cross-talk. Often, the extent of cold acclimation of the chloroplast is tightly correlated with the overall plant tolerance to chilling and freezing temperatures, a finding suggesting that the chloroplast cold acclimation could be the rate limiting factor in the adaptation to low temperature.
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Abstract
Plant cells regulate many cellular processes controlling the half-life of critical proteins through ubiquitination. Previously, we characterized two interacting RING-type E3 ubiquitin ligases of Triticum durum, TdRF1 and WVIP2. We revealed their role in tolerance to dehydration, and existing knowledge about their partners also indicated their involvement in the regulation of some aspects of plant development. Here we located WVIP2 in the regulation of the ABA signaling, based on sequence similarities. Further we acquired general evidence about the versatility of ubiquitination in plant cells. A protein can be target of different E3 ligases for a perfect tuning of its abundance as well as the same E3 ligase can ubiquitinate different and unrelated proteins, thus representing a cross-connections between different signaling pathways for a global coordination of cellular processes.
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Guerra D, Mastrangelo AM, Lopez-Torrejon G, Marzin S, Schweizer P, Stanca AM, del Pozo JC, Cattivelli L, Mazzucotelli E. Identification of a protein network interacting with TdRF1, a wheat RING ubiquitin ligase with a protective role against cellular dehydration. Plant Physiol 2012; 158:777-89. [PMID: 22167118 PMCID: PMC3271766 DOI: 10.1104/pp.111.183988] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Plants exploit ubiquitination to modulate the proteome with the final aim to ensure environmental adaptation and developmental plasticity. Ubiquitination targets are specifically driven to degradation through the action of E3 ubiquitin ligases. Genetic analyses have indicated wide functions of ubiquitination in plant life; nevertheless, despite the large number of predicted E3s, only a few of them have been characterized so far, and only a few ubiquitination targets are known. In this work, we characterized durum wheat (Triticum durum) RING Finger1 (TdRF1) as a durum wheat nuclear ubiquitin ligase. Moreover, its barley (Hordeum vulgare) homolog was shown to protect cells from dehydration stress. A protein network interacting with TdRF1 has been defined. The transcription factor WHEAT BEL1-TYPE HOMEODOMAIN1 (WBLH1) was degraded in a TdRF1-dependent manner through the 26S proteasome in vivo, the mitogen-activated protein kinase TdWNK5 [for Triticum durum WITH NO LYSINE (K)5] was able to phosphorylate TdRF1 in vitro, and the RING-finger protein WHEAT VIVIPAROUS-INTERACTING PROTEIN2 (WVIP2) was shown to have a strong E3 ligase activity. The genes coding for the TdRF1 interactors were all responsive to cold and/or dehydration stress, and a negative regulative function in dehydration tolerance was observed for the barley homolog of WVIP2. A role in the control of plant development was previously known, or predictable based on homology, for wheat BEL1-type homeodomain1(WBLH1). Thus, TdRF1 E3 ligase might act regulating the response to abiotic stress and remodeling plant development in response to environmental constraints.
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Mazzucotelli E, Belloni S, Marone D, De Leonardis A, Guerra D, Di Fonzo N, Cattivelli L, Mastrangelo A. The e3 ubiquitin ligase gene family in plants: regulation by degradation. Curr Genomics 2011; 7:509-22. [PMID: 18369404 DOI: 10.2174/138920206779315728] [Citation(s) in RCA: 172] [Impact Index Per Article: 13.2] [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: 09/26/2006] [Revised: 10/19/2006] [Accepted: 10/22/2006] [Indexed: 02/02/2023] Open
Abstract
The regulation of protein expression and activity has been for long time considered only in terms of transcription/translation efficiency. In the last years, the discovery of post-transcriptional and post-translational regulation mechanisms pointed out that the key factor in determining transcript/protein amount is the synthesis/degradation ratio, together with post-translational modifications of proteins. Polyubiquitinaytion marks target proteins directed to degradation mediated by 26S-proteasome. Recent functional genomics studies pointed out that about 5% of Arabidopsis genome codes for proteins of ubiquitination pathway. The most of them (more than one thousand genes) correspond to E3 ubiquitin ligases that specifically recognise target proteins. The huge size of this gene family, whose members are involved in regulation of a number of biological processes including hormonal control of vegetative growth, plant reproduction, light response, biotic and abiotic stress tolerance and DNA repair, indicates a major role for protein degradation in control of plant life.
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Affiliation(s)
- E Mazzucotelli
- C.R.A.-Experimental Institute for Cereal Research, Section of Foggia, S.S. 16 km 675, 71100 Foggia, Italy
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Mazzucotelli E, Tartari A, Cattivelli L, Forlani G. Metabolism of gamma-aminobutyric acid during cold acclimation and freezing and its relationship to frost tolerance in barley and wheat. J Exp Bot 2006; 57:3755-66. [PMID: 16997899 DOI: 10.1093/jxb/erl141] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Amino acid homeostasis was investigated in frost-resistant barley seedlings under either cold- or freezing-stress conditions. Total free amino acid content varied only slightly, but a substantial conversion of glutamate to gamma-aminobutyric acid (GABA) was found that was proportional to the severity of the stress. Cold acclimation caused a significant increase in amino acid pools, and induced the expression of the GABA-shunt genes. As a consequence, GABA accumulated to a higher extent during the subsequent exposure to lower temperature. A different picture was obtained with a frost-sensitive genotype, in which glutamate decarboxylation occurred during the stress as well, but the activation of the GABA shunt seemed not to take place, and free glutamate was almost depleted. Analogous results were found in frost-resistant and frost-sensitive wheat cultivars. Feeding non-hardened plants with exogenous glutamate resulted in increased GABA accumulation under low temperature. The possibility that glutamate decarboxylation and GABA metabolism would play a role in frost tolerance is discussed.
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Affiliation(s)
- Elisabetta Mazzucotelli
- Dipartimento di Biologia, Università di Ferrara, via L. Borsari 46, 44100 Ferrara (FE), Italy
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Marè C, Mazzucotelli E, Crosatti C, Francia E, Stanca AM, Cattivelli L. Hv-WRKY38: a new transcription factor involved in cold- and drought-response in barley. Plant Mol Biol 2004; 55:399-416. [PMID: 15604689 DOI: 10.1007/s11103-004-0906-7] [Citation(s) in RCA: 182] [Impact Index Per Article: 9.1] [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
WRKY proteins constitute a large family of plant specific transcription factors implicated in many different processes. Here we describe Hv-WRKY38, a barley gene coding for a WRKY protein, whose expression is involved in cold and drought stress response. Hv-WRKY38 was early and transiently expressed during exposure to low non-freezing temperature, in ABA-independent manner. Furthermore, it showed a continuous induction during dehydration and freezing treatments. A WRKY38:YFP fusion protein was found to localise into the nucleus upon introduction into epidermal onion cells. Bacterially expressed Hv-WRKY38 was able to bind in vitro to the W-box element (T)TGAC(C/T) also recognisable by other WRKY proteins. Hv-WRKY38 genomic DNA was sequenced and mapped onto the centromeric region of the barley chromosome 6H. Arabidopsis and rice sequences homologous to Hv-WRKY38 were also identified. Our results indicate that Hv-WRKY38 transcription factor may play a regulatory role in abiotic stress response.
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Affiliation(s)
- Caterina Marè
- Istituto Sperimentale per la Cerealicoltura, Via S. Protaso 302, Italy.
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Crosatti C, Marè C, Mazzucotelli E, Belloni S, Barilli S, Bassi R, Dubcovskyi J, Galiba G, Stanca AM, Cattivelli L. Genetic analysis of the expression of the cold-regulated gene cor14b: a way toward the identification of components of the cold response signal transduction in Triticeae. ACTA ACUST UNITED AC 2003. [DOI: 10.1139/b03-114] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Extensive molecular biological studies have led to the cloning of many cold-regulated genes (cor) whose expression is up-regulated in winter cereals during exposure to cold. Among them is cor14b, a nuclear gene coding for a chloroplast-localized protein whose expression level has been associated with frost resistance in Triticeae. Although frost tolerance is recognised as a complex quantitative character, members of homologous group 5 in Triticeae are known to carry major loci determining frost tolerance. In this work we summarize a number of recent experiments where the cold-regulated gene cor14b was used as a tool (i) to understand the genetic relationship between the expression of cor genes and the frost resistance loci and (ii) to identify barley mutants revealing a chloroplast role in the signal transduction pathway leading to the molecular cold response.Key words: Triticeae, cold hardening, frost resistance, cor genes.
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