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Talukder ZI, Underwood W, Misar CG, Li X, Seiler GJ, Cai X, Qi L. Genetic analysis of basal stalk rot resistance introgressed from wild Helianthus petiolaris into cultivated sunflower ( Helianthus annuus L.) using an advanced backcross population. FRONTIERS IN PLANT SCIENCE 2023; 14:1278048. [PMID: 37920712 PMCID: PMC10619160 DOI: 10.3389/fpls.2023.1278048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 09/29/2023] [Indexed: 11/04/2023]
Abstract
Introduction Sclerotinia sclerotiorum is a serious pathogen causing severe basal stalk rot (BSR) disease on cultivated sunflower (Helianthus annuus L.) that leads to significant yield losses due to insufficient resistance. The wild annual sunflower species H. petiolaris, commonly known as prairie sunflower is known for its resistance against this pathogen. Sunflower resistance to BSR is quantitative and determined by many genes with small effects on the resistance phenotype. The objective of this study was to identify loci governing BSR resistance derived from H. petiolaris using a quantitative trait loci (QTL) mapping approach. Methods BSR resistance among lines of an advanced backcross population (AB-QTL) with 174 lines developed from a cross of inbred line HA 89 with H. petiolaris PI 435843 was determined in the field during 2017-2019, and in the greenhouse in 2019. AB-QTL lines and the HA 89 parent were genotyped using genotyping-by-sequencing and a genetic linkage map was developed spanning 997.51 cM and using 1,150 SNP markers mapped on 17 sunflower chromosomes. Results and discussion Highly significant differences (p<0.001) for BSR response among AB-QTL lines were observed disease incidence (DI) in all field seasons, as well as disease rating (DR) and area under the disease progress curve (AUDPC) in the greenhouse with a moderately high broad-sense heritability (H 2) of 0.61 for the tested resistance parameters. A total of 14 QTL associated with BSR resistance were identified on nine chromosomes, each explaining a proportion of the phenotypic variation ranging from 3.5% to 28.1%. Of the 14 QTL, eight were detected for BSR resistance in the field and six were detected under greenhouse conditions. Alleles conferring increased BSR resistance were contributed by the H. petiolaris parent at 11 of the 14 QTL.
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Affiliation(s)
- Zahirul I. Talukder
- United States Department of Agriculture (USDA)-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - William Underwood
- United States Department of Agriculture (USDA)-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Christopher G. Misar
- United States Department of Agriculture (USDA)-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Xuehui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Gerald J. Seiler
- United States Department of Agriculture (USDA)-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Xiwen Cai
- Wheat, Sorghum and Forage Research Unit, United States Department of Agriculture (USDA)-Agricultural Research Service, Lincoln, NE, United States
| | - Lili Qi
- United States Department of Agriculture (USDA)-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
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Ribone AI, Fass M, Gonzalez S, Lia V, Paniego N, Rivarola M. Co-Expression Networks in Sunflower: Harnessing the Power of Multi-Study Transcriptomic Public Data to Identify and Categorize Candidate Genes for Fungal Resistance. PLANTS (BASEL, SWITZERLAND) 2023; 12:2767. [PMID: 37570920 PMCID: PMC10421300 DOI: 10.3390/plants12152767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023]
Abstract
Fungal plant diseases are a major threat to food security worldwide. Current efforts to identify and list loci involved in different biological processes are more complicated than originally thought, even when complete genome assemblies are available. Despite numerous experimental and computational efforts to characterize gene functions in plants, about ~40% of protein-coding genes in the model plant Arabidopsis thaliana L. are still not categorized in the Gene Ontology (GO) Biological Process (BP) annotation. In non-model organisms, such as sunflower (Helianthus annuus L.), the number of BP term annotations is far fewer, ~22%. In the current study, we performed gene co-expression network analysis using eight terabytes of public transcriptome datasets and expression-based functional prediction to categorize and identify loci involved in the response to fungal pathogens. We were able to construct a reference gene network of healthy green tissue (GreenGCN) and a gene network of healthy and stressed root tissues (RootGCN). Both networks achieved robust, high-quality scores on the metrics of guilt-by-association and selective constraints versus gene connectivity. We were able to identify eight modules enriched in defense functions, of which two out of the three modules in the RootGCN were also conserved in the GreenGCN, suggesting similar defense-related expression patterns. We identified 16 WRKY genes involved in defense related functions and 65 previously uncharacterized loci now linked to defense response. In addition, we identified and classified 122 loci previously identified within QTLs or near candidate loci reported in GWAS studies of disease resistance in sunflower linked to defense response. All in all, we have implemented a valuable strategy to better describe genes within specific biological processes.
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Affiliation(s)
| | | | | | | | | | - Máximo Rivarola
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA—Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Los Reseros y Nicolás Repetto, Hurlingham 1686, Argentina; (A.I.R.); (M.F.); (S.G.); (V.L.); (N.P.)
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Calderón-González Á, Pérez-Vich B, Pouilly N, Boniface MC, Louarn J, Velasco L, Muños S. Association mapping for broomrape resistance in sunflower. FRONTIERS IN PLANT SCIENCE 2023; 13:1056231. [PMID: 36714707 PMCID: PMC9875907 DOI: 10.3389/fpls.2022.1056231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/14/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Sunflower breeding for resistance to the parasitic plant sunflower broomrape (Orobanche cumana Wallr.) requires the identification of novel resistance genes. In this research, we conducted a genome-wide association study (GWAS) to identify QTLs associated with broomrape resistance. METHODS The marker-trait associations were examined across a germplasm set composed of 104 sunflower accessions. They were genotyped with a 600k AXIOM® genome-wide array and evaluated for resistance to three populations of the parasite with varying levels of virulence (races EFR, FGV, and GTK) in two environments. RESULTS AND DISCUSSION The analysis of the genetic structure of the germplasm set revealed the presence of two main groups. The application of optimized treatments based on the general linear model (GLM) and the mixed linear model (MLM) allowed the detection of 14 SNP markers significantly associated with broomrape resistance. The highest number of marker-trait associations were identified on chromosome 3, clustered in two different genomic regions of this chromosome. Other associations were identified on chromosomes 5, 10, 13, and 16. Candidate genes for the main genomic regions associated with broomrape resistance were studied and discussed. Particularly, two significant SNPs on chromosome 3 associated with races EFR and FGV were found at two tightly linked SWEET sugar transporter genes. The results of this study have confirmed the role of some QTL on resistance to sunflower broomrape and have revealed new ones that may play an important role in the development of durable resistance to this parasitic weed in sunflower.
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Affiliation(s)
- Álvaro Calderón-González
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Córdoba, Spain
| | - Begoña Pérez-Vich
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Córdoba, Spain
| | - Nicolas Pouilly
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), Université de Toulouse, CNRS, INRAE, Castanet-Tolosan, France
| | - Marie-Claude Boniface
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), Université de Toulouse, CNRS, INRAE, Castanet-Tolosan, France
| | - Johann Louarn
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), Université de Toulouse, CNRS, INRAE, Castanet-Tolosan, France
| | - Leonardo Velasco
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Córdoba, Spain
| | - Stéphane Muños
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), Université de Toulouse, CNRS, INRAE, Castanet-Tolosan, France
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Genome-Wide Association Studies in Sunflower: Towards Sclerotinia sclerotiorum and Diaporthe/Phomopsis Resistance Breeding. Genes (Basel) 2022; 13:genes13122357. [PMID: 36553624 PMCID: PMC9777803 DOI: 10.3390/genes13122357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/24/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022] Open
Abstract
Diseases caused by necrotrophic fungi, such as the cosmopolitan Sclerotinia sclerotiorum and the Diaporthe/Phomopsis complex, are among the most destructive diseases of sunflower worldwide. The lack of complete resistance combined with the inefficiency of chemical control makes assisted breeding the best strategy for disease control. In this work, we present an integrated genome-wide association (GWA) study investigating the response of a diverse panel of sunflower inbred lines to both pathogens. Phenotypic data for Sclerotinia head rot (SHR) consisted of five disease descriptors (disease incidence, DI; disease severity, DS; area under the disease progress curve for DI, AUDPCI, and DS, AUDPCS; and incubation period, IP). Two disease descriptors (DI and DS) were evaluated for two manifestations of Diaporthe/Phomopsis: Phomopsis stem canker (PSC) and Phomopsis head rot (PHR). In addition, a principal component (PC) analysis was used to derive transformed phenotypes as inputs to a univariate GWA (PC-GWA). Genotypic data comprised a panel of 4269 single nucleotide polymorphisms (SNP), generated via genotyping-by-sequencing. The GWA analysis revealed 24 unique marker-trait associations for SHR, 19 unique marker-trait associations for Diaporthe/Phomopsis diseases, and 7 markers associated with PC1 and PC2. No common markers were found for the response to the two pathogens. Nevertheless, epistatic interactions were identified between markers significantly associated with the response to S. sclerotiorum and Diaporthe/Phomopsis. This suggests that, while the main determinants of resistance may differ for the two pathogens, there could be an underlying common genetic basis. The exploration of regions physically close to the associated markers yielded 364 genes, of which 19 were predicted as putative disease resistance genes. This work presents the first simultaneous evaluation of two manifestations of Diaporthe/Phomopsis in sunflower, and undertakes a comprehensive GWA study by integrating PSC, PHR, and SHR data. The multiple regions identified, and their exploration to identify candidate genes, contribute not only to the understanding of the genetic basis of resistance, but also to the development of tools for assisted breeding.
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Talukder ZI, Underwood W, Misar CG, Seiler GJ, Cai X, Li X, Qi L. Genomic Insights Into Sclerotinia Basal Stalk Rot Resistance Introgressed From Wild Helianthus praecox Into Cultivated Sunflower ( Helianthus annuus L.). FRONTIERS IN PLANT SCIENCE 2022; 13:840954. [PMID: 35665155 PMCID: PMC9158519 DOI: 10.3389/fpls.2022.840954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Crop wild relatives of the cultivated sunflower (Helianthus annuus L.) are a valuable resource for its sustainable production. Helianthus praecox ssp. runyonii is a wild sunflower known for its resistance against diseases caused by the fungus, Sclerotinia sclerotiorum (Lib.) de Bary, which infects over 400 broadleaf hosts including many important food crops. The objective of this research was to dissect the Sclerotinia basal stalk rot (BSR) resistance introgressed from H. praecox ssp. runyonii into cultivated sunflower. An advanced backcross quantitative trait loci (AB-QTL) mapping population was developed from the cross of a H. praecox accession with cultivated sunflower lines. The AB-QTL population was evaluated for BSR resistance in the field during the summers of 2017-2018 and in the greenhouse in the spring of 2018. Highly significant genetic variations (p < 0.001) were observed for the BSR disease in the field and greenhouse with a moderately high broad-sense heritability (H 2) ranging from 0.66 to 0.73. Genotyping-by-sequencing approach was used to genotype the parents and the progeny lines of the AB-QTL population. A genetic linkage map spanning 1,802.95 cM was constructed using 1,755 single nucleotide polymorphism (SNP) markers mapped on 17 sunflower chromosomes. A total of 19 BSR resistance QTL were detected on nine sunflower chromosomes, each explaining 2.21%-16.99% of the phenotypic variance for resistance in the AB-QTL population. Sixteen of the 19 QTL had alleles conferring increased BSR resistance derived from the H. praecox parent. SNP markers flanking the identified QTL will facilitate marker-assisted breeding to combat the disease in sunflower.
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Affiliation(s)
- Zahirul I. Talukder
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - William Underwood
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Christopher G. Misar
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Gerald J. Seiler
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Xiwen Cai
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Xuehui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Lili Qi
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
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Talukder ZI, Underwood W, Misar CG, Seiler GJ, Liu Y, Li X, Cai X, Qi L. Unraveling the Sclerotinia Basal Stalk Rot Resistance Derived From Wild Helianthus argophyllus Using a High-Density Single Nucleotide Polymorphism Linkage Map. FRONTIERS IN PLANT SCIENCE 2021; 11:617920. [PMID: 33613588 PMCID: PMC7886805 DOI: 10.3389/fpls.2020.617920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/21/2020] [Indexed: 05/30/2023]
Abstract
Basal stalk rot (BSR), caused by the fungus Sclerotinia sclerotiorum, is a serious disease of sunflower (Helianthus annuus L.) in the humid temperate growing areas of the world. BSR resistance is quantitative and conditioned by multiple genes. Our objective was to dissect the BSR resistance introduced from the wild annual species Helianthus argophyllus using a quantitative trait loci (QTL) mapping approach. An advanced backcross population (AB-QTL) with 134 lines derived from the cross of HA 89 with a H. argophyllus Torr. and Gray accession, PI 494573, was evaluated for BSR resistance in three field and one greenhouse growing seasons of 2017-2019. Highly significant genetic variations (p < 0.001) were observed for BSR disease incidence (DI) in all field screening tests and disease rating and area under the disease progress curve in the greenhouse. The AB-QTL population and its parental lines were genotyped using the genotyping-by-sequencing method. A genetic linkage map spanning 2,045.14 cM was constructed using 3,110 SNP markers mapped on 17 sunflower chromosomes. A total of 21 QTL associated with BSR resistance were detected on 11 chromosomes, each explaining a phenotypic variation ranging from 4.5 to 22.6%. Of the 21 QTL, eight were detected for BSR DI measured in the field, seven were detected for traits measured in the greenhouse, and six were detected from both field and greenhouse tests. Thirteen of the 21 QTL had favorable alleles from the H. argophyllus parent conferring increased BSR resistance.
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Affiliation(s)
- Zahirul I. Talukder
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - William Underwood
- United States Department of Agriculture – Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Christopher G. Misar
- United States Department of Agriculture – Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Gerald J. Seiler
- United States Department of Agriculture – Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Yuan Liu
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Xuehui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Xiwen Cai
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Lili Qi
- United States Department of Agriculture – Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
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Ma L, Sun Y, Ruan X, Huang PC, Wang S, Li S, Zhou Y, Wang F, Cao Y, Wang Q, Wang Z, Kolomiets MV, Gao X. Genome-Wide Characterization of Jasmonates Signaling Components Reveals the Essential Role of ZmCOI1a-ZmJAZ15 Action Module in Regulating Maize Immunity to Gibberella Stalk Rot. Int J Mol Sci 2021; 22:E870. [PMID: 33467172 PMCID: PMC7830991 DOI: 10.3390/ijms22020870] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/24/2020] [Accepted: 01/05/2021] [Indexed: 12/20/2022] Open
Abstract
Gibberella stalk rot (GSR) by Fusarium graminearum causes significant losses of maize production worldwide. Jasmonates (JAs) have been broadly known in regulating defense against pathogens through the homeostasis of active JAs and COI-JAZ-MYC function module. However, the functions of different molecular species of JAs and COI-JAZ-MYC module in maize interactions with Fusarium graminearum and regulation of diverse metabolites remain unknown. In this study, we found that exogenous application of MeJA strongly enhanced resistance to GSR. RNA-seq analysis showed that MeJA activated multiple genes in JA pathways, which prompted us to perform a genome-wide screening of key JA signaling components in maize. Yeast Two-Hybrid, Split-Luciferase, and Pull-down assays revealed that the JA functional and structural mimic coronatine (COR) functions as an essential ligand to trigger the interaction between ZmCOIa and ZmJAZ15. By deploying CRISPR-cas9 knockout and Mutator insertional mutants, we demonstrated that coi1a mutant is more resistant, whereas jaz15 mutant is more susceptible to GSR. Moreover, JA-deficient opr7-5opr8-2 mutant displayed enhanced resistance to GSR compared to wild type. Together, these results provide strong evidence that ZmJAZ15 plays a pivotal role, whereas ZmCOIa and endogenous JA itself might function as susceptibility factors, in maize immunity to GSR.
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Affiliation(s)
- Liang Ma
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; (L.M.); (Y.S.); (X.R.); (S.W.); (S.L.); (F.W.); (Y.C.); (Q.W.)
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yali Sun
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; (L.M.); (Y.S.); (X.R.); (S.W.); (S.L.); (F.W.); (Y.C.); (Q.W.)
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinsen Ruan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; (L.M.); (Y.S.); (X.R.); (S.W.); (S.L.); (F.W.); (Y.C.); (Q.W.)
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Pei-Cheng Huang
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77840-2132, USA; (P.-C.H.); (M.V.K.)
| | - Shi Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; (L.M.); (Y.S.); (X.R.); (S.W.); (S.L.); (F.W.); (Y.C.); (Q.W.)
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shunfa Li
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; (L.M.); (Y.S.); (X.R.); (S.W.); (S.L.); (F.W.); (Y.C.); (Q.W.)
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Zhou
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (Z.W.)
| | - Fang Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; (L.M.); (Y.S.); (X.R.); (S.W.); (S.L.); (F.W.); (Y.C.); (Q.W.)
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Cao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; (L.M.); (Y.S.); (X.R.); (S.W.); (S.L.); (F.W.); (Y.C.); (Q.W.)
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Qing Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; (L.M.); (Y.S.); (X.R.); (S.W.); (S.L.); (F.W.); (Y.C.); (Q.W.)
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhenhua Wang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (Z.W.)
| | - Michael V. Kolomiets
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77840-2132, USA; (P.-C.H.); (M.V.K.)
| | - Xiquan Gao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; (L.M.); (Y.S.); (X.R.); (S.W.); (S.L.); (F.W.); (Y.C.); (Q.W.)
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
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Fass MI, Rivarola M, Ehrenbolger GF, Maringolo CA, Montecchia JF, Quiroz F, García-García F, Blázquez JD, Hopp HE, Heinz RA, Paniego NB, Lia VV. Exploring sunflower responses to Sclerotinia head rot at early stages of infection using RNA-seq analysis. Sci Rep 2020; 10:13347. [PMID: 32770047 PMCID: PMC7414910 DOI: 10.1038/s41598-020-70315-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 07/24/2020] [Indexed: 12/24/2022] Open
Abstract
Sclerotinia head rot (SHR), caused by the necrotrophic fungus Sclerotinia sclerotiorum, is one of the most devastating sunflower crop diseases. Despite its worldwide occurrence, the genetic determinants of plant resistance are still largely unknown. Here, we investigated the Sclerotinia-sunflower pathosystem by analysing temporal changes in gene expression in one susceptible and two tolerant inbred lines (IL) inoculated with the pathogen under field conditions. Differential expression analysis showed little overlapping among ILs, suggesting genotype-specific control of cell defense responses possibly related to differences in disease resistance strategies. Functional enrichment assessments yielded a similar pattern. However, all three ILs altered the expression of genes involved in the cellular redox state and cell wall remodeling, in agreement with current knowledge about the initiation of plant immune responses. Remarkably, the over-representation of long non-coding RNAs (lncRNA) was another common feature among ILs. Our findings highlight the diversity of transcriptional responses to SHR within sunflower breeding lines and provide evidence of lncRNAs playing a significant role at early stages of defense.
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Affiliation(s)
- Mónica I Fass
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham B1686IGC, Buenos Aires, Argentina.
| | - Máximo Rivarola
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham B1686IGC, Buenos Aires, Argentina
| | - Guillermo F Ehrenbolger
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham B1686IGC, Buenos Aires, Argentina
| | - Carla A Maringolo
- Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce, Balcarce, Argentina
| | - Juan F Montecchia
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham B1686IGC, Buenos Aires, Argentina
| | - Facundo Quiroz
- Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce, Balcarce, Argentina
| | | | - Joaquín Dopazo Blázquez
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain.,INB-ELIXIR-Es, FPS, Hospital Virgen del Rocío, 42013, Sevilla, Spain
| | - H Esteban Hopp
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham B1686IGC, Buenos Aires, Argentina.,Departamento de Fisiología, Biología Molecular y Celular (FBMC), Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), 1428, Ciudad Universitaria, Buenos Aires, Argentina
| | - Ruth A Heinz
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham B1686IGC, Buenos Aires, Argentina
| | - Norma B Paniego
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham B1686IGC, Buenos Aires, Argentina
| | - Verónica V Lia
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham B1686IGC, Buenos Aires, Argentina
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9
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Filippi CV, Zubrzycki JE, Di Rienzo JA, Quiroz FJ, Puebla AF, Alvarez D, Maringolo CA, Escande AR, Hopp HE, Heinz RA, Paniego NB, Lia VV. Unveiling the genetic basis of Sclerotinia head rot resistance in sunflower. BMC PLANT BIOLOGY 2020; 20:322. [PMID: 32641108 PMCID: PMC7346337 DOI: 10.1186/s12870-020-02529-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 06/26/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Sclerotinia sclerotiorum is a necrotrophic fungus that causes Sclerotinia head rot (SHR) in sunflower, with epidemics leading to severe yield losses. In this work, we present an association mapping (AM) approach to investigate the genetic basis of natural resistance to SHR in cultivated sunflower, the fourth most widely grown oilseed crop in the world. RESULTS Our association mapping population (AMP), which comprises 135 inbred breeding lines (ILs), was genotyped using 27 candidate genes, a panel of 9 Simple Sequence Repeat (SSR) markers previously associated with SHR resistance via bi-parental mapping, and a set of 384 SNPs located in genes with molecular functions related to stress responses. Moreover, given the complexity of the trait, we evaluated four disease descriptors (i.e, disease incidence, disease severity, area under the disease progress curve for disease incidence, and incubation period). As a result, this work constitutes the most exhaustive AM study of disease resistance in sunflower performed to date. Mixed linear models accounting for population structure and kinship relatedness were used for the statistical analysis of phenotype-genotype associations, allowing the identification of 13 markers associated with disease reduction. The number of favourable alleles was negatively correlated to disease incidence, disease severity and area under the disease progress curve for disease incidence, whereas it was positevily correlated to the incubation period. CONCLUSIONS Four of the markers identified here as associated with SHR resistance (HA1848, HaCOI_1, G33 and G34) validate previous research, while other four novel markers (SNP117, SNP136, SNP44, SNP128) were consistently associated with SHR resistance, emerging as promising candidates for marker-assisted breeding. From the germplasm point of view, the five ILs carrying the largest combination of resistance alleles provide a valuable resource for sunflower breeding programs worldwide.
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Affiliation(s)
- C V Filippi
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - J E Zubrzycki
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina
- Present address: Biocódices, San Martín, Buenos Aires, Argentina
| | - J A Di Rienzo
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Ing Agr. Felix Aldo Marrone 746 (5000), Córdoba, Argentina
| | - F J Quiroz
- Estación Experimental Agropecuaria INTA Balcarce, Ruta 226 Km 73.5 (7620), Balcarce, Buenos Aires, Argentina
| | - A F Puebla
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina
| | - D Alvarez
- Estación Experimental Agropecuaria INTA Manfredi, Ruta 9 Km 636 (5988), Manfredi, Córdoba, Argentina
| | - C A Maringolo
- Estación Experimental Agropecuaria INTA Balcarce, Ruta 226 Km 73.5 (7620), Balcarce, Buenos Aires, Argentina
| | - A R Escande
- Estación Experimental Agropecuaria INTA Balcarce, Ruta 226 Km 73.5 (7620), Balcarce, Buenos Aires, Argentina
| | - H E Hopp
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires, Intendente Güiraldes 2160, (1428), Ciudad Autónoma de Buenos Aires, Argentina
| | - R A Heinz
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires, Intendente Güiraldes 2160, (1428), Ciudad Autónoma de Buenos Aires, Argentina
| | - N B Paniego
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - V V Lia
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Ciudad Autónoma de Buenos Aires, Argentina.
- Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires, Intendente Güiraldes 2160, (1428), Ciudad Autónoma de Buenos Aires, Argentina.
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10
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Fernandez O, Urrutia M, Berton T, Bernillon S, Deborde C, Jacob D, Maucourt M, Maury P, Duruflé H, Gibon Y, Langlade NB, Moing A. Metabolomic characterization of sunflower leaf allows discriminating genotype groups or stress levels with a minimal set of metabolic markers. Metabolomics 2019; 15:56. [PMID: 30929085 PMCID: PMC6441456 DOI: 10.1007/s11306-019-1515-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/18/2019] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Plant and crop metabolomic analyses may be used to study metabolism across genetic and environmental diversity. Complementary analytical strategies are useful for investigating metabolic changes and searching for biomarkers of response or performance. METHODS AND OBJECTIVES The experimental material consisted in eight sunflower lines with two line status, four restorers (R, used as males) and four maintainers (B, corresponding to females) routinely used for sunflower hybrid varietal production, respectively to complement or maintain the cytoplasmic male sterility PET1. These lines were either irrigated at full soil capacity (WW) or submitted to drought stress (DS). Our aim was to combine targeted and non-targeted metabolomics to characterize sunflower leaf composition in order to investigate the effect of line status genotypes and environmental conditions and to find the best and smallest set of biomarkers for line status and stress response using a custom-made process of variables selection. RESULTS Five hundred and eighty-eight metabolic variables were measured by using complementary analytical methods such as 1H-NMR, MS-based profiles and targeted analyses of major metabolites. Based on statistical analyses, a limited number of markers were able to separate WW and DS samples in a more discriminant manner than previously published physiological data. Another metabolic marker set was able to discriminate line status. CONCLUSION This study underlines the potential of metabolic markers for discriminating genotype groups and environmental conditions. Their potential use for prediction is discussed.
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Affiliation(s)
- Olivier Fernandez
- UMR1332 Biologie du Fruit et Pathologie, INRA, Centre INRA de Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- Present Address: Laboratoire RIBP, Université de Reims Champagne Ardenne, Moulin de la Housse Chemin des Rouliers, 51100 Reims, France
| | - Maria Urrutia
- UMR1332 Biologie du Fruit et Pathologie, INRA, Centre INRA de Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- UMR AgroImpact, INRA, Estrées-Mons, 80203 Péronne, France
- Present Address: Enza Zaden Centro de Investigacion S.L., Santa Maria del Aguila, 04710 Almeria, Spain
| | - Thierry Berton
- UMR1332 Biologie du Fruit et Pathologie, INRA, Centre INRA de Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- Present Address: Centre for CardioVascular and Nutrition, UMR INRA-INSERM, Aix-Marseille Univ, INSERM, 13005 Marseilles, France
| | - Stéphane Bernillon
- UMR1332 Biologie du Fruit et Pathologie, INRA, Centre INRA de Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- Plateforme Métabolome Bordeaux, CGFB, MetaboHUB-PHENOME, 33140 Villenave d’Ornon, France
| | - Catherine Deborde
- UMR1332 Biologie du Fruit et Pathologie, INRA, Centre INRA de Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- Plateforme Métabolome Bordeaux, CGFB, MetaboHUB-PHENOME, 33140 Villenave d’Ornon, France
| | - Daniel Jacob
- UMR1332 Biologie du Fruit et Pathologie, INRA, Centre INRA de Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- Plateforme Métabolome Bordeaux, CGFB, MetaboHUB-PHENOME, 33140 Villenave d’Ornon, France
| | - Mickaël Maucourt
- UMR1332 Biologie du Fruit et Pathologie, INRA, Centre INRA de Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- Plateforme Métabolome Bordeaux, CGFB, MetaboHUB-PHENOME, 33140 Villenave d’Ornon, France
- Present Address: Enza Zaden Centro de Investigacion S.L., Santa Maria del Aguila, 04710 Almeria, Spain
| | - Pierre Maury
- UMR LIPM, INRA, CNRS, Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Harold Duruflé
- UMR LIPM, INRA, CNRS, Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Yves Gibon
- UMR1332 Biologie du Fruit et Pathologie, INRA, Centre INRA de Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- Plateforme Métabolome Bordeaux, CGFB, MetaboHUB-PHENOME, 33140 Villenave d’Ornon, France
| | - Nicolas B. Langlade
- UMR LIPM, INRA, CNRS, Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Annick Moing
- UMR1332 Biologie du Fruit et Pathologie, INRA, Centre INRA de Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- Plateforme Métabolome Bordeaux, CGFB, MetaboHUB-PHENOME, 33140 Villenave d’Ornon, France
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11
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Horn R, Radanovic A, Fuhrmann L, Sprycha Y, Hamrit S, Jockovic M, Miladinovic D, Jansen C. Development and Validation of Markers for the Fertility Restorer Gene Rf1 in Sunflower. Int J Mol Sci 2019; 20:ijms20061260. [PMID: 30871146 PMCID: PMC6471545 DOI: 10.3390/ijms20061260] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/05/2019] [Accepted: 03/10/2019] [Indexed: 01/14/2023] Open
Abstract
Hybrid breeding in sunflowers based on CMS PET1 requires development of restorer lines carrying, in most cases, the restorer gene Rf1. Markers for marker-assisted selection have been developed, but there is still need for closer, more versatile, and co-dominant markers linked to Rf1. Homology searches against the reference sunflower genome using sequences of cloned markers, as well as Bacterial Artificial Chromosome (BAC)-end sequences of clones hybridizing to them, allowed the identification of two genomic regions of 30 and 3.9 Mb, respectively, as possible physical locations of the restorer gene Rf1 on linkage group 13. Nine potential candidate genes, encoding six pentatricopeptide repeat proteins, one tetratricopeptide-like helical domain, a probable aldehyde dehydrogenase 22A1, and a probable poly(A) polymerase 3 (PAPS3), were identified in these two genomic regions. Amplicon targeted next generation sequencing of these nine candidate genes for Rf1 was performed in an association panel consisting of 27 maintainer and 32 restorer lines and revealed the presence of 210 Single Nucleotide Polymorphisms (SNPs) and 67 Insertions/Deletions (INDELs). Association studies showed significant associations of 10 SNPs with fertility restoration (p-value < 10−4), narrowing Rf1 down to three candidate genes. Three new markers, one co-dominant marker 67N04_P and two dominant markers, PPR621.5R for restorer, and PPR621.5M for maintainer lines were developed and verified in the association panel of 59 sunflower lines. The versatility of the three newly developed markers, as well as of three existing markers for the restorer gene Rf1 (HRG01 and HRG02, Cleaved Amplified Polymorphic Sequence (CAPS)-marker H13), was analyzed in a large association panel consisting of 557 accessions.
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Affiliation(s)
- Renate Horn
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany.
| | - Aleksandra Radanovic
- Industrial Crops Department, Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia.
| | - Lena Fuhrmann
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany.
| | - Yves Sprycha
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany.
| | - Sonia Hamrit
- Strube Research GmbH & Co. KG, Hauptstr. 1, D-38387 Söllingen, Germany.
| | - Milan Jockovic
- Industrial Crops Department, Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia.
| | - Dragana Miladinovic
- Industrial Crops Department, Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia.
| | - Constantin Jansen
- Strube Research GmbH & Co. KG, Hauptstr. 1, D-38387 Söllingen, Germany.
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12
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Talukder ZI, Long Y, Seiler GJ, Underwood W, Qi L. Introgression and monitoring of wild Helianthus praecox alien segments associated with Sclerotinia basal stalk rot resistance in sunflower using genotyping-by-sequencing. PLoS One 2019; 14:e0213065. [PMID: 30822322 PMCID: PMC6396933 DOI: 10.1371/journal.pone.0213065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 02/14/2019] [Indexed: 11/19/2022] Open
Abstract
Sclerotinia basal stalk rot (BSR) and downy mildew are major diseases of sunflowers worldwide. Breeding for BSR resistance traditionally relies upon cultivated sunflower germplasm that has only partial resistance thus lacking an effective resistance against the pathogen. In this study, we report the transfer of BSR resistance from sunflower wild species, Helianthus praecox, into cultivated sunflower and molecular assessment of the introgressed segments potentially associated with BSR resistance using the genotyping-by-sequencing (GBS) approach. Eight highly BSR-resistant H. praecox introgression lines (ILs), H.pra 1 to H.pra 8, were developed. The mean BSR disease incidence (DI) for H.pra 1 to H.pra 8 across environments for four years ranged from 1.2 to 11.1%, while DI of Cargill 270 (susceptible check), HA 89 (recurrent parent), HA 441 and Croplan 305 (resistant checks) was 36.1, 31.0, 19.5, and 11.6%, respectively. Molecular assessment using GBS detected the presence of H. praecox chromosome segments in chromosomes 1, 8, 10, 11, and 14 of the ILs. Both shared and unique polymorphic SNP loci were detected throughout the entire genomes of the ILs, suggesting the successful transfer of common and novel introgression regions that are potentially associated with BSR resistance. Downy mildew (DM) disease screening and molecular tests revealed that a DM resistance gene, Pl17, derived from one of the inbred parent HA 458 was present in four ILs. Introgression germplasms possessing resistance to both Sclerotinia BSR and DM will extend the useful diversity of the primary gene pool in the fight against two destructive sunflower diseases.
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Affiliation(s)
- Zahirul I. Talukder
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Yunming Long
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Gerald J. Seiler
- Sunflower and Plant Biology Research Unit, USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, North Dakota, United States of America
| | - William Underwood
- Sunflower and Plant Biology Research Unit, USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, North Dakota, United States of America
| | - Lili Qi
- Sunflower and Plant Biology Research Unit, USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, North Dakota, United States of America
- * E-mail:
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13
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Zubrzycki JE, Maringolo CA, Filippi CV, Quiróz FJ, Nishinakamasu V, Puebla AF, Di Rienzo JA, Escande A, Lia VV, Heinz RA, Hopp HE, Cervigni GDL, Paniego NB. Main and epistatic QTL analyses for Sclerotinia Head Rot resistance in sunflower. PLoS One 2017; 12:e0189859. [PMID: 29261806 PMCID: PMC5738076 DOI: 10.1371/journal.pone.0189859] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 12/04/2017] [Indexed: 02/04/2023] Open
Abstract
Sclerotinia Head Rot (SHR), a disease caused by Sclerotinia sclerotiorum, is one of the most limiting factors in sunflower production. In this study, we identified genomic loci associated with resistance to SHR to support the development of assisted breeding strategies. We genotyped 114 Recombinant Inbred Lines (RILs) along with their parental lines (PAC2 -partially resistant-and RHA266 -susceptible-) by using a 384 single nucleotide polymorphism (SNP) Illumina Oligo Pool Assay to saturate a sunflower genetic map. Subsequently, we tested these lines for SHR resistance using assisted inoculations with S. sclerotiorum ascospores. We also conducted a randomized complete-block assays with three replicates to visually score disease incidence (DI), disease severity (DS), disease intensity (DInt) and incubation period (IP) through four field trials (2010-2014). We finally assessed main effect quantitative trait loci (M-QTLs) and epistatic QTLs (E-QTLs) by composite interval mapping (CIM) and mixed-model-based composite interval mapping (MCIM), respectively. As a result of this study, the improved map incorporates 61 new SNPs over candidate genes. We detected a broad range of narrow sense heritability (h2) values (1.86-59.9%) as well as 36 M-QTLs and 13 E-QTLs along 14 linkage groups (LGs). On LG1, LG10, and LG15, we repeatedly detected QTLs across field trials; which emphasizes their putative effectiveness against SHR. In all selected variables, most of the identified QTLs showed high determination coefficients, associated with moderate to high heritability values. Using markers shared with previous Sclerotinia resistance studies, we compared the QTL locations in LG1, LG2, LG8, LG10, LG11, LG15 and LG16. This study constitutes the largest report of QTLs for SHR resistance in sunflower. Further studies focusing on the regions in LG1, LG10, and LG15 harboring the detected QTLs are necessary to identify causal alleles and contribute to unraveling the complex genetic basis governing the resistance.
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Affiliation(s)
- Jeremías Enrique Zubrzycki
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
| | - Carla Andrea Maringolo
- Laboratorio de Patología Vegetal, Unidad Integrada Universidad Nacional de Mar del Plata, Estación Experimental Agropecuaria INTA Balcarce, Balcarce, Buenos Aires, Argentina
| | - Carla Valeria Filippi
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Facundo José Quiróz
- Laboratorio de Patología Vegetal, Unidad Integrada Universidad Nacional de Mar del Plata, Estación Experimental Agropecuaria INTA Balcarce, Balcarce, Buenos Aires, Argentina
| | - Verónica Nishinakamasu
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
| | - Andrea Fabiana Puebla
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
| | - Julio A. Di Rienzo
- Cátedra de Estadística y Biometría, Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Alberto Escande
- Laboratorio de Patología Vegetal, Unidad Integrada Universidad Nacional de Mar del Plata, Estación Experimental Agropecuaria INTA Balcarce, Balcarce, Buenos Aires, Argentina
| | - Verónica Viviana Lia
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Ruth Amalia Heinz
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Horacio Esteban Hopp
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Gerardo D. L. Cervigni
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- Centro de Estudios Fotosintéticos y Bioquímicos, Rosario, Santa Fe, Argentina
| | - Norma Beatriz Paniego
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
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14
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Rana K, Atri C, Gupta M, Akhatar J, Sandhu PS, Kumar N, Jaswal R, Barbetti MJ, Banga SS. Mapping resistance responses to Sclerotinia infestation in introgression lines of Brassica juncea carrying genomic segments from wild Brassicaceae B. fruticulosa. Sci Rep 2017; 7:5904. [PMID: 28724956 PMCID: PMC5517529 DOI: 10.1038/s41598-017-05992-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 06/07/2017] [Indexed: 11/30/2022] Open
Abstract
Sclerotinia stem rot (Sclerotinia sclerotiorum) is a major disease of Brassica oilseeds. As suitable donors to develop resistant cultivars are not available in crop Brassicas, we introgressed resistance from a wild Brassicaceae species, B. fruticulosa. We produced 206 B. juncea-B. fruticulosa introgression lines (ILs). These were assessed for pollen grain fertility, genome size variations and resistance responses to Sclerotinia following stem inoculations under disease-conducive conditions. Of these, 115 ILs showing normal fertility and genome size were selected for cytogenetic characterization using florescent genomic in situ hybridization (Fl-GISH). B. fruticulosa segment substitutions were indicated in 28 ILs. These were predominantly terminal and located on B-genome chromosomes. A final set of 93 highly fertile and euploid (2n = 36) ILs were repeat-evaluated for their resistance responses during 2014-15. They were also genotyped with 202 transferable and 60 candidate gene SSRs. Association mapping allowed detection of ten significant marker trait associations (MTAs) after Bonferroni correction. These were: CNU-m157-2, RA2G05, CNU-m353-3, CNU-m442-5, ACMP00454-2, ACMP00454-3, EIN2-3-1, M641-1, Na10D09-1 and Na10D11-1. This is the first time such a molecular mapping technique has been deployed with introgression lines carrying genomic segments from B. fruticulosa, and the first to show that they possess high levels of resistance against S. sclerotiorum.
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Affiliation(s)
- Kusum Rana
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Chhaya Atri
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Mehak Gupta
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Javed Akhatar
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Prabhjodh S Sandhu
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Nitin Kumar
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Ravinder Jaswal
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Martin J Barbetti
- School of Agriculture and Environment and the UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Surinder S Banga
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India.
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15
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Goossens J, Fernández-Calvo P, Schweizer F, Goossens A. Jasmonates: signal transduction components and their roles in environmental stress responses. PLANT MOLECULAR BIOLOGY 2016; 91:673-89. [PMID: 27086135 DOI: 10.1007/s11103-016-0480-9] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 04/09/2016] [Indexed: 05/20/2023]
Abstract
Jasmonates, oxylipin-type plant hormones, are implicated in diverse aspects of plant growth development and interaction with the environment. Following diverse developmental and environmental cues, jasmonate is produced, conjugated to the amino acid isoleucine and perceived by a co-receptor complex composed of the Jasmonate ZIM-domain (JAZ) repressor proteins and an E3 ubiquitin ligase complex containing the F-box CORONATINE INSENSITIVE 1 (COI1). This event triggers the degradation of the JAZ proteins and the release of numerous transcription factors, including MYC2 and its homologues, which are otherwise bound and inhibited by the JAZ repressors. Here, we will review the role of the COI1, JAZ and MYC2 proteins in the interaction of the plant with its environment, illustrating the significance of jasmonate signalling, and of the proteins involved, for responses to both biotic stresses caused by insects and numerous microbial pathogens and abiotic stresses caused by adverse climatic conditions. It has also become evident that crosstalk with other hormone signals, as well as light and clock signals, plays an important role in the control and fine-tuning of these stress responses. Finally, we will discuss how several pathogens exploit the jasmonate perception and early signalling machinery to decoy the plants defence systems.
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Affiliation(s)
- Jonas Goossens
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Patricia Fernández-Calvo
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Fabian Schweizer
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, Technologiepark 927, 9052, Ghent, Belgium.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
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16
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Li P, Zhang F, Chen S, Jiang J, Wang H, Su J, Fang W, Guan Z, Chen F. Genetic diversity, population structure and association analysis in cut chrysanthemum (Chrysanthemum morifolium Ramat.). Mol Genet Genomics 2016; 291:1117-25. [PMID: 26780102 DOI: 10.1007/s00438-016-1166-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 01/06/2016] [Indexed: 02/04/2023]
Abstract
Characterizing the genetic diversity present in a working set of plant germplasm can contribute to its effective management and genetic improvement. The cut flower chrysanthemum (Chrysanthemum morifolium Ramat.) is an economically important ornamental species. With the repeated germplasm exchange and intensive breeding activities, it remains a major task in genetic research. The purpose of the present study was to characterize the genetic diversity and the population structure of a worldwide collection of 159 varieties, and to apply an association mapping approach to identify DNA-based markers linked to five plant architecture traits and six inflorescence traits. The genotyping demonstrated that there was no lack of genetic diversity in the collection and that pair-wise kinship values were relatively low. The clustering based on a Bayesian model of population structure did not reflect known variation in either provenance or inflorescence type. A principal coordinate analysis was, however, able to discriminate most of the varieties according to both of these criteria. About 1 in 100 marker pairs exhibited a degree of linkage disequilibrium. The association analysis identified a number of markers putatively linked to one or more of the traits. Some of these associations were robust over two seasons. The findings provide an in-depth understanding of genetic diversity and population structure present in cut flower chrysanthemum varieties, and an insight into the genetic control of plant architecture and inflorescence-related traits.
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Affiliation(s)
- Pirui Li
- College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Fei Zhang
- College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Sumei Chen
- College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Jiafu Jiang
- College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Haibin Wang
- College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Jiangshuo Su
- College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Zhiyong Guan
- College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China.
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17
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Filippi CV, Aguirre N, Rivas JG, Zubrzycki J, Puebla A, Cordes D, Moreno MV, Fusari CM, Alvarez D, Heinz RA, Hopp HE, Paniego NB, Lia VV. Population structure and genetic diversity characterization of a sunflower association mapping population using SSR and SNP markers. BMC PLANT BIOLOGY 2015; 15:52. [PMID: 25848813 PMCID: PMC4351844 DOI: 10.1186/s12870-014-0360-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 11/27/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Argentina has a long tradition of sunflower breeding, and its germplasm is a valuable genetic resource worldwide. However, knowledge of the genetic constitution and variability levels of the Argentinean germplasm is still scarce, rendering the global map of cultivated sunflower diversity incomplete. In this study, 42 microsatellite loci and 384 single nucleotide polymorphisms (SNPs) were used to characterize the first association mapping population used for quantitative trait loci mapping in sunflower, along with a selection of allied open-pollinated and composite populations from the germplasm bank of the National Institute of Agricultural Technology of Argentina. The ability of different kinds of markers to assess genetic diversity and population structure was also evaluated. RESULTS The analysis of polymorphism in the set of sunflower accessions studied here showed that both the microsatellites and SNP markers were informative for germplasm characterization, although to different extents. In general, the estimates of genetic variability were moderate. The average genetic diversity, as quantified by the expected heterozygosity, was 0.52 for SSR loci and 0.29 for SNPs. Within SSR markers, those derived from non-coding regions were able to capture higher levels of diversity than EST-SSR. A significant correlation was found between SSR and SNP- based genetic distances among accessions. Bayesian and multivariate methods were used to infer population structure. Evidence for the existence of three different genetic groups was found consistently across data sets (i.e., SSR, SNP and SSR + SNP), with the maintainer/restorer status being the most prevalent characteristic associated with group delimitation. CONCLUSION The present study constitutes the first report comparing the performance of SSR and SNP markers for population genetics analysis in cultivated sunflower. We show that the SSR and SNP panels examined here, either used separately or in conjunction, allowed consistent estimations of genetic diversity and population structure in sunflower breeding materials. The generated knowledge about the levels of diversity and population structure of sunflower germplasm is an important contribution to this crop breeding and conservation.
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Affiliation(s)
- Carla V Filippi
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
- />Consejo Nacional de Investigaciones Científicas y Técnicas–CONICET, Saavedra 15, C1083ACA Ciudad Autónoma de Buenos Aires, Argentina
| | - Natalia Aguirre
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
| | - Juan G Rivas
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
| | - Jeremias Zubrzycki
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
- />Consejo Nacional de Investigaciones Científicas y Técnicas–CONICET, Saavedra 15, C1083ACA Ciudad Autónoma de Buenos Aires, Argentina
| | - Andrea Puebla
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
| | - Diego Cordes
- />Estación Experimental Agropecuaria Manfredi, Ruta Nac. nro. 9 km 636 (5988), Manfredi, Córdoba (INTA) Argentina
| | - Maria V Moreno
- />Estación Experimental Agropecuaria Manfredi, Ruta Nac. nro. 9 km 636 (5988), Manfredi, Córdoba (INTA) Argentina
| | - Corina M Fusari
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
- />Currently at System Regulation Group, Metabolic Networks Department, Max Planck Institute of Molecular Plant Physiology, Am Mühlemberg 1, D-14476 Potsdam-Golm, Germany
| | - Daniel Alvarez
- />Estación Experimental Agropecuaria Manfredi, Ruta Nac. nro. 9 km 636 (5988), Manfredi, Córdoba (INTA) Argentina
| | - Ruth A Heinz
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
- />Consejo Nacional de Investigaciones Científicas y Técnicas–CONICET, Saavedra 15, C1083ACA Ciudad Autónoma de Buenos Aires, Argentina
- />Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria (1428), Buenos Aires, Argentina
| | - Horacio E Hopp
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
- />Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria (1428), Buenos Aires, Argentina
| | - Norma B Paniego
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
- />Consejo Nacional de Investigaciones Científicas y Técnicas–CONICET, Saavedra 15, C1083ACA Ciudad Autónoma de Buenos Aires, Argentina
| | - Veronica V Lia
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
- />Consejo Nacional de Investigaciones Científicas y Técnicas–CONICET, Saavedra 15, C1083ACA Ciudad Autónoma de Buenos Aires, Argentina
- />Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria (1428), Buenos Aires, Argentina
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18
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Talukder ZI, Gong L, Hulke BS, Pegadaraju V, Song Q, Schultz Q, Qi L. A high-density SNP Map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R12. PLoS One 2014; 9:e98628. [PMID: 25014030 PMCID: PMC4094432 DOI: 10.1371/journal.pone.0098628] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 05/06/2014] [Indexed: 11/19/2022] Open
Abstract
A high-resolution genetic map of sunflower was constructed by integrating SNP data from three F2 mapping populations (HA 89/RHA 464, B-line/RHA 464, and CR 29/RHA 468). The consensus map spanned a total length of 1443.84 cM, and consisted of 5,019 SNP markers derived from RAD tag sequencing and 118 publicly available SSR markers distributed in 17 linkage groups, corresponding to the haploid chromosome number of sunflower. The maximum interval between markers in the consensus map is 12.37 cM and the average distance is 0.28 cM between adjacent markers. Despite a few short-distance inversions in marker order, the consensus map showed high levels of collinearity among individual maps with an average Spearman's rank correlation coefficient of 0.972 across the genome. The order of the SSR markers on the consensus map was also in agreement with the order of the individual map and with previously published sunflower maps. Three individual and one consensus maps revealed the uneven distribution of markers across the genome. Additionally, we performed fine mapping and marker validation of the rust resistance gene R12, providing closely linked SNP markers for marker-assisted selection of this gene in sunflower breeding programs. This high resolution consensus map will serve as a valuable tool to the sunflower community for studying marker-trait association of important agronomic traits, marker assisted breeding, map-based gene cloning, and comparative mapping.
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Affiliation(s)
- Zahirul I. Talukder
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Li Gong
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Brent S. Hulke
- Northern Crop Science Laboratory, USDA- Agricultural Research Service, Fargo, North Dakota, United States of America
| | | | - Qijian Song
- Soybean Genomics and Improvement Lab, USDA- Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Quentin Schultz
- BioDiagnostics Inc., River Falls, Wisconsin, United States of America
| | - Lili Qi
- Northern Crop Science Laboratory, USDA- Agricultural Research Service, Fargo, North Dakota, United States of America
- * E-mail:
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