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Guerra-García A, Trněný O, Brus J, Renzi JP, Kumar S, Bariotakis M, Coyne CJ, Chitikineni A, Bett KE, Varshney R, Pirintsos S, Berger J, von Wettberg EJB, Smýkal P. Genetic structure and ecological niche space of lentil's closest wild relative, Lens orientalis (Boiss.) Schmalh. Plant Biol (Stuttg) 2024; 26:232-244. [PMID: 38230798 DOI: 10.1111/plb.13615] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/27/2023] [Indexed: 01/18/2024]
Abstract
Crops arose from wild ancestors and to understand their domestication it is essential to compare the cultivated species with their crop wild relatives. These represent an important source of further crop improvement, in particular in relation to climate change. Although there are about 58,000 Lens accessions held in genebanks, only 1% are wild. We examined the geographic distribution and genetic diversity of the lentil's immediate progenitor L. orientalis. We used Genotyping by Sequencing (GBS) to identify and characterize differentiation among accessions held at germplasm collections. We then determined whether genetically distinct clusters of accessions had been collected from climatically distinct locations. Of the 195 genotyped accessions, 124 were genuine L. orientalis with four identified genetic groups. Although an environmental distance matrix was significantly correlated with geographic distance in a Mantel test, the four identified genetic clusters were not found to occupy significantly different environmental space. Maxent modelling gave a distinct predicted distribution pattern centred in the Fertile Crescent, with intermediate probabilities of occurrence in parts of Turkey, Greece, Cyprus, Morocco, and the south of the Iberian Peninsula with NW Africa. Future projections did not show any dramatic alterations in the distribution according to the climate change scenarios tested. We have found considerable diversity in L. orientalis, some of which track climatic variability. The results of the study showed the genetic diversity of wild lentil and indicate the importance of ongoing collections and in situ conservation for our future capacity to harness the genetic variation of the lentil progenitor.
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Affiliation(s)
- A Guerra-García
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| | - O Trněný
- Agriculture Research Ltd, Troubsko, Czech Republic
| | - J Brus
- Department of Geoinformatics, Palacký University, Olomouc, Czech Republic
| | - J P Renzi
- Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
| | - S Kumar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - M Bariotakis
- Department of Biology, University of Crete, Heraklion, Greece
- Botanical Garden, Rethymnon, Greece
| | - C J Coyne
- Western Regional Plant Introduction Station, USDA-ARS, Pullman, WA, USA
| | - A Chitikineni
- International Crop Research Institute for the semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - K E Bett
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - R Varshney
- International Crop Research Institute for the semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
- Murdoch University, Murdoch, WA, Australia
| | - S Pirintsos
- Department of Biology, University of Crete, Heraklion, Greece
| | - J Berger
- CSIRO Plant Industry, Wembley, WA, Australia
| | - E J B von Wettberg
- Department of Plant and Soil Sciences, Gund Institute for the Environment, University of Vermont, Burlington, VT, USA
| | - P Smýkal
- Department of Botany, Palacký University, Olomouc, Czech Republic
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Woods DP, Li W, Sibout R, Shao M, Laudencia-Chingcuanco D, Vogel JP, Dubcovsky J, Amasino RM. PHYTOCHROME C regulation of photoperiodic flowering via PHOTOPERIOD1 is mediated by EARLY FLOWERING 3 in Brachypodium distachyon. PLoS Genet 2023; 19:e1010706. [PMID: 37163541 PMCID: PMC10171608 DOI: 10.1371/journal.pgen.1010706] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 03/17/2023] [Indexed: 05/12/2023] Open
Abstract
Daylength sensing in many plants is critical for coordinating the timing of flowering with the appropriate season. Temperate climate-adapted grasses such as Brachypodium distachyon flower during the spring when days are becoming longer. The photoreceptor PHYTOCHROME C is essential for long-day (LD) flowering in B. distachyon. PHYC is required for the LD activation of a suite of genes in the photoperiod pathway including PHOTOPERIOD1 (PPD1) that, in turn, result in the activation of FLOWERING LOCUS T (FT1)/FLORIGEN, which causes flowering. Thus, B. distachyon phyC mutants are extremely delayed in flowering. Here we show that PHYC-mediated activation of PPD1 occurs via EARLY FLOWERING 3 (ELF3), a component of the evening complex in the circadian clock. The extreme delay of flowering of the phyC mutant disappears when combined with an elf3 loss-of-function mutation. Moreover, the dampened PPD1 expression in phyC mutant plants is elevated in phyC/elf3 mutant plants consistent with the rapid flowering of the double mutant. We show that loss of PPD1 function also results in reduced FT1 expression and extremely delayed flowering consistent with results from wheat and barley. Additionally, elf3 mutant plants have elevated expression levels of PPD1, and we show that overexpression of ELF3 results in delayed flowering associated with a reduction of PPD1 and FT1 expression, indicating that ELF3 represses PPD1 transcription consistent with previous studies showing that ELF3 binds to the PPD1 promoter. Indeed, PPD1 is the main target of ELF3-mediated flowering as elf3/ppd1 double mutant plants are delayed flowering. Our results indicate that ELF3 operates downstream from PHYC and acts as a repressor of PPD1 in the photoperiod flowering pathway of B. distachyon.
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Affiliation(s)
- Daniel P. Woods
- Dept. Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Weiya Li
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Richard Sibout
- Institut Jean-Pierre Bourgin, UMR1318 INRAE-AgroParisTech, Versailles Cedex, France
- UR1268 BIA, INRAE, Nantes, France
| | - Mingqin Shao
- DOE Joint Genome Institute, Berkeley, California, United States of America
| | - Debbie Laudencia-Chingcuanco
- USDA-Agricultural Research Service, Western Regional Research Center, Albany, California, United States of America
| | - John P. Vogel
- DOE Joint Genome Institute, Berkeley, California, United States of America
| | - Jorge Dubcovsky
- Dept. Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Richard M. Amasino
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, United States of America
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, United States of America
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Ma G, Song Q, Li X, Qi L. High-Density Mapping and Candidate Gene Analysis of Pl18 and Pl20 in Sunflower by Whole-Genome Resequencing. Int J Mol Sci 2020; 21:E9571. [PMID: 33339111 PMCID: PMC7765508 DOI: 10.3390/ijms21249571] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/17/2022] Open
Abstract
Downy mildew (DM) is one of the severe biotic threats to sunflower production worldwide. The inciting pathogen, Plasmopara halstedii, could overwinter in the field for years, creating a persistent threat to sunflower. The dominant genes Pl18 and Pl20 conferring resistance to known DM races have been previously mapped to 1.5 and 1.8 cM intervals on sunflower chromosomes 2 and 8, respectively. Utilizing a whole-genome resequencing strategy combined with reference sequence-based chromosome walking and high-density mapping in the present study, Pl18 was placed in a 0.7 cM interval on chromosome 2. A candidate gene HanXRQChr02g0048181 for Pl18 was identified from the XRQ reference genome and predicted to encode a protein with typical NLR domains for disease resistance. The Pl20 gene was placed in a 0.2 cM interval on chromosome 8. The putative gene with the NLR domain for Pl20, HanXRQChr08g0210051, was identified within the Pl20 interval. SNP markers closely linked to Pl18 and Pl20 were evaluated with 96 diverse sunflower lines, and a total of 13 diagnostic markers for Pl18 and four for Pl20 were identified. These markers will facilitate to transfer these new genes to elite sunflower lines and to pyramid these genes with broad-spectrum DM resistance in sunflower breeding.
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Affiliation(s)
- Guojia Ma
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.M.); (X.L.)
| | - Qijian Song
- USDA-Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, MD 20705-2350, USA;
| | - Xuehui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.M.); (X.L.)
| | - Lili Qi
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102-2765, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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