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Wang W, Sun T, Fang Z, Yang D, Wang Y, Xiang L, Chan Z. Genome-wide identification of DREB1 transcription factors in perennial ryegrass and functional profiling of LpDREB1H2 in response to cold stress. PHYSIOLOGIA PLANTARUM 2024; 176:e14210. [PMID: 38380683 DOI: 10.1111/ppl.14210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/19/2024] [Accepted: 02/02/2024] [Indexed: 02/22/2024]
Abstract
Perennial ryegrass (Lolium perenne L.) is an outstanding turfgrass and forage cultivated in temperate regions worldwide. However, poor tolerance to extreme cold, heat, or drought limits wide extension and cultivation. DEHYDRATION-RESPONSIVE ELEMENT BINDING FACTOR1s (DREB1s) play a vital role in enhancing plant tolerance to abiotic stress, specifically for low-temperature stress. In this study, a total of 24 LpDREB1 family members were identified from the released genome of perennial ryegrass. Phylogenetic analysis showed that the LpDREB1 genes are divided into 7 groups that have close relationships with rice homologues. Conserved motif analysis revealed that members within the same group have similar conserved motif compositions. All LpDREB1s lack introns, and the promoter sequences of LpDREB1 genes contain multiple cis-acting elements associated with stress response, phytohormone signal transduction and plant growth and development. The majority of LpDREB1 genes were upregulated by drought, submergence, heat and cold stress treatments, including LpDREB1H2. Further investigation showed that LpDREB1H2 is localized in the nucleus. Overexpression of LpDREB1H2 in Arabidopsis induced the expression of cold-responsive (COR) genes, increased the levels of osmotic adjusting substances, and enhanced antioxidant enzyme activities, thus improving the cold tolerance of Arabidopsis. This study lays a foundation for further understanding the function of LpDREB1 genes in perennial ryegrass and provides insights for plant stress tolerance breeding.
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Affiliation(s)
- Weiliang Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Tianxiao Sun
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhengfu Fang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Di Yang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yanping Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lin Xiang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhulong Chan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, China
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Keep T, Sampoux J, Barre P, Blanco‐Pastor J, Dehmer KJ, Durand J, Hegarty M, Ledauphin T, Muylle H, Roldán‐Ruiz I, Ruttink T, Surault F, Willner E, Volaire F. To grow or survive: Which are the strategies of a perennial grass to face severe seasonal stress? Funct Ecol 2021. [DOI: 10.1111/1365-2435.13770] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | - Klaus J. Dehmer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Malchow/Poel Germany
| | | | | | | | - Hilde Muylle
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) ‐ Plant Sciences Unit Melle Belgium
| | - Isabel Roldán‐Ruiz
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) ‐ Plant Sciences Unit Melle Belgium
| | - Tom Ruttink
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) ‐ Plant Sciences Unit Melle Belgium
| | | | - Evelin Willner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Malchow/Poel Germany
| | - Florence Volaire
- CEFEUniv MontpellierCNRSEPHE, IRDUniversité Paul Valéry Montpellier 3INRAE Montpellier France
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Ghaleb W, Barre P, Teulat B, Ahmed LQ, Escobar-Gutiérrez AJ. Divergent Selection for Seed Ability to Germinate at Extreme Temperatures in Perennial Ryegrass ( Lolium perenne L.). FRONTIERS IN PLANT SCIENCE 2021; 12:794488. [PMID: 35173750 PMCID: PMC8841656 DOI: 10.3389/fpls.2021.794488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/14/2021] [Indexed: 05/03/2023]
Abstract
Various adaptive mechanisms can ensure that seedlings are established at the most favourable time and place. These mechanisms include seed dormancy i.e., incapacity to germinate in any environment without a specific environmental trigger and inhibition i.e., incapacity to germinate in an unfavourable environment (water availability, temperature: thermoinhibition and light). The objective of this research was to study in the temperate range for germination of forage and turf grass species perennial ryegrass, if the thermal requirements for germination are under genetic controlled and could be selectively bred. Two divergent selections of three cycles were realized on a natural population: one to select for the capacity to germinate at 10°C vs. the impossibility to germinate at 10°C, and one to select for the capacity to germinate at 32°C vs. the impossibility to germinate at 32°C. Seeds of all the lots obtained from the two divergent selections were then germinated at constant temperatures from 5 to 35°C to evaluate their germination ability. Concerning the positive selection, the first cycle of positive selection at 10°C was highly efficient with a very strong increase in the germination percentage. However, afterward no selection effect was observed during the next two cycles of positive selection. By contrast, the positive selection at 32°C was efficient during all cycles with a linear increase of the percentage of germination at 32°C. Concerning the negative selection, we observed only a large positive effect of the first cycle of selection at 10°C. These findings demonstrate that seed thermoinhibition at 10 and 32°C observed in a natural population of perennial ryegrass has a genetic basis and a single recessive gene seems to be involved at 10°C.
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Affiliation(s)
- Wagdi Ghaleb
- INRAE, URP3F, F-86600 Lusignan, France
- Biotechnology Research Center (BTRC), Tripoli, Libya
| | - Philippe Barre
- INRAE, URP3F, F-86600 Lusignan, France
- *Correspondence: Philippe Barre,
| | - Béatrice Teulat
- Univ. Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F-49000 Angers, France
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Blanco-Pastor JL, Barre P, Keep T, Ledauphin T, Escobar-Gutiérrez A, Roschanski AM, Willner E, Dehmer KJ, Hegarty M, Muylle H, Veeckman E, Vandepoele K, Ruttink T, Roldán-Ruiz I, Manel S, Sampoux JP. Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass. Mol Ecol Resour 2020; 21:849-870. [PMID: 33098268 DOI: 10.1111/1755-0998.13289] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/10/2020] [Accepted: 10/12/2020] [Indexed: 11/28/2022]
Abstract
Germplasm from perennial ryegrass (Lolium perenne L.) natural populations is useful for breeding because of its adaptation to a wide range of climates. Climate-adaptive genes can be detected from associations between genotype, phenotype and climate but an integrated framework for the analysis of these three sources of information is lacking. We used two approaches to identify adaptive loci in perennial ryegrass and their effect on phenotypic traits. First, we combined Genome-Environment Association (GEA) and GWAS analyses. Then, we implemented a new test based on a Canonical Correlation Analysis (CANCOR) to detect adaptive loci. Furthermore, we improved the previous perennial ryegrass gene set by de novo gene prediction and functional annotation of 39,967 genes. GEA-GWAS revealed eight outlier loci associated with both environmental variables and phenotypic traits. CANCOR retrieved 633 outlier loci associated with two climatic gradients, characterized by cold-dry winter versus mild-wet winter and long rainy season versus long summer, and pointed out traits putatively conferring adaptation at the extremes of these gradients. Our CANCOR test also revealed the presence of both polygenic and oligogenic climatic adaptations. Our gene annotation revealed that 374 of the CANCOR outlier loci were positioned within or close to a gene. Co-association networks of outlier loci revealed a potential utility of CANCOR for investigating the interaction of genes involved in polygenic adaptations. The CANCOR test provides an integrated framework to analyse adaptive genomic diversity and phenotypic responses to environmental selection pressures that could be used to facilitate the adaptation of plant species to climate change.
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Affiliation(s)
| | - Philippe Barre
- INRAE, Centre Nouvelle-Aquitaine-Poitiers, Lusignan, France
| | - Thomas Keep
- INRAE, Centre Nouvelle-Aquitaine-Poitiers, Lusignan, France
| | | | | | - Anna Maria Roschanski
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Malchow/Poel, Germany
| | - Evelyn Willner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Malchow/Poel, Germany
| | - Klaus J Dehmer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Malchow/Poel, Germany
| | - Matthew Hegarty
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, UK
| | - Hilde Muylle
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) - Plant Sciences Unit, Melle, Belgium
| | - Elisabeth Veeckman
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) - Plant Sciences Unit, Melle, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Klaas Vandepoele
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) - Plant Sciences Unit, Melle, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Tom Ruttink
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) - Plant Sciences Unit, Melle, Belgium
| | - Isabel Roldán-Ruiz
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) - Plant Sciences Unit, Melle, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Stéphanie Manel
- CEFE, University of Montpellier, CNRS, EPHE-PSL University, IRD, Univ Paul Valéry Montpellier, Montpellier, France
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High-Throughput Genome-Wide Genotyping To Optimize the Use of Natural Genetic Resources in the Grassland Species Perennial Ryegrass ( Lolium perenne L.). G3-GENES GENOMES GENETICS 2020; 10:3347-3364. [PMID: 32727925 PMCID: PMC7466994 DOI: 10.1534/g3.120.401491] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The natural genetic diversity of agricultural species is an essential genetic resource for breeding programs aiming to improve their ecosystem and production services. A large natural ecotype diversity is usually available for most grassland species. This could be used to recombine natural climatic adaptations and agronomic value to create improved populations of grassland species adapted to future regional climates. However describing natural genetic resources can be long and costly. Molecular markers may provide useful information to help this task. This opportunity was investigated for Lolium perenne L., using a set of 385 accessions from the natural diversity of this species collected right across Europe and provided by genebanks of several countries. For each of these populations, genotyping provided the allele frequencies of 189,781 SNP markers. GWAS were implemented for over 30 agronomic and/or putatively adaptive traits recorded in three climatically contrasted locations (France, Belgium, Germany). Significant associations were detected for hundreds of markers despite a strong confounding effect of the genetic background; most of them pertained to phenology traits. It is likely that genetic variability in these traits has had an important contribution to environmental adaptation and ecotype differentiation. Genomic prediction models calibrated using natural diversity were found to be highly effective to describe natural populations for almost all traits as well as commercial synthetic populations for some important traits such as disease resistance, spring growth or phenological traits. These results will certainly be valuable information to help the use of natural genetic resources of other species.
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Harper J, De Vega J, Swain S, Heavens D, Gasior D, Thomas A, Evans C, Lovatt A, Lister S, Thorogood D, Skøt L, Hegarty M, Blackmore T, Kudrna D, Byrne S, Asp T, Powell W, Fernandez-Fuentes N, Armstead I. Integrating a newly developed BAC-based physical mapping resource for Lolium perenne with a genome-wide association study across a L. perenne European ecotype collection identifies genomic contexts associated with agriculturally important traits. ANNALS OF BOTANY 2019; 123:977-992. [PMID: 30715119 PMCID: PMC6589518 DOI: 10.1093/aob/mcy230] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 11/28/2018] [Indexed: 05/27/2023]
Abstract
BACKGROUND AND AIMS Lolium perenne (perennial ryegrass) is the most widely cultivated forage and amenity grass species in temperate areas worldwide and there is a need to understand the genetic architectures of key agricultural traits and crop characteristics that deliver wider environmental services. Our aim was to identify genomic regions associated with agriculturally important traits by integrating a bacterial artificial chromosome (BAC)-based physical map with a genome-wide association study (GWAS). METHODS BAC-based physical maps for L. perenne were constructed from ~212 000 high-information-content fingerprints using Fingerprint Contig and Linear Topology Contig software. BAC clones were associated with both BAC-end sequences and a partial minimum tiling path sequence. A panel of 716 L. perenne diploid genotypes from 90 European accessions was assessed in the field over 2 years, and genotyped using a Lolium Infinium SNP array. The GWAS was carried out using a linear mixed model implemented in TASSEL, and extended genomic regions associated with significant markers were identified through integration with the physical map. KEY RESULTS Between ~3600 and 7500 physical map contigs were derived, depending on the software and probability thresholds used, and integrated with ~35 k sequenced BAC clones to develop a resource predicted to span the majority of the L. perenne genome. From the GWAS, eight different loci were significantly associated with heading date, plant width, plant biomass and water-soluble carbohydrate accumulation, seven of which could be associated with physical map contigs. This allowed the identification of a number of candidate genes. CONCLUSIONS Combining the physical mapping resource with the GWAS has allowed us to extend the search for candidate genes across larger regions of the L. perenne genome and identified a number of interesting gene model annotations. These physical maps will aid in validating future sequence-based assemblies of the L. perenne genome.
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Affiliation(s)
- J Harper
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - J De Vega
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - S Swain
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - D Heavens
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - D Gasior
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - A Thomas
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - C Evans
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - A Lovatt
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - S Lister
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - D Thorogood
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - L Skøt
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - M Hegarty
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - T Blackmore
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - D Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - S Byrne
- Teagasc, Department of Crop Science, Carlow, Ireland
| | - T Asp
- Department of Molecular Biology and Genetics, Crop Genetics and Biotechnology, Aarhus University, Slagelse, Denmark
| | - W Powell
- Scotland’s Rural College, Edinburgh, UK
| | - N Fernandez-Fuentes
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - I Armstead
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
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Capstaff NM, Miller AJ. Improving the Yield and Nutritional Quality of Forage Crops. FRONTIERS IN PLANT SCIENCE 2018; 9:535. [PMID: 29740468 PMCID: PMC5928394 DOI: 10.3389/fpls.2018.00535] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 04/06/2018] [Indexed: 05/02/2023]
Abstract
Despite being some of the most important crops globally, there has been limited research on forages when compared with cereals, fruits, and vegetables. This review summarizes the literature highlighting the significance of forage crops, the current improvements and some of future directions for improving yield and nutritional quality. We make the point that the knowledge obtained from model plant and grain crops can be applied to forage crops. The timely development of genomics and bioinformatics together with genome editing techniques offer great scope to improve forage crops. Given the social, environmental and economic importance of forage across the globe and especially in poorer countries, this opportunity has enormous potential to improve food security and political stability.
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Haploid and Doubled Haploid Techniques in Perennial Ryegrass (Lolium perenne L.) to Advance Research and Breeding. AGRONOMY-BASEL 2016. [DOI: 10.3390/agronomy6040060] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Taranto F, D'Agostino N, Greco B, Cardi T, Tripodi P. Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by sequencing. BMC Genomics 2016; 17:943. [PMID: 27871227 PMCID: PMC5117568 DOI: 10.1186/s12864-016-3297-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 11/15/2016] [Indexed: 01/03/2023] Open
Abstract
Background Knowledge on population structure and genetic diversity in vegetable crops is essential for association mapping studies and genomic selection. Genotyping by sequencing (GBS) represents an innovative method for large scale SNP detection and genotyping of genetic resources. Herein we used the GBS approach for the genome-wide identification of SNPs in a collection of Capsicum spp. accessions and for the assessment of the level of genetic diversity in a subset of 222 cultivated pepper (Capsicum annum) genotypes. Results GBS analysis generated a total of 7,568,894 master tags, of which 43.4% uniquely aligned to the reference genome CM334. A total of 108,591 SNP markers were identified, of which 105,184 were in C. annuum accessions. In order to explore the genetic diversity of C. annuum and to select a minimal core set representing most of the total genetic variation with minimum redundancy, a subset of 222 C. annuum accessions were analysed using 32,950 high quality SNPs. Based on Bayesian and Hierarchical clustering it was possible to divide the collection into three clusters. Cluster I had the majority of varieties and landraces mainly from Southern and Northern Italy, and from Eastern Europe, whereas clusters II and III comprised accessions of different geographical origins. Considering the genome-wide genetic variation among the accessions included in cluster I, a second round of Bayesian (K = 3) and Hierarchical (K = 2) clustering was performed. These analysis showed that genotypes were grouped not only based on geographical origin, but also on fruit-related features. Conclusions GBS data has proven useful to assess the genetic diversity in a collection of C. annuum accessions. The high number of SNP markers, uniformly distributed on the 12 chromosomes, allowed the accessions to be distinguished according to geographical origin and fruit-related features. SNP markers and information on population structure developed in this study will undoubtedly support genome-wide association mapping studies and marker-assisted selection programs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3297-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- F Taranto
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-Centro di ricerca per l'orticoltura (CREA-ORT), Via dei Cavalleggeri 25, 84098, Pontecagnano Faiano, SA, Italy
| | - N D'Agostino
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-Centro di ricerca per l'orticoltura (CREA-ORT), Via dei Cavalleggeri 25, 84098, Pontecagnano Faiano, SA, Italy
| | - B Greco
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-Centro di ricerca per l'orticoltura (CREA-ORT), Via dei Cavalleggeri 25, 84098, Pontecagnano Faiano, SA, Italy
| | - T Cardi
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-Centro di ricerca per l'orticoltura (CREA-ORT), Via dei Cavalleggeri 25, 84098, Pontecagnano Faiano, SA, Italy
| | - P Tripodi
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-Centro di ricerca per l'orticoltura (CREA-ORT), Via dei Cavalleggeri 25, 84098, Pontecagnano Faiano, SA, Italy.
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