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Chapuis M, Leménager N, Piou C, Roumet P, Marche H, Centanni J, Estienne C, Ecarnot M, Vasseur F, Violle C, Kazakou E. Domestication provides durum wheat with protection from locust herbivory. Ecol Evol 2023; 13:e9741. [PMID: 36694552 PMCID: PMC9843534 DOI: 10.1002/ece3.9741] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 12/17/2022] [Accepted: 12/28/2022] [Indexed: 01/19/2023] Open
Abstract
Lower plant resistance to herbivores following domestication has been suggested as the main cause for higher feeding damage in crops than in wild progenitors. While herbivore compensatory feeding has also been proposed as a possible mechanism for raised damage in crops with low nutritional quality, predictions regarding the effects of plant domestication on nutritional quality for herbivores remain unclear. In particular, data on primary metabolites, even major macronutrients, measured in the organs consumed by herbivores, are scarce. In this study, we used a collection of 10 accessions of wild ancestors and 10 accessions of modern progenies of Triticum turgidum to examine whether feeding damage and selectivity by nymphs of Locusta migratoria primarily depended on five leaf traits related to structural resistance or nutrient profiles. Our results unexpectedly showed that locusts favored wild ancestors over domesticated accessions and that leaf toughness and nitrogen and soluble protein contents increased with the domestication process. Furthermore, the quantitative relationship between soluble protein and digestible carbohydrates was found to poorly meet the specific requirements of the herbivore, in all wheat accessions, both wild and modern. The increase in leaf structural resistance to herbivores in domesticated tetraploid wheat accessions suggested that resource allocation trade-offs between growth and herbivory resistance may have been disrupted by domestication in the vegetative organs of this species. Since domestication did not result in a loss of nutritional quality in the leaves of the tetraploid wheat, our results rather provides evidence for a role of the content of plants in nonnutritive nitrogenous secondary compounds, possibly deterrent or toxic, at least for grasshopper herbivores.
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Affiliation(s)
- Marie‐Pierre Chapuis
- CIRAD, CBGPMontpellierFrance,CBGP, CIRAD, Montpellier SupAgro, INRA, IRD, Univ MontpellierMontpellierFrance
| | - Nicolas Leménager
- CIRAD, CBGPMontpellierFrance,CBGP, CIRAD, Montpellier SupAgro, INRA, IRD, Univ MontpellierMontpellierFrance
| | - Cyril Piou
- CIRAD, CBGPMontpellierFrance,CBGP, CIRAD, Montpellier SupAgro, INRA, IRD, Univ MontpellierMontpellierFrance
| | - Pierre Roumet
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
| | - Héloïse Marche
- CIRAD, CBGPMontpellierFrance,CBGP, CIRAD, Montpellier SupAgro, INRA, IRD, Univ MontpellierMontpellierFrance
| | - Julia Centanni
- CEFE, Univ Montpellier, CNRS, EPHE, IRDMontpellierFrance
| | - Christophe Estienne
- CIRAD, CBGPMontpellierFrance,CBGP, CIRAD, Montpellier SupAgro, INRA, IRD, Univ MontpellierMontpellierFrance
| | - Martin Ecarnot
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
| | | | - Cyrille Violle
- CEFE, Univ Montpellier, CNRS, EPHE, IRDMontpellierFrance
| | - Elena Kazakou
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Institut AgroMontpellierFrance
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2
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Brault C, Lazerges J, Doligez A, Thomas M, Ecarnot M, Roumet P, Bertrand Y, Berger G, Pons T, François P, Le Cunff L, This P, Segura V. Interest of phenomic prediction as an alternative to genomic prediction in grapevine. Plant Methods 2022; 18:108. [PMID: 36064570 PMCID: PMC9442960 DOI: 10.1186/s13007-022-00940-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/24/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Phenomic prediction has been defined as an alternative to genomic prediction by using spectra instead of molecular markers. A reflectance spectrum provides information on the biochemical composition within a tissue, itself being under genetic determinism. Thus, a relationship matrix built from spectra could potentially capture genetic signal. This new methodology has been mainly applied in several annual crop species but little is known so far about its interest in perennial species. Besides, phenomic prediction has only been tested for a restricted set of traits, mainly related to yield or phenology. This study aims at applying phenomic prediction for the first time in grapevine, using spectra collected on two tissues and over two consecutive years, on two populations and for 15 traits, related to berry composition, phenology, morphological and vigour. A major novelty of this study was to collect spectra and phenotypes several years apart from each other. First, we characterized the genetic signal in spectra and under which condition it could be maximized, then phenomic predictive ability was compared to genomic predictive ability. RESULTS For the first time, we showed that the similarity between spectra and genomic relationship matrices was stable across tissues or years, but variable across populations, with co-inertia around 0.3 and 0.6 for diversity panel and half-diallel populations, respectively. Applying a mixed model on spectra data increased phenomic predictive ability, while using spectra collected on wood or leaves from one year or another had less impact. Differences between populations were also observed for predictive ability of phenomic prediction, with an average of 0.27 for the diversity panel and 0.35 for the half-diallel. For both populations, a significant positive correlation was found across traits between predictive ability of genomic and phenomic predictions. CONCLUSION NIRS is a new low-cost alternative to genotyping for predicting complex traits in perennial species such as grapevine. Having spectra and phenotypes from different years allowed us to exclude genotype-by-environment interactions and confirms that phenomic prediction can rely only on genetics.
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Affiliation(s)
- Charlotte Brault
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
- Institut Français de la vigne et du vin, 34398, Montpellier, France
| | - Juliette Lazerges
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
| | - Agnès Doligez
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
| | - Miguel Thomas
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
| | - Martin Ecarnot
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
| | - Pierre Roumet
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
| | - Yves Bertrand
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
| | - Gilles Berger
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
| | - Thierry Pons
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
| | - Pierre François
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
| | - Loïc Le Cunff
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
- Institut Français de la vigne et du vin, 34398, Montpellier, France
| | - Patrice This
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
| | - Vincent Segura
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France.
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France.
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Villesseche H, Ecarnot M, Ballini E, Bendoula R, Gorretta N, Roumet P. Unsupervised analysis of NIRS spectra to assess complex plant traits: leaf senescence as a use case. Plant Methods 2022; 18:100. [PMID: 35962438 PMCID: PMC9373489 DOI: 10.1186/s13007-022-00927-6] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND As a rapid and non-destructive method, Near Infrared Spectroscopy is classically proposed to assess plant traits in many scientific fields, to observe enlarged genotype panels and to document the temporal kinetic of some biological processes. Most often, supervised models are used. The signal is calibrated thanks to reference measurements, and dedicated models are generated to predict biological traits. An alternative unsupervised approach considers the whole spectra information in order to point out various matrix changes. Although more generic, and faster to implement, as it does not require a reference data set, this latter approach is rarely used to document biological processes, and does requires more information of the process. METHODS In our work, an unsupervised model was used to document the flag leaf senescence of durum wheat (Triticum turgidum durum). Leaf spectra changes were observed using Moving Window Principal Component Analysis (MWPCA). The dates related to earlier and later spectra changes were compared to two key points on the senescence time course: senescence onset (T0) and the end of the leaf span (T1) derived from a supervised strategy. RESULTS For almost all leaves and whatever the signal pre-treatments and window size considered, the MWPCA found significant spectral changes. The latter was highly correlated with T1 (0.59 ≤ r ≤ 0.86) whereas the correlations between the first significant spectrum changes and T0 were lower (0.09 ≤ r ≤ 0.56). These different relationships are discussed below since they define the potential as well as the limitations of MWPCA to model biological processes. CONCLUSION Overall, our study demonstrates that the information contained in the spectra can be used when applying an unsupervised method, here the MWPCA, to characterize a complex biological phenomenon such leaf senescence. It also means that using whole spectra may be relevant in agriculture and plant biology.
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Affiliation(s)
| | - Martin Ecarnot
- AGAP, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Elsa Ballini
- PHIM, CIRAD, INRAE, IRD, Institut Agro, Univ Montpellier, Montpellier, France
| | - Ryad Bendoula
- ITAP, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Nathalie Gorretta
- AGAP, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Pierre Roumet
- AGAP, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
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Colombo M, Roumet P, Salon C, Jeudy C, Lamboeuf M, Lafarge S, Dumas AV, Dubreuil P, Ngo W, Derepas B, Beauchêne K, Allard V, Le Gouis J, Rincent R. Genetic Analysis of Platform-Phenotyped Root System Architecture of Bread and Durum Wheat in Relation to Agronomic Traits. Front Plant Sci 2022; 13:853601. [PMID: 35401645 PMCID: PMC8992431 DOI: 10.3389/fpls.2022.853601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
Roots are essential for water and nutrient uptake but are rarely the direct target of breeding efforts. To characterize the genetic variability of wheat root architecture, the root and shoot traits of 200 durum and 715 bread wheat varieties were measured at a young stage on a high-throughput phenotyping platform. Heritability of platform traits ranged from 0.40 for root biomass in durum wheat to 0.82 for the number of tillers. Field phenotyping data for yield components and SNP genotyping were already available for all the genotypes. Taking differences in earliness into account, several significant correlations between root traits and field agronomic performances were found, suggesting that plants investing more resources in roots in some stressed environments favored water and nutrient uptake, with improved wheat yield. We identified 100 quantitative trait locus (QTLs) of root traits in the bread wheat panels and 34 in the durum wheat panel. Most colocalized with QTLs of traits measured in field conditions, including yield components and earliness for bread wheat, but only in a few environments. Stress and climatic indicators explained the differential effect of some platform QTLs on yield, which was positive, null, or negative depending on the environmental conditions. Modern breeding has led to deeper rooting but fewer seminal roots in bread wheat. The number of tillers has been increased in bread wheat, but decreased in durum wheat, and while the root-shoot ratio for bread wheat has remained stable, for durum wheat it has been increased. Breeding for root traits or designing ideotypes might help to maintain current yield while adapting to specific drought scenarios.
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Affiliation(s)
- Michel Colombo
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Pierre Roumet
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Christophe Salon
- Univ. Bourgogne, Agroecol Lab, Univ. Bourgogne Franche Comte, AgroSup Dijon, INRAE, Dijon, France
| | - Christian Jeudy
- Univ. Bourgogne, Agroecol Lab, Univ. Bourgogne Franche Comte, AgroSup Dijon, INRAE, Dijon, France
| | - Mickael Lamboeuf
- Univ. Bourgogne, Agroecol Lab, Univ. Bourgogne Franche Comte, AgroSup Dijon, INRAE, Dijon, France
| | | | | | | | - Wa Ngo
- INRAE-Universite Clermont-Auvergne, UMR 1095, GDEC, Clermont-Ferrand, France
| | - Brice Derepas
- INRAE-Universite Clermont-Auvergne, UMR 1095, GDEC, Clermont-Ferrand, France
| | | | - Vincent Allard
- INRAE-Universite Clermont-Auvergne, UMR 1095, GDEC, Clermont-Ferrand, France
| | - Jacques Le Gouis
- INRAE-Universite Clermont-Auvergne, UMR 1095, GDEC, Clermont-Ferrand, France
| | - Renaud Rincent
- INRAE-Universite Clermont-Auvergne, UMR 1095, GDEC, Clermont-Ferrand, France
- GQE-Le Moulon, INRAE, Univ. Paris-Sud, CNRS, AgroParisTech, Universite Paris-Saclay, Gif-sur-Yvette, France
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5
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Montazeaud G, Violle C, Roumet P, Rocher A, Ecarnot M, Compan F, Maillet G, Fort F, Fréville H. Multifaceted functional diversity for multifaceted crop yield: Towards ecological assembly rules for varietal mixtures. J Appl Ecol 2020. [DOI: 10.1111/1365-2664.13735] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Germain Montazeaud
- AGAPUniversité de MontpellierCIRADINRAEL'institut Agro Montpellier France
- CEFEUniversité de MontpellierCNRSEPHEIRDL'institut AgroUniversité Paul Valéry Montpellier France
| | - Cyrille Violle
- CEFEUniversité de MontpellierCNRSEPHEIRDUniversité Paul Valéry Montpellier France
| | - Pierre Roumet
- AGAPUniversité de MontpellierCIRADINRAEL'institut Agro Montpellier France
| | - Aline Rocher
- AGAPUniversité de MontpellierCIRADINRAEL'institut Agro Montpellier France
| | - Martin Ecarnot
- AGAPUniversité de MontpellierCIRADINRAEL'institut Agro Montpellier France
| | - Frédéric Compan
- AGAPUniversité de MontpellierCIRADINRAEL'institut Agro Montpellier France
| | - Guillaume Maillet
- AGAPUniversité de MontpellierCIRADINRAEL'institut Agro Montpellier France
| | - Florian Fort
- CEFEUniversité de MontpellierCNRSEPHEIRDL'institut AgroUniversité Paul Valéry Montpellier France
| | - Hélène Fréville
- AGAPUniversité de MontpellierCIRADINRAEL'institut Agro Montpellier France
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6
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Fréville H, Roumet P, Rode NO, Rocher A, Latreille M, Muller M, David J. Preferential helping to relatives: A potential mechanism responsible for lower yield of crop variety mixtures? Evol Appl 2019; 12:1837-1849. [PMID: 31548861 PMCID: PMC6752151 DOI: 10.1111/eva.12842] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 06/19/2019] [Accepted: 07/02/2019] [Indexed: 12/23/2022] Open
Abstract
Variety mixtures, the cultivation of different genotypes within a field, have been proposed as a way to increase within-crop diversity, allowing the development of more sustainable agricultural systems with reduced environmental costs. Although mixtures have often been shown to over-yield the average of component varieties in pure stands, decreased yields in mixtures have also been documented. Kin selection may explain such pattern, whenever plants direct helping behaviors preferentially toward relatives and thus experience stronger competition when grown with less related neighbors, lowering seed production of mixtures. Using varieties of durum wheat originating from traditional Moroccan agrosystems, we designed a greenhouse experiment to address whether plants reduced competition for light by limiting stem elongation when growing with kin and whether such phenotypic response resulted in higher yield of kin groups. Seeds were sown in groups of siblings and nonkin, each group containing a focal plant surrounded by four neighbors. At the group level, mean plant height and yield did not depend upon relatedness among competing plants. At the individual level, plant height was not affected by genetic relatedness to neighbors, after accounting for direct genetic effects that might induce among-genotype differences in the ability to capture resources that do not depend on relatedness. Moreover, in contrast to our predictions, shorter plants had lower inclusive fitness. Phenotypic plasticity in height was very limited in response to neighbor genotypes. This suggests that human selection in crops may have attenuated shade-avoidance responses to competition for light. Future research on preferential helping to relatives in crops might thus target social traits that drive competition for other resources than light. Overall, our study illustrates the relevance of tackling agricultural issues from an evolutionary standpoint and calls for extending such approaches to a larger set of crop species.
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Affiliation(s)
- Hélène Fréville
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgroMontpellierFrance
| | - Pierre Roumet
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgroMontpellierFrance
| | - Nicolas Olivier Rode
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgroMontpellierFrance
- CBGP, Univ Montpellier, CIRAD, Montpellier SupAgro, INRAIRDMontpellierFrance
| | - Aline Rocher
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgroMontpellierFrance
| | - Muriel Latreille
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgroMontpellierFrance
| | | | - Jacques David
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgroMontpellierFrance
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7
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Pommier C, Michotey C, Cornut G, Roumet P, Duchêne E, Flores R, Lebreton A, Alaux M, Durand S, Kimmel E, Letellier T, Merceron G, Laine M, Guerche C, Loaec M, Steinbach D, Laporte MA, Arnaud E, Quesneville H, Adam-Blondon AF. Applying FAIR Principles to Plant Phenotypic Data Management in GnpIS. Plant Phenomics 2019; 2019:1671403. [PMID: 33313522 PMCID: PMC7718628 DOI: 10.34133/2019/1671403] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/08/2019] [Indexed: 05/19/2023]
Abstract
GnpIS is a data repository for plant phenomics that stores whole field and greenhouse experimental data including environment measures. It allows long-term access to datasets following the FAIR principles: Findable, Accessible, Interoperable, and Reusable, by using a flexible and original approach. It is based on a generic and ontology driven data model and an innovative software architecture that uncouples data integration, storage, and querying. It takes advantage of international standards including the Crop Ontology, MIAPPE, and the Breeding API. GnpIS allows handling data for a wide range of species and experiment types, including multiannual perennial plants experimental network or annual plant trials with either raw data, i.e., direct measures, or computed traits. It also ensures the integration and the interoperability among phenotyping datasets and with genotyping data. This is achieved through a careful curation and annotation of the key resources conducted in close collaboration with the communities providing data. Our repository follows the Open Science data publication principles by ensuring citability of each dataset. Finally, GnpIS compliance with international standards enables its interoperability with other data repositories hence allowing data links between phenotype and other data types. GnpIS can therefore contribute to emerging international federations of information systems.
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Affiliation(s)
- C. Pommier
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - C. Michotey
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - G. Cornut
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - P. Roumet
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - E. Duchêne
- UMR SVQV, 28 rue de Herrlisheim, B.P. 20507, 68021 Colmar, France
| | - R. Flores
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - A. Lebreton
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - M. Alaux
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - S. Durand
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - E. Kimmel
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - T. Letellier
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - G. Merceron
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - M. Laine
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - C. Guerche
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - M. Loaec
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - D. Steinbach
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - M. A. Laporte
- Bioversity International, parc Scientifique Agropolis II, 34397 Montpellier cedex 5, France
| | - E. Arnaud
- Bioversity International, parc Scientifique Agropolis II, 34397 Montpellier cedex 5, France
| | - H. Quesneville
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
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8
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Affiliation(s)
- Agathe Roucou
- CEFE; CNRS; Univ. Montpellier; Univ Paul Valéry Montpellier 3; EPHE, IRD; Montpellier France
- LEPSE; Univ Montpellier; INRA; SupAgro Montpellier; Montpellier France
| | - Cyrille Violle
- CEFE; CNRS; Univ. Montpellier; Univ Paul Valéry Montpellier 3; EPHE, IRD; Montpellier France
| | - Florian Fort
- CEFE; Montpellier SupAgro; CNRS; Univ. Montpellier; Univ Paul Valéry Montpellier 3; EPHE, IRD; Montpellier France
| | - Pierre Roumet
- AGAP; Univ Montpellier; CIRAD; INRA; Montpellier SupAgro; Montpellier France
| | - Martin Ecarnot
- AGAP; Univ Montpellier; CIRAD; INRA; Montpellier SupAgro; Montpellier France
| | - Denis Vile
- LEPSE; Univ Montpellier; INRA; SupAgro Montpellier; Montpellier France
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9
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Holtz Y, Bonnefoy M, Viader V, Ardisson M, Rode NO, Poux G, Roumet P, Marie-Jeanne V, Ranwez V, Santoni S, Gouache D, David JL. Epistatic determinism of durum wheat resistance to the wheat spindle streak mosaic virus. Theor Appl Genet 2017; 130:1491-1505. [PMID: 28451771 PMCID: PMC5487696 DOI: 10.1007/s00122-017-2904-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 03/27/2017] [Indexed: 05/29/2023]
Abstract
KEY MESSAGE The resistance of durum wheat to the Wheat spindle streak mosaic virus (WSSMV) is controlled by two main QTLs on chromosomes 7A and 7B, with a huge epistatic effect. Wheat spindle streak mosaic virus (WSSMV) is a major disease of durum wheat in Europe and North America. Breeding WSSMV-resistant cultivars is currently the only way to control the virus since no treatment is available. This paper reports studies of the inheritance of WSSMV resistance using two related durum wheat populations obtained by crossing two elite cultivars with a WSSMV-resistant emmer cultivar. In 2012 and 2015, 354 recombinant inbred lines (RIL) were phenotyped using visual notations, ELISA and qPCR and genotyped using locus targeted capture and sequencing. This allowed us to build a consensus genetic map of 8568 markers and identify three chromosomal regions involved in WSSMV resistance. Two major regions (located on chromosomes 7A and 7B) jointly explain, on the basis of epistatic interactions, up to 43% of the phenotypic variation. Flanking sequences of our genetic markers are provided to facilitate future marker-assisted selection of WSSMV-resistant cultivars.
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Affiliation(s)
- Yan Holtz
- Montpellier SupAgro, UMR AGAP, 34060, Montpellier, France.
| | - Michel Bonnefoy
- Montpellier SupAgro, UMR BGPI, 34398, Montpellier Cedex 5, France
| | | | | | | | | | | | | | - Vincent Ranwez
- Montpellier SupAgro, UMR AGAP, 34060, Montpellier, France
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Jaillais B, Roumet P, Pinson-Gadais L, Bertrand D. Detection of Fusarium head blight contamination in wheat kernels by multivariate imaging. Food Control 2015. [DOI: 10.1016/j.foodcont.2015.01.048] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Sahri A, Chentoufi L, Arbaoui M, Ardisson M, Belqadi L, Birouk A, Roumet P, Muller MH. Towards a comprehensive characterization of durum wheat landraces in Moroccan traditional agrosystems: analysing genetic diversity in the light of geography, farmers' taxonomy and tetraploid wheat domestication history. BMC Evol Biol 2014; 14:264. [PMID: 25528060 PMCID: PMC4300848 DOI: 10.1186/s12862-014-0264-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 12/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Crop diversity managed by smallholder farmers in traditional agrosystems is the outcome of historical and current processes interacting at various spatial scales, and influenced by factors such as farming practices and environmental pressures. Only recently have studies started to consider the complexity of these processes instead of simply describing diversity for breeding purposes. A first step in that aim is to add multiple references to the collection of genetic data, including the farmers' varietal taxonomy and practices and the historical background of the crop. RESULTS On the basis of interview data collected in a previous study, we sampled 166 populations of durum wheat varieties in two traditional Moroccan agrosystems, in the Pre-Rif and Atlas Mountains regions. Using a common garden experiment, we detected a high phenotypic variability on traits indicative of taxonomical position and breeding status, namely spike shape and plant height. Populations often combined modern (short) with traditional-like (tall) statures, and classical durum squared spike shape (5 flowers/spikelet) with flat spike shape (3 flowers/ spikelet) representative of primitive domesticated tetraploid wheat (ssp. dicoccum). By contrast, the genetic diversity assessed using 14 microsatellite markers was relatively limited. When compared to the genetic diversity found in a large collection of tetraploid wheat, it corresponded to free-threshing tetraploid wheat. Within Morocco, the two studied regions differed for both genetic diversity and variety names. Within regions, neither geography nor variety names nor even breeding status constituted strong barriers to gene exchange despite a few significant patterns. CONCLUSIONS This first assessment of morphological and genetic diversity allowed pointing out some important factors that may have influenced the structure and evolutionary dynamics of durum wheat in Morocco: the significance of variety names, the occurrence of mixtures within populations, the relative strength of seed exchange between farmers and local adaptation, as well as the fate of modern varieties once they have been introduced. Further, multidisciplinary studies at different spatial scales are needed to better understand these complex agrosystems of invaluable importance for food security.
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Affiliation(s)
- Ali Sahri
- Département de Production, Protection et Biotechnologies Végétales, Institut Agronomique et Vétérinaire Hassan II, B.P. 6202, Rabat-Instituts, Rabat, Morocco.
| | - Lamyae Chentoufi
- Département de Production, Protection et Biotechnologies Végétales, Institut Agronomique et Vétérinaire Hassan II, B.P. 6202, Rabat-Instituts, Rabat, Morocco.
| | - Mustapha Arbaoui
- Département de Production, Protection et Biotechnologies Végétales, Institut Agronomique et Vétérinaire Hassan II, B.P. 6202, Rabat-Instituts, Rabat, Morocco.
| | - Morgane Ardisson
- INRA, UMR 1334, Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP), 2 place Pierre Viala, F-34060, Montpellier Cedex 1, France.
| | - Loubna Belqadi
- Département de Production, Protection et Biotechnologies Végétales, Institut Agronomique et Vétérinaire Hassan II, B.P. 6202, Rabat-Instituts, Rabat, Morocco.
| | - Ahmed Birouk
- Département de Production, Protection et Biotechnologies Végétales, Institut Agronomique et Vétérinaire Hassan II, B.P. 6202, Rabat-Instituts, Rabat, Morocco.
| | - Pierre Roumet
- INRA, UMR 1334, Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP), 2 place Pierre Viala, F-34060, Montpellier Cedex 1, France.
| | - Marie-Hélène Muller
- INRA, UMR 1334, Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP), 2 place Pierre Viala, F-34060, Montpellier Cedex 1, France.
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Chentoufi L, Sahri A, Arbaoui M, Belqadi L, Birouk A, Roumet P, Muller MH. Anchoring durum wheat diversity in the reality of traditional agricultural systems: varieties, seed management, and farmers' perception in two Moroccan regions. J Ethnobiol Ethnomed 2014; 10:58. [PMID: 25027694 PMCID: PMC4132198 DOI: 10.1186/1746-4269-10-58] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 07/03/2014] [Indexed: 06/03/2023]
Abstract
BACKGROUND Traditional agrosystems are the places were crop species have evolved and continue to evolve under a combination of human and environmental pressures. A better knowledge of the mechanisms underlying the dynamics of crop diversity in these agrosystems is crucial to sustain food security and farmers' self-reliance. It requires as a first step, anchoring a description of the available diversity in its geographical, environmental, cultural and socio-economic context. METHODS We conducted interviews with farmers cultivating durum wheat in two contrasted traditional agrosystems of Morocco in the Pre-Rif (163 farmers) and in the oases of the Atlas Mountains (110 farmers). We documented the varietal diversity of durum wheat, the main characteristics of the farms, the farming and seed management practices applied to durum wheat, and the farmers' perception of their varieties. RESULTS As expected in traditional agrosystems, farmers largely practiced diversified subsistence agriculture on small plots and relied on on-farm seed production or informal seed exchange networks. Heterogeneity nevertheless prevailed on many variables, especially on the modernization of practices in the Pre-Rif region. Fourteen (resp. 11) traditional and 5 (resp. 3) modern varieties were identified in the Pre-Rif region (resp. in the Atlas Mountains). The majority of farmers grew a single variety, and most traditional varieties were distributed in restricted geographical areas. At the farm level, more than half of the varieties were renewed in the last decade in the Pre-Rif, a more rapid renewal than in the Atlas Mountain. Modern varieties were more prevalent in the Pre-Rif region and were integrated in the traditional practices of seed production, selection and exchange. They were clearly distinguished by the farmers from the landraces, the last ones being appreciated for their quality traits. CONCLUSIONS The surveyed traditional agrosystems constitute open, dynamic and heterogeneous entities. We suggest that competing factors could favour or limit the cultivation of improved varieties and the erosion of original durum wheat diversity. This first description opens the way to focused further investigations, including complementing variety names with cultural, genetic and phenotypic information and unravelling the multidimensional factors and consequences of modern variety adoption.
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Affiliation(s)
- Lamyae Chentoufi
- Département de Production, Protection et Biotechnologies Végétales, Institut Agronomique et Vétérinaire Hassan II, B.P. 6202, Rabat-Instituts, Rabat, Morocco
| | - Ali Sahri
- Département de Production, Protection et Biotechnologies Végétales, Institut Agronomique et Vétérinaire Hassan II, B.P. 6202, Rabat-Instituts, Rabat, Morocco
| | - Mustapha Arbaoui
- Département de Production, Protection et Biotechnologies Végétales, Institut Agronomique et Vétérinaire Hassan II, B.P. 6202, Rabat-Instituts, Rabat, Morocco
| | - Loubna Belqadi
- Département de Production, Protection et Biotechnologies Végétales, Institut Agronomique et Vétérinaire Hassan II, B.P. 6202, Rabat-Instituts, Rabat, Morocco
| | - Ahmed Birouk
- Département de Production, Protection et Biotechnologies Végétales, Institut Agronomique et Vétérinaire Hassan II, B.P. 6202, Rabat-Instituts, Rabat, Morocco
| | - Pierre Roumet
- INRA, UMR 1334, Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP), 2 place Pierre Viala, F-34060 Montpellier Cedex 1, France
| | - Marie-Hélène Muller
- INRA, UMR 1334, Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP), 2 place Pierre Viala, F-34060 Montpellier Cedex 1, France
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Lacaze X, Roumet P. Environment characterisation for the interpretation of environmental effect and genotype x environment interaction. Theor Appl Genet 2004; 109:1632-1640. [PMID: 15372155 DOI: 10.1007/s00122-004-1786-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2004] [Accepted: 07/31/2004] [Indexed: 05/24/2023]
Abstract
Increasing attention is being paid to environment characterisation as a means of identifying the environmental factors determining grain protein content (GPC) in durum wheat. New insights in crop physiology and agronomy have led to the development of crop simulation models. Those models can reconstruct plant development for past cropping seasons. One major advantage of these models is that they can also indicate the intensity of limiting factors affecting plants during particular developmental stages. The main environmental factors determining GPC in durum wheat can be investigated by introducing the intensity of limiting factors into genotype x environment (GxE) models. In our case, limiting factors corresponding to water deficit and nitrogen availability were calculated for the development period between booting and heading. These variables were then introduced into a clustering model. This model is an extension of factorial regression applied to discrete environment and genotypic variables. This procedure effectively described the environment main effect: around 30.9% of the sum of squares of the environment main effect was accounted for, using less than 33% of the degrees of freedom. It also partially accounted for GxE interaction. Our methodology, coupling the use of crop simulation and GxE analysis models, is of potential value for improving our understanding of the main development stages and identification of environmental limiting factors for the development of GPC.
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Affiliation(s)
- Xavier Lacaze
- UMR 1097 Diversité et Génome des Plantes Cultivées : Institut de la Recherche Agronomique INRA-SGAP, Domaine de Melgueil, 34130 Mauguio, France.
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Thuillet AC, Bru D, David J, Roumet P, Santoni S, Sourdille P, Bataillon T. Direct estimation of mutation rate for 10 microsatellite loci in durum wheat, Triticum turgidum (L.) Thell. ssp durum desf. Mol Biol Evol 2002; 19:122-5. [PMID: 11752198 DOI: 10.1093/oxfordjournals.molbev.a003977] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Anne-Céline Thuillet
- INRA-Station de Génétique et d'Amélioration des Plantes, Mauguio, Domaine de Melgueil, 34130 Mauguio, France.
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David JL, Dusautoir JC, Raynaud C, Roumet P. Heritable variation in the ability to produce haploid embryos via pollination with maize and embryo rescue in durum wheat. Genome 1999. [DOI: 10.1139/g98-140] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pollination with maize is commonly used to produce fertile doubled haploid plants in durum wheat. However, the genetic basis for the ability of parental lines to produce haploid seedlings is not well documented. A maximum likelihood procedure was used to analyse the response of 15 F1, from a half diallel design involving six inbred lines, and to document rigorously the existence of heritable variation for haploid embryo production. Cross-effects and "general combining abilities" (GCA) were computed to estimate the ability to produce swollen ovaries and viable embryos. On average, the ovary swelling production was 56% and 11% of emasculated flowers produced a viable embryo. For both variables, cross-effect was significant. Based on GCA estimations, the 6 parental lines could be distributed in 3 different groups. The GCA values explained respectively 69% and 79% of the cross-effect for each variable. On the whole, ovary swelling was a poor predictor of embryo formation. No significant correlation was found between the per se values of the 6 parental lines and their GCA.Key words: Triticum durum, haploid, general combining ability.
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