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Bourion V, Heulin-Gotty K, Aubert V, Tisseyre P, Chabert-Martinello M, Pervent M, Delaitre C, Vile D, Siol M, Duc G, Brunel B, Burstin J, Lepetit M. Co-inoculation of a Pea Core-Collection with Diverse Rhizobial Strains Shows Competitiveness for Nodulation and Efficiency of Nitrogen Fixation Are Distinct traits in the Interaction. Front Plant Sci 2018; 8:2249. [PMID: 29367857 PMCID: PMC5767787 DOI: 10.3389/fpls.2017.02249] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 12/21/2017] [Indexed: 05/07/2023]
Abstract
Pea forms symbiotic nodules with Rhizobium leguminosarum sv. viciae (Rlv). In the field, pea roots can be exposed to multiple compatible Rlv strains. Little is known about the mechanisms underlying the competitiveness for nodulation of Rlv strains and the ability of pea to choose between diverse compatible Rlv strains. The variability of pea-Rlv partner choice was investigated by co-inoculation with a mixture of five diverse Rlv strains of a 104-pea collection representative of the variability encountered in the genus Pisum. The nitrogen fixation efficiency conferred by each strain was determined in additional mono-inoculation experiments on a subset of 18 pea lines displaying contrasted Rlv choice. Differences in Rlv choice were observed within the pea collection according to their genetic or geographical diversities. The competitiveness for nodulation of a given pea-Rlv association evaluated in the multi-inoculated experiment was poorly correlated with its nitrogen fixation efficiency determined in mono-inoculation. Both plant and bacterial genetic determinants contribute to pea-Rlv partner choice. No evidence was found for co-selection of competitiveness for nodulation and nitrogen fixation efficiency. Plant and inoculant for an improved symbiotic association in the field must be selected not only on nitrogen fixation efficiency but also for competitiveness for nodulation.
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Affiliation(s)
- Virginie Bourion
- Agroécologie, INRA, AgroSup Dijon, Université Bourgogne Franche-Comté, Dijon, France
| | - Karine Heulin-Gotty
- Laboratoire des Symbioses Tropicales et Méditerranéennes, INRA, IRD, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Véronique Aubert
- Agroécologie, INRA, AgroSup Dijon, Université Bourgogne Franche-Comté, Dijon, France
| | - Pierre Tisseyre
- Laboratoire des Symbioses Tropicales et Méditerranéennes, INRA, IRD, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | | | - Marjorie Pervent
- Laboratoire des Symbioses Tropicales et Méditerranéennes, INRA, IRD, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Catherine Delaitre
- Agroécologie, INRA, AgroSup Dijon, Université Bourgogne Franche-Comté, Dijon, France
| | - Denis Vile
- Laboratoire d'Ecophysiologie des Plantes Sous Stress Environnementaux, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Mathieu Siol
- Agroécologie, INRA, AgroSup Dijon, Université Bourgogne Franche-Comté, Dijon, France
| | - Gérard Duc
- Agroécologie, INRA, AgroSup Dijon, Université Bourgogne Franche-Comté, Dijon, France
| | - Brigitte Brunel
- Laboratoire des Symbioses Tropicales et Méditerranéennes, INRA, IRD, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Judith Burstin
- Agroécologie, INRA, AgroSup Dijon, Université Bourgogne Franche-Comté, Dijon, France
| | - Marc Lepetit
- Laboratoire des Symbioses Tropicales et Méditerranéennes, INRA, IRD, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
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Siol M, Jacquin F, Chabert-Martinello M, Smýkal P, Le Paslier MC, Aubert G, Burstin J. Patterns of Genetic Structure and Linkage Disequilibrium in a Large Collection of Pea Germplasm. G3 (Bethesda) 2017; 7:2461-2471. [PMID: 28611254 PMCID: PMC5555454 DOI: 10.1534/g3.117.043471] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/22/2017] [Indexed: 12/18/2022]
Abstract
Pea (Pisum sativum, L.) is a major pulse crop used both for animal and human alimentation. Owing to its association with nitrogen-fixing bacteria, it is also a valuable component for low-input cropping systems. To evaluate the genetic diversity and the scale of linkage disequilibrium (LD) decay in pea, we genotyped a collection of 917 accessions, gathering elite cultivars, landraces, and wild relatives using an array of ∼13,000 single nucleotide polymorphisms (SNP). Genetic diversity is broadly distributed across three groups corresponding to wild/landraces peas, winter types, and spring types. At a finer subdivision level, genetic groups relate to local breeding programs and type usage. LD decreases steeply as genetic distance increases. When considering subsets of the data, LD values can be higher, even if the steep decay remains. We looked for genomic regions exhibiting high level of differentiation between wild/landraces, winter, and spring pea, respectively. Two regions on linkage groups 5 and 6 containing 33 SNPs exhibit stronger differentiation between winter and spring peas than would be expected under neutrality. Interestingly, QTL for resistance to cold acclimation and frost resistance have been identified previously in the same regions.
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Affiliation(s)
- Mathieu Siol
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche (UMR) 1347, Agroécologie, 21065 Dijon, France
| | - Françoise Jacquin
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche (UMR) 1347, Agroécologie, 21065 Dijon, France
| | - Marianne Chabert-Martinello
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche (UMR) 1347, Agroécologie, 21065 Dijon, France
| | - Petr Smýkal
- Palacky University, Faculty of Science, Department of Botany, Holice, 783 71 Olomouc, Czech Republic
| | - Marie-Christine Le Paslier
- INRA, US 1279 Etude du Polymorphisme des Génomes Végétaux (EPGV), Centre de Recherche Ile-de-France-Versailles-Grignon, Commissariat à l'énergie atomique (CEA)-Institut de Génomique, Centre national de génotypage (CNG), Université Paris-Saclay, 91000 Evry, France
| | - Grégoire Aubert
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche (UMR) 1347, Agroécologie, 21065 Dijon, France
| | - Judith Burstin
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche (UMR) 1347, Agroécologie, 21065 Dijon, France
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Burstin J, Salloignon P, Chabert-Martinello M, Magnin-Robert JB, Siol M, Jacquin F, Chauveau A, Pont C, Aubert G, Delaitre C, Truntzer C, Duc G. Genetic diversity and trait genomic prediction in a pea diversity panel. BMC Genomics 2015; 16:105. [PMID: 25765216 PMCID: PMC4355348 DOI: 10.1186/s12864-015-1266-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 01/22/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pea (Pisum sativum L.), a major pulse crop grown for its protein-rich seeds, is an important component of agroecological cropping systems in diverse regions of the world. New breeding challenges imposed by global climate change and new regulations urge pea breeders to undertake more efficient methods of selection and better take advantage of the large genetic diversity present in the Pisum sativum genepool. Diversity studies conducted so far in pea used Simple Sequence Repeat (SSR) and Retrotransposon Based Insertion Polymorphism (RBIP) markers. Recently, SNP marker panels have been developed that will be useful for genetic diversity assessment and marker-assisted selection. RESULTS A collection of diverse pea accessions, including landraces and cultivars of garden, field or fodder peas as well as wild peas was characterised at the molecular level using newly developed SNP markers, as well as SSR markers and RBIP markers. The three types of markers were used to describe the structure of the collection and revealed different pictures of the genetic diversity among the collection. SSR showed the fastest rate of evolution and RBIP the slowest rate of evolution, pointing to their contrasted mode of evolution. SNP markers were then used to predict phenotypes -the date of flowering (BegFlo), the number of seeds per plant (Nseed) and thousand seed weight (TSW)- that were recorded for the collection. Different statistical methods were tested including the LASSO (Least Absolute Shrinkage ans Selection Operator), PLS (Partial Least Squares), SPLS (Sparse Partial Least Squares), Bayes A, Bayes B and GBLUP (Genomic Best Linear Unbiased Prediction) methods and the structure of the collection was taken into account in the prediction. Despite a limited number of 331 markers used for prediction, TSW was reliably predicted. CONCLUSION The development of marker assisted selection has not reached its full potential in pea until now. This paper shows that the high-throughput SNP arrays that are being developed will most probably allow for a more efficient selection in this species.
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Affiliation(s)
- Judith Burstin
- UMR1347, Agroecology, INRA, 17 rue de Sully, Dijon Cedex, 21065, France.
| | - Pauline Salloignon
- Clinical and Innovation Proteomic Platform (CLIPP), CHU Dijon, Université de Bourgogne, 1 rue du Professeur Marion, Dijon, 21000, France.
| | | | | | - Mathieu Siol
- UMR1347, Agroecology, INRA, 17 rue de Sully, Dijon Cedex, 21065, France.
| | - Françoise Jacquin
- UMR1347, Agroecology, INRA, 17 rue de Sully, Dijon Cedex, 21065, France.
| | - Aurélie Chauveau
- UMR1347, Agroecology, INRA, 17 rue de Sully, Dijon Cedex, 21065, France.
- Present address: US EPGV, IG-CEA, Centre National de Génotypage, 2 rue Gaston Crémieux, Evry Cedex, 91057, France.
| | - Caroline Pont
- UMR GDEC, Plateforme Gentyane, Clermont Ferrand, 63100, France.
| | - Grégoire Aubert
- UMR1347, Agroecology, INRA, 17 rue de Sully, Dijon Cedex, 21065, France.
| | - Catherine Delaitre
- UMR1347, Agroecology, INRA, 17 rue de Sully, Dijon Cedex, 21065, France.
| | - Caroline Truntzer
- Clinical and Innovation Proteomic Platform (CLIPP), CHU Dijon, Université de Bourgogne, 1 rue du Professeur Marion, Dijon, 21000, France.
| | - Gérard Duc
- UMR1347, Agroecology, INRA, 17 rue de Sully, Dijon Cedex, 21065, France.
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Tayeh N, Klein A, Le Paslier MC, Jacquin F, Houtin H, Rond C, Chabert-Martinello M, Magnin-Robert JB, Marget P, Aubert G, Burstin J. Genomic Prediction in Pea: Effect of Marker Density and Training Population Size and Composition on Prediction Accuracy. Front Plant Sci 2015; 6:941. [PMID: 26635819 PMCID: PMC4648083 DOI: 10.3389/fpls.2015.00941] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 10/16/2015] [Indexed: 05/18/2023]
Abstract
Pea is an important food and feed crop and a valuable component of low-input farming systems. Improving resistance to biotic and abiotic stresses is a major breeding target to enhance yield potential and regularity. Genomic selection (GS) has lately emerged as a promising technique to increase the accuracy and gain of marker-based selection. It uses genome-wide molecular marker data to predict the breeding values of candidate lines to selection. A collection of 339 genetic resource accessions (CRB339) was subjected to high-density genotyping using the GenoPea 13.2K SNP Array. Genomic prediction accuracy was evaluated for thousand seed weight (TSW), the number of seeds per plant (NSeed), and the date of flowering (BegFlo). Mean cross-environment prediction accuracies reached 0.83 for TSW, 0.68 for NSeed, and 0.65 for BegFlo. For each trait, the statistical method, the marker density, and/or the training population size and composition used for prediction were varied to investigate their effects on prediction accuracy: the effect was large for the size and composition of the training population but limited for the statistical method and marker density. Maximizing the relatedness between individuals in the training and test sets, through the CDmean-based method, significantly improved prediction accuracies. A cross-population cross-validation experiment was further conducted using the CRB339 collection as a training population set and nine recombinant inbred lines populations as test set. Prediction quality was high with mean Q (2) of 0.44 for TSW and 0.59 for BegFlo. Results are discussed in the light of current efforts to develop GS strategies in pea.
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Affiliation(s)
- Nadim Tayeh
- INRA, UMR1347 AgroécologieDijon, France
- *Correspondence: Nadim Tayeh
| | | | - Marie-Christine Le Paslier
- INRA, US1279 Etude du Polymorphisme des Génomes Végétaux, CEA-IG/Centre National de GénotypageEvry, France
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