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Duarte J, Rivière N, Baranger A, Aubert G, Burstin J, Cornet L, Lavaud C, Lejeune-Hénaut I, Martinant JP, Pichon JP, Pilet-Nayel ML, Boutet G. Transcriptome sequencing for high throughput SNP development and genetic mapping in Pea. BMC Genomics 2014; 15:126. [PMID: 24521263 PMCID: PMC3925251 DOI: 10.1186/1471-2164-15-126] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 02/05/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Pea has a complex genome of 4.3 Gb for which only limited genomic resources are available to date. Although SNP markers are now highly valuable for research and modern breeding, only a few are described and used in pea for genetic diversity and linkage analysis. RESULTS We developed a large resource by cDNA sequencing of 8 genotypes representative of modern breeding material using the Roche 454 technology, combining both long reads (400 bp) and high coverage (3.8 million reads, reaching a total of 1,369 megabases). Sequencing data were assembled and generated a 68 K unigene set, from which 41 K were annotated from their best blast hit against the model species Medicago truncatula. Annotated contigs showed an even distribution along M. truncatula pseudochromosomes, suggesting a good representation of the pea genome. 10 K pea contigs were found to be polymorphic among the genetic material surveyed, corresponding to 35 K SNPs.We validated a subset of 1538 SNPs through the GoldenGate assay, proving their ability to structure a diversity panel of breeding germplasm. Among them, 1340 were genetically mapped and used to build a new consensus map comprising a total of 2070 markers. Based on blast analysis, we could establish 1252 bridges between our pea consensus map and the pseudochromosomes of M. truncatula, which provides new insight on synteny between the two species. CONCLUSIONS Our approach created significant new resources in pea, i.e. the most comprehensive genetic map to date tightly linked to the model species M. truncatula and a large SNP resource for both academic research and breeding.
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Affiliation(s)
- Jorge Duarte
- Biogemma, route d’Ennezat, CS 90126, Chappes 63720, France
| | | | - Alain Baranger
- INRA UMR 1349 IGEPP, BP35327, Le Rheu Cedex 35653, France
| | - Grégoire Aubert
- INRA UMR 1347 Agroécologie, Bat. Mendel, 17 rue Sully BP 86510, Dijon 21065, France
| | - Judith Burstin
- INRA UMR 1347 Agroécologie, Bat. Mendel, 17 rue Sully BP 86510, Dijon 21065, France
| | - Laurent Cornet
- Biogemma, route d’Ennezat, CS 90126, Chappes 63720, France
| | - Clément Lavaud
- INRA UMR 1349 IGEPP, BP35327, Le Rheu Cedex 35653, France
| | | | - Jean-Pierre Martinant
- Limagrain Europe, centre de recherche route d’Ennezat, CS 3911, Chappes 63720, France
| | | | | | - Gilles Boutet
- INRA UMR 1349 IGEPP, BP35327, Le Rheu Cedex 35653, France
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Gallardo K, Courty PE, Le Signor C, Wipf D, Vernoud V. Sulfate transporters in the plant's response to drought and salinity: regulation and possible functions. FRONTIERS IN PLANT SCIENCE 2014; 5:580. [PMID: 25400648 PMCID: PMC4212607 DOI: 10.3389/fpls.2014.00580] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 10/08/2014] [Indexed: 05/20/2023]
Abstract
Drought and salinity are two frequently combined abiotic stresses that affect plant growth, development, and crop productivity. Sulfate, and molecules derived from this anion such as glutathione, play important roles in the intrinsic responses of plants to such abiotic stresses. Therefore, understanding how plants facing environmental constraints re-equilibrate the flux of sulfate between and within different tissues might uncover perspectives for improving tolerance against abiotic stresses. In this review, we took advantage of genomics and post-genomics resources available in Arabidopsis thaliana and in the model legume species Medicago truncatula to highlight and compare the regulation of sulfate transporter genes under drought and salt stress. We also discuss their possible function in the plant's response and adaptation to abiotic stresses and present prospects about the potential benefits of mycorrhizal associations, which by facilitating sulfate uptake may assist plants to cope with abiotic stresses. Several transporters are highlighted in this review that appear promising targets for improving sulfate transport capacities of crops under fluctuating environmental conditions.
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Affiliation(s)
- Karine Gallardo
- Institut National de la Recherche Agronomique, UMR1347 Agroécologie, DijonFrance
- *Correspondence: Karine Gallardo, Institut National de la Recherche Agronomique, UMR1347 Agroécologie, 17 rue de Sully, BP 86510, Dijon, France e-mail:
| | - Pierre-Emmanuel Courty
- Zurich-Basel Plant Science Center, Department of Environmental Sciences, Botany, University of Basel, BaselSwitzerland
| | - Christine Le Signor
- Institut National de la Recherche Agronomique, UMR1347 Agroécologie, DijonFrance
| | - Daniel Wipf
- Université de Bourgogne, UMR1347 Agroécologie, DijonFrance
| | - Vanessa Vernoud
- Institut National de la Recherche Agronomique, UMR1347 Agroécologie, DijonFrance
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53
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Satovic Z, Avila CM, Cruz-Izquierdo S, Díaz-Ruíz R, García-Ruíz GM, Palomino C, Gutiérrez N, Vitale S, Ocaña-Moral S, Gutiérrez MV, Cubero JI, Torres AM. A reference consensus genetic map for molecular markers and economically important traits in faba bean (Vicia faba L.). BMC Genomics 2013; 14:932. [PMID: 24377374 PMCID: PMC3880837 DOI: 10.1186/1471-2164-14-932] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 12/12/2013] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Faba bean (Vicia faba L.) is among the earliest domesticated crops from the Near East. Today this legume is a key protein feed and food worldwide and continues to serve an important role in culinary traditions throughout Middle East, Mediterranean region, China and Ethiopia. Adapted to a wide range of soil types, the main faba bean breeding objectives are to improve yield, resistance to biotic and abiotic stresses, seed quality and other agronomic traits. Genomic approaches aimed at enhancing faba bean breeding programs require high-quality genetic linkage maps to facilitate quantitative trait locus analysis and gene tagging for use in a marker-assisted selection. The objective of this study was to construct a reference consensus map in faba bean by joining the information from the most relevant maps reported so far in this crop. RESULTS A combination of two approaches, increasing the number of anchor loci in diverse mapping populations and joining the corresponding genetic maps, was used to develop a reference consensus map in faba bean. The map was constructed from three main recombinant inbreed populations derived from four parental lines, incorporates 729 markers and is based on 69 common loci. It spans 4,602 cM with a range from 323 to 1041 loci in six main linkage groups or chromosomes, and an average marker density of one locus every 6 cM. Locus order is generally well maintained between the consensus map and the individual maps. CONCLUSION We have constructed a reliable and fairly dense consensus genetic linkage map that will serve as a basis for genomic approaches in faba bean research and breeding. The core map contains a larger number of markers than any previous individual map, covers existing gaps and achieves a wider coverage of the large faba bean genome as a whole. This tool can be used as a reference resource for studies in different genetic backgrounds, and provides a framework for transferring genetic information when using different marker technologies. Combined with syntenic approaches, the consensus map will increase marker density in selected genomic regions and will be useful for future faba bean molecular breeding applications.
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Affiliation(s)
- Zlatko Satovic
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
- Present addresses: Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Carmen M Avila
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - Serafin Cruz-Izquierdo
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
- Colegio de Postgraduados, Recursos Genéticos y Productividad – Genética, Campus Montecillo, Km 36.5 Carretera México-Texcoco, C.P., Texcoco, Edo. de México 56230, México
| | - Ramón Díaz-Ruíz
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
- Colegio de Postgraduados, Campus Puebla, Km 125.5 Carretera México-Puebla, C.P., Puebla, Pue 72760, México
| | - Gloria M García-Ruíz
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - Carmen Palomino
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - Natalia Gutiérrez
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - Stefania Vitale
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - Sara Ocaña-Moral
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - María Victoria Gutiérrez
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - José I Cubero
- Departamento de Mejora Genética, IAS-CSIC, Apdo. 4084, Córdoba 14080, Spain
| | - Ana M Torres
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
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Tayeh N, Bahrman N, Sellier H, Bluteau A, Blassiau C, Fourment J, Bellec A, Debellé F, Lejeune-Hénaut I, Delbreil B. A tandem array of CBF/DREB1 genes is located in a major freezing tolerance QTL region on Medicago truncatula chromosome 6. BMC Genomics 2013; 14:814. [PMID: 24261852 PMCID: PMC4046650 DOI: 10.1186/1471-2164-14-814] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 11/04/2013] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Freezing provokes severe yield losses to different fall-sown annual legumes. Understanding the molecular bases of freezing tolerance is of great interest for breeding programs. Medicago truncatula Gaertn. is an annual temperate forage legume that has been chosen as a model species for agronomically and economically important legume crops. The present study aimed to identify positional candidate genes for a major freezing tolerance quantitative trait locus that was previously mapped to M. truncatula chromosome 6 (Mt-FTQTL6) using the LR3 population derived from a cross between the freezing-tolerant accession F83005-5 and the freezing-sensitive accession DZA045-5. RESULTS The confidence interval of Mt-FTQTL6 was narrowed down to the region comprised between markers MTIC153 and NT6054 using recombinant F7 and F8 lines. A bacterial-artificial chromosome (BAC) clone contig map was constructed in an attempt to close the residual assembly gap existing therein. Twenty positional candidate genes including twelve C-repeat binding factor (CBF)/dehydration-responsive element binding factor 1 (DREB1) genes were identified from BAC-derived sequences and whole-genome shotgun sequences (WGS). CBF/DREB1 genes are organized in a tandem array within an approximately 296-Kb region. Eleven CBF/DREB1 genes were isolated and sequenced from F83005-5 and DZA045-5 which revealed high polymorphism among these accessions. Unique features characterizing CBF/DREB1 genes from M. truncatula, such as alternative splicing and large tandem duplication, are elucidated for the first time. CONCLUSIONS Overall, twenty genes were identified as potential candidates to explain Mt-FTQTL6 effect. Their future functional characterization will uncover the gene(s) involved in freezing tolerance difference observed between F83005-5 and DZA045-5. Knowledge transfer for breeding improvement of crop legumes is expected. Furthermore, CBF/DREB1 related data will certainly have a large impact on research studies targeting this group of transcriptional activators in M. truncatula and other legume species.
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Affiliation(s)
- Nadim Tayeh
- />Université Lille 1, UMR 1281 Stress Abiotiques et Différenciation des Végétaux cultivés (SADV), Bâtiment SN2, F-59655 Villeneuve d’Ascq Cedex, France
| | - Nasser Bahrman
- />Université Lille 1, UMR 1281 Stress Abiotiques et Différenciation des Végétaux cultivés (SADV), Bâtiment SN2, F-59655 Villeneuve d’Ascq Cedex, France
- />INRA, UMR 1281 Stress Abiotiques et Différenciation des Végétaux cultivés (SADV), Estrées-Mons, BP 50136, F-80203 Péronne Cedex, France
| | - Hélène Sellier
- />INRA, UMR 1281 Stress Abiotiques et Différenciation des Végétaux cultivés (SADV), Estrées-Mons, BP 50136, F-80203 Péronne Cedex, France
| | - Aurélie Bluteau
- />Université Lille 1, UMR 1281 Stress Abiotiques et Différenciation des Végétaux cultivés (SADV), Bâtiment SN2, F-59655 Villeneuve d’Ascq Cedex, France
- />INRA, UMR 1281 Stress Abiotiques et Différenciation des Végétaux cultivés (SADV), Estrées-Mons, BP 50136, F-80203 Péronne Cedex, France
| | - Christelle Blassiau
- />Université Lille 1, UMR 1281 Stress Abiotiques et Différenciation des Végétaux cultivés (SADV), Bâtiment SN2, F-59655 Villeneuve d’Ascq Cedex, France
| | - Joëlle Fourment
- />INRA, Centre National de Ressources Génomiques Végétales (CNRGV), BP 52627, F-31326 Castanet-Tolosan Cedex, France
| | - Arnaud Bellec
- />INRA, Centre National de Ressources Génomiques Végétales (CNRGV), BP 52627, F-31326 Castanet-Tolosan Cedex, France
| | - Frédéric Debellé
- />INRA/CNRS, UMR 441/2594, Laboratoire des Interactions Plantes-Microorganismes (LIPM), BP 52627, F-31326 Castanet-Tolosan Cedex, France
| | - Isabelle Lejeune-Hénaut
- />INRA, UMR 1281 Stress Abiotiques et Différenciation des Végétaux cultivés (SADV), Estrées-Mons, BP 50136, F-80203 Péronne Cedex, France
| | - Bruno Delbreil
- />Université Lille 1, UMR 1281 Stress Abiotiques et Différenciation des Végétaux cultivés (SADV), Bâtiment SN2, F-59655 Villeneuve d’Ascq Cedex, France
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Jain S, McPhee KE. Isolation and characterization of novel EST-derived genic markers in Pisum sativum (Fabaceae). APPLICATIONS IN PLANT SCIENCES 2013; 1:apps.1300026. [PMID: 25202494 PMCID: PMC4103456 DOI: 10.3732/apps.1300026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 06/17/2013] [Indexed: 06/03/2023]
Abstract
UNLABELLED PREMISE OF THE STUDY Novel markers were developed for pea (Pisum sativum) from pea expressed sequence tags (ESTs) having significant homology to Medicago truncatula gene sequences to investigate genetic diversity, linkage mapping, and cross-species transferability. • METHODS AND RESULTS Seventy-seven EST-derived genic markers were developed through comparative mapping between M. truncatula and P. sativum in which 75 markers produced PCR products and 33 were polymorphic among 16 pea genotypes. • CONCLUSIONS The novel markers described here will be useful for future genetic studies of P. sativum; their amplification in lentil (Lens culinaris) demonstrates their potential for use in closely related species.
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Affiliation(s)
- Shalu Jain
- Department of Plant Sciences, North Dakota State University Fargo, North Dakota 58108-6050 USA
| | - Kevin E. McPhee
- Department of Plant Sciences, North Dakota State University Fargo, North Dakota 58108-6050 USA
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Hamon C, Coyne CJ, McGee RJ, Lesné A, Esnault R, Mangin P, Hervé M, Le Goff I, Deniot G, Roux-Duparque M, Morin G, McPhee KE, Delourme R, Baranger A, Pilet-Nayel ML. QTL meta-analysis provides a comprehensive view of loci controlling partial resistance to Aphanomyces euteiches in four sources of resistance in pea. BMC PLANT BIOLOGY 2013; 13:45. [PMID: 23497245 PMCID: PMC3680057 DOI: 10.1186/1471-2229-13-45] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 03/04/2013] [Indexed: 05/21/2023]
Abstract
BACKGROUND Development of durable plant genetic resistance to pathogens through strategies of QTL pyramiding and diversification requires in depth knowledge of polygenic resistance within the available germplasm. Polygenic partial resistance to Aphanomyces root rot, caused by Aphanomyces euteiches, one of the most damaging pathogens of pea worldwide, was previously dissected in individual mapping populations. However, there are no data available regarding the diversity of the resistance QTL across a broader collection of pea germplasm. In this study, we performed a meta-analysis of Aphanomyces root rot resistance QTL in the four main sources of resistance in pea and compared their genomic localization with genes/QTL controlling morphological or phenological traits and with putative candidate genes. RESULTS Meta-analysis, conducted using 244 individual QTL reported previously in three mapping populations (Puget x 90-2079, Baccara x PI180693 and Baccara x 552) and in a fourth mapping population in this study (DSP x 90-2131), resulted in the identification of 27 meta-QTL for resistance to A. euteiches. Confidence intervals of meta-QTL were, on average, reduced four-fold compared to mean confidence intervals of individual QTL. Eleven consistent meta-QTL, which highlight seven highly consistent genomic regions, were identified. Few meta-QTL specificities were observed among mapping populations, suggesting that sources of resistance are not independent. Seven resistance meta-QTL, including six of the highly consistent genomic regions, co-localized with six of the meta-QTL identified in this study for earliness and plant height and with three morphological genes (Af, A, R). Alleles contributing to the resistance were often associated with undesirable alleles for dry pea breeding. Candidate genes underlying six main meta-QTL regions were identified using colinearity between the pea and Medicago truncatula genomes. CONCLUSIONS QTL meta-analysis provided an overview of the moderately low diversity of loci controlling partial resistance to A. euteiches in four main sources of resistance in pea. Seven highly consistent genomic regions with potential use in marker-assisted-selection were identified. Confidence intervals at several main QTL regions were reduced and co-segregation among resistance and morphological/phenological alleles was identified. Further work will be required to identify the best combinations of QTL for durably increasing partial resistance to A. euteiches.
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Affiliation(s)
- Céline Hamon
- INRA, UMR1349 IGEPP, Le Rheu F-35653, France
- Current address: Vegenov-BBV, Penn ar Prat, Saint Pol de Léon, 29250, France
| | - Clarice J Coyne
- USDA, ARS, Western Regional Plant Introduction Station, Washington State University, Pullman, WA, 99164-6402, USA
| | - Rebecca J McGee
- USDA, ARS, Grain Legume Genetics and Physiology Research Unit, Pullman, WA, 99164-6434, USA
| | | | | | - Pierre Mangin
- INRA, Domaine Expérimental d’Epoisses, UE0115, Bretenières, F-21110, France
| | - Marie Hervé
- INRA, UMR1349 IGEPP, Le Rheu F-35653, France
- Current address: HM CLAUSE, 1 chemin ronzières, La Bohalle, 49800, France
| | - Isabelle Le Goff
- INRA, UMR1349 IGEPP, Le Rheu F-35653, France
- Current address: INRA, UMR1301 IBSV Interactions Biotiques en Santé Végétale, 400 route des Chappes, Sophia Antipolis Cedex, 06903, France
| | | | - Martine Roux-Duparque
- GSP, Domaine Brunehaut, Estrées-Mons, 80200, France
- Current address: Chambre d'Agriculture de l'Aisne, 1 rue René Blondelle, Laon Cedex, 02007, France
| | | | - Kevin E McPhee
- Department 7670, North Dakota State University, 370G Loftsgard Hall, Fargo, ND, 58108-6050, USA
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Abstract
The primary model legumes to date have been Medicago truncatula and Lotus japonicus. Both species are tractable both genetically and in the greenhouse, and for both, substantial sets of tools and resources for molecular genetic research have been assembled. As sequencing costs have declined, however, additional legume genomes have been sequenced, and the funding available to crops such as soybean has enabled these to be developed to the status of genetic models in their own right. This chapter, therefore, describes a broader set of model species in the legumes, and discusses similarities and differences between the genomes sequenced to date, as well as computational resources available for various legume species. Genome structural characteristics in, for example, Medicago truncatula and Glycine max, can have large impacts on the kinds of functional genomic research that may be carried out in these species. Both of these genomes have substantial redundancy for many gene families, but the nature of the redundancy is different in the two genomes-with the redundancy typically being in the form of local gene duplications in Medicago, and in whole-genome-duplication-derived duplications in Glycine. Similar considerations (about gene environments and genome structure) will likely need to be taken into account for any model or crop species.
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Affiliation(s)
- Steven B Cannon
- United States Department of Agriculture, Agricultural Research Service, Ames, IA, USA
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58
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Weller JL, Hecht VFG, Sussmilch FC. Isolation and forward genetic analysis of developmental genes in pea. Methods Mol Biol 2013; 1069:147-61. [PMID: 23996314 DOI: 10.1007/978-1-62703-613-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Understanding of developmental processes relies heavily on isolation and functional characterization of relevant genes. The garden pea (Pisum sativum L.) is one of the classic model species in plant genetics and has been used for a wide range of physiological and molecular studies of plant development. Here we describe the resources and approaches available for isolation of genes and genetic characterization of loci affecting development in pea.
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Affiliation(s)
- James L Weller
- School of Plant Science, University of Tasmania, Hobart, TAS, Australia
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Weller JL, Liew LC, Hecht VFG, Rajandran V, Laurie RE, Ridge S, Wenden B, Vander Schoor JK, Jaminon O, Blassiau C, Dalmais M, Rameau C, Bendahmane A, Macknight RC, Lejeune-Hénaut I. A conserved molecular basis for photoperiod adaptation in two temperate legumes. Proc Natl Acad Sci U S A 2012; 109:21158-63. [PMID: 23213200 PMCID: PMC3529011 DOI: 10.1073/pnas.1207943110] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Legumes were among the first plant species to be domesticated, and accompanied cereals in expansion of agriculture from the Fertile Crescent into diverse environments across the Mediterranean basin, Europe, Central Asia, and the Indian subcontinent. Although several recent studies have outlined the molecular basis for domestication and eco-geographic adaptation in the two main cereals from this region, wheat and barley, similar questions remain largely unexplored in their legume counterparts. Here we identify two major loci controlling differences in photoperiod response between wild and domesticated pea, and show that one of these, high response to photoperiod (HR), is an ortholog of early flowering 3 (ELF3), a gene involved in circadian clock function. We found that a significant proportion of flowering time variation in global pea germplasm is controlled by HR, with a single, widespread functional variant conferring altered circadian rhythms and the reduced photoperiod response associated with the spring habit. We also present evidence that ELF3 has a similar role in lentil, another major legume crop, with a distinct functional variant contributing to reduced photoperiod response in cultivars widely deployed in short-season environments. Our results identify the factor likely to have permitted the successful prehistoric expansion of legume cultivation to Northern Europe, and define a conserved genetic basis for major adaptive changes in flowering phenology and growth habit in an important crop group.
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Affiliation(s)
- James L Weller
- School of Plant Science, University of Tasmania, Hobart, Tasmania 7001, Australia.
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D'Erfurth I, Le Signor C, Aubert G, Sanchez M, Vernoud V, Darchy B, Lherminier J, Bourion V, Bouteiller N, Bendahmane A, Buitink J, Prosperi JM, Thompson R, Burstin J, Gallardo K. A role for an endosperm-localized subtilase in the control of seed size in legumes. THE NEW PHYTOLOGIST 2012; 196:738-751. [PMID: 22985172 DOI: 10.1111/j.1469-8137.2012.04296.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 07/25/2012] [Indexed: 05/08/2023]
Abstract
Here, we report a subtilase gene (SBT1.1) specifically expressed in the endosperm of Medicago truncatula and Pisum sativum seeds during development, which is located at a chromosomal position coinciding with a seed weight quantitative trait locus (QTL). Association studies between SBT1.1 polymorphisms and seed weights in ecotype collections provided further evidence for linkage disequilibrium between the SBT1.1 locus and a seed weight locus. To investigate the possible contribution of SBT1.1 to the control of seed weight, a search for TILLING (Targeting Induced Local Lesions in Genomes) mutants was performed. An inspection of seed phenotype revealed a decreased weight and area of the sbt1.1 mutant seeds, thus inferring a role of SBT1.1 in the control of seed size in the forage and grain legume species. Microscopic analyses of the embryo, representing the major part of the seed, revealed a reduced number of cells in the MtP330S mutant, but no significant variation in cell size. SBT1.1 is therefore most likely to be involved in the control of cotyledon cell number, rather than cell expansion, during seed development. This raises the hypothesis of a role of SBT1.1 in the regulation of seed size by providing molecules that can act as signals to control cell division within the embryo.
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Affiliation(s)
- I D'Erfurth
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - C Le Signor
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - G Aubert
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - M Sanchez
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - V Vernoud
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - B Darchy
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - J Lherminier
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - V Bourion
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - N Bouteiller
- INRA/CNRS (Centre National de la Recherche Scientifique), Unité de Recherche en Génomique Végétale, CP5708, 91057, Evry, France
| | - A Bendahmane
- INRA/CNRS (Centre National de la Recherche Scientifique), Unité de Recherche en Génomique Végétale, CP5708, 91057, Evry, France
| | - J Buitink
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, 49045, Angers, France
| | - J M Prosperi
- INRA, UMR1334 Amélioration Génétique et Adaptation des Plantes, 34060, Montpellier, France
| | - R Thompson
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - J Burstin
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - K Gallardo
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
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Charon C, Bruggeman Q, Thareau V, Henry Y. Gene duplication within the Green Lineage: the case of TEL genes. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:5061-5077. [PMID: 22865910 DOI: 10.1093/jxb/ers181] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Recent years have witnessed a breathtaking increase in the availability of genome sequence data, providing evidence of the highly duplicate nature of eukaryotic genomes. Plants are exceptional among eukaryotic organisms in that duplicate loci compose a large fraction of their genomes, partly because of the frequent occurrence of polyploidy (or whole-genome duplication) events. Tandem gene duplication and transposition have also contributed to the large number of duplicated genes in plant genomes. Evolutionary analyses allowed the dynamics of duplicate gene evolution to be studied and several models were proposed. It seems that, over time, many duplicated genes were lost and some of those that were retained gained new functions and/or expression patterns (neofunctionalization) or subdivided their functions and/or expression patterns between them (subfunctionalization). Recent studies have provided examples of genes that originated by duplication with successive diversification within plants. In this review, we focused on the TEL (TERMINAL EAR1-like) genes to illustrate such mechanisms. Emerged from the mei2 gene family, these TEL genes are likely to be land plant-specific. Phylogenetic analyses revealed one or two TEL copies per diploid genome. TEL gene degeneration and loss in several Angiosperm species such as in poplar and maize seem to have occurred. In Arabidopsis thaliana, whose genome experienced at least three polyploidy events followed by massive gene loss and genomic reorganization, two TEL genes were retained and two new shorter TEL-like (MCT) genes emerged. Molecular and expression analyses suggest for these genes sub- and neofunctionalization events, but confirmation will come from their functional characterization.
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Affiliation(s)
- Céline Charon
- Institut de Biologie des Plantes-CNRS (UMR8618), Université Paris-Sud 11, Saclay Plant Sciences, F-91405 Orsay Cedex, France.
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Moreau D, Burstin J, Aubert G, Huguet T, Ben C, Prosperi JM, Salon C, Munier-Jolain N. Using a physiological framework for improving the detection of quantitative trait loci related to nitrogen nutrition in Medicago truncatula. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:755-68. [PMID: 22113590 DOI: 10.1007/s00122-011-1744-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 10/28/2011] [Indexed: 05/19/2023]
Abstract
Medicago truncatula is used as a model plant for exploring the genetic and molecular determinants of nitrogen (N) nutrition in legumes. In this study, our aim was to detect quantitative trait loci (QTL) controlling plant N nutrition using a simple framework of carbon/N plant functioning stemming from crop physiology. This framework was based on efficiency variables which delineated the plant's efficiency to take up and process carbon and N resources. A recombinant inbred line population (LR4) was grown in a glasshouse experiment under two contrasting nitrate concentrations. At low nitrate, symbiotic N(2) fixation was the main N source for plant growth and a QTL with a large effect located on linkage group (LG) 8 affected all the traits. Significantly, efficiency variables were necessary both to precisely localize a second QTL on LG5 and to detect a third QTL involved in epistatic interactions on LG2. At high nitrate, nitrate assimilation was the main N source and a larger number of QTL with weaker effects were identified compared to low nitrate. Only two QTL were common to both nitrate treatments: a QTL of belowground biomass located at the bottom of LG3 and another one on LG6 related to three different variables (leaf area, specific N uptake and aboveground:belowground biomass ratio). Possible functions of several candidate genes underlying QTL of efficiency variables could be proposed. Altogether, our results provided new insights into the genetic control of N nutrition in M. truncatula. For instance, a novel result for M. truncatula was identification of two epistatic interactions in controlling plant N(2) fixation. As such this study showed the value of a simple conceptual framework based on efficiency variables for studying genetic determinants of complex traits and particularly epistatic interactions.
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Affiliation(s)
- Delphine Moreau
- INRA, UMR 102 Génétique et Ecophysiologie des Légumineuses, 17 rue Sully, BP 86510, 21065, Dijon cedex, France.
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