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Open Access Research article

QTL meta-analysis provides a comprehensive view of loci controlling partial resistance to Aphanomyces euteiches in four sources of resistance in pea

Céline Hamon17, Clarice J Coyne2, Rebecca J McGee3, Angélique Lesné1, Robert Esnault1, Pierre Mangin4, Marie Hervé19, Isabelle Le Goff18, Gwenaëlle Deniot1, Martine Roux-Duparque105, Gérard Morin1, Kevin E McPhee6, Régine Delourme1, Alain Baranger1 and Marie-Laure Pilet-Nayel1*

Author Affiliations

1 INRA, UMR1349 IGEPP, Le Rheu F-35653, France

2 USDA, ARS, Western Regional Plant Introduction Station, Washington State University, Pullman, WA, 99164-6402, USA

3 USDA, ARS, Grain Legume Genetics and Physiology Research Unit, Pullman, WA, 99164-6434, USA

4 INRA, Domaine Expérimental d’Epoisses, UE0115, Bretenières, F-21110, France

5 GSP, Domaine Brunehaut, Estrées-Mons, 80200, France

6 Department 7670, North Dakota State University, 370G Loftsgard Hall, Fargo, ND, 58108-6050, USA

7 Current address: Vegenov-BBV, Penn ar Prat, Saint Pol de Léon, 29250, France

8 Current address: INRA, UMR1301 IBSV Interactions Biotiques en Santé Végétale, 400 route des Chappes, Sophia Antipolis Cedex, 06903, France

9 Current address: HM CLAUSE, 1 chemin ronzières, La Bohalle, 49800, France

10 Current address: Chambre d'Agriculture de l'Aisne, 1 rue René Blondelle, Laon Cedex, 02007, France

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BMC Plant Biology 2013, 13:45  doi:10.1186/1471-2229-13-45

Published: 16 March 2013

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.

Keywords:
Aphanomyces root rot; Pisum sativum; Meta-QTL; QTL diversity; Consistent genomic regions; Resistance alleles; Undesirable alleles