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Open Access Research article

Transcriptome sequencing for high throughput SNP development and genetic mapping in Pea

Jorge Duarte1, Nathalie Rivière1, Alain Baranger2, Grégoire Aubert4, Judith Burstin4, Laurent Cornet1, Clément Lavaud2, Isabelle Lejeune-Hénaut5, Jean-Pierre Martinant3, Jean-Philippe Pichon1, Marie-Laure Pilet-Nayel2 and Gilles Boutet2*

Author Affiliations

1 Biogemma, route d’Ennezat, CS 90126, Chappes 63720, France

2 INRA UMR 1349 IGEPP, BP35327, Le Rheu Cedex 35653, France

3 Limagrain Europe, centre de recherche route d’Ennezat, CS 3911, Chappes 63720, France

4 INRA UMR 1347 Agroécologie, Bat. Mendel, 17 rue Sully BP 86510, Dijon 21065, France

5 INRA, UMR 1281 SADV, Estrées-Mons BP 50136, Péronne 80203, France

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BMC Genomics 2014, 15:126  doi:10.1186/1471-2164-15-126

Published: 12 February 2014

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.

Keywords:
Pisum sativum; Medicago truncatula; Next generation sequencing; Genetic diversity; Composite genetic map; Synteny; Marker assisted selection