title: Transcriptome sequencing for high throughput SNP development and genetic mapping in Pea.
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.
authors: Jorge
authors: J
authors: Duarte
authors: Nathalie
authors: N
authors: Rivière
authors: Alain
authors: A
authors: Baranger
authors: Grégoire
authors: G
authors: Aubert
authors: Judith
authors: J
authors: Burstin
authors: Laurent
authors: L
authors: Cornet
authors: Clément
authors: C
authors: Lavaud
authors: Isabelle
authors: I
authors: Lejeune-Hénaut
authors: Jean-Pierre
authors: JP
authors: Martinant
authors: Jean-Philippe
authors: JP
authors: Pichon
authors: Marie-Laure
authors: ML
authors: Pilet-Nayel
authors: INRA UMR 1349 IGEPP, BP35327, Le Rheu Cedex 35653, France. gilles.boutet@rennes.inra.fr.
authors: Gilles
authors: G
authors: Boutet
mesh_terms: D002874:Chromosome Mapping; D020451:Contig Mapping; D017343:Genes, Plant; D014644:Genetic Variation; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D018532:Pisum sativum / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA