Transcriptome sequencing for high throughput SNP development and genetic mapping in Pea - Archive ouverte HAL Accéder directement au contenu
Article Dans Une Revue BMC Genomics Année : 2014

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

Jorge Duarte
  • Fonction : Auteur
  • PersonId : 962084
Nathalie Rivière
Gregoire Aubert
Judith Burstin
Laurent Cornet
  • Fonction : Auteur
Jean-Philippe Pichon
  • Fonction : Auteur

Résumé

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.[br/] 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.[br/] 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.
Fichier principal
Vignette du fichier
2014_Duarte_BMC Genomics_1.pdf (1.67 Mo) Télécharger le fichier
Origine : Fichiers éditeurs autorisés sur une archive ouverte
Loading...

Dates et versions

hal-01208693 , version 1 (27-05-2020)

Identifiants

Citer

Jorge Duarte, Nathalie Rivière, Alain Baranger, Gregoire Aubert, Judith Burstin, et al.. Transcriptome sequencing for high throughput SNP development and genetic mapping in Pea. BMC Genomics, 2014, 15 (126), pp.1-15. ⟨10.1186/1471-2164-15-126⟩. ⟨hal-01208693⟩
94 Consultations
46 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More