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. 2014 Feb 12:15:126.
doi: 10.1186/1471-2164-15-126.

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

Jorge Duarte, Nathalie Rivière, Alain Baranger, Grégoire Aubert, Judith Burstin, Laurent Cornet, Clément Lavaud, Isabelle Lejeune-Hénaut, Jean-Pierre Martinant, Jean-Philippe Pichon, Marie-Laure Pilet-Nayel, Gilles Boutet  1
Affiliations

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

Jorge Duarte et al. BMC Genomics. .

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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Figures

Figure 1
Figure 1
Conserved distribution along M. truncatula pseudo-chromosomes (MT_chr) of the 10,522 pea polymorphic cDNA contigs (grey bars) and the 1,920 pea cDNA contigs (pink bars) selected for genotyping.
Figure 2
Figure 2
Classification of a diversity panel of 92 pea accessions using 1,538 SNPs. Rogers’ distances were computed for all pairs of accessions and a Ward hierarchical classification procedure was used to classify the accessions in clusters (Cx) and subclusters (Cx-x). Unnamed branches are non-registered breeding lines currently in the registration process.
Figure 3
Figure 3
Colinearity of common markers between our study (middle) and the Bordat et al. ([39]; left) and Loridon et al. ([38]; right) composite maps on LGII.
See this image and copyright information in PMC

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