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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

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

Jorge Duarte, Nathalie Rivière, Alain Baranger

¹INRA UMR 1349 IGEPP, BP35327, Le Rheu Cedex 35653, France. gilles.boutet@rennes.inra.fr.

|February 14, 2014

Summary

This summary is machine-generated.

Researchers developed a comprehensive pea genetic map and a large single nucleotide polymorphism (SNP) resource. This enhances pea genetic diversity studies and modern breeding efforts.

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Area of Science:

Plant genomics
Molecular biology
Agricultural science

Background:

Pea (Pisum sativum) possesses a complex genome (4.3 Gb) with limited genomic resources.
Single nucleotide polymorphism (SNP) markers are crucial for genetic diversity and linkage analysis but are scarce in pea.

Purpose of the Study:

To develop a comprehensive genetic map for pea.
To create a substantial resource of single nucleotide polymorphism (SNP) markers.
To enhance genetic diversity studies and breeding in pea.

Main Methods:

cDNA sequencing of 8 pea genotypes using Roche 454 technology.
Assembly of sequencing data into a unigene set and annotation against Medicago truncatula.
SNP discovery, validation using GoldenGate assay, and genetic mapping.
Construction of a consensus genetic map and comparison with M. truncatula.

Main Results:

Generated a 68K unigene set with 41K annotated contigs, showing even distribution across M. truncatula pseudochromosomes.
Discovered 35K SNPs from polymorphic pea contigs.
Validated 1538 SNPs and genetically mapped 1340, contributing to a 2070-marker consensus map.
Established 1252 syntenic bridges between the pea map and M. truncatula.

Conclusions:

Developed significant new genomic resources for pea.
Created the most comprehensive pea genetic map to date, linked to M. truncatula.
Generated a large SNP resource valuable for academic research and crop improvement.