Genomics-Assisted Plant Breeding for Cool Season Food Legume

Genomics-Assisted Plant Breeding for Cool Season Food Legume

Clarice Coyne, Doreen Main, Rebecca McGee and George Vandemark

Abstract

The cool season food legumes have not fully participated in the new technologies of genetic and genomic analysis that have directly contributed to the significant and rapid expansion of gene discovery, knowledge of gene function (including tolerance to biotic and abiotic stresses), and genetic improvement of many crops.  The development of inexpensive, fast methodologies for DNA sequencing (e.g. Roche 454-pyrosequencing) and computational strategies has allowed the development of expressed sequence tag (EST) libraries for many crops that contain hundreds of thousands to millions of sequences.  ESTs, sequences of cDNAs made by reverse transcription of mRNAs, are particularly valuable for discovering new genes, for obtaining data on gene expression and regulation, for constructing genomic maps and for the development of single nucleotide polymorphism (SNP) markers.  SNPs are ‘perfect’ genetic markers. They are abundant, they represent the highest resolution of sequencing (a single base) and they can be used to create high density genetic maps.  They are also useful tools as molecular markers in crop improvement; including QTL discovery, assessment of genetic diversity, association mapping and marker assisted selection (MAS).  An international public EST database is maintained by National Center for Biotechnology Information, USA (NCBI).  Of the 63,579,220 ESTs in NCBI, 2,018,798 are from corn, 1,422,604 are from soybean, 1,249,110 are from rice, but only 18,552 are from pea.  Therefore, there is a critical need to develop a significant database of pea ESTs in order to enable breeders, pathologists, physiologists and other researchers to take advantage of this very powerful tool. This study will generate several cDNA libraries that represent a vast amount of the transcriptome of pea.  The EST database will be valuable for genomic research and a high density SNP map that will be ideally suited for MAS.  These powerful tools will be useful to all scientists who work on Pisum.  They will seed the acquisition of further resources for cool season legumes through application to competitive federal programs such as the Specialty Crop Research Initiative, thereby significantly leveraging the investment of the Cool Season Food Legume Research Program.