Development of Novel Genomic Resources in Pea (Pisum sativum L.) Revolutionizes Applications in Selection

Pea (Pisum sativum L.) is an important food and feed crop and a valuable component of low-input farming systems. Pea breeding has achieved great success since the time of Mendel’s experiments in the mid-1800s. However, several traits still require significant improvement for better yield stability in a larger growing area. Key breeding objectives in pea include improving biotic and abiotic stress resistance and enhancing yield components and seed quality. Pea has recently benefited from next-generation sequencing and high-throughput genotyping technologies. The GenoPea 13.2K SNP Array, powered by Illumina Infinium® II technology, was developed. Twelve recombinant inbred line populations were genotyped using this SNP array and 12,802 transcript-derived SNP markers could be placed on a 15,079-marker high density, high resolution consensus map. This allowed (1) the localization of a large set of genes, (2) the identification of ohnolog-rich regions within the pea genome, and (3) the establishment of dense syntenic networks with sequenced legume genomes. The genomic prediction of important agronomical traits was evaluated in a collection of 339 genetic resource accessions (CRB339) genotyped using the GenoPea 13.2K SNP Array. Prediction quality was high even in cross-population experiments where the CRB339 collection was used as a training set and 9 recombinant inbred lines populations as a test set. The significant development and deployment of genomic resources is expected to enhance breeding by paving the way for genome-wide association studies and genomic selection approaches and also strengthen pea as a model for genetics and physiology.

This work was supported by the French National Institute for Agricultural Research (INRA) and funded by the French National Research Agency (Project ANR-09-GENM-026 “GENOPEA” and Project Investissements d’Avenir ANR-11-BTBR-0002 “PeaMUST”).