Allele Mining and Enhanced Genetic Recombination for Stress Resistant Crops

Traditional varieties or landraces of rice harbour a large store of valuable genes that can be used to develop new varieties with improved yield potential, better suited to the stresses of future climate, with higher nutritional quality, and improved tolerance of pests and diseases. The recent completion of re-sequencing of 3,000 Genebank accessions (The 3000 Rice Genomes Project 2014. GigaScience 3:7) has revealed allelic diversity of multiple rice genomes at an average sequencing depth of 14X. The sequence data provide a “digital library” of the 3,000 accessions, presenting opportunities to identify natural genetic variations in rice.  However, use of landraces for breeding is often hampered by linkage drag. An efficient mating design is needed to break the undesirable linkages and to convert landraces to breeding-ready genetic resources. Multi-parent Advanced Generation InterCross (MAGIC) is a breeding method to produce highly recombined germplasm. The increased recombination in MAGIC populations can lead to novel rearrangements of alleles and greater genotypic diversity.  Inclusion of elite varieties together with the landraces in such crosses can produce pre-breeding materials with reduced linkage drag.  We aim to generate a gene pool enriched in resistance genes to multiple diseases.  We will use several disease resistance to illustrate the extraction of useful germplasm from the 3,000 sequenced accessions and propose a breeding scheme to accumulate multiple stress tolerance.