Rice MAGIC Populations for Genetic Research and Breeding

MAGIC (Multi-parent Advanced Generation Inter-Cross) is a breeding design that increases precision in mapping quantitative trait loci (QTL). The highly recombined germplasm can be used directly for the development of breeding lines and varieties adapted to different environments. We have developed four multi-parent populations: indica MAGIC (8 indica founder parents); MAGIC PLUS (8 indica parents with two additional rounds of 8-way F1 inter-crossing); japonica MAGIC (8 japonica parents); and Global MAGIC (16 parents—8 indica and 8 japonica). Using 9,012 SNP markers, we estimated 87–100 recombinations per advanced inbred line of the indica MAGIC and MAGIC PLUS populations. The number of detectable recombinations is expected to increase with a higher SNP marker coverage across the genome. Evaluation of two large populations (>1,300 lines) of indica MAGIC and Global MAGIC showed transgressive segregation in yield. Our results show that the MAGIC populations can serve a dual purpose: (a) as a permanent resource for QTL mapping and (b) for direct and indirect use in variety development. Subsets of the populations are being tested in multiple locations in Southeast Asia and South Asia for yield and adaptability. Although new genotypic combinations can be generated by MAGIC, the source of alleles from the founders is still limited. The recently published 3,000 genomes present an opportunity to select accessions with new diversity. We propose a strategy to combine allele mining and the MAGIC approach to introduce new allelic diversity into breeding programs. This approach has the advantage of simultaneously breaking up undesirable linkages and recombining favorable alleles. The resulting MAGIC populations with multiple traits in breeding-ready background can serve as bridging resources to deliver diverse germplasm for breeding.