MAGIC Indica: A New Genetic Resource for Multiple Trait Improvement and QTL Discovery in the Indica Rice Subspecies.

Indica rice is one of two major subspecies of the cultivated Asian rice species Oryza sativa L. that is the staple food of more than half of the world’s population. Key economic traits in indica rice, such as tolerances to biotic and abiotic stresses, are quantitatively inherited and influenced by large GxE interactions. Their complex inheritance and oftentimes narrow genetic resource base for mining favourable alleles make trait improvement through breeding inherently difficult. To harness natural allelic variation comprehensively in breeding while allowing the genetic dissection of complex traits individually, we generated a multi-parent advanced generation intercross (MAGIC) population using, as the founder parents, eight elite indica cultivars with desirable traits such as high yield, good grain quality, and tolerance to a suite of stresses. After several rounds of selective intercrossing, genotyping, and generation advancement that began in 2007, we have generated 1,439 S6 lines that are being further advanced and tested in multilocation trials in Southeast Asia and East Africa. Early generation selection has yielded plants with tolerances to salinity, submergence, and drought. Disease screening data suggest transmission of blast and bacterial blight resistances from the founders to a majority of the progeny. Genome-wide association mapping using genotyping-by-sequencing was able to tag known genes/QTLs such the Sub1 for submergence tolerance, qBR9.1 for blast disease resistance, and Saltol for salinity tolerance, with SNP markers within or very close to the gene/QTL itself. Moreover, several novel QTLs for these same traits were also identified. The new and diverse genetic resource, which we now refer to as ‘MAGIC Indica’, promises to be a valuable source of breeding-ready materials for the extraction of new commercial varieties with multiple economically important traits as well as a rich resource for fine mapping known QTLs and/or precisely identifying multiple QTLs for multiple traits in indica rice.