Decades of genetic research have identified dozens of genes controlling traits valuable to breeding programs. However, when the availability of these genes in elite breeding programs is assessed, the majority are either absent (almost half) or very rare (~15%). This means they are very difficult or impossible to use in elite population improvement breeding programs; they are only available from poor-quality landraces, often from different cultivar groups (e.g. japonica) or different species (Oryza glaberrima) than the elite indica material used in most breeding programs. Thus breeders face a difficult choice—they can use these genes, but that comes with substantial penalties in yield, grain quality, etc. Alternatively, they can improve yields but will miss out on the value these major genes could bring.
IRRI has been working to break this trade-off by creating high-quality introgressions of major genes into fully elite genomic backgrounds. QC criteria for these introgressions include stringent background recovery (>95% elite indica genome recovery) to eliminate the unfavorable donor background, and aggressive foreground recombinant selection (<2cM introgression size; <0.125% of the rice genome) to eliminate linkage drag. In many cases these QC targets are exceeded by a wide margin, with background recoveries of 98%+ and introgression sizes of <1cM being common.
Currently, most introgressions have been into the IRRI 154 genomic background, which is a widely adapted and high-yielding cultivar that has been released as a variety in both the Philippines and Bangladesh, and contains restorer alleles at both Rf3 and Rf4. This makes it useful as a parent in breeding programs targeted at diverse geographies.
The near-isogenic lines thus produced are excellent donors to introduce the genes into the elite breeding program. They also find significant application in the testing of gene effects and value. For example, blast resistance genes have previously only been available from landraces, or from japonica introgressions (IRBL lines) with very different maturity and genomic backgrounds used in the breeding programs. Having high-quality NILs in a fully-elite indica background allows confident determination of the effectiveness of these resistance genes, and thus the value of the genes for breeding programs.
In addition to deploying individual genes, substantial effort is underway to create pyramids (particularly for disease resistance genes, to enhance durability), coupled linkages of genes in the same genomic region (enhancing their value), and diversifying the genomic backgrounds and foreground elite haplotypes in which the genes are available. As time goes on the diversity of genes, pyramids and genomic backgrounds will increase substantially so watch this space for updates!