QTLs in rice breeding: examples for abiotic stresses

Abstract

Despite the status of rice as a model agricultural crop and hundreds of studies identifying quantitative trait loci (QTLs), the applications of these results in breeding have been limited. However, the success of plant breeders in developing varieties with high yield, excellent grain quality, and wide adaptation that are widely grown by farmers (i.e., mega varieties) has provided an opportunity to deploy the most useful QTLs for rice improvement. Marker-assisted backcrossing (MAB) facilitates the precise introgression of a desired trait into the original genetic background of such mega varieties. QTLs with a large effect are rare for complex agronomic traits like yield, but are more common for other traits such as resistance to abiotic stresses. Here we discuss the example of submergence tolerance. Much of the tolerance in varieties such as FR13A has been shown to be under the control of the Sub1 locus, which includes 2–3 tightly-linked putative transcription factors. Sub1 was transferred into the Indian cultivar Swarna, resulting in a new version of this mega variety with tolerance of submergence. Large QTLs also exist for tolerance of salinity, P deficiency, Al toxicity, and low temperature. With some modifications, this approach may be applicable for traits controlled by multiple smaller QTLs. However, strategies for transferring multiple QTLs into mega varieties need to be developed such that negative effects of the transferred segments (linkage drag) do not adversely affect the resulting varieties. Furthermore, strategies for reducing the costs associated with marker genotyping and efficient phenotyping also need to be developed and adopted in order to apply MAB on a larger scale.