Marker-evaluated selection in rice: shifts in allele frequency among bulks selected in contrasting agricultural environments identify genomic regions of importance to rice adaptation and breeding

Conventional methods for quantitative trait locus (QTL) mapping require the selection of particular traits to be measured based on assumptions as to their importance. We have tested an alternative approach for the location of QTLs—marker-evaluated selection—that makes no prior assumptions as to which traits are important. The results of phenotype selection were evaluated in the products of modified bulk-population breeding that was replicated across a range of rice ecosystems. Selection was carried out in close collaboration with farmers in bulk populations that were all derived from a cross between an Indian upland variety (Kalinga III) and a high-yielding semi-dwarf variety (IR64). Twenty-seven diverse bulks were produced that were screened with molecular markers in order to determine whether shifts could be detected in marker allele frequency as a result of selection and if such changes varied by genomic region across ecosystems. Marker loci linked to important traits for adaptation to specific environments were identified without making any prior assumptions about which traits might be important. Genomic regions from Kalinga III were strongly selected in the upland environments and regions from IR64 in the lowland ones. However, exceptions occurred where the upland parent contributed positively to lowland adaptation and vice versa. The results can be used as a basis for the development of second-cycle varieties, using marker-assisted selection to produce genotypic ideotypes for specific target environments. The very strong selection for genomic regions from the adapted parents of the wide (upland × lowland) cross indicates that, in non-marker-assisted breeding, where genetically distant parents have been used, modified backcross breeding should be efficient. A single backcross to the adapted parent for a specific ecosystem will result in a higher frequency of segregants with the desired high genetic contribution from the adapted parent.