A Backcross Breeding Strategy for Improving Multiple Complex Traits – A Case Study in Rice (Oryza sativa L.)

Breeding superior rice varieties with high yield potential and superior resistance/tolerances to multiple abiotic and biotic stresses has been the greatest challenge to breeders. Traditional backcross (BC) breeding is believed to be effective only for improving single highly heritable traits but not for multiple complex traits. Here, we demonstrate that a BC breeding strategy for simultaneous improvement and genetic dissection of multiple complex traits. We used Huang-Hua-Zhan (HHZ), an indica variety with high yield and wide adaptability from China as the recurrent parent (RP), crossed with eight indica donors of diverse origin, and developed 8 random BC₁F₂ populations. All BC₁F₂ populations were screened for high yield (HY), drought tolerance (DT), salt tolerance (ST) and submergence tolerance (SUT) at International Rice Research Institute (IRRI), resulting in total of 311 trait-specific plants. Then, all selected BC₁F₃ lines were selected for high yield performances under both stress (drought, salinity, and submergence) and normal conditions, producing 512 selected BC₁F₄ introgression lines (ILs). From them, 68 promising lines were identified, each with 1-3 target traits for further evaluation in replicated preliminary yield trials under multiple environments, resulting in identification of 12 superior lines with high yield and multiple abiotic stress tolerance recommended for evaluation in the national coordinated yield trials in several Asia countries in 2011. Based on genotypic data of trait-specific ILs, QTL and genetic networks underlying the target traits were identified using linkage mapping and linkage disequilibrium (LD) mapping. Interestingly, the 512 ILs showed a wide range of resistance spectrum to the 14 tropic races of rice bacterial leaf blight (BLB). Preliminary analyses of the genotypic and phenotypic data allowed us to identify at least 51 resistance loci across the rice genome. These ILs also provide valuable genetic materials for genetic and molecular dissection of the relationships between biotic and abiotic tolerances in rice using various – omic tools.