Genome-Wide Responses to Selection and Genetic Networks Underlying Submergence Tolerance in Rice

Submergence is an important factor limiting rice (Oryza sativa L.) yield in many rain-fed lowland areas of Asia. Here we explored the genetic basis of submergence tolerance (ST) in rice and facilitated simultaneous improvement of ST of rice. The genome-wide patterns of donor introgressions in 162 backcross (BC) progenies selected for ST from 12 populations of nine crosses between three recipients and three donors were characterized using simple sequence repeat (SSR) markers. The genome-wide responses of donor alleles to strong phenotypic selection for ST were reflected in three aspects: (i) significant over introgression of the donor alleles at 295 loci in 167 functional genetic units (FGUs) across the rice genome, (ii) greatly increased homozygosity or loss of heterozygosity genome-wide, and (iii) pronounced nonrandom associations between or among the detected ST loci, which led us to discovery of putative genetic networks (multilocus structures) underlying ST of rice. Our results suggest that ST of rice is controlled by large numbers of loci involved in multiple positively regulated signaling pathways. Restoration of one or more of these broken pathways in the BC progeny by genetic complementation from introgressed functional donor alleles at ST loci provide an appropriate explanation for transgressive segregation of ST and other complex traits in rice.