Characterization of Salt-Induced Epigenetic Segregation by Genome-Wide Loss of Heterozygosity and its Association with Salt Tolerance in Rice (Oryza sativa L.)

In a breeding effort to develop salt tolerant (ST) rice varieties by designed QTL pyramiding, large numbers of progenies derived from four crosses between salt-or drought-tolerant BC2F5 IR64 introgression lines, were subjected to severe salt stress, resulting in 422 ST plants. The progeny testing of the selected F-3 lines under more severe salt stress resulted in identification of 16 promising homozygous lines with high levels of ST. Genetic characterization of the 422 ST F3 progeny and 318 random F-2 plants from the same four crosses using 105 segregating SSR markers lead to three interesting discoveries: (1) salt stress can induce genome-wide epigenetic segregation (ES) characterized by complete loss of heterozygosity (LOH) and nearly complete loss of an allele (LOA) in the F3 progenies of four rice populations in a single generation; (2) similar to 25% of the stress-induced ES loci were transgenerational and inherited from their salt-and drought-selected parents; and (3) the salt-induced LOH and LOA loci (regions) appeared to contain genes/alleles associated with ST and/or drought tolerance. 32 genomic regions that showed one or more types of salt-induced ES in the random and salt-selected progenies from these crosses. The same or different types of ES were detected with two large genomic regions on chromosomes 1 and 6 where more and the strongest ES were found across different populations. 14 genomic regions were found where the salt-induced ES regions were overlapping with QTL affecting ST related traits. The discovery of the three types of salt-induced ES showed several interesting characteristics and had important implications in evolution and future breeding for developing stress-resilient rice and crops.