Patterns of Salinity-Induced ncRNA Expression Across the Genomes of Sibling Recombinant Inbred Lines of Rice: What Do They Tell Us about Transcriptome Reconfiguration and Network Rewiring in Hybrids?

The mechanisms of genetic network rewiring and how they configure novel phenotypes in transgressive segregants are largely unknown. We hypothesize that in biparental recombinant inbreds, genome shuffling after several rounds of meiosis may modify the epigenomic landscapes and transcriptome configuration of recombinants. A major question under this hypothesis is the extent by which non-coding RNAs (ncRNA) contribute to changes in epigenomic landscapes and transcriptome reconfiguration in recombinants. We have begun to map the genome-wide tracts of salinity stress-induced ncRNAs across F₈ recombinant inbred lines (RIL) derived from IR29 (salt-sensitive) x Pokkali (salt-tolerant), and compared such patterns with their mRNA transcriptomes. Our comparative panel includes representative RILs covering the spectrum of salinity tolerance in the population, including positive and negative transgressive segregants.

Our preliminary results revealed ncRNA signatures among RILs that are distinct from IR29 and Pokkali and between siblings, particularly with respect to tracts occurring outside the retrotransposon-rich regions of the genome. These results suggest that recombination between genetically diverse genomes alters the global patterns of ncRNA expression. We are investigating the potential biological significance of these findings in context of two possible cause-and-effect scenarios. First, distinct ncRNA signatures have possible implications to altered genome methylation patterns, reconfiguring the transcriptomes of certain RILs. Second, ncRNA patterns in RILs may reflect different magnitudes of erroneous transcription due to stress, and are consequences of genomic shock brought about by recombination between diverse parents. Erroneous transcription may impose a penalty to the fidelity of the stress response transcriptome in certain RILs.