Novel Transcriptional and Physiological Profiles in Recombinant Inbred Lines of Rice Exhibiting Transgressive Traits for Salinity Tolerance: Preliminary Evidence of miRNA-Mediated Network Rewiring

Apart from the contributions of genomics-assisted breeding and biotechnology to the incremental increases in stress tolerance and yield potential of rice, we believe that modern paradigms for examining the functional consequences of genetic recombination should reveal rewired genetic networks that define the novel attributes of transgressive segregants. Outcomes of recombination-mediated network rewiring will be hard to recreate with the one-gene-centric paradigm of genetic engineering. Our aim is to elucidate the molecular underpinnings of novel stress tolerance phenotypes created by transgressive segregation, by understanding how the coupling or uncoupling of miRNAs and their targets facilitate physiological and biochemical reconfiguration.

We performed an in-depth phenotyping of the recombinant inbred line (F₈-RIL) population of IR29 (salt-sensitive) x Pokkali (salt-tolerant) across a battery of physiological and biochemical parameters to identify unique signatures of transgressive segregants relevant to salinity tolerance. Parallel analysis of miRNA and mRNA transcriptomes across the phenotypic range identified several reverse coexpression clusters, i.e., upregulated miRNA and downregulated target gene(s) or vice versa. Many of the reverse coexpressing pairs were RIL-specific or their patterns were distinct from the parental patterns, suggesting that miRNA expression could be gained or lost after multiple rounds of meiosis. The functional implications of these trends to network rewiring in recombinants could be very significant given how post-transcriptional silencing of regulatory genes by miRNAs could potentially reconfigure the transcriptome, which could lead to either enhanced tolerance or enhanced sensitivity relative to the parents. The physiological and biochemical implications of miRNA-mediated transcriptional reconfiguration in certain transgressive RILs are discussed.