Unraveling regulatory divergence, heterotic malleability, and allelic imbalance switching in rice due to drought stress

Abstract

The indica ecotypes, IR64, an elite drought-susceptible variety adapted to irrigated ecosystem, and Apo (IR55423-01 or NSIC RC9), a moderate drought-tolerant upland genotype together with their hybrid (IR64 × Apo) were exposed to non- and water-stress conditions. By sequencing (RNA-seq) these genotypes, we were able to map genes diverging in cis and/or trans factors. Under non-stress condition, cis dominantly explains (11.2%) regulatory differences, followed by trans (8.9%). Further analysis showed that water-limiting condition largely affects trans and cis + trans factors. On the molecular level, cis and/or trans regulatory divergence explains their genotypic differences and differential drought response. Between the two parental genotypes, Apo appears to exhibit more photosynthetic efficiency even under water-limiting condition and is ascribed to trans. Statistical analyses showed that regulatory divergence is significantly influenced by environmental conditions. Likewise, the mode of parental expression inheritance which drives heterosis (HET) is significantly affected by environmental conditions indicating the malleability of heterosis to external factors. Further analysis revealed that the HET class, dominance, was significantly enriched under water-stress condition. We also identified allelic imbalance switching in which several genes prefer IR64- (or Apo-) specific allele under non-stress condition but switched to Apo- (or IR64-) specific allele when exposed to water-stress condition.

Assessing Loss of Regulatory Divergence, Genome–Transcriptome Incongruence, and Preferential Expression Switching in Abaca/ Banana Backcrosses

“…The finding that cis regulatory factors explaining interspecific divergence has been widely reported in literature (e.g. [10,14,17,49,50]). On the other hand, trans regulatory factor (purple in Fig.…”

“…binomial and Fisher exact tests, FDR < 0.5%) in the Results and Discussions as previously performed (e.g. [12,17]). For cis/trans regulatory assignments, see our github repository site: https://bit.ly/3tP4BtE.…”

“…Trans, on the other hand, is robust to changes in genomic composition (P = 0.3817). In recent papers, trans is significantly affected by changes in external factors [17,51] but not in changes in genetic make-up. On the contrary, cis is robust to environmental changes [17,52].…”

“…ASE has been a subject of a number of papers in different organisms such as humans [8,9], Drosophila [10,11,12], maize [13], stickleback [14], coffee [15], and rice [16,17]. There are several approaches in assessing ASE which include single-base extension [18], pyrosequencing [10], and most recently RNA-seq (e.g.…”

RNA-Seq Reveals Differentially Expressed Genes Associated with High Fiber Quality in Abaca (Musa textilis Nee)

“…Bandala is also grown in several areas in Visayas, the central region of the Philippines, and in Mindanao, besides Luzon [42]. This indicates its ability to adapt to multiple environmental conditions owing to its heterozygous alleles, which confer it with transcriptional versatility or heterotic malleability, as recently shown in rice hybrids [47].…”