Analysis of Allelic Imbalance in Rice Hybrids Under Water Stress and Association of Asymmetrically Expressed Genes with Drought-Response QTLs

Abstract

BackgroundInformation on the effect of stress on the allele-specific expression (ASE) profile of rice hybrids is limited. More so, the association of allelically imbalanced genes to important traits is yet to be understood. Here we assessed allelic imbalance (AI) in the heterozygote state of rice under non- and water-stress treatments and determined association of asymmetrically expressed genes with grain yield (GY) under drought stress by in-silico co-localization analysis and selective genotyping. The genotypes IR64, Apo and their F1 hybrid (IR64 × Apo) were grown under normal and water-limiting conditions. We sequenced the total RNA transcripts for all genotypes then reconstructed the two chromosomes in the heterozygote.ResultsWe are able to estimate the transcript abundance of and the differential expression (DE) between the two parent-specific alleles in the rice hybrids. The magnitude and direction of AI are classified into two categories: (1) symmetrical or biallelic and (2) asymmetrical. The latter can be further classified as either IR64- or Apo-favoring gene. Analysis showed that in the hybrids grown under non-stress conditions, 179 and 183 favor Apo- and IR64-specific alleles, respectively. Hence, the number of IR64- and Apo-favoring genes is relatively equal. Under water-stress conditions, 179 and 255 favor Apo- and IR64-specific alleles, respectively, indicating that the number of allelically imbalanced genes is skewed towards IR64. This is nearly 40–60 % preference for Apo and IR64 alleles, respectively, to the hybrid transcriptome. We also observed genes which exhibit allele preference switching when exposed to water-stress conditions. Results of in-silico co-localization procedure and selective genotyping of Apo/IR64 F3:5 progenies revealed significant association of several asymmetrically expressed genes with GY under drought stress conditions.ConclusionOur data suggest that water stress skews AI on a genome-wide scale towards the IR64 allele, the cross-specific maternal allele. Several asymmetrically expressed genes are strongly associated with GY under drought stress which may shed hints that genes associated with important traits are allelically imbalanced. Our approach of integrating hybrid expression analysis and QTL mapping analysis may be an efficient strategy for shortlisting candidate genes for gene discovery.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-016-0123-4) contains supplementary material, which is available to authorized users.

cis dominantly explains regulatory divergence between two indica rice genotypes; drought further enhances regulatory differences

“…In a companion paper, we have described our approach of assessing allelic imbalance in rice hybrid including the description of the datasets (Ereful et al 2016). In this current work, we report evidence of regulatory divergence of the two genotypes which has not been described before.…”

“…In a companion paper (Ereful et al 2016), we used mRNA-seq to describe allelespecific expression (ASE) imbalance in IR64×Apo hybrid exposed to both water-stressed and unstressed conditions. Here, we further tested our datasets for evidence of cis and/or trans regulatory differences.…”

“…Reports showed that natural selection reduces the level of variability of local genomic regions leaving molecular patterns of selection such as increased genetic divergence around adaptive loci (Nielsen et al 2005;Verta and Jones, 2019;Wachowiak et al 2018). We further tested this hypothesis by co-localizing cis-diverging genes to drought-yield QTL marker regions (shown below; also see Ereful et al 2016).…”

“…3. Several genes harboring cis divergence were found to co-localize with QTL marker regions (boxed in blue) identified to participate in drought-yield response in the same bi-parental population background (IR64/Apo) under drought conditions (Venuprasad et al 2009;Ereful et al 2016). Genes appended with "Trans" exhibited no ASE (as described in the text) but were found to diverge in trans.…”

“…Markers which have been previously reported to be involved in drought -yield response were taken from previous papers (Ereful et al 2016;Venuprassad et al 2009).…”