Genome-wide analysis of allele specific expression imbalance and copy number variation in rice (Oryza sativa L.) under normal and drought conditions

To understand the possible roles of allele-specific expression (ASE) imbalance in genetic regulation of drought response in rice, IR64, a drought-sensitive indica and Apo, a drought-tolerant indica and their F1 hybrid were grown under normal and drought stress condition. SNPs were identified between the two parents and were used to identify parent-specific alleles in the F1 mRNA. The authors assayed 29 drought-responsive genes in the F1 hybrid for ASE imbalance by SNaPshot single-base extension assay. Surprisingly, results showed allele-specific copy number variation (CNV). This happens when, in a bi-allelic organism such as rice, one of the parent-specific alleles were replicated several times relative to the other allele. These asymmetric copies of alleles may contribute to ASE imbalance. To further investigate ASE imbalance in a genome-wide scale, the authors sequenced the total RNA transcripts of the same parents (Apo and IR64) and their F1 hybrid in both conditions. Analysis of reads revealed that more than 80% of the genes showed ASE imbalance. In a genome-wide scale, ASE imbalance occurs in both control and stress conditions indicating that such phenomenon is inherent to the organism regardless of the environmental conditions. The imbalance, however, is directed towards the maternal allele in both conditions. More than 25% of the whole transcript population exhibited 'dynamic' expression behavior between the two conditions, that is, a gene preferentially expresses IR64-specific allele in the normal condition but then shifts to Apo-specific allele in the drought stress-condition, or vice-versa. Most of these genes encode for stress-related or signal transduction protein. This implies that such genes are directly affected by environmental changes. This study shows that ASE imbalance is common in rice and reveals potentially new regulatory mechanisms that have bearings on drought response, phenotypic variation, and heterosis in rice.