Allele-specific genomic variations and transcriptomic research on quantitative phenotyping in plants

Genomes and interactions among gene products with other molecules are the physical fundamentals of biological systems. This is especially true for research in plants, which usually have complicated genomes and many important traits like yield, plant height, and stress tolerance are quantitative. Many quantitative traits are usually controlled by more than one Quantitative expression Loci (QTL) through the regulation of gene expression. The expression of a gene could be associated with a genetic variant far away from it, which is called trans-eQTL (expression QTL) or be affected by a local variant, which is named cis-eQTL. With a widespread existence throughout the plant genome, cis-acting genetic variants have been proven to account for a larger proportion of variation in gene expression. However, it is challenging for identifying cis-eQTL in the population with sequencing data because the power of eQTL mapping is either constrained by sample size or reduced by confounding factors. For organisms with a diploid genome, the information of AlleleSpecific Expression (ASE) which could provide more direct evidence of cis-eQTL is often ignored or discarded due to the unavailability of haplotype information and mapping bias.