Lessons from eQTL mapping studies: non-coding regions and their role behind natural phenotypic variation in plants

► A larger proportion of the explained transcript abundance variation is due to local regulators (likely cis-acting) compared to distant regulators (trans-acting). ► Allelic variation in gene expression levels is a strong contributor to phenotype diversity. ► Local epigenetic variation may be an important contributor to gene expression diversity. ► Studying differentially expressed alleles helps to reconstruct regulatory networks, providing candidates in classical linkage studies. ► High-throughput RNA-sequencing technologies on F1 hybrids (RNA-seq) has already proven fruitful in other systems. Even if considerable progress has been achieved towards the understanding of natural variation in plant systems, the contribution of transcript abundance variation to phenotypic diversity remains unappreciated. Over the last decade, efforts to characterise the genome-wide expression variation in natural accessions, structured populations and hybrids have improved our knowledge of the contribution of non-coding polymorphisms to gene expression regulation. Moreover, new studies are helping to unravel the role of expression polymorphisms and their orchestrated performance. Recent advances involving classical linkage analysis, GWAS and improved eQTL mapping strategies will provide a greater resolution to determine the genetic variants shaping the broad diversity in plant systems.