A Very Oil Yellow1 Modifier of the Oil Yellow1-N1989 Allele Uncovers a Cryptic Phenotypic Impact of Cis-regulatory Variation in Maize

G3: Genes, Genomes, Genetics

article

Rajdeep S. Khangura¹  Sandeep Marla¹  Bala P. Venkata¹  Nicholas J. Heller¹  Gurmukh S. Johal¹  Brian P. Dilkes² 

[1] Department of Botany and Plant Pathology, Purdue University, IN 47907;Center for Plant Biology, Purdue University, IN 47907;Department of Biochemistry, Purdue University, IN 47907

关键词: Chlorophyll biosynthesis;    cryptic variation;    cis-acting;    complex traits;    epistasis;   

DOI  :  10.1534/g3.118.200798

学科分类：社会科学、人文和艺术（综合）

来源: Genetics Society of America

【 摘 要 】

Forward genetics determines the function of genes underlying trait variation by identifying the change in DNA responsible for changes in phenotype. Detecting phenotypically-relevant variation outside protein coding sequences and distinguishing this from neutral variants is not trivial; partly because the mechanisms by which DNA polymorphisms in the intergenic regions affect gene regulation are poorly understood. Here we utilized a dominant genetic reporter to investigate the effect of cis and trans -acting regulatory variation. We performed a forward genetic screen for natural variation that suppressed or enhanced the semi-dominant mutant allele Oy1-N1989 , encoding the magnesium chelatase subunit I of maize. This mutant permits rapid phenotyping of leaf color as a reporter for chlorophyll accumulation, and mapping of natural variation in maize affecting chlorophyll metabolism. We identified a single modifier locus segregating between B73 and Mo17 that was linked to the reporter gene itself, which we call very oil yellow1 ( vey1 ). Based on the variation in OY1 transcript abundance and genome-wide association data, vey1 is predicted to consist of multiple cis -acting regulatory sequence polymorphisms encoded at the wild-type oy1 alleles. The vey1 locus appears to be a common polymorphism in the maize germplasm that alters the expression level of a key gene in chlorophyll biosynthesis. These vey1 alleles have no discernable impact on leaf chlorophyll in the absence of the Oy1-N1989 reporter. Thus, the use of a mutant as a reporter for magnesium chelatase activity resulted in the detection of expression-level polymorphisms not readily visible in the laboratory.

【 授权许可】

CC BY|CC BY-NC