Identifying a candidate mutation underlying a reduced cuticle wax mutant of rice using targeted exon capture and sequencing

Authors: KIM, HYUNJUNG - University Of California, Davis; Tai, Thomas

Submitted to: Plant Breeding and Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/26/2018
Publication Date: 3/1/2019
Citation: Kim, H., Tai, T. 2019. Identifying a candidate mutation underlying a reduced cuticle wax mutant of rice using targeted exon capture and sequencing. Plant Breeding and Biotechnology. 7(1):1-11. https://doi.org/10.9787/PBB.2019.7.1.1.
DOI: https://doi.org/10.9787/PBB.2019.7.1.1

Interpretive Summary: Land plants have an outer protective covering call a cuticle layer or membrane, which consists of various waxes embedded in a structural matrix of cutin, a polyester compound. The cuticle is a barrier that prevents uncontrolled water and gas diffusion and protects plants from physical and biological stresses from the environment (e.g., drought, plant pathogens). In this study, a rice mutantwith reduced cuticle wax content was analyzed using a technique called targeted exon capture and sequencing. This method facilitates the selective sequence analysis of a relatively small set of genes more efficiently than traditional Sanger sequencing-based approach. The resulting sequence data revealed one candidate mutation meeting the criteria of 1) predicted to cause an amino acid change, and 2) existing in both copies of the chromosome (i.e., homozygous or fixed mutation). Based on previous studies and our genetic analysis of the mutant, this mutation is in a gene known to be involved in cuticle wax synthesis and accumulation. The exon capture and sequencing method enabled rapid detection of the mutation. The corresponding mutant will be useful in characterizing the importance of epicuticular wax in the interaction of rice plants with their growing environment.

Technical Abstract: Aerial surfaces of terrestrial plants are protected from the uncontrolled loss of water and gas by the cuticle, a membrane of fatty acid polymers on the outer surface of epidermal cells. Composed of cutin and waxes, the cuticle protects against a wide range of external stresses and has an important role in plant development and reproduction. Plants with reduced cuticular waxes often exhibit glossy, bright green leaves, which in rice are only observed in the presence of water adhesion. In this study, a wet leaf/glossy (wlg) mutant KDS-2249D was subjected to targeted exon capture and sequencing to identify candidate mutations. A single nonsynonymous, homozygous mutation was found in the KDS-2249D mutant. The mutation (G1080A) is predicted to change a tryptophan at position 360 to a stop codon in the Glossy1-like-1/wax crystal-sparse leaf 2 gene. This mutation completely co-segregated with the wlg phenotype in an F2 mapping population (n = 435) and the KDS-2249 mutant exhibited a 40-50% decrease in total wax and significant increase in membrane permeability. This mutant will be useful for studies examining the role of cuticle waxes in protecting rice plants from environmental stresses.