The dominant and poor penetrant phenotypes of the maize mutation Unstable factor for orange1 are caused by DNA methylation changes at a linked transposon

Transcriptional analysis of the Ufo1-1 mutant allele and wild type plants were used to identify the candidate gene using a k-mer based approach. The transcriptome data also revealed the altered expression of carbohydrate metabolic genes, which translates into elevated levels of soluble sugars in leaves and light-induced lesions found in mature Ufo1-1 leaves. Genome-wide RNA and sRNA profiling was done by Illumina TruSeq sample preparation followed by high-throughput sequencing with Illumina HiSeq 2000 platform.