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Lentinula edodes is a globally important edible mushroom species that is appreciated for its medicinal properties as well as its nutritional value. During commercial cultivation, a mycelial brown film forms on the surface of the sawdust growth medium at the late vegetative stage. Mycelial film formation is a critical developmental process that contributes to the quantity and quality of the mushroom yield. However, little is known regarding the genetic underpinnings of brown film formation on the surface of mycelial tissue. A novel causal gene associated with the formation of the mycelial brown film, named ABL (Abnormal browning related to light), was identified in this study. The comparative genetic analysis by dihybrid crosses between normal and abnormal browning film cultivars demonstrated that a single dominant allele was responsible for the abnormal mycelium browning phenotype. Whole-genome sequencing analysis of hybrid isolates revealed five missense single-nucleotide polymorphisms (SNPs) in the ABL locus of individuals forming abnormal partial brown films. Additional whole-genome resequencing of a further 16 cultivars showed that three of the five missense SNPs were strongly associated with the abnormal browning phenotype. Overexpression of the dominant abl-D allele in a wild-type background conferred the abnormal mycelial browning phenotype upon transformants, with slender hyphae observed as a general defective mycelial growth phenotype. Our methodology will aid the future discovery of candidate genes associated with favorable traits in edible mushrooms. The discovery of a novel gene, ABL, associated with mycelial film formation will facilitate marker-associated breeding in L. edodes. [ABSTRACT FROM AUTHOR]

Rice, being a staple food crop for over one-third of the world's population, has become a potential target for many dishonest traders and stakeholders for mixing with low-grade, low-cost grains/products and poorly nutritious adulterants to make a profit with the least effort. Single-nucleotide and insertion-deletion (InDel) polymorphisms have been widely used as DNA markers, not only in plant breeding but also to identify various traits in rice. Recently, next-generation sequencing (NGS) has produced sequences that allow for genome-wide detection of these molecular markers. These polymorphisms can potentially be used to develop high-accuracy polymerase chain reaction (PCR)-based markers. PCR-based techniques are rapid and successful methods to deal with the problem of adulteration at a commercial level. Here, we report the genome-wide analysis of InDel markers of 17 commercially available Chinese cultivars. In order to achieve accurate results, all samples were sequenced at approximately 30 genome coverage using Illumina HiSeq 2500™system. An average of 10.6 GB clean reads per sample was produced and ~96.3% of the reads could be mapped to the rice genome reference IRGSP 1.0. After a series of filtering, we selected five InDel markers for PCR validation. The results revealed that these InDel markers can be used for authentication of Korean elite cultivars from the adulterants. [ABSTRACT FROM AUTHOR]