RNA sequencing for candidate gene identification for habitat specific clock varaition in natural ecotypes of Neurospora discreta

Purpose: The goal of the current study was to find the candidate genes responsible for the habita specific clock variation in N. discreta. Methods: We performed RNA-seq experiment using four strains ; African parent (FGSC8831), North American parent (FGSC 8578) and two representative progeny representing African clock phenotype (N309-89) and North American clock phenotype (N309-50). Results: We identified one candidate gene that meets our criteria; confirmed it's expression by qPCR and it's expression pattern is associated with parent genotype. Conclusions: Our approach using the expression profiles and SNP data of two parents and two representative progeny led us to identify a candidate gene for a complex clock adaptation phenotype. Samples are prepared from cells at different time of the cycling environement, 12 h light: 12 h dark; 2h dark phase (2DK), and 15m, 1h and 2h light phase. We also used the identified SNPs in the transcripts to perform association study.