Genetic Mapping of SNP Markers and Candidate Genes Associated with Day-Neutral Flowering in Cannabis sativa L

Hemp ( Cannabis sativa L.) is a primarily short-day crop grown for grain, fiber, and secondary metabolites. Although terminal flowering of most non-domesticated hemp is regarded as photoperiod sensitive, limited germplasm is available for the development of day-neutral hemp. Day-neutral plants experience flower maturation independently of the short-day photoperiod cue which is typically triggered by photoperiods of less than 14 hours. The day-neutral trait is the subject of increased commercial interest for the purpose of breeding varieties with accelerated flowering time or cultivars that do not require labor- and cost-intensive light deprivation production systems. Genetic markers for the photoperiodic response would help breeders make early selection in the design of suitable cultivars for specific environments and cultivation calendars. Limited refereed information has been produced regarding the genetic regulation of photoperiodism in C. sativa . A population of 318 F2 individuals segregating for day-neutral flowering was developed, phenotyped, and genotyped. Genome-wide association analysis identified markers associated with the day-neutral trait indicating that a single recessive gene controlling photoperiod sensitivity is located within a large region of Chromosome 1. Flanking region sequence data of linked SNP markers was used in the development and validation of a TaqMan-based qPCR assay for the day-neutral trait. A genetic linkage map was produced, and QTL mapping identified two additional markers on Chromosome 1. Candidate genes, TARGET OF EARLY ACTIVATION TAGGED (TOE )/ APETALA2 ( AP2 ), and PSEUDO-RESPONSE REGULATOR 3 ( PRR3 ), may work together to impact phase transition and photoperiodic flowering respectively and have key domains that are disrupted in day-neutral plants. The day-neutral flowering (a.k.a. “autoflower”) phenotype is a valuable and understudied trait in Cannabis sativa The phenotype may result from a conserved linkage block of phase transition and photoperiodic flowering genes A segregating population was developed, genome wide analyses identified markers linked to the day-neutral trait Correlated markers were mapped to Chromosome 1 across a sizable region that appears to be largely non-recombining ### Competing Interest Statement Authors A.R.G, B.M.R., and S.C. work for the company Oregon CBD at the time of submission of this manuscript. All other authors declare no conflict of interest.