Auto x Photo F2 Mapping Population SNPs

Methods:An F2 population was developed between an auto-flowering and photoperiod sensitive cross to construct a genetic map. A total of 192 F2 plants were grown indoors and genotyped using a SeqSNP chip with 5,000 custom markers selected from our GBS dataset covering the cannabis genome. Biosearch Technologies performed the mapping of reads and SNP calling using the Purple Kush genome (ASM23057v4, GCA_000230575.4) as reference. In brief, variant calling was done using GATK (McKenna et al., 2010) and identified SNPs were filtered by biallelic variants. Only those SNPs for which a definitive parental origin could be assigned were used for genetic map construction. Of the 4004 markers available, only 484 remained after filtering for missing genotypes and segregation distortion. A linkage map was constructed with the R package Rqtl using the ‘est.map’ function with a genotyping error rate set to 0.01. Genetic distances were calculated from the observed recombination fractions using the Kosambi function.