Genetic Mapping of SNP Markers and Candidate Genes Associated with Day-Neutral Flowering inCannabis sativaL.

Abstract

Hemp (Cannabis sativaL.) 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 inC. 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), andPSEUDO-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.

Domesticated cannabinoid synthases amid a wild mosaic cannabis pangenome

“…In Arabidopsis and rice many tested populations show segregation distortion, which may be due to seed dormancy and lethal epistatic interactions 24,25 . However, the segregation distortion could be the result of the SV noted across the pangenome, and consistent with this chromosome 1, where DN alleles have been mapped 21,26 , displays the largest size variation (Supplemental Fig. 4).…”

“…1b). Segregation distortion patterns observed across many regions of the genome were noted in a prior study of this population 21 , and may be caused by differences in seed germination rates. A study done by Beutler and Der Marderosian reported a delay in seed germination in crosses between DN and SD plants; the authors speculate this trait is a carryover from the hypothesized species “ Cannabis ruderalis ,” or DN, parent 22 .…”

“…Indeed, the 17 instances of this inversion were found to be heterozygous in 15 samples and homozygous in one. This inverted region contains 1,203 genes, spanning many functions, including the core circadian and flowering time gene PSEUDO RESPONSE REGULATOR 3 ( PRR3 ) implicated in the DN behavior of “autoflower” cannabis 21,26,58 , but are significantly enriched for catalytic activity, transport activity, and binding gene ontology (GO) categories. Pairwise SNP r 2 values and local PCA plots of this area suggest some level of haplotype formation and elevated linkage disequilibrium (LD) across this region, especially at the interior breakpoint (Supplemental Fig.…”

A FLOWERING LOCUS T ortholog is associated with photoperiod‐insensitive flowering in hemp (Cannabis sativa L.)

“…Two recent mapping studies have suggested C. sativa homologues of APETALA2 and PSEUDO-RESPONSE REGU-LATOR 37 (PRR37) as candidate genes within Autoflower1 (Garfinkel et al, 2023;Leckie et al, 2023). Alterations of PRR37 homologues in T. aestivum, O. sativa, and Sorghum bicolor are known to confer photoperiod insensitivity due to de-repressed FT expression (Beales et al, 2007;Koo et al, 2013;Murphy et al, 2011).…”