Natural variation in PHY causes differential response to R/FR light following a latitudinal cline in Norway spruce

Detection of the genomic basis of local adaptation to environmental conditions is challenging in forest trees. Phytochromes ( PHY ) and cryptochromes ( CRY ) perceive the red (R)/far-red (FR) and blue light respectively and, play a fundamental role in regulating the light pathway in plants contributing to plant growth and development. Norway spruce shows an adaptive latitudinal cline for shade (low R:FR or FR-enriched light) tolerance and requirement of FR light for its growth, thus showing differential response to light quality. We analyzed the exome capture data that included a uniquely large data set of 1654 Norway spruce trees sampled from different latitudes across Sweden that differ in exposure to photoperiod and FR light received during the growing season. Statistically significant clinal variation was detected in allele and genotype frequencies of missense mutations in coding regions belonging to well-defined functional domains of PHYO (PAS-B), PHYP2 (PAS fold-2), CRY1 (CCT1) and CRY2 (CCT2) that strongly correlates with the latitudinal gradient in response to variable light quality in Norway spruce. Asn835Ser in PHYO displayed the steepest cline among all other polymorphisms. We propose that these variations represent signs of local adaptation to light quality in Norway spruce. ### Competing Interest Statement The authors have declared no competing interest. * CCT/CCE : CRY C-terminal domain/ CRY C-terminal extension CRY : Cryptochrome FR : Far-red light PAS : Drosophila period clock protein ( P ER), vertebrate aryl hydrocarbon receptor nuclear translocator ( A RNT) and Drosophila single-minded protein ( S IM) PHY : Phytochrome R : Red light SNP : Single nucleotide polymorphism