Functional copy number variation inSQUALENE EPOXIDASE-LIKEgenes affects photosystem II efficiency in Arabidopsis

ABSTRACT In this study, we found a single quantitative trait locus for photosystem II efficiency (Φ PSII ) in the Arabidopsis Ler-0 x Col-0 recombinant inbred line population. This locus on chromosome 5 is caused by genetic variation in a cluster of tandemly repeated SQUALENE EPOXIDASE - LIKE ( SQE-like ) genes, with unknown function. We show the QTL is caused by variation in the SQE5 , SQE6 and SQE7 genes affecting Φ PSII in a dose-dependent manner, due to a combination of functional copies. Col-0 carries only one functional copy, SQE5 , while Ler-0 carries functional copies of SQE6 and SQE 7 . Overexpression of a functional copy of SQE6 enhances Φ PSII to exceed that of the Ler-0 parent in Arabidopsis, but does not affect Φ PSII in tobacco. Phylogenetic analysis of the SQE and SQE-likes in 135 plant species revealed that the SQE -likes are evolutionary confined to two sister families, the Cleomaceae and Brassicaceae, and diversified independently. The tandem cluster of four SQE-like genes in Arabidopsis is likely the result of two recent gene duplication events, one generating SQE5 from SQE4 , the next one generating SQE6 and SQE7 from SQE5 . The involvement of SQE-like genes in photosynthesis will open up new avenues to determine the function of these novel genes.