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

Abstract

ABSTRACTIn this study, we found a single quantitative trait locus for photosystem II efficiency (ΦPSII) 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 repeatedSQUALENE EPOXIDASE-LIKE(SQE-like) genes, with unknown function. We show the QTL is caused by variation in theSQE5,SQE6andSQE7genes affecting ΦPSIIin 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 ofSQE6and SQE7. Overexpression of a functional copy ofSQE6enhances ΦPSIIto exceed that of the Ler-0 parent in Arabidopsis, but does not affect ΦPSIIin tobacco. Phylogenetic analysis of theSQEandSQE-likesin 135 plant species revealed that theSQE-likes are evolutionary confined to two sister families, the Cleomaceae and Brassicaceae, and diversified independently. The tandem cluster of fourSQE-likegenes in Arabidopsis is likely the result of two recent gene duplication events, one generatingSQE5fromSQE4, the next one generatingSQE6andSQE7fromSQE5. The involvement ofSQE-likegenes in photosynthesis will open up new avenues to determine the function of these novel genes.