Origin of the presence/absence variation of the LTIA1/LTIA2mini-ribonuclease III genes required for low-temperature growth in rice

A rice low temperature-induced albino variant was determined by the recessive ltia1and ltia2genes. LTIA1and LTIA2encode highly conserved mini-ribonucleases III located in chloroplasts and expressed in aerial parts of the plant. At low temperature, LTIA1and LTIA2redundantly affect chlorophyll levels, non-photochemical quenching, photosynthetic quantum yield of PS II and seedling growth. LTIA1 and LTIA2 proteins are involved in splicing of atpFand the biogenesis of 16S and 23S rRNA in chloroplasts. Presence/absence variation of LTIA1, the ancestral copy, was found only in japonicabut that of LTIA2in all rice subgroups. Accessions with LTIA2presence tended to be distributed more remote from the equator compared to those with LTIA2absence. LTIA2duplicated from LTIA1at the early stage of divergence of the AA genome Oryzaspecies but deleted againin O. nivara. In cultivated rice, absence of LTIA2is derived from O. nivara. LTIA1absence occurred more recently in japonica.