Origin of the presence/absence variation of the LTIA1/LTIA2 mini-ribonuclease Ⅲ genes required for low-temperature growth in rice

A rice low temperature-induced albino variant was determined by the recessive ltia1 and ltia2 genes. LTIA1 and LTIA2 encode highly conserved mini-ribonucleases Ⅲ located in chloroplasts and expressed in aerial parts of the plant. At low temperature, LTIA1 and LTIA2 redundantly affect chlorophyll levels, non-photochemical quenching, photosynthetic quantum yield of PS Ⅱ and seedling growth. LTIA1 and LTIA2 proteins are involved in splicing of atpF and the biogenesis of 16S and 23S rRNA in chloroplasts. Presence/absence variation of LTIA1, the ancestral copy, was found only in japonica but that of LTIA2 in all rice subgroups. Accessions with LTIA2 presence tended to be distributed more remote from the equator compared to those with LTIA2 absence. LTIA2 duplicated from LTIA1 at the early stage of divergence of the AA genome Oryza species but deleted againin O. nivara. In cultivated rice, absence of LTIA2 is derived from O. nivara. LTIA1 absence occurred more recently in japonica.