Recent and frequent insertions of chloroplast DNA into maize nuclear chromosomes

Organellar DNA transfer into the nucleus and incorporation into chromosomes are continuing processes. We have examined chloroplast DNA insertions in maize chromosomes using fluorescence in situ hybridization (FISH). Probes to detect the nuclear-plastid sequences (NUPTs) were generated using 14 overlapping fragments of the chloroplast genome. Using current FISH methods, detection of NUPTs on mitotic metaphase chromosomes requires relatively large insertions (>3 kb) with strong sequence similarity to chloroplast DNA. In the B73 inbred line, hybridization of each fragment separately resolved a total of 49 NUPT sites; fewer sites (30) were detectable when all the probes were combined. The combined set of probes was hybridized to 10 genetically useful maize inbred lines and identified 19-30 NUPTs in each line. In all but two of the lines, a prominent NUPT was present on the long arm of chromosome 5. Collectively, the number of NUPTs exceeds the number of nuclear-mitochondrial (NUMT) sites identified within the same set of inbred lines. A majority of the NUPTs are found at sites that are different from the NUMTs. Like NUMTs, the positions of the NUPTs vary greatly among the lines, suggesting that the transfers are recent as well as frequent. Thus, insertions of large segments of chloroplast and mitochondrial DNA are components of the dynamic fraction of maize nuclear genomes.