A universal chromosome identification system for maize and wild Zea species

Maize was one of the first eukaryotic species in which individual chromosomes can be identified cytologically, which made maize one of the earliest models for genetics and cytogenetics research. Nevertheless, consistent identification of all 10 chromosomes from different maize lines as well as from wild Zea species has been a challenge. We developed a new technique for maize chromosome identification based on fluorescence in situ hybridization (FISH) using two oligonucleotide (oligo)-based probes. The two oligo probes hybridize to 24 chromosomal regions, which generate distinct signal patterns on 10 maize chromosomes and allow universal identification of all chromosomes from different Zea species. We developed karyotypes from six Zea species and subspecies based on individually identified chromosomes. A putative paracentric inversion was discovered on the long arm of chromosome 4 in Z. nicaraguensis and Z. luxurians based on modification of the FISH signal pattern, supporting Z. nicaraguensis and Z. luxurians to be closely related species.