Chromosome identification and comparative molecular cytogenetic mapping based on oligo-fish in model plants

Abstract

Since the discovery of chromosomes and the association of their behavior with Mendel’s “factors”, different strategies have been used to study their organization and function. In this way, the development of an accurate system of chromosome identification is crucial for the success in cytogenetic research. At the beginning, morphological data like chromosome length, centromere and secondary constriction position were used as marks for distinguishing chromosomes from each other. Chromosome banding methods like G-band were a great advance, but the most informative, the G-banding, never produced consistent results in plants. After the development of fluorescent in situ hybridization technique a variety of probes were developed which allowed cytogeneticists to create a vast amount of chromosome marks and identify homologous chromosomes. Recently developed, oligo-based FISH probes showed to be a powerful, cheap and repeatable strategy for chromosome identification in mammals and plants cytogenetics. Here we developed a comparative cytogenetics mapping based on oligoFISH probes. Basically, we selected specifics regions of potato and corn chromosomes to create a “barcode” system combining two colors (green and red). This strategy allowed us to distinguish all individual chromosomes from each other of potato, corn and their relatives using only one round of FISH preparation. In potato each of 12 chromosomes from diploid and polyploid species were accurately identified, as well as from distantly related Solanum species like tomato and eggplant. Two reciprocal chromosomal translocations were identified in Solanum etuberosum and S. caripense, which were validated using oligo-based chromosome painting. In corn, we identified each of 10 chromosomes in mitotic and pachytene preparations. We used our oligo-based probes in “teosinte” species which allowed us to identify all homeologous chromosomes of these species. The chromosomes of those species are similar except by the knob distribution and size. A homolozygous paracentric inversion was identified in Zea luxurians. Oligo-based FISH showed to be a powerful method for chromosome identification and karyotype evolution studies.