Development and Applications of Chromosome-Specific Cytogenetic BAC-FISH Probes in S. spontaneum

Guangrui Dong, Jiao Shen, Qing Zhang, Jianping Wang, Qingyi Yu, Ray Ming, Kai Wang, Jisen Zhang

Saccharum spontaneum is a majorSaccharumspecies that contributed to the origin of modern sugarcane cultivars, and due to a high degree of polyploidy is considered to be a plant species with one of the most complex genetics. Fluorescencein situhybridization (FISH) is a powerful and widely used tool in genome studies. Here, we demonstrated that FISH based on bacterial artificial chromosome (BAC) clones can be used as a specific cytological marker to identifyS. spontaneumindividual chromosomes and study the relationship betweenS. spontaneumand other related species. We screened low-copy BACs as probes from the sequences of a high coverage ofS. spontaneumBAC library based on BLAST search of the sorghum genome. In total, we isolated 49 positive BAC clones, and identified 27 BAC clones that can give specific signals on theS. spontaneumchromosomes. Of the 27 BAC probes, 18 were confirmed to be able to discriminate the eight basic chromosomes ofS. spontaneum. Moreover, BAC-24, BAC-66, BAC-78, BAC-69, BAC-71, BAC-73, and BAC-77 probes were used to construct physical maps of chromosome 1 and chromosome 2 ofS. spontaneum, which indicated synteny in Sb01 betweenS. spontaneumand sorghum. Furthermore, we found that BAC-14 and BAC-19 probes, corresponding to the sorghum chromosomes 2 and 8, respectively, localized to different arms of the sameS. spontaneumchromosome, suggesting that there was an inter-chromosomal rearrangement event betweenS. spontaneumand sorghum. Our study provides the first set of chromosome-specific cytogenetic markers inSaccharumand is critical for future advances in cytogenetics and genome sequencing studies inSaccharum.