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A simple and efficient non-denaturing FISH method for maize chromosome differentiation using single-strand oligonucleotide probes

Zhu, Minqiu, Du, Pei, Zhuang, Lifang, Chu, Chenggen, Zhao, Han, Qi, Zengjun
Genome 2017 v.60 no.8 pp. 657-664
Zea mays, chromosome painting, chromosomes, corn, genetic variation, genotype, hybrids, inbred lines, oligonucleotide probes, oligonucleotides
Single-strand oligonucleotides (SSONs hereafter) as probes are becoming a powerful method of chromosome painting in many species. In this study, nine SSONs ((ACT)₁₀, (ACT)₁₉, Knob-1, Knob-2, Knob-3, CentC69-1, MR68-3, K10-72-1, and TR1-357-2) were developed and used for chromosome identification in 16 maize (Zea mays L., 2n = 20) inbred lines and hybrids by non-denaturing fluorescence in situ hybridization (ND-FISH). Each SSON produced clear signals on 2–10 chromosomes of inbred lines B73 and Mo17. A multiplex probe set containing four SSONs ((ACT)₁₀, Knob-2, CentC69-1, and MR68-3) clearly characterized all maize chromosomes in the 16 lines by a single round of ND-FISH and revealed genetic variation at a chromosome level. For example, unique signals on chromosome 6 clearly distinguished all 16 genotypes. The SSONs and multiplex probe developed in this research will facilitate genotype identification and chromosome research in maize.