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Physical organization of repetitive sequences and chromosome diversity of barley revealed by fluorescence in situ hybridization (FISH)

Zhang, Siyu, Zhu, Minqiu, Shang, Yi, Wang, Jiaqi, Dawadundup,, Zhuang, Lifang, Zhang, Jinlong, Chu, Chenggen, Qi, Zengjun
Genome 2019 v.62 no.5 pp. 329-339
barley, centromeres, clones, cultivars, fluorescence in situ hybridization, heterochromatin, karyotyping, landraces, mutants, oligonucleotides, plasmids, repetitive sequences, ribosomal DNA
Fluorescence in situ hybridization (FISH) using oligonucleotides is a simple and convenient method for chromosome research. In this study, 34 of 46 previously developed oligonucleotides produced signals in barley. Together with two plasmid clones and one PCR-amplified cereal centromere repeat (CCS1) probe, 37 repetitive sequences were chromosomally located produced three types of signals covering different positions on the chromosomes. The centromeric and pericentric regions had a more complex genomic organization and sequence composition probably indicative of higher contents of heterochromatin. An efficient multi-plex probe containing eight oligonucleotides and a plasmid clone of 45S rDNA was developed. Thirty-three barley karyotypes were developed and compared. Among them, 11 irradiation-induced mutants of cultivar 08-49 showed no chromosomal variation, whereas 22 cultivar and landrace accessions contained 28 chromosomal polymorphisms. Chromosome 4H was the most variable and 6H was the least variable based on chromosome polymorphic information content (CPIC). Five polymorphic chromosomes (1H-2, 2H-1, 3H-3, 5H-2, and 6H-2) were dominant types, each occurring in more than 50% of accessions. The multi-plex probe should facilitate identification of further chromosomal polymorphisms in barley.