Abstract
The genus Saccharum is composed of species with high polyploidy and highly varied chromosome numbers, laying a challenge for uncovering its genomic structure and evolution. We developed a chromosome 2 painting (CP2) probe by designing oligonucleotides covering chromosome 2 of Saccharum spontaneum (2n = 8x = 64). Fluorescence in situ hybridization (FISH) using this CP2 probe revealed six types of ploidies from twenty S. spontaneum clones, including 6x, 8x, 10x, 11x, 12x, and 13x clones. The finding of S. spontaneum clones with uneven of ploid suggested that certain S. spontaneum clones come from hybridization. It renews our knowledge that S. spontaneum is derived from autopolyploidization. Combined with a S. spontaneum-specific probe, chromosome 2-derived chromosome or fragments from either S. spontaneum or Saccharum officinarum can be identified in sugarcane modern cultivars. We revealed unexpected high level of interspecific recombination from introgressive S. spontaneum chromosomes (>50.0%) in cultivars ROC22 and ZZ1, indicating frequent chromosome exchange in cultivars. Intriguingly, we observed interspecific recombination recurring among either homoeologous or non-homoeologous chromosomes in sugarcane cultivars. These results demonstrated that chromosome painting FISH is a powerful tool in the genome dissection of sugarcane and provide new insights into the genome structure and evolution of the complex genus Saccharum.
Highlights
Chromosome painting (CP) is a technique to visualize the entire chromosome via fluorescence in situ hybridization (FISH) using chromosome-specific painting probes (Pinkel et al, 1988)
We developed an oligo-based chromosome 2 painting (CP2) probe based on the genome assembly of S. spontaneum AP85441 (x = 8) chromosome 2 (Zhang et al, 2018)
No unspecific signals were detectable from any other chromosomes, indicating that these oligos were specific to chromosome 2 and could potentially be used as reliable markers for chromosome 2 identification in the highly polyploid species S. spontaneum
Summary
Chromosome painting (CP) is a technique to visualize the entire chromosome via fluorescence in situ hybridization (FISH) using chromosome-specific painting probes (Pinkel et al, 1988). A major cause is the prevalence of repetitive DNAs in the genomes, which results in unfavorable non-specific hybridization signals. To overcome this problem, CP based on large insert DNA clone (YAC/BAC) probes with low amounts of repetitive sequences has been developed and successfully applied in studies of the genomic structure and evolution of plants (Fransz et al, 2000; Xiaomin et al, 2008; Dóra et al, 2010; Kai et al, 2010; Mandakova et al, 2010; Peters et al, 2012). PCR amplification of single-copy genes from the entire chromosome is labor-intensive and time consuming
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