Recent advances in rice genome and chromosome structure research by fluorescence <i>in situ</i> hybridization (FISH)

Abstract

Fluorescence in situ hybridization (FISH) is an effective method for the physical mapping of genes and repetitive DNA sequences on chromosomes. Physical mapping of unique nucleotide sequences on specific rice chromosome regions was performed using a combination of chromosome identification and highly sensitive FISH. Increases in the detection sensitivity of smaller DNA sequences and improvements in spatial resolution have ushered in a new phase in FISH technology. Thus, it is now possible to perform in situ hybridization on somatic chromosomes, pachytene chromosomes, and even on extended DNA fibers (EDFs). Pachytene-FISH allows the integration of genetic linkage maps and quantitative chromosome maps. Visualization methods using FISH can reveal the spatial organization of the centromere, heterochromatin/euchromatin, and the terminal structures of rice chromosomes. Furthermore, EDF-FISH and the DNA combing technique can resolve a spatial distance of 1 kb between adjacent DNA sequences, and the detection of even a 300-bp target is now feasible. The copy numbers of various repetitive sequences and the sizes of various DNA molecules were quantitatively measured using the molecular combing technique. This review describes the significance of these advances in molecular cytology in rice and discusses future applications in plant studies using visualization techniques.

Dual-color FISH karyotype analyses using rDNAs in three Cucurbitaceae species

“…This would favor the transposition and higher dispersion of the 45S rDNA in the genome over the 5S rDNA. These findings could also explain the higher number of 45S rDNA loci when compared to the 5S rDNA, as observed in many plant species such as Brasicca rapa (Lim et al, 2005), Cucumis sativus (Koo et al, 2005;Han et al, 2008), some rice species (Ohmido et al, 2010), Luffa cylindrica (Xu et al, 2007), Passiflora spp. (de Melo and Guerra, 2003), and in all three species evaluated in this study.…”

Dual-color FISH karyotype and rDNA distribution analyses on four Cucurbitaceae species

“…The results also show significantly higher number of 45S rDNA signals than 5S rDNA, a pattern following the trend of rDNA distribution among plant species like Brasicca rapa (Lim et al, 2005), Crotalaria juncea (Mondin et al, 2007), Passiflora spp. (de Melo and Guerra, 2003), some rice species (Ohmido et al, 2010), and wild Lilium (Sultana et al, 2010) among others, as revealed by FISH.…”

“…Karyotyping, coupled with fluorescence in situ hybridization (FISH) using specific DNA markers, is an indispensable tool for cytogenetics in expediting the development and improvement of economically important plant species (Sadder and Webber, 2001;Vasconcelos et al, 2010), such as Cucumis sativus (Chen et al, 1998;Koo et al, 2002), Oryza (Ohmido et al, 2010), and Zea mays (Kato et al, 2004).…”

Genomic in situ Hybridization in Triticeae: A Methodological Approach

“…Since the discovery of the nucleic acid hybridization reaction by Hall & Spiegelmann [7], and later by using fluorescent detection rather than radioactive isotopes [8], the fluorescent in situ hybridization (FISH) and its variations have been largely employed in karyotype characterization of plants [9]. The technique basically consists on the pairing of a given probe (a DNA or RNA fragment) with a specific sequence on the target genome, aiming to indicate its exact location in a chromosome.…”

“…Therefore, the GISH has efficiently contributed for the analysis on the karyotypic stability of plant materials, indicating the best genotypes, and helping the assisted selection in different phases of crop improvement [9,14].…”