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

Molecular combing and its application in clinical settings

Molecular combing technology (MCT) is an effective means for stretching DNA molecules and making them thus accessible for in situ studies. MCT uses the force exerted in the process of liquid flow via surface tension to stretch DNA molecules and spread them on solid surfaces, i.e. glass cover slips. Many DNA molecules can be stretched at the same time in parallel and neatly arranged side-by-side, making the approach convenient for statistical analysis. Accordingly, DNA replication and transcription can be studied at the single molecule level. In this paper, the principle, experimental methods, important applications, advantages and shortcuts of MCT in medical field are presented and discussed.

Production and First Assessment of Iranian Secondary Tritipyrum Genotypes by GISH and AFLP Markers

Background

Non-Iranian Primary Tritipyrum (2n=6x=42, AABBE^bE^b) set seed after Triticale (2n=6x=42, AABBRR) and Tritordeum (2n=6x=42, AABBH^cH^c) but, due to a few undesirable agronomic traits, it cannot fulfil the commercial expectations of farming.

Objectives

To remove these deficiencies, six hexaploid Tritipyrum lines were crossed with four Iranian bread wheat cultivars which led to the production of 107 (F₁), 479 (F₂), 768 (F₃), and 1539 (F₄) Iranian Secondary Tritipyrum Genotypes (ISTG) seeds. This study was carried out for selecting the plants potentially carry the 5E^b chromosome/s and are good candidates for salt tolerant by GISH and RFLP markers.

Materials and Methods

The procedure involved extracting the total DNA content of 209 plants, including non-Iranian primary Tritipyrum lines, Iranian wheat cultivars, Chinese Spring addition, and substitution lines for 5E^b and Iranian secondary Tritipyrum genotypes (ISTG: F₁, F₂, F₃, F₄). Genomic in situ Hybridization (GISH) on mitotic spreads of fertile new Iranian secondary Tritipyrum genotypes (ISTG) was carried out to demonstrate the feasibility of single E^b chromosomes. There were three trials of 18 Fragment Length Polymorphism (AFLP) EcoRI/MseI primers to identify the presence of the 5E^b chromosome in 105 ISTG plants, along with four wheat addition lines and substitution lines for the 5E^b chromosome.

Results

GISH on mitotic spreads demonstrated the feasibility of producing 75 plants out of 105 fertile new Iranian secondary Tritipyrum genotypes (ISTG) with 0-14 single E^b chromosomes. Among the mentioned markers, only the E₃₆/M₅₉ marker showed 43, 50, 30 and 47 identical bands, respectively, in contrast to 53 expected bands in all plants with the 5E^b chromosome which indicated 21, 33, 9 and 6 out of 75 ISTG plants, respectively, with the 5E^b chromosome.

Conclusion

This study indicated that 69 ISTG Tritipyrum plants were potentially carry the 5E^b chromosome/s and are good candidates for salt tolerant tests in comparison with Iranian modern bread wheat cultivars.

Technical Review: Cytogenetic Tools for Studying Mitotic Chromosomes

Significant advances in chromosome preparation and other techniques have greatly increased the potential of plant cytogenetics in recent years. Increase in longitudinal resolution using DNA extended fibers as well as new developments in imaging and signal amplification technologies have enhanced the ability of FISH to detect small gene targets. The combination of fluorescence in situ hybridization with immunocytochemistry allows the investigation of cell events, chromosomal rearrangements and chromatin features typical for plant nuclei. Chromosome manipulation techniques using microdissection and flow sorting have accelerated the analysis of complex plant genomes. Together, the different cytogenetic approaches are invaluable for the unravelling of detailed structures of plant chromosomes, which are of utmost importance for the study of genome properties, DNA replication and gene regulation. In this technical review, different cytogenetic approaches are discussed for the analysis of plant chromosomes, with a focus on mitotic chromosomes.

Ribosomal DNA locus variation and REMAP analysis of the diploid and triploid complexes of Lilium lancifolium

Lilium lancifolium Thunb. (2n = 2x = 24) is a cytologically conspicuous species with both diploids and triploids in nature. Cytological and molecular genetic analyses were carried out in both diploids and triploids that were collected from 55 geographical locations in Korea, Japan, and China. While the 5S rRNA gene loci were located at duplicated loci on the long arm of chromosome 2, the 45S rRNA gene loci were present in chromosomes 1, 2, 4, 6, 7, and 11. While the loci on chromosomes 1 and 7 were constant, the loci on chromosomes 2, 4, 6, 7, and 11 were variable in some plants so that the L. lancifolium accessions were grouped into 7 cytotypes in diploids and 12 cytotypes in triploids. REMAP marker analysis revealed that the diploids were classified into seven clusters, and the triploids were classified into a large cluster. Geographic, cytological, and genetic differentiations were not related in both the diploid and triploid accessions of L. lancifolium. Thus, current genetic variations occurred prior to the geographic differentiation in both diploids and triploids, and the 45S rDNA cytotype variations occurred after geographic differentiation in the current habitats of L. lancifolium.

Visualization of large elongated DNA molecules

Long and linear DNA molecules are the mainstream single-molecule analytes for a variety of biochemical analysis within microfluidic devices, including functionalized surfaces and nanostructures. However, for biochemical analysis, large DNA molecules have to be unraveled, elongated, and visualized to obtain biochemical and genomic information. To date, elongated DNA molecules have been exploited in the development of a number of genome analysis systems as well as for the study of polymer physics due to the advantage of direct visualization of single DNA molecule. Moreover, each single DNA molecule provides individual information, which makes it useful for stochastic event analysis. Therefore, numerous studies of enzymatic random motions have been performed on a large elongated DNA molecule. In this review, we introduce mechanisms to elongate DNA molecules using microfluidics and nanostructures in the beginning. Secondly, we discuss how elongated DNA molecules have been utilized to obtain biochemical and genomic information by direct visualization of DNA molecules. Finally, we reviewed the approaches used to study the interaction of proteins and large DNA molecules. Although DNA-protein interactions have been investigated for many decades, it is noticeable that there have been significant achievements for the last five years. Therefore, we focus mainly on recent developments for monitoring enzymatic activity on large elongated DNA molecules.

Sample preparation for single cell transcriptomics: essential oil glands in Citrus fruit peel as an example

Many plant natural products are synthesized in specialized cells and tissues. To learn more about metabolism in these cells, they have to be studied in isolation. Here, we describe a protocol for the isolation of epithelial cells that surround secretory cavities in Citrus fruit peel. Cells isolated using laser microdissection are suitable for RNA isolation and downstream transcriptome analyses.

Variability of stomata and 45S and 5S rDNAs loci characteristics in two species of Anthoxanthum genus: A. aristatum and A. odoratum (Poaceae)

Diploid Anthoxanthum odoratum and tetraploid A. aristatum were compared with respect to stomatal guard cell lengths, and stomatal density at adaxial and abaxial surfaces of the lamina. Further, the genome size of both species was determined by flow cytometry, and the number as well as the chromosomal distribution of 5S and 45S rDNAs were examined using FISH with ribosomal DNA (rDNA) probes. The average length of stomatal guard cells in A. odoratum was shown to be greater than that for A. aristatum, but the ranges overlapped. Moreover, reduction in stomatal frequency was found at higher ploidy levels.The genome size was 6.863 pg/2C DNA for A. aristatum and 13.252 pg/2C DNA for A. odoratum. A. aristatum has four sites of 5S rDNA in its root-tip meristematic cells, whereas A. odoratum has six. Both species have six sites of 45S rDNA. Chromosomal localization of the rDNA varied, which suggests that chromosome rearrangements took place during Anthoxanthum genome evolution.

Comparative sequence analysis of the Ghd7 orthologous regions revealed movement of Ghd7 in the grass genomes

Ghd7 is an important rice gene that has a major effect on several agronomic traits, including yield. To reveal the origin of Ghd7 and sequence evolution of this locus, we performed a comparative sequence analysis of the Ghd7 orthologous regions from ten diploid Oryza species, Brachypodium distachyon, sorghum and maize. Sequence analysis demonstrated high gene collinearity across the genus Oryza and a disruption of collinearity among non-Oryza species. In particular, Ghd7 was not present in orthologous positions except in Oryza species. The Ghd7 regions were found to have low gene densities and high contents of repetitive elements, and that the sizes of orthologous regions varied tremendously. The large transposable element contents resulted in a high frequency of pseudogenization and gene movement events surrounding the Ghd7 loci. Annotation information and cytological experiments have indicated that Ghd7 is a heterochromatic gene. Ghd7 orthologs were identified in B. distachyon, sorghum and maize by phylogenetic analysis; however, the positions of orthologous genes differed dramatically as a consequence of gene movements in grasses. Rather, we identified sequence remnants of gene movement of Ghd7 mediated by illegitimate recombination in the B. distachyon genome.