Completely Distinguishing Individual A-Genome Chromosomes and Their Karyotyping Analysis by Multiple Bacterial Artificial Chromosome–Fluorescence in Situ Hybridization

Abstract

Twenty bacterial artificial chromosome (BAC) clones that could produce bright signals and no or very low fluorescence in situ hybridization (FISH) background were identified from Gossypium arboreum cv. JLZM, and G. hirsutum accession (acc.) TM-1 and 0-613-2R. Combining with 45S and 5S rDNA, a 22-probe cocktail that could identify all 13 G. arboreum chromosomes simultaneously was developed. According to their homology with tetraploid cotton, the G. arboreum chromosomes were designated as A1-A13, and a standard karyotype analysis of G. arboreum was presented. These results demonstrated an application for multiple BAC-FISH in cotton cytogenetic studies and a technique to overcome the problem of simultaneous chromosome recognition in mitotic cotton cells.

Chromosome-Specific Painting in Cucumis Species Using Bulked Oligonucleotides

“…Most common FISH probes used in chromosome identification have been repetitive DNA elements (Mukai et al 1993;Fransz et al 1998;Lim et al 2000;Kato et al 2004;Fonseca et al 2010;Xiong et al 2011;Chester et al 2012Chester et al , 2013 or large genomic DNA clones such as BACs (Dong et al 2000;Cheng et al 2001;Kim et al 2002;Wang et al 2008;Findley et al 2010). It often takes a significant effort to develop such probes or probe sets to identify all chromosomes in each species.…”

Individual chromosome identification, chromosomal collinearity and genetic-physical integrated map in <i>Gossypium darwinii</i> and four D genome cotton species revealed by BAC-FISH

“…BAC- FISH, which probes are BAC clones screened from BAC library with genetic molecular markers, has proved to be a high efficient method to identify plant chromosomes (Cheng et al, 2001;Dong et al, 2000;Gan et al, 2011;Hasterok et al, 2006;Kim et al, 2002;Kim et al, 2009;Kulikova et al, 2001;Wang et al, 2007Wang et al, , 2008. With the improvement of cotton genomics research, cotton cytogenetics has made a lot of progress and chromosome recognition of several species has been finished, including G. hirsutum , G. arboreum (Wang et al, 2008), G. thurberi and G. trilobum and D subgenome of G. barbadense (Gan et al, 2011). In present study, the relative chromosomal positions of centromere and the individual chromosome-specific BAC clones have been successfully located to the corresponding chromosomes in D d , D 3k , D 3d , D 2-1 and D 4 using D genome centromerespecific and chromosome-specific BAC clone.…”

“…Chromosomes of G. hirsutum were identified by BAC-FISH and named as A01-13 and D01-13 for A and D subgenome, respectively (Wang et al, 2006). With the same process, chromosomes of G. arboreum were assigned and named A01-13 (Wang et al, 2008). The chromosome designations of the two species were both linked to genetic map, however, it seemed to be confused in different species.…”

“…Therefore, a simplified and reproducible karyotype method for identifying individual chromosomes in plants is necessarily to be developed. Recently, fluorescence in situ hybridization (FISH), which is used to localize DNA probes and identify chromosomes or chromosomal segments, have been adapted successfully to identify the chromosome for many plant species, including rice, potato, cotton and so on (Cheng et al, 2001;Dong et al, 2000;Gan et al, 2011;Kim et al, 2002;Ma et al, 2005;Peng et al, 2012;Wang et al, 2007Wang et al, , 2008Zhang et al, 2004). This technique has been developed from highly repeated copies sequences probe to singlecopy probe (Desel et al, 2001;Zhu et al, 1999) and from single-color to multiple-color (Tang et al, 2009).…”

Histone Modifications Define Expression Bias of Homoeologous Genomes in Allotetraploid Cotton

“…S3, C and D). There are three 45S rDNA loci, two major and one minor loci, in G. arboreum (in some cases, minor loci could not be detected by fluorescence in situ hybridization (FISH; Hanson et al, 1995;Wang et al, 2008). H3K27me2 antibody signals were colocalized with one of the rDNA loci, but not with the other rDNA loci (Supplemental Fig.…”