An integrated map of Oryza sativa L. chromosome 5

Abstract

The developments of molecular marker-based genetic linkage maps are now routine. Physical maps based on contigs of large insert genomic clones have been established in several plant species. However, integration of genetic, physical, and cytological maps is still a challenge for most plant species. Here we present an integrated map of rice (Oryza sativa L.) chromosome 5, developed by fluorescence in situ hybridization mapping of 18 bacterial artificial chromosome (BAC) clones or PI-derived artificial chromosome (PAC) clones on meiotic pachytene chromosomes. Each BAC/PAC clone was anchored by a restriction fragment length polymorphism marker mapped to the rice genetic linkage map. This molecular cytogenetic map shows the genetic recombination and sequence information of a physical map, correlated to the cytological features of rice chromosome 5. Detailed comparisons of the distances between markers on genetic, cytological, and physical maps, revealed the distributions of recombination events and molecular organization of the chromosomal features of rice chromosome 5 at the pachytene stage. Discordance of distances between the markers was found among the different maps. Our results revealed that neither the recombination events nor the degree of chromatin condensation were evenly distributed along the entire length of chromosome 5. Detailed comparisons of the correlative positions of markers on the genetic, cytological, and physical maps of rice chromosome 5 provide insight into the molecular architecture of rice chromosome 5, in relation to its cytological features and recombination events on the genetic map. The prospective applications of such an integrated cytogenetic map are discussed.

Chromosome pairing affinities in interspecific hybrids reflect phylogenetic distances among lady's slipper orchids (Paphiopedilum)

“…PMCs were macerated with an enzyme mixture containing 6 % cellulose (Onoauka R-10, Yakult Honsha, Japan) and 6 % pectinase (Sigma Chemical Co., St Louis, MO.) in 75 m m KCl, pH 4·0 at 37 °C for 30 min then squashed in 1 % aceto-carmine according to the method of Kao et al (2006). Slides with good quality MI spreads were stored at –80 °C for GISH and FISH analysis.…”

Expression and regulation of two novel anther-specific genes in Lilium longiflorum

“…DIG-labeled RNA probes were synthesized using a DIG RNA labeling kit (SP6/T7) (Roche Diagnostics GmbH, Penzberg, Germany). In situ hybridization was carried out essentially according to the DNA in situ hybridization protocol previously described in Kao et al (2006) with some modifications. Hybridization sites were immunologically detected by using an alkaline phosphataseconjugated anti-DIG antibody dilute in 1:500 with 1 Â TNB buffer [0.1 M Tris-HCl, pH 7.5, 0.15 M NaCl and 0.5% blocking reagent (Roche Diagnostics GmbH, Penzberg, Germany)].…”

An integrated molecular cytogenetic map of Cucumis sativus L. chromosome 2

“…Not only do the pachytene chromosomes provide superior mapping resolution compared to somatic metaphase chromosomes, but the euchromatin and heterochromatin features can be visualized on pachytene chromosomes, thereby allowing DNA probes to be mapped to specific euchromatic or heterochromatic regions. To date, FISH-based cytogenetic maps on pachytene chromosomes have been developed in A. thaliana for chromosome 4 [10], maize chromosome 9 [11,12], potato chromosome 6 [13,14], Brassica oleracea chromosome 6 [15], rice chromosomes 5 and 10 [4,16], tomato chromosomes 1, 2 and 6 [17-19], soybean chromosome 19 [20], cotton chromosomes 12A and 12D [21] and for all the Sorghum chromosomes [22,23]. We previously reported integrated cytogenetic maps for cucumber chromosomes 6 and 7 [24].…”