A cytogenetic map of common bean was built by in situ hybridization of 35 bacterial artificial chromosomes (BACs) selected with markers mapping to eight linkage groups, plus two plasmids for 5S and 45S ribosomal DNA and one bacteriophage. Together with three previously mapped chromosomes (chromosomes 3, 4, and 7), 43 anchoring points between the genetic map and the cytogenetic map of the species are now available. Furthermore, a subset of four BAC clones was proposed to identify the 11 chromosome pairs of the standard cultivar BAT93. Three of these BACs labelled more than a single chromosome pair, indicating the presence of repetitive DNA in their inserts. A repetitive distribution pattern was observed for most of the BACs; for 38% of them, highly repetitive pericentromeric or subtelomeric signals were observed. These distribution patterns corresponded to pericentromeric and subtelomeric heterochromatin blocks observed with other staining methods. Altogether, the results indicate that around half of the common bean genome is heterochromatic and that genes and repetitive sequences are intermingled in the euchromatin and heterochromatin of the species.Electronic supplementary materialThe online version of this article (doi:10.1007/s10577-010-9129-8) contains supplementary material, which is available to authorized users.

The heterochromatin banding patterns in the karyotypes of 17 species belonging to 15 genera of Rutaceae subfamily Aurantioideae (= Citroideae) were analyzed with the fluorochromes chromomycin (CMA) and 4'-6-diamidino-2-phenylindole-2HCl (DAPI). All species were diploids, except one tetraploid (Clausena excavata) and two hexaploids [Glycosmis parviflora agg. (aggregate) and G. pentaphylla agg.]. There are only CMA/DAPI bands, including those associated with the nucleolus. Using recent cpDNA (chloroplast DNA) sequence data as a phylogenetic background, it becomes evident that generally more basal genera with rather plesiomorphic traits in their morphology, anatomy, and phytochemistry exhibit very small amounts of heterochromatin (e.g., Glycosmis, Severinia, Swinglea), whereas relatively advanced genera from different clades with more apomorphic characters display numerous large CMA bands (e.g., Merrillia, Feroniella, Fortunella). Heterochromatin increase (from 0.7 to 13.7%) is interpreted as apomorphic. The bands are mostly located in the larger chromosomes and at telomeric regions of larger arms. However, one of the largest chromosome pair has been conserved throughout the subfamily with only very little heterochromatin. The heterochromatin-rich patterns observed in different clades of Aurantioideae appear quite similar, suggesting a kind of parallel chromosomal evolution. In respect to the current classification of the subfamily, it is proposed to divide Murraya s.l. (sensu lato) into Bergera and Murraya s.s. (sensu stricto) and to place the former near Clausena into Clauseneae s.s. and the latter together with Merrillia into Citreae s.l. The subtribes recognized within Clauseneae s.s. and Citreae s.l. appear heterogeneous and should be abandoned. On the other hand, the monophyletic nature of the core group of Citrinae, i.e., the Citrus clade with Eremocitrus, Microcitrus, Clymenia, Poncirus, Fortunella, and Citrus, is well supported.

Most species of Citrus and related genera display a similar karyotype with 2n = 18 and a variable number of terminal heterochromatic blocks positively stained with chromomycin A(3) (CMA(+) bands). Some of these blocks are 45S rDNA sites, whereas others may correspond to the main GC-rich satellite DNA found in several Citrus species. In the present work, the distribution of the 45S rDNA and the main satellite DNA isolated from C. sinensis (CsSat) were investigated by in situ hybridization in seven species of Citrus, two species of closely related genera (Fortunella obovata and Poncirus trifoliata) and four species of the subfamily Aurantioideae, which were less related to Citrus (Atalantia monophylla, Murraya paniculata, Severinia buxifolia, and Triphasia trifolia). In Citrus, Fortunella, and Poncirus, most CMA(+) bands colocalized only with CsSat sites, whereas others colocalized only with rDNA sites. However, some of these species displayed a few CMA(+) bands that colocalized with sites of both probes and other CMA(+) bands that did not colocalized with any of the probes. On the other hand, in the four species less related to Citrus, no CsSat signal was found on chromosomes. On Southern blot, the CsSat probe hybridized with genomic DNA from Citrus, Fortunella, and Poncirus at high stringency only, while under the less stringent conditions, it also hybridized with distantly related species. Therefore, CsSat sequences are the principal component of the heterochromatic blocks of Citrus, Poncirus, and Fortunella, whereas CsSat-like sequences seem to be widespread in the subfamily Aurantioideae. These data further suggest that the variable number of terminal CMA(+) bands observed on chromosomes of Citrus and related genera are probably the consequence of amplification or reduction in the number of CsSat-like sequences distributed on chromosome termini, paralleled by mutation and homogenization events, as proposed by the library hypothesis.

The common bean (Phaseolus vulgaris) and lima bean (P. lunatus) are among the most important legumes in terms of direct human consumption. The present work establishes a comparative cytogenetic map of P. lunatus, using previously mapped markers from P. vulgaris, in association with analyses of heterochromatin distribution using the fluorochromes chromomycin A3 (CMA) and 4',6-diamidino-2-phenylindole (DAPI) and localization of the 5S and 45S ribosomal DNA (rDNA) probes. Seven BACs selected from different common bean chromosomes demonstrated a repetitive pericentromeric pattern corresponding to the heterochromatic regions revealed by CMA/DAPI and could not be mapped. The subtelomeric repetitive pattern observed for BAC 63H6 in most of the chromosome ends of common bean was not detected in lima bean, indicating lack of conservation of this subtelomeric repeat. All chromosomes could be identified and 16 single-copy clones were mapped. These results showed a significant conservation of synteny between species, although change in centromere position suggested the occurrence of pericentric inversions on chromosomes 2, 9 and 10. The low number of structural rearrangements reflects the karyotypic stability of the genus.