Coffee genome sizes were estimated using flow cytometry. Four main conclusions were drawn: (i) the genome size of diploid coffee varies from 1.03 (C. racemosa) to 1.76 pg (C. humilis) (Cros et al., 1995, 1998; Hamon et al., 2009; Noirot et al., 2003); (ii) species native to dry areas (mostly in East Africa) have a smaller genome size (<1.3 pg) than those native to evergreen forest (1.3 < x < 1.76 pg); (iii) a difference in genome size greater than 0.25 pg is associated with high rates failure in crosses and marked sterility of hybrids; (iv) by coupling flow cytometry tools with cytometry images, the 1C nuclear DNA content of C. canephora and C. arabica was evaluated and results confirmed the true allotetraploidy of C. arabica (Clarindo and Carvalho, 2008).
As far as chromosome morphology is concerned, early observations clearly showed that diploid coffee chromosomes (2n = 2x = 22) are small, metacentric and submetacentric (Sybenga, 1960). For a long time, the limited number of metaphases in root meristem cells has strongly limited coffee cytogenetic investigations. But recently, the development of pachytene chromosome analysis (Pinto-Maglio and Da Cruz, 1987, 1998) and improved methods of chromosome preparations (Clarindo and Carvalho, 2008) enabled an overview of heterochromatin versus euchromatin distribution along the chromosomes and led to karyotyping of both C. arabica and C. canephora.
FISH and heterochromatin staining techniques have been used for coffee (Barre et al., 1998; Hamon et al., 2009; Raina et al., 1998). These techniques enabled improved resolution for the physical mapping of ribosomal genes and heterochromatin AT- or GC-rich regions. This approach, which was extended to a large set of Coffea species (Hamon et al., 2009), showed that there is a correlation between the number of secondary constrictions (one or two satellite chromosomes (SAT-chromosomes)), the number of rDNA sites (5S and 18S), the geographic origin of the species (West and Central Africa vs. East Africa) and the genome size. However, it was impossible to assign a causality relationship between these traits and rDNA distribution patterns.
FISH techniques also permitted visual location of BAC clones on C. arabica (Herrera et al., 2007) and C. canephora chromosomes (Guyot et al., 2009). Combined BAC-FISH technology for use on pachytene chromosomes is a very promising tool for complementary studies of the organization of the coffee tree genomes, as well as for the comparison of species genetic relationships and of physical maps.
Genomic in situ hybridization (GISH) was used to study the genome organization of interspecific hybrids. In interspecific F1 hybrids, Barre et al. (1998) demonstrated that there is a linear relationship between the number of chromosomes of one parental species and the nuclear DNA content. It was also helpful to analyze the DNA content of the backcrossed derived hybrids and to monitor species evolution of C. Arabica. Lashermes et al. (1999) focused on the origin of the tetraploid Arabica and concluded on the allopolyploid origin of the species. Hamon et al. (2009) provided clear cytogenetic evidence that one C. arabica progenitor is native to East Africa and the other to West or Central Africa. More detailed analysis of the organization of the coffee genome will certainly be undertaken in the very near future by combining BAC-FISH, DNA fiber, FISH and genetic maps.
The organization of gene-rich regions along C. canephora chromosomes remains unknown. However, previous cytological observations in C. canephora and C. arabica chromosomes by Pinto-Maglio and Da Cruz (1987, 1998) revealed the presence of intensely and lightly stained patterns in some regions indicating an overall chromosome organization in condensed heterochromatin and decondensed euchromatin regions. Similarly to the architecture of Medi-cago and tomato chromosomes (Kulikova et al., 2001; Lin et al., 2005), C. canephora heterochromatin regions are mainly located around centromeric regions, while euchromatin forms the distal parts of chromosomes. As for other studied plants, it is expected to find gene-rich regions in the distal euchromatine of the C. canephora genome.
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