Physical mapping of rDNA and heterochromatin in chromosomes of 16 Coffea species: A revised view of species differentiation

Abstract

The chromosome organization among 15 wild diploid Coffea species and cultivated tetraploid C. arabica was determined by fluorochrome banding (CMA, DAPI) and double fluorescence in-situ hybridization (FISH) of 5S and 18S rDNA achieved on the same chromosome plates. Two to five chromosome pairs (plus one putative chromosome B) are marked. Overall, there are two SAT-chromosome pairs for East African species and one for the Malagasy and the West and Central African species. 18S rDNA loci are telomeric and strongly marked the SAT-chromosome pairs. Generally, only one pericentromeric 5S rDNA locus characterized East African species, while an additional minor locus co-localized with the 18S rDNA-SAT locus for the Malagasy species and West and Central African species. A combination of rDNA FISH plus CMA and DAPI banding patterns enables identification of almost all the species, even those for which the genetic or botanical status is still being discussed. C. arabica clearly appears to be an allotetraploid species, including one genome from East Africa and one from West and Central Africa. However, since the minor 5S rDNA-SAT locus present in West/Central African genomes is not detected, two evolutionary hypotheses could be put forward for C. arabica. Considering only the diploid species, global trends are obvious in rDNA signal patterns, genome size variations, and geographic distribution of the species, but there are no clear evolutionary trends. However, complex interactions between these factors and environmental growing conditions exist, which have resulted in loss and gain of rDNA loci and probably also in copy repeat number variations in each rDNA family.

A Karyological Study in Some Species of Coffea L. and in the Closest Relative Psilanthus travancorensis (Wight & Arn.) J.-F. Leroy

“…2), only one pair was marked after silver impregnation, which presumably would be number three, as observed by Pierozzi et al (1999) in C. canephora and in C. dewevrei. The presence of only one chromosome pair carrying nucleolar organizer region site in C. canephora, C. kapakata and P. travancorensis, has also been reported by Lombelo and Pinto-Maglio (2004 a, b) as well as in C. dewevrei by Hamon et al (2009), with the in situ hybridization with 45S rDNA probe. Conversely, C. racemosa and C. salvatrix showed silver impregnation (NOR band) in both chromosome pairs.…”

“…salvatrix displayed the highest mean values for THCL, χchrom, S (µm) and S%, however, the lowest valtempt to visualize and count the mitotic chromosomes of the ovules. Thenceforth, the studies developed in the genus of species ranged from the identification of the most probable genomes involved in the Arabica origin (Pinto-Maglio and Cruz, 1987), the establishment of the first karyogram and ideogram for C. arabica based on pachytene chromosomes (Pinto-Maglio and Cruz, 1998), following studies in several diploid species to determine the nuclear content (Cros et al, 1998), the heterochromatin localization and quantification in mitotic chromosomes (Pierozzi et al, 1999) and subsequently the heterochromatin molecular composition, as reviewed by Pinto-Maglio (2006) and Hamon et al (2009). The first approaches in coffee chromosome studies however concerned the establishment of chromosome number which led to the finding that wild species are diploid (2n=22) while the Arabica varieties and cultivars are predominantly tetraploid (2n=44) with several hexaploid (2n=66) and octoploid (2n=88) exceptions (Krug, 1934(Krug, , 1945.…”

“…A comprehensive median ideogram however, with the localization of centromere and heterochromatin at chromosomes after orcein and C-banding, was obtained by Pierozzi et al (1999) for C. canephora and C. dewevrei. Later, the characterization at cytomolecular level using fluorochromes and in situ hybridization with rDNA probes was performed by Lombello and Pinto-Maglio (2004 a, b, c) and afterwards by Hamon et al (2009) in some coffee species which showed one to two pairs of chromosomes carrying rDNA sites. Despite these efforts, few diploid species have some chromosome morphometric information or an average ideogram based on mitotic chromosome measures with centromere, secondary constriction and satellite segment positioned (Pierozzi et al, 1999;Pierozzi and Silvarolla, 2011).…”

Characterization and physical mapping of nuclear ribosomal RNA (rRNA) genes in the haploid gametophytes of Saccharina japonica (Phaeophyta)

“…However, using the sensitive fluorescence in situ hybridization (FISH) technique, especially with nuclear ribosomal RNA (rRNA) genes as probes, has been proven to be efficient for the investigation of species with small or similarly sized chromosomes (Leitch and Heslop-Harison, 1992;Garcia et al 2012). Thus, this enables the identification and discrimination of different chromosomes within and between chromosome complements (Hamon et al 2009). …”

Orcein, C- and NOR-banding on mitotic chromosomes of some wild diploid coffee species (CoffeaL.)

“…Bouharmont (1959Bouharmont ( , 1963, Pinto-Maglio and Cruz (1998), Campa et al (2003), Lombello and Pinto-Maglio (2004a, 2004b, 2004c, Hamon et al (2009) and Razafinarivo et al (2012). The studies regarding the total amount of DNA showed similarities between C. congensis and C. liberica (1.53 pg/1.54 pg and 1.59 pg, respectively) and also between C. eugenioides and C. stenophylla (1.36 pg/1.45 pg and 1.28 pg, respectively), despite the differences between these two pairs of species (Cros et al 1994;Noirot et al 2003;Razafinarivo et al 2012).…”