Comparison of the Coffea canephora and C. arabica karyotype based on chromosomal DNA content

Abstract

Nuclear genome size has been measured in various plants, seeing that knowledge of the DNA content is useful for taxonomic and evolutive studies, plant breeding programs and genome sequencing projects. Besides the nuclear DNA content, tools and protocols to quantify the chromosomal DNA content have been also applied, expanding the data about genomic structure. This study was conducted in order to calculate the Coffea canephora and Coffea arabica chromosomal DNA content, associating cytogenetic methodologies with flow cytometry (FCM) and image cytometry (ICM) tools. FCM analysis showed that the mean nuclear DNA content of C. canephora and C. arabica is 2C = 1.41 and 2.62 pg, respectively. The cytogenetic methodology provided prometaphase and metaphase cells exhibiting adequate chromosomes for the ICM measurements and karyogram assembly. Based on cytogenetic, FCM and ICM results; it was possible to calculate the chromosomal DNA content of the two species. The 1C chromosomal DNA content of C. canephora ranged from 0.09 (chromosome 1) to 0.05 pg (chromosome 11) and C. arabica from 0.09 (chromosome 1) to 0.03 pg (chromosome 22). The methodology presented in this study was suitable for DNA content measuring of each chromosome of C. canephora and C. arabica. The cytogenetic characterization and chromosomal DNA content analyses evidenced that C. arabica is a true allotetraploid originated from a cross between Coffea diploid species. Besides, the same analyses also reinforce that C. canephora is a possible progenitor of C. arabica.

Development and validation of SSR markers for Coffea arabica L.

“…Garner (2002) observed that the percentage of SSR primers that do not produce PCR products is high and positively correlated to the size of the genomes. We found, however, that the conversion rate in C. arabica (93.7%) was higher than in C. canephora (75.8%, Hendre et al 2008), nevertheless the double of the size of C. arabica genome, respectively, 2,56x10 9 bp and 1,38x10 9 bp (Clarindo and Carvalho 2009). Conversion rates similar of C. arabica were reported for Corchorus capsularis (91.0%, Mir et al 2008), Lolium multiflorum (90.4%, Hirata et al 2006), Cucurbitaceas (94.0%, Gong et al 2008), Humulus lupulus (92.2%, Stajner et al 2005), and Avena sativa (95.5%, Li et al 2000).…”

Genome size, base composition and karyotype of Carica papaya L.

“…Subsequently, 0.5 mL of the same buffer was added and the homogenate was filtered in a 30 μm nylon filter (Partec ® ) into a 2.0 microcentrifuge tube (Eppendorf ® ), and then centrifuged at 100 g for 5 min. The supernatant was poured out and the pellet was resuspended and incubated for 10 min in a 100 μL OTTO I lysis buffer [13].…”

Cytogenetic and flow cytometry data expand knowledge of genome evolution in three Coffea species

“…arabica originated from a cross between two diploid species of the genus Coffea with similar genomes (Raina et al 1998;Yu et al 2011). Some diploid species have been especially pointed out as possible progenitors of this species, for instance, C. canephora (Lashermes et al 1997;Clarindo and Carvalho 2009;Yu et al 2011), and C. congensis (Lashermes et al 1997;Raina et al 1998). However, more recent evolutive data, obtained by Hamon et al (2009) from 16 species of Coffea, support the view of Raina et al (1998) that C. arabica is a hybrid of Coffea eugenioides and C. congensis.…”

“…A. Froehner Carvalho 2006, 2009) and C. arabica Carvalho 2008, 2009), and accurate karyograms were assembled for these species. Karyomorphological features indicated that C. arabica is a true allotetraploid species Carvalho 2008, 2009), and C. canephora may be one of its diploid progenitors (Clarindo and Carvalho 2009). Despite these improvements, assembling the karyotype of other Coffea species is important to accomplish evolutive studies and identify the progenitor species of C. arabica, which is a matter of general interest (Clarindo and Carvalho 2009).…”