High resolution synteny maps allowing direct comparisons between the coffee and tomato genomes

Abstract

Tomato (Solanum lycopersicum) and coffee (Coffea canephora) belong to the sister families Solanaceae and Rubiaceae, respectively. We report herein the mapping of a common set of 257 Conserved Ortholog Set II genes in the genomes of both species. The mapped markers are well distributed across both genomes allowing the first syntenic comparison between species from these two families. The majority (75%) of the synteny blocks are short (<4 cM); however, some extend up to 50 cM. In an effort to further characterize the synteny between these two genomes, we took advantage of the available sequence for the tomato genome to show that tomato chromosome 7 is syntenic to half of the two coffee linkage groups E and F with the putative break point in tomato localized to the boundary of the heterochromatin and euchromatin on the long arm. In addition to the new insight on genome conservation and evolution between the plant families Solanaceae and Rubiaceae, the comparative maps presented herein provide a translational tool by which coffee researchers may take benefit of DNA sequence and genetic information from tomato and vice versa. It is thus expected that these comparative genome information will help to facilitate and expedite genetic and genomic research in coffee.

Improving the quality of African robustas: QTLs for yield- and quality-related traits in Coffea canephora

“…Another map has been developed using doubled haploids for the analysis of segregation distortion . Recently, a map has been developed (Lefebvre-Pautigny et al 2010) from a segregating population of 93 individuals resulting from a cross between heterozygous genotypes, using mainly RFLP, simple sequence repeat (SSR), and expressed sequence tag (EST)-SSR markers. Maps were also developed for interspecific crosses (Akaffou et al 2003;Coulibaly et al 2003;Ky et al 2000b;N'Diaye et al 2007) to identify QTLs involved in contrasting traits between wild species using mainly AFLP markers.…”

Identification and mapping of conserved ortholog set (COS) II sequences of cacao and their conversion to SNP markers for marker-assisted selection in Theobroma cacao and comparative genomics studies

“…We were therefore interested in taking advantage of the rapid advances being made in the sequencing of genomes from various plant species to develop a set of genetic markers for cacao that were based on single-copy genes. Because single-copy conserved orthologs have been well defined and used for mapping in a variety of plants (Wu et al 2009a, b;Lefebvre-Pautigny et al 2010), we undertook this study of them in cacao. Our hope was that, as more COSII sequences are identified in other crop plants and co-located with existing QTLs, we could use SNP markers for those loci for MAS in cacao.…”

“…In a further refinement, Wu et al (2006) identified 2,869 single-copy orthologs, referred to as COSII sequences, that are found in most plant species and are particularly useful for evolutionary and systematic studies. COS sequences have been studied in tree species (Krutovsky et al 2007;Cabrera et al 2009) and used as universal markers in the Asteraceae (Chapman et al 2007) and for synteny mapping in tomato, eggplant (Wu et al 2009b), pepper (Wu et al 2009a), coffee (Lefebvre-Pautigny et al 2010), and the Rosaceae (Cabrera et al 2009). We therefore set out to identify and map COSII markers in cacao.…”

Comparison of three QTL detection models on biochemical, sensory, and yield characters in Coffea canephora

“…The SSRs segregating F2 type (a/b×c/d or e/f×e/g) were chosen in priority due to their higher levels of genetic information. The SSR genotyping was performed according to Lefebvre-Pautigny et al (2010).…”