AFLP and SSR polymorphism in a Coffea interspecific backcross progeny [(C. heterocalyx × C. canephora) × C. canephora]

Abstract

An interspecific cross (BC 1) involving a species with one of the largest genomes in the Coffea genus [ Coffea heterocalyx (HET), qDNA = 1.74 pg] and a species with a medium-sized genome [ Coffea canephora (CAN), qDNA = 1.43 pg] was studied using two types of molecular markers, AFLP and SSR. One hundred and eighty eight AFLP bands and 34 SSR primer pairs were suitable for mapping. The total map length was 1,360 cM with 190 loci distributed in 15 linkage groups. The results were compared to those obtained previously on an interspecific BC 1 progeny involving a species with a medium-sized genome ( Coffea liberica var dewevrei, DEW) and a species with one of the smallest genomes ( Coffea pseudozanguebariae, PSE). They are discussed relative to three main points: (1) the relevance of the different marker types, (2) the genomic distribution of AFLP and SSR markers, and (3) the relation between AFLP polymorphism and genome size.

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

“…However, we wonder whether the same chromosomes always remained unpaired? Other markers, including SSRs, EST-SSRs, and cloned genes, are currently being developed for coffee trees (Poncet et al 2004(Poncet et al , 2006 and their mapping on interspecific progenies is under way (Campa et al 2003;Coulibaly et al 2003;Mahesh et al 2006;Bustamante-Porras et al 2007). Combined with BAC-FISH, these markers will enable precise identification of univalents.…”

SSR mining in coffee tree EST databases: potential use of EST–SSRs as markers for the Coffea genus

“…Polymerase chain reaction ampliWcations were carried out as described in Coulibaly et al (2003) and Poncet et al (2004) using a touchdown PCR proWle optimised for each set of primers: touchdown 60-55°C or touchdown 55-50°C. PCR products were detected on an IR 2 Automated DNA Sequencer (LI-COR, model 4200L-2, Lincoln, NE, USA) using an M13 primer coupled to the infrared tag IRD700 or IRD800 and after migration on 25 cm 6.5% KBplus (LI-COR, CAT# 827-05607) polyacrylamide gels.…”

“…Good crossspecies transferability and high genetic diversity were generally observed. However, only a handful of linkage maps have been constructed, including these markers (Lashermes et al 2001;Coulibaly et al 2003;N'Diaye et al 2006). These maps were mainly constructed using AFLP markers but their relevance for coVee tree breeding programs is limited.…”

Genetic diversity of Cuban pineapple germplasm assessed by AFLP Markers

“…AFLP markers (Vos et al 1995) have also been widely used to study diversity in several species such as Arabidopsis (Breyne et al 1999), coffee (Coulibaly et al 2003), Rubus (Marulanda et al 2007) and Jatropha curcas (Santos et al 2010). The technique has also been employed to identify varieties in pineapple (Leal et al ARTICLE EY Paz et al 1986) and carry out classical genetic mapping studies (Carlier et al 2004).…”