AFLP analysis of genetic diversity within and among Coffea arabica cultivars

Abstract

Genetic diversity of Coffea arabica cultivars was estimated using amplified fragment length polymorphism (AFLP) markers. Sixty one Coffea accessions composed of six arabica cultivars, including Typica, Bourbon, Catimor, Catuai, Caturra and Mokka Hybrid, plus two diploid Coffea species, were analyzed with six EcoRI- MseI primer combinations. A total of 274 informative AFLP markers were generated and scored as binary data. These data were analyzed using cluster methods in the software package NTSYSpc. The differences among cultivars at the DNA level were small, with an average genetic similarity of 0.933. Most accessions within a cultivar formed a cluster, although deviant samples occurred in five of the six cultivars examined due to residual heterozygosity from ancestral materials. Among the six cultivars fingerprinted, the highest level of genetic diversity was found within the cultivar Catimor, with an average genetic similarity of 0.880. The lowest level was found within Caturra accessions, with an average genetic similarity of 0.993. Diversity between C. arabica and two other Coffea species, Coffea canephora and Coffea liberica, was also estimated with average genetic similarities of 0.540 and 0.413, respectively, suggesting that C. canephora is more closely related to C. arabica than is C. liberica. The genetic variation among arabica cultivars was similar to the variation within cultivars, and no cultivar-specific DNA marker was detected. Although arabica cultivars appear to have a narrow genetic base, our results show that sufficient polymorphism can be found among some arabica cultivars with a genetic similarity as low as 0.767 for genetic/QTL mapping and breeding. The assessment of genetic diversity among arabica cultivars provided the necessary information to estimate the potential for using marker-assisted breeding for coffee improvement.

Construction of a genetic map for arabica coffee

“…DNA fingerprinting of arabica coffee cultivars has shown very low genetic diversity, which has been attributed to the restricted number of starting ancestral plants and the reproductive consequence of self-pollination Steiger et al 2002). This is confirmed in our present linkage map.…”

“…This is confirmed in our present linkage map. Although Catimor and Mokka hybrid were separated by Catuai and Caturra in the previously published dendrogram (Steiger et al 2002), only a very low level of polymorphism (an average 1.6 markers per primer pair) was detected between the two parental cultivars. Comparing our two parental cultivars, Catimor is more heterozygous with 68% of the total marker generated as Catimor-dominant; the higher heterozygosity occurs because Catimor was derived from an interspecific cross.…”

“…Coffee genomic DNA isolation was described previously (Steiger et al 2002). DNA digestions were performed according to the protocol of Vos et al (1995) with the modification that 250 ng of DNA was digested at 37C for 3 h with 2.5 U each of EcoRI, PstI, and MseI.…”

Screening interspecific hybrids of Populus (P. ciliata × maximowiczii) using AFLP markers

“…This speciesspecific clustering pattern of the hybrids has also been observed in papaya (Van Droogenbroeck et al 2002) and coffee (Steiger et al 2002). Our results show the clustering of the P. ciliata maximowiczii hybrids with the two parent species, with the hybrid cluster being closer to the P. ciliata cluster.…”

Genetic diversity within Pisum sativum using protein- and PCR-based markers

“…Together with a need for biodiversity conservation, the need for an assessment of crop diversity and a better understanding of the impact of breeding on this diversity has emerged. Molecular markers have allowed the study of diversity through DNA sequence variation, thus facilitating (1) the understanding of crop species domestication (White and Doebley 1998), (2) the deciphering of elite cultivar breeding history (Dubreuil and Charcosset 1999;Narvel et al 2000;Russell et al 2000), (3) the assessment of genetic diversity within germplasm and/or cultivated types for various species (Prasad et al 2000;Liu et al 2001;MØtais et al 2002;Steiger et al 2002) and (4) the identification of cultivars (Rongwen et al 1995;Russell et al 1997). Recently, molecular markers have been used to examine the effect of modern plant breeding methods on genetic diversity in barley (Russell et al 2000;Koebner et al 2003), wheat (Christiansen et al 2002;Soleimani et al 2002), and maize (Lu and Bernardo 2001).…”