Simple Sequence Repeats : the markers of choice in apple breeding

Simple sequence repeats (SSR), also called microsatellites, are becoming the most important molecular markers in both animals and plants.

SSR are stretches of 1 to 6 nucleotide units repeated in tandem and randomly spread in eucaryotic genomes. SSR are very polymorphic due to the high mutation rate affecting the number of repeat units. Such length-polymorphisms can be easily detected on high resolution gels (e. g. sequencing gels), by running PCR amplified fragments obtained using a unique pair of primers flanking the repeat (Weber and May 1989). SSR have several advantages over other molecular markers. For example, (i) microsatellites allow the identification of many alleles at a single locus, (ii) they are evenly distributed all over the genome, (iii) they are co-dominant, (iv) little DNA is required and (v) the analysis can be semi-automated and performed without the need of radioactivity. In our lab as well as in others (Gianfranceschi et al. 1998, Guilford et al. 1997, Maliepaard et al. 1998) SSRs for the genetic analysis of apple have been developed. We focused on the isolation and characterisation of (GA)n repeats, since those are the most abundant class of repeats in plants, after (TA)n, which have some technical disadvantages that hinder the selection of TA rich sequences.

SSRs proved to be very informative markers for the analysis of apple genome

We could test the incredible utility of SSR in detecting outcross plants present in segregating populations and to verify parental relationships of apple selections. Some microsatellite loci have already been placed on apple linkage maps and more have been developed or are under development to be used in the present European apple project. Thanks to the high number of alleles and to their co-dominance, SSRs will be mapped in more populations becoming the "backbone" of all linkage maps generated during the project. Thus allowing the alignment of linkage groups and the detection of homologous chromosomes in the different maps. SSRs will also be extremely important for the genetic analysis of quantitative traits (QT), in order to evaluate the relative importance of different QT alleles in different genetic backgrounds and environments. Finally, the use of SSRs will be extremely important to fully exploit information generated in the previous European project (EAGMAP) comparing results obtained on the Prima x Fiesta population where a detailed linkage map already exists (see the paper of King, Maliepaar and chevreau in the present newsletter).

References

Gianfranceschi et al. , 1998. Simple Sequence Repeat for the genetic analysis of apple. Theor Appl Genet (in press).

Guilford et al.,1997. Microsatellites in Malus x domestica (apple), abundance, polymorphism and cultivar identification. Theor Appl Genet 94 : 249-254.

Maliepaard et al., 1998. Integrating male and female linkage maps of apple (Malus x domestica Borkh) using multi-allelic markers. Theor Appl Genet (in press).

Weber & May, 1989. Abundant class of human DNA polymorphism which can be typed using the polymerase chain reaction. Am J Hum Genet 44 : 388-396.

Luca Gianfranceschi

ETHZ
Swiss Federal Inst.
of Technology
Zürich, Switzerland

fax 41-1.632.11.08