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The detection of association between DNA markers and traits of interest in an outbred population is complicated and requires highly polymorphic markers. A genetic linkage map of avocado (Persea americana Mill.) recently generated consists of simple sequence repeat (SSR) markers as well as DNA fingerprint (DFP) and randomly amplified polymorphic DNA (RAPD) markers. These markers were used to detect putative quantitative trait loci (QTLs) of eight avocado fruit traits. Two statistical methods were used: one-way analysis of variance and interval mapping. Six traits were found to be associated with at least one of the 90 DNA markers. Based on the two statistical approaches, a putative QTL associated with the presence of fibers in the flesh, was found to be located on linkage group 3. This putative QTL was found to be associated with the SSR marker AVA04 having a high significant value (P = 4.4 × 10-8). The haplotype analysis of linkage group 3 showed a putative dominant interaction between the alleles of this locus.
To estimate heterozygosity level in the avocado (Persea americana Mill.) genome, two types of variable number of tandem repeat (VNTR) markers were used. Multilocus DNA fingerprints (DFPs) were analyzed on avocado progeny resulting from either crosses or selfing of cultivars. In five crosses, heterozygosity was 100%, while in two self-pollinated families, heterozygosity was 90% and 94%. Single locus, simple sequence repeat (SSR) DNA markers were analyzed by typing 59 loci on five avocado cultivars. Average heterozygosity varied from 0.50 to 0.66, while gene diversity varied from 0.42 to 0.66. Heterozygosity varied from 38% to 70%. The percentage of fragments that exhibited Mendelian inheritance was 62.5% to 85% (P < 0.05) for the DFP fragments and 85% for the SSR alleles.
Plant genomes contain polymorphic repetitive sequences that can be used as DNA markers. Minisatellites (16 to 64 bp per repeat) and simple-sequence repeats (2 to 6 bp per repeat) are the most polymorphic markers found in plant and animal genomes. In this study, the hybridizations between genomic DNA and variable number of tandem repeat probes were examined in Arabidopsis thaliana L. (Heynn), onion (Allium cepa L.), tomato (Lycopersicon esculentum L.), wheat (Triticum aestivum L.), avocado (Persea americana Mill.), litchi (Chinensis Sonn.), mango (Mangifera indica L.), and Carica species. Some of the probes detected polymorphic sequences in all the species, but others were useful only for one or two species. None of the probes gave clear band patterns in either onion or wheat. The in-gel hybridization method was similar to Southern blot hybridization using the simple-sequence repeat probes.