Genetic linkage mapping in Acacia mangium 1. Evaluation of restriction endonucleases, inheritance of RFLP loci and their conservation across species

Random genomic probes were used to assess levels of restriction fragment le ngth polymorphism (RFLP) in two 2-generation outbred pedigrees of Acacia ma ngium Willd. Probes; were evaluated for their ability to detect polymorphic loci in each pedigree and to determine the relative efficiency of differen t restriction enzymes in revealing polymorphisms. Sixty two percent of the probes which detected single- or low-copy number sequences revealed polymor phisms with at least one restriction enyzme. HpaII was the most efficient i n detecting polymorphism among first-generation individuals. The recognitio n sequence of HpaII contains a CpG dimer. suggesting that cytosines in the CpG sequence may be hotspots for mutation in plant genomes, as previously r eported in bacterial and mammalian genomes. Mendelian inheritance of 230 lo ci was demonstrated based on single-locus segregation in second-generation individuals. Less than 5% of loci showed evidence of segregation distortion . The proportion of fully informative loci (15%) was lower than previously reported in eucalypts reflecting the lower level of genetic diversity in A. mangium. The RFLP probes are suitable for the construction of a high-densi ty genetic linkage map in A. mangium. Cross-hybridization of the A. mangium RFLPs to DNA from species representing the three subgenera of the genus Ac acia indicates that these markers could be used in breeding programs of oth er diploid acacias, for comparative studies of genome organisation, and for phylogenetic studies.