This study deals with the structure and genetic diversity of a species typical of the Brazilian Cerrado, Qualea grandiflora Mart (Vochysiaceae), present in different physiognomies of this biome. We developed eight microsatellite loci to analyze 420 samples of adult individuals from four populations distributed in the state of São Paulo, three of them in units managed by the Forestry Institute of Sao Paulo (Assis, Itirapina and Pedregulho) and one in a private property (Brotas). We also analyzed 300 progeny collected from 25 matrix in Assis. The results showed an average occurrence of 12.9 alleles per locus. The average number of effective alleles was six, and 26 exclusive alleles were found in the populations. The average expected heterozygosity was 0.803 while the observed heterozygosity was 0.512. The polymorphic information content ranged from 0.708 to 0.801 at the loci studied. The mean fixation was 0.349, therefore indicating the presence of inbreeding within populations. There is no presence of clones in the populations. The test of adherence to the Hardy Weinberg Equilibrium confirms the deviation from equilibrium in all populations. There is formation of population structure in the first distance classes in all populations studied, ranging from 30 to 40 meters, and there is a formation of three possible genotype groups. The influence of the Wahlund effect varied among populations (from 8.5% to 53.3%). The effective population size estimates were low (less than 10 individuals) and the minimum viable area was estimated between 4 to 184 hectares, taking into account estimates of short, medium and long terms. Regarding the reproductive system, results indicate that Q. grandiflora Mart reproduces by crosses between relatives and unrelated individuals (0.913). The single locus rate was 0.632, indicating that there are more crosses between unrelated than related individuals. The self-fertilization rate was low (0.087), therefore indicating that the species is allogamous, with little predisposition for self-fertilization. Approximately 35% of the plants within progenies were full-sibs and approximately 57% were half-sibs. In addition, approximately 8% of progenies were self-fertilized brothers. The estimated coefficient of coancestry in progenies was 0.139, while the rate of fixation was about 27%. The estimated effective size indicated that the genetic representativeness of the offspring is lower than the expected in random cross progenies: the samples analyzed account for only 13.2 individuals in a ideal panmitic population. The results show that this species has potential for in situ genetic conservation, although the collection of seeds to maintain the effective size should use a large number of trees. It is suggested that the studied areas be treated as evolutionary significant units and as independent units for management.
