The genetic diversity and population structure of genipa americana (Rubiaceae) in Northern Mato Grosso, Brazil

Abstract

Genipa americana (Rubiaceae) is an endemic Amazon-region species that may be subject to inbreeding, since it grows in fragmented environments. To examine this possibility, we examined the genetic diversity and population structure of three G. americana populations naturally grown in Northern Mato Grosso State using SSR markers. Sixty-four individuals were sampled from the three populations: 20 in AFL, 20 in MTP, and 24 in NBD. DNA extraction was performed according to the CTAB method, with modifications. Six SSR primers developed for the species were used. The allele frequency, the observed and expected heterozygosity, polymorphism information content), and the fixation Index were estimated. Molecular variance and principal coordinates analyses were conducted, and the most likely number of groups was inferred using the Structure software to help understand the genetic structure of the populations. The six microsatellite loci used showed 17 alleles, in total, ranging from 2 to 4 alleles per locus, with a mean of 2.83. The expected heterozygosity ranged from 0.35 to 0.67 and remained higher than the observed heterozygosity for all loci. The three populations showed genetic diversity, shared genetic material and presented high inbreeding indexes. Cluster analysis results showed genetic material sharing between populations, as well as a lack of genetic structuring among individuals according to their geographical origins. The molecular characterization revealed that the genetic diversity is higher within than between populations. The three populations had shared genetic material and a high inbreeding index due to low observed heterozygosity. This could be a consequence of the fragmented environment where these populations currently live in, since it reduces the number of G. americana individuals and can increase inbreeding.