Contrasting clonal and population genetic structure in two endangered Costa Rican Vanilla species of commercial interest

Abstract

Wild relatives of the commercially grown Vanilla planifolia, such as Vanilla odorata and V. pompona, are understudied despite their ecological and agricultural importance. Both species are listed as endangered by the IUCN, but limited research on their genetic diversity hinders effective management. While Vanilla species reproduce extensively by cloning, wild populations may retain significant genetic diversity valuable for crop improvement and conservation. To evaluate genetic diversity and structure, we analyzed 146 individuals from 10 V. pompona populations and 75 individuals from six V. odorata populations in Costa Rica, using 11 and 10 microsatellites, respectively. Vanilla odorata showed higher clonality than V. pompona (63% vs. 35%). Both species exhibited low to moderate genetic diversity (V. odorata: H_O = 0.47, H_E = 0.29; V. pompona: H_O = 0.43, H_E = 0.41). Vanilla odorata populations revealed greater genetic differentiation than V. pompona populations (Nei's G_ST = 0.51 vs. 0.091), with V. odorata also exhibiting isolation by distance (R² = 0.704, p < 0.05). Both species showed fine-scale genetic structure, with higher levels linked to clonality. Gene flow in V. pompona benefits from broad distribution and sexual reproduction, while V. odorata experiences limited gene flow due to its high clonality and restricted range. Protecting habitats and promoting outcrossing may aid V. odorata viability while V. pompona serves as an important resource for increasing genetic diversity in cultivated vanilla.

Keywords: Fine-scale genetic structure; Microsatellites; Pacific region; Population genetics.

Fig. 1

Discriminant analysis of principal components (DAPC) (A) clustering of six populations of V. odorata, including clones (IC). (B) clustering of ten populations in V. pompona, including clones. Colors denote the geographical allocation of V. pompona populations (clusters) to designated regions: Green = South Pacific - Peninsula; Yellow = South Pacific - Térraba; Pink = Central Pacific - Carara; Blue = North Pacific; Purple = Central Pacific - Puriscal.

Fig. 2

Correlograms showing the spatial autocorrelation of the coancestry Loiselle coefficient (Loiselle et al., 1995) as a function of distance for V. odorata populations: (A) dataset including clones, (B) dataset excluding clones. Dashed lines represent the lower and upper 95% confidence limits for the null hypothesis of no spatial genetic structure.

Fig. 3

Correlograms showing the spatial autocorrelation of the coancestry Loiselle coefficient (Loiselle et al., 1995) as a function of distance for V. pompona populations: (A) dataset including clones, (B) dataset excluding clones. Dashed lines represent the lower and upper 95% confidence limits for the null hypothesis of no spatial genetic structure.

Fig. 4

A map of Costa Rica showing the locations of V. odorata (triangles) and V. pompona (circles) populations. The colors grouping the circles in V. pompona correspond to the five regions in which the populations are categorized: Blue = North Pacific; Pink = Central Pacific - Carara; Purple = Central Pacific - Puriscal, Yellow = South Pacific - Térraba Green = South Pacific - Peninsula. The numbers in brackets indicate the number of individuals collected at each site. In the zoomed-in view of the Piro Biological Station, the names in light orange represent V. odorata populations, while the names in light green represent V. pompona populations. Abbreviations are as follows: VT = Vanilla Trail, PST = Piro Station Trail, PPT = Pica Pica Trail, STH = Stairway to Heaven. The map was created using QGIS software (version 3.30.3-‘s-Hertogenbosch, available at https://qgis.org/), with minor modifications made in Adobe Photoshop^® CC (Adobe Systems Inc., California, U.S.A.). QGIS is licensed under the GNU General Public License (https://www.gnu.org/licenses).