A new look at genetic variability in pomegranate: Landscape genetics and structural equation modeling (SEM)

Abstract

Pomegranate (Punica granatum L.) is an important horticultural plant in Iran and has been a food source since ancient times. Despite several genetic diversity studies conducted on these taxa, there are no reports on the landscape genetics of these important plants in Iran, nor is there any information on the effects of environmental, spatial, and climatic variables on the genetic structure of pomegranate. Therefore, this study used genetics, structural equation modeling (SEM), and species distribution modeling (SDM) approaches to explore the above-mentioned objectives. We used both cytogenetic and molecular analyses (SSR and SCoT markers) of several pomegranate samples along with environmental, spatial, and climatic variables. The redundancy analysis (RDA) analysis showed a significant positive association between terminal chiasmata with the longitudinal distribution of the pomegranate accession, while total chiasma number and interstitial chiasmata have an association with the altitude. The spatial PCA analysis indicated the role played by both global and local spatial variables in the cytogenetic variability like the univalent and terminal chiasmata formation. The Mantel test indicates that the cytogenetic difference in pomegranate plants is not related to their geographical distance, while the Moran I test result shows that geographical regions with similar spatial conditions affect the cytogenetic structuring of pomegranate plants in a similar way. SEM methods showed a strong negative association between bivalent formation and the environmental variables, while they showed both positive and negative associations between some of the environmental variables and different kinds of chiasmata. The sPCA analysis of molecular data showed a significant global, and local, spatial structuring of the molecular data and the genetic cline formation within the pomegranate accessions studied. Similarly, the spatial PCA analysis of climate variables, precipitation, and temperature revealed a significant structuring of genetic diversity and the formation of genetic clines by these factors. RDA analysis identified some of the loci that are significantly associated with temperature and precipitation. Therefore, both geographical/ or spatial variables and climate factors contribute to the genetic structure of the pomegranate accessions studied. SEM models based on genetic data revealed a positive association between environmental and climate variables with genetic diversity parameters and SSR-SCoT molecular loci studied. Climate change is unlikely to hurt pomegranate growing areas due to the high genetic diversity of pomegranate plants and the diverse genetic lineages present in the country.