Genetic diversity and population structure in Cary’s Beardtongue Penstemon caryi (Plantaginaceae), a rare plant endemic to the eastern Rocky Mountains of Wyoming and Montana

Study on the characteristics of genetic diversity and population structure of a rare and endangered species of Rhododendron nymphaeoides (Ericaceae) based on microsatellite markers

BACKGROUND

Rhododendron nymphaeoides is explicitly listed as an endangered species in the "the International Union for Conservation of Nature's Red List (IUCN)", "The Red List of Rhododendrons", "Red List of China's Higher Plants" and "Threatened Species List of China's Higher Plants". It is also listed as a provincial-level key protected wild plant in Sichuan, with few individuals in the wild and significant conservation value. The genetic diversity and population structure have never been described, making it difficult to plan conservation strategies for this plant.

RESULTS

This study utilized 15 pairs of microsatellite markers to examine the genetic diversity of 79 samples of R. nymphaeoides sourced from five different geographic populations. A total of 214 alleles were detected, with the average effective number of alleles (Ne) of 7.0324. The averages for the polymorphism information index (PIC) and expected heterozygosity (He) were 0.7832 and 0.8102, respectively, indicating that the R. nymphaeoides populations harbor a rich genetic information content, the genetic differentiation coefficients (FST) average was 1.2607. There was high genetic diversity among populations, with average observed heterozygosity (Ho) and expected heterozygosity (He) values of 0.6375 and 0.6663, respectively, suggesting a degree of inbreeding within populations. Mantel test results showed a significant positive correlation between geographic distance and genetic distance amongst populations (r = 0.8456, P = 0.0021), which conforms to the isolation-by-distance (IBD) model. Due to geographical barriers, there is also a high level of genetic differentiation among populations, with an average genetic differentiation coefficient (FST) of 0.2685. Analysis of molecular variance (AMOVA) indicated that the main source of molecular variance exists within populations (73%), rather than between populations (27%). There was higher historical gene flow (average = 1.0850) and lower contemporary gene flow (average = 1.2849), with seed and pollen dispersal being impeded. Under the Two-Phase Model (TPM) assumption, findings are consistent with the mutation-migration model, suggesting that there has been no genetic bottleneck. STRUCTURE analysis, principal coordinate analysis (PCoA), and UPGMA analysis all support the division of the five natural populations into three genetic clusters.

CONCLUSIONS

This is the first comprehensive analysis of the genetic diversity and population structure of the endangered plant R. nymphaeoides using microsatellite markers. The study results indicate that this endangered plant's natural populations maintain a high level of genetic diversity. Due to geographical barriers, there is also a high level of genetic differentiation, with the primary source of genetic variation originating within populations. There is higher historical gene flow and lower contemporary gene flow, with seed and pollen dispersal being obstructed. The five populations can be divided into three evolutionary units, for which corresponding conservation management units should be established. These findings will benefit the conservation and development of the species and provide a theoretical basis for further studies on its evolution and biogeography.

Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis

Global climate change has increased concerns regarding biodiversity loss. However, many key conservation issues still required further research, including demographic history, deleterious mutation load, adaptive evolution, and putative introgression. Here we generated the first chromosome-level genome of the endangered Chinese hazelnut, Corylus chinensis, and compared the genomic signatures with its sympatric widespread C. kwechowensis-C. yunnanensis complex. We found large genome rearrangements across all Corylus species and identified species-specific expanded gene families that may be involved in adaptation. Population genomics revealed that both C. chinensis and the C. kwechowensis-C. yunnanensis complex had diverged into two genetic lineages, forming a consistent pattern of southwestern-northern differentiation. Population size of the narrow southwestern lineages of both species have decreased continuously since the late Miocene, whereas the widespread northern lineages have remained stable (C. chinensis) or have even recovered from population bottlenecks (C. kwechowensis-C. yunnanensis complex) during the Quaternary. Compared with C. kwechowensis-C. yunnanensis complex, C. chinensis showed significantly lower genomic diversity and higher inbreeding level. However, C. chinensis carried significantly fewer deleterious mutations than C. kwechowensis-C. yunnanensis complex, as more effective purging selection reduced the accumulation of homozygous variants. We also detected signals of positive selection and adaptive introgression in different lineages, which facilitated the accumulation of favorable variants and formation of local adaptation. Hence, both types of selection and exogenous introgression could have mitigated inbreeding and facilitated survival and persistence of C. chinensis. Overall, our study provides critical insights into lineage differentiation, local adaptation, and the potential for future recovery of endangered trees.

Comparative epigenetic and genetic spatial structure in Mediterranean mountain plants: a multispecies study

Changes in epigenetic states can allow individuals to cope with environmental changes. If such changes are heritable, this may lead to epigenetic adaptation. Thus, it is likely that in sessile organisms such as plants, part of the spatial epigenetic variation found across individuals will reflect the environmental heterogeneity within populations. The departure of the spatial epigenetic structure from the baseline genetic variation can help in understanding the value of epigenetic regulation in species with different breadth of optimal environmental requirements. Here, we hypothesise that in plants with narrow environmental requirements, epigenetic variability should be less structured in space given the lower variability in suitable environmental conditions. We performed a multispecies study that considered seven pairs of congeneric plant species, each encompassing a narrow endemic with habitat specialisation and a widespread species. In three populations per species we used AFLP and methylation-sensitive AFLP markers to characterise the spatial genetic and epigenetic structures. Narrow endemics showed a significantly lower epigenetic than genetic differentiation between populations. Within populations, epigenetic variation was less spatially structured than genetic variation, mainly in narrow endemics. In these species, structural equation models revealed that such pattern was associated to a lack of correlation between epigenetic and genetic information. Altogether, these results show a greater decoupling of the spatial epigenetic variation from the baseline spatial genetic pattern in endemic species. These findings highlight the value of studying genetic and epigenetic spatial variation to better understand habitat specialisation in plants.

Study on the characteristics of genetic diversity of different populations of Guizhou endemic plant Rhododendron pudingense based on microsatellite markers

BACKGROUND

Rhododendron pudingense, firstly discovered in Puding county of Guizhou province in 2020, have adapted to living in rocky fissure habitat, which has important ornamental and economic values. However, the genetic diversity and population structure of this species have been rarely described, which seriously affects the collection and protection of wild germplasm resources.

RESULTS

In the present study, 13 pairs of primers for polymorphic microsatellite were used to investigate the genetic diversity of 65 R. pudingense accessions from six different geographic populations. A total of 254 alleles (Na) were obtained with an average of 19.5 alleles per locus. The average values of polymorphic information content (PIC), observed heterozygosity (Ho), and expected heterozygosity (He) were 0.8826, 0.4501, and 0.8993, respectively, These results indicate that the microsatellite primers adopted demonstrate good polymorphism, and the R. pudingense exhibits a high level of genetic diversity at the species level. The average genetic differentiation coefficient (Fst) was 0.1325, suggested that moderate divergence occurred in R. pudingense populations. The average values of genetic differentiation coefficient and gene flow among populations were 0.1165 and 3.1281, respectively. The analysis of molecular variance (AMOVA) indicated that most of the population differences (88%) were attributed to within-population variation. The PCoA results are consistent with the findings of the UPGMA clustering analysis, supporting the conclusion that the six populations of R. pudingense can be clearly grouped into two separate clusters. Based on Mantel analysis, we speculate that the PD population may have migrated from WM-1 and WM-2. Therefore, it is advised to protect the natural habitat of R. pudingense in situ as much as possible, in order to maximize the preservation of its genetic diversity.

CONCLUSIONS

This is the first comprehensive analysis of genetic diversity and population structure of R. pudingense in Guizhou province. The research results revealed the high genetic diversity and moderate population diferentiation in this horticulture plant. This study provide a theoretical basis for the conservation of wild resources of the R. pudingense and lay the foundation for the breeding or cultivation of this new species.

Genetic diversity and structure of Rhododendron meddianum, a plant species with extremely small populations

Rhododendron meddianum is a critically endangered species with important ornamental value and is also a plant species with extremely small populations. In this study, we used double digest restriction-site-associated DNA sequencing (ddRAD) technology to assess the genetic diversity, genetic structure and demographic history of the three extant populations of R. meddianum. Analysis of SNPs indicated that R. meddianum populations have a high genetic diversity (π = 0.0772 ± 0.0024, H _E  = 0.0742 ± 0.002). Both F _ST values (0.1582-0.2388) and AMOVA showed a moderate genetic differentiation among the R. meddianum populations. Meanwhile, STRUCTURE, PCoA and NJ trees indicated that the R. meddianum samples were clustered into three distinct genetic groups. Using the stairway plot, we found that R. meddianum underwent a population bottleneck about 70,000 years ago. Furthermore, demographic models of R. meddianum and its relative, Rhododendron cyanocarpum, revealed that these species diverged about 3.05 (2.21-5.03) million years ago. This divergence may have been caused by environmental changes that occurred after the late Pliocene, e.g., the Asian winter monsoon intensified, leading to a drier climate. Based on these findings, we recommend that R. meddianum be conserved through in situ, ex situ approaches and that its seeds be collected for germplasm.