RADseq‐based population genomic analysis and environmental adaptation of rare and endangered recretohalophyte Reaumuria trigyna

Abstract

Genetic diversity reflects the survival potential, history, and population dynamics of an organism. It underlies the adaptive potential of populations and their response to environmental change. Reaumuria trigyna is an endemic species in the Eastern Alxa and West Ordos desert regions in China. The species has been considered a good candidate to explore the unique survival strategies of plants that inhabit this area. In this study, we performed population genomic analyses based on restriction‐site associated DNA sequencing to understand the genetic diversity, population genetic structure, and differentiation of the species. Analyses of 92,719 high‐quality single‐nucleotide polymorphisms (SNPs) indicated that overall genetic diversity of R. trigyna was low (HO = 0.249 and HE = 0.208). No significant genetic differentiation was observed among the investigated populations. However, a subtle population genetic structure was detected. We suggest that this might be explained by adaptive diversification reinforced by the geographical isolation of populations. Overall, 3513 outlier SNPs were located in 243 gene‐coding sequences in the R. trigyna transcriptome. Potential sites under diversifying selection occurred in genes (e.g., AP2/EREBP, E3 ubiquitin‐protein ligase, FLS, and 4CL) related to phytohormone regulation and synthesis of secondary metabolites which have roles in adaptation of species. Our genetic analyses provide scientific criteria for evaluating the evolutionary capacity of R. trigyna and the discovery of unique adaptions. Our findings extend knowledge of refugia, environmental adaption, and evolution of germplasm resources that survive in the Ordos area.

Unravelling some factors affecting sexual reproduction in rock-specialist shrub: Insight from an endemic Daphne arbuscula (Thymelaeaceae)

“…Genetic mechanisms may contribute to seed and/or fruit abortion, leading to low fecundity and posing a risk to the long-term survival of plants [e.g., 108 – 113 ]. Endemic species, often occurring in small and isolated populations, may be more vulnerable to reduced gene flow within and among populations, potentially experiencing genetic drift or inbreeding depression [ 10 , 11 , 15 – 17 , 114 , 115 ].…”

Exploring the genomics of abiotic stress tolerance and crop resilience to climate change

“…Technologies like restriction-site-associated DNA sequencing (RADseq/GBS) have opened avenues for acquiring precise information on population genetic diversity, significantly expediting the exploration of adaptive evolutionary mechanisms (Feng et al, 2020). Dang et al (2023) employed RADseq technology for a population genomic analysis, unveiling the genetic variation and structure of Reaumuria trigyna. The analysis identified probable sites under diversifying selection in genes associated with phytohormone regulation and the synthesis of secondary metabolites, providing major insights into the adaptive diversification of R. trigyna species.…”

“…Dang et al. (2023) employed RADseq technology for a population genomic analysis, unveiling the genetic variation and structure of Reaumuria trigyna . The analysis identified probable sites under diversifying selection in genes associated with phytohormone regulation and the synthesis of secondary metabolites, providing major insights into the adaptive diversification of R. trigyna species.…”

Genetic Diversity and Structure of Geodorum eulophioides, a Plant Species with Extremely Small Populations in China

“…RAD-seq methods have been used on plant communities to reveal their evolutionary history and local adaptability, identify the genetic structure of populations, and determine how environmental and topographical elements affect genetic diversity and differentiation. They have also been used to identify genetic lineages of plants, thereby creating references for the conservation of rare species [9][10][11][12].…”