Conservation genetics and genetic vulnerability of Craigia yunnanensis (Malvaceae), a relict plant species with extremely small populations from Southwest China.

Authors

Lei Cai, Yang Liu, Ya-Ling Chen, Zhi-Ling Dao, Wei-Bang Sun, Jing Yang

Published in

Annals of botany. Volume 138. Issue 1. Pages 88-100. Jul 28, 2026.

Abstract

Conservation genomics research on endangered plants can provide insights for their genetic rescue and adaptive potential. Craigia yunnanensis is one of two species of the relict genus Craigia that has survived to the present day, and is naturally scattered in southwestern China to northern Vietnam and northern Myanmar. It has been listed as a PSESP species (Plant Species with Extremely Small Populations) in China due to its small populations, scattered distribution and significant human disturbances. Thus, we aimed to use genomic data to conduct research on the conservation genetics and genetic vulnerability of C. yunnanensis to provide insights for its population conservation and genetic rescue, and to investigate its potential for adaptation under future climate change.
We developed genetic markers (SNPs: single nucleotide polymorphisms) for 122 samples from 12 locations based on double digest restriction-site associated DNA sequencing data. Based on commonly used analysis methods in conservation genetics, Stairway Plot 2, genotype-environment association (GEA) and environmental factors, we then made a detailed analysis of its genetic diversity, population structure, genetic vulnerability and demographic history.
A total of 1354 common loci with 20 758 SNPs were generated. The results showed that genetic diversity was moderate to high for C. yunnanensis when compared to other rare and endangered plant species. Low genetic differentiation is reflected in all populations and can be used to divide them into two genetic clusters. The demographic history revealed that the effective population shows a trough (Ne value: 500) during the period 10-20 ka that may correspond to the end of the Last Glacial Period (11.5 ka) and the Last Glacial Maximum (19-26.5 ka), and a period of recovery (Ne value: 5500) between 4 and 10 ka. Analysis of genetic vulnerability demonstrates that with non-significant genetic offset (future maladaptabilty with climate change) the ability of the populations to persist into the future will also probably be impacted by other factors such as population size and geographical distance.
Overall, habitat fragmentation and loss of genetic diversity, coupled with severe human interference, have led to the endangered status of C. yunnanensis. Additionally, different patterns of genetic vulnerability suggested constructive conservation strategies for different populations. This study also provides additional evidence that the 'Tanaka-Kaiyong Line' (TKL) is an obvious phytogeographical boundary in southwestern China.

PMID:
41163571
Bibliographic data and abstract were imported from PubMed on 15 Sep 2026.

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