Candidate Genes for the High-Altitude Adaptations of Two Mountain Pine Taxa

Genomic Insights into High-Altitude Adaptation: A Comparative Analysis of Roscoea alpina and R. purpurea in the Himalayas

Environmental stress at high altitudes drives the development of distinct adaptive mechanisms in plants. However, studies exploring the genetic adaptive mechanisms of high-altitude plant species are scarce. In the present study, we explored the high-altitude adaptive mechanisms of plants in the Himalayas through whole-genome resequencing. We studied two widespread members of the Himalayan endemic alpine genus Roscoea (Zingiberaceae): R. alpina (a selfing species) and R. purpurea (an outcrossing species). These species are distributed widely in the Himalayas with distinct non-overlapping altitude distributions; R. alpina is distributed at higher elevations, and R. purpurea occurs at lower elevations. Compared to R. purpurea, R. alpina exhibited higher levels of linkage disequilibrium, Tajima's D, and inbreeding coefficient, as well as lower recombination rates and genetic diversity. Approximately 96.3% of the genes in the reference genome underwent significant genetic divergence (FST ≥ 0.25). We reported 58 completely divergent genes (FST = 1), of which only 17 genes were annotated with specific functions. The functions of these genes were primarily related to adapting to the specific characteristics of high-altitude environments. Our findings provide novel insights into how evolutionary innovations promote the adaptation of mountain alpine species to high altitudes and harsh habitats.

Population structure analysis to explore genetic diversity and geographical distribution characteristics of wild tea plant in Guizhou Plateau

BACKGROUND

Tea, the second largest consumer beverage in the world after water, is widely cultivated in tropical and subtropical areas. However, the effect of environmental factors on the distribution of wild tea plants is unclear.

RESULTS

A total of 159 wild tea plants were collected from different altitudes and geological types of the Guizhou Plateau. Using the genotyping-by-sequencing method, 98,241 high-quality single nucleotide polymorphisms were identified. Genetic diversity, population structure analysis, principal component analysis, phylogenetic analysis, and linkage disequilibrium were performed. The genetic diversity of the wild tea plant population from the Silicate Rock Classes of Camellia gymnogyna was higher than that from the Carbonate Rock Classes of Camellia tachangensis. In addition, the genetic diversity of wild tea plants from the second altitude gradient was significantly higher than that of wild tea plants from the third and first altitude gradients. Two inferred pure groups (GP01 and GP02) and one inferred admixture group (GP03) were identified by population structure analysis and were verified by principal component and phylogenetic analyses. The highest differentiation coefficients were determined for GP01 vs. GP02, while the lowest differentiation coefficients were determined for GP01 vs. GP03.

CONCLUSIONS

This study revealed the genetic diversity and geographical distribution characteristics of wild tea plants in the Guizhou Plateau. There are significant differences in genetic diversity and evolutionary direction between Camellia tachangensis with Carbonate Rock Classes at the first altitude gradient and Camellia gymnogyna with Silicate Rock Classes at the third altitude gradient. Geological environment, soil mineral element content, soil pH, and altitude markedly contributed to the genetic differentiation between Camellia tachangensis and Camellia gymnogyna.