Genomic basis of high-altitude adaptation in Tibetan Prunus fruit trees
Background: The Great Himalayan Mountains and their foothills are recognized as the primary centers of origin and genetic diversity for numerous cultivated plant species. While the genetic mechanisms of adaptation to the extreme Himalayan climate have been studied in several animal species, the genetic basis for adaptation in long-lived perennials, such as trees, remains largely unexplored. Tibetan peach (Prunus mira) is an ancient progenitor of the cultivated peach and is endemic to the high-altitude regions of the Himalayas (2,000 to 4,500 m above sea level). This study aimed to investigate the genetic and metabolic foundations that allowed Tibetan Prunus species to adapt to harsh environments characterized by low temperatures, low atmospheric pressure, and high UV light intensity.
Results: The research team de novo assembled high-quality genomes for Tibetan peach, Tibetan Mei, and Tibetan apricot, discovering a significant expansion of SINE retrotransposons in these Tibetan species compared to their cultivated relatives. Through population genomic analysis of 377 Prunus accessions, they identified strong genetic differentiation between high- and low-altitude populations, with selection signals concentrated in genes related to UV stress signaling (such as UVR8) and light response (the FAR1/FHY3 family). Metabolomic profiling of 1,768 metabolites revealed that 379 compounds are genetically correlated with altitude, specifically showing that phenylpropanoids like 3-O-feruloyl quinic acid accumulate at much higher levels in high-altitude fruits. Functional analysis demonstrated that a specific SINE2 insertion upstream of the NAC transcription factor Pmira3g006670 is predominant in high-altitude populations; this insertion enhances the gene's expression, which in turn promotes the accumulation of beneficial phenylpropanoids that help the plants cope with intense UV radiation.
Conclusions: The expansion of SINE retrotransposons played a critical role in the adaptation of Tibetan Prunus species to the Himalayan plateau. These SINE insertions drive the accumulation of beneficial metabolites like phenylpropanoids, which provide essential protection against intense UV radiation. This research provides a rare and valuable gene bank for adaptation genomics and offers new strategies for the genetic improvement of crops and fruit trees through molecular breeding.
https://pubmed.ncbi.nlm.nih.gov/34314676/
Download