[LAB Search] Successful Decoding of the Standard Genome of Korean Pine 'Jeongipumsong'

Research Team Led by Professor Kim Seung-il, Department of Environmental Horticulture, University of Seoul

The research team led by Professor Kim Seung-il from the Department of Environmental Horticulture at the University of Seoul has constructed a haploid genotype-reflecting standard genome of pine and published research results on the evolution of the giant genome and genetic differences between haploids.

Research team led by Professor Seung-il Kim from the Department of Environmental Horticulture, University of Seoul
[Photo by University of Seoul]

This study was conducted with Professor Kim Seung-il as the corresponding author, and Dr. Jang Min-jung and Dr. Cho Hye-jung as first authors. Additionally, it was carried out as a joint research project with the National Institute of Forest Science, with Dr. Park Eung-jun participating as a co-corresponding author. The research was supported by the Korea Research Foundation’s Early Career Research Program, the Ministry of Agriculture, Food and Rural Affairs’ Digital Breeding Transition Technology Development Project, and the Korea Forest Service’s Forest Science and Technology Development Project.

This study is the first case among gymnosperms to construct a haploid unit standard genome of pine and to attempt the exploration of genetic variation in wild haploid individuals. The research team analyzed pine genome variations in detail based on haploid genotype information and elucidated genetic differences arising during the evolution of the giant genome.

In particular, it is evaluated to have contributed to clarifying genome rearrangements and the evolutionary roles of important functional transcription factors during the speciation process within the genus Pinus. The research results were published online on the 20th in the journal Nature Genetics under the title “Haplotype-resolved genome assembly and resequencing analysis provide insights into genome evolution and allelic imbalance in Pinus densiflora.”

Most plants exist as diploids composed of two pairs of haploids, one pair inherited from the mother and the other from the father. The research team constructed two sets of high-quality haploid genomes totaling 21.7 gigabytes (GB) using the latest genome assembly method called the “phasing technique” targeting Korea’s symbolic pine, Jeongipumsong. This corresponds to more than seven times the size of the human genome.

A part of the research using the genome information of the Jeongipumsong pine by Professor Kim Seung-il's research team

Furthermore, as part of a study on gene diversity within the genus Pinus, the team attempted for the first time a sequence variation analysis reflecting haploid information on 30 wild pine individuals in Korea. Through this, they revealed the impact of individual genetic variation on pine gene diversity and suggested the necessity of constructing data reflecting genome information from multiple individuals.

Professor Kim said, “This study is significant in that it laid an important foundation for breeding research on pine and major trees,” adding, “We expect it to contribute to developing varieties that can respond to climate change, such as resistance to pine wilt disease, pine cone breeding, and carbon reduction.”