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News — Admired for their vibrant colors and durability, carnations are among the most popular ornamental plants globally. However, breeding efforts aimed at enhancing traits like extended blooming periods and disease resistance have been slowed by a lack of high-quality genetic information. Although genome sequencing technologies have evolved, fully assembled, gap-free genomes remain rare. This has forced breeders to rely on traditional, time-intensive cross-breeding methods. To address these challenges, comprehensive genetic research is necessary to unlock the full potential of carnations and accelerate the development of improved varieties.

A team of researchers from the Agricultural Genomics Institute at Shenzhen, Murdoch University, and Huazhong Agricultural University has made a significant leap forward by the first telomere-to-telomere genome assembly of the carnation variety 'Baltico' in , on November 27, 2023. Using cutting-edge sequencing techniques, including HiFi and nanopore technologies, the researchers have produced a complete genome map. This resource represents a major advancement over previous carnation genome drafts, offering valuable insights for future molecular breeding strategies.

The study successfully mapped the entire genome of the carnation variety 'Baltico,' offering an in-depth view of the species’ genetic makeup. By leveraging high-resolution sequencing data from PacBio and Oxford Nanopore technologies, the researchers created a gap-free genome. One of the most significant discoveries was the impact of transposable elements (TEs) on gene expression. These elements, often found within gene regions, were shown to suppress gene activity, influencing the regulatory networks that control traits like flower color and vase life. Additionally, the study identified a strong link between gene structure—such as gene and intron length—and gene expression levels. This comprehensive genomic resource now serves as a guide for developing carnation varieties with improved traits, such as disease resistance and extended flowering periods, through more precise molecular breeding techniques.

Dr. Zhiqiang Wu, a lead author from the Agricultural Genomics Institute at Shenzhen, remarked: "This genome assembly marks a critical advancement in carnation genetics. By resolving gaps in earlier genome versions, we can now examine gene expression with much higher precision. This opens the door for breeders to develop varieties that not only meet but exceed, the expectations of both consumers and growers, particularly in terms of disease resistance and ornamental qualities."

This gap-free carnation genome offers a significant milestone for molecular breeding, allowing for more accurate genetic modifications. Beyond carnations, the research establishes a framework for enhancing other ornamental plants by using similar genetic approaches. The findings will help breeders focus on refining traits such as color, fragrance, and resilience. This will accelerate the development of new plant varieties that are more aligned with market trends and consumer preferences, providing a strategic advantage in the competitive horticulture industry.

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Funding information

This work was funded by the National Natural Science Foundation of China (32002074); the Shenzhen Fundamental Research Program (JCYJ20220818103212025); Major Scientific Research Tasks, Kunpeng Institute of Modern Agriculture at Foshan (KIMA-ZDKY2022004); the Scientific Research Foundation for the Principal Investigator, Kunpeng Institute of Modern Agriculture at Foshan (KIMA-QD2022004); and the Chinese Academy of Agricultural Sciences Elite Youth Program (110243160001007) to Z.W. This work was also supported by the Innovation Program of Chinese Academy of Agricultural Sciences, Science Technology and Innovation Commission of Shenzhen Municipality of China (ZDSYS20200811142605017).

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is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2022. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.