Journal of Tea Science Research, 2024, Vol.14, No.5, 293-303 http://hortherbpublisher.com/index.php/jtsr 293 Research Insight Open Access Structural Variations in Tea Genome and Their Role in Trait Diversity Chuchu Liu , Xichen Wang Institute of Life Sciences, Jiyang Colloge of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China Corresponding author: chuchu.liu@jicat.org Journal of Tea Science Research, 2024, Vol.14, No.5 doi: 10.5376/jtsr.2024.14.0027 Received: 20 Aug., 2024 Accepted: 28 Sep., 2024 Published: 25 Oct., 2024 Copyright © 2024 Liu and Wang, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Liu C.C., and Wang X.C., 2024, Structural variations in tea genome and their role in trait diversity, Journal of Tea Science Research, 14(5): 293-303 (doi: 10.5376/jtsr.2024.14.0027) Abstract Tea (Camellia sinensis) has important economic and cultural significance. The tea aroma, taste and even morphological diversity that everyone is familiar with are actually related to the genomic mechanisms behind it. With the release of high-quality reference genomes and the construction of the pan-genome of tea, more than 217,000 structural variations (SVs) and 56,000 presence/absence variations (PAVs) have been identified. This study analyzed the types and distribution of these SVs and their roles in secondary metabolism, stress resistance, morphological traits, etc. By integrating SV data with multi-omics data such as transcriptome and metabolome, we found that the expression of many key traits is indeed affected by SV regulation. Some SVs directly affect whether genes are expressed or change the location of regulatory elements, thereby promoting the evolution of certain traits. SVs are expected to become targets for trait improvement and are gradually showing their potential for application in molecular breeding. This study provides a more solid theoretical basis and technical support for the precision breeding and genetic resource protection of tea. Keywords Tea tree (Camellia sinensis); Structural variation; Trait diversity; Pan-genome; Molecular breeding; Multi-omics integration 1 Introduction Tea (Camellia sinensis) is an important economic crop around the world. It also plays a special role in cultural exchange and health-related consumption. As the tea industry grows, interest in its genetic background has also increased. In recent years, there have been many advances in tea genome research. For example, high-quality reference genomes have been released, and pangenomes based on diverse tea resources have been built. These are major foundational breakthroughs. Kong et al. (2022) developed a pan-transcriptome dataset including 134 tea accessions. They identified 30,482 expressed genes. Among them, 4,940 genes came from de novo transcriptome assembly without a reference, and 5,506 were newly annotated based on the reference genome. These studies help us better understand the genetic diversity of tea plants. They have revealed more than 217,000 large structural variations (SVs) and around 56,000 presence/absence variations (PAVs), which have greatly enriched the genomic resources of tea (Xia et al., 2020; Tong et al., 2024; Tariq et al., 2024). However, there are still many challenges. The tea genome is large and contains a high proportion of repetitive sequences. In particular, the presence of many LTR retrotransposons makes both genome assembly and annotation more difficult (Xia et al., 2020; Tariq et al., 2024). On top of that, the population structure of tea plants is quite complex. It is still hard to fully understand the genetic mechanisms behind key agronomic traits. In the past, researchers mainly used SNPs and small Indels for population studies and trait association analysis (Niu et al., 2019; Hazra et al., 2021). But now, more and more studies are shifting attention to SVs. These structural variants tend to affect larger genomic regions and often have stronger effects. Yet, they are usually overlooked in traditional analyses. SVs can cause large deletions, duplications, inversions, or even gene rearrangements. Many traits are closely linked to these changes, such as leaf shape, tea aroma, flavonoid biosynthesis, and cold resistance (Tong et al., 2024; Tariq et al., 2024). For instance, aroma-related pathways like terpenoid biosynthesis and phenylalanine
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