Pan-genome analysis of Liriodendron reveals presence/absence variations associated with growth traits

In this study, we constructed a pan-genome of Liriodendron based on 24 accessions. Comparative analysis with the reference genome revealed 116 Mb of non-reference sequences and obtained 32,773 genes, including 3,558 novel genes. We subsequently employed resequencing data from 247 Liriodendron genotypes to identify PAVs, comprising 13,779 core genes and 18,179 dispensable genes. To further assess PAV applicability, a genome-wide association study (GWAS) was conducted to link gene PAVs with growth traits, including tree height (H), diameter at breast height (DBH), clear bole height (CBH), and crown length ratio (CLR), in hybrid Liriodendron. This approach identified 14 candidate genes associated with these growth traits above. Additionally, gene PAVs appeared to predominantly contribute to heterosis in growth traits, displaying a dominant expression pattern when comparing leaf, shoot, and phloem tissues of strong and weak heterotic combinations. Additionally, we identified two key candidate genes, Litul.02G164100 and Litul.01G057400, which appear to drive hybrid vigor by exhibiting high parental expression patterns in strong heterotic combinations of leaf and shoot tissues. Altogether, this study expands the Liriodendron genomic dataset, identifies candidate genes linked to growth traits, and provides insights into their heterotic mechanisms in hybrid Liriodendron. These findings offer a valuable genetic resource for molecular breeding and functional genomics research in Liriodendron.

本研究基于24份鹅掌楸属种质资源构建了泛基因组。与参考基因组的比较分析揭示了116 Mb的非参考序列，并获得32773个基因，其中包括3558个新基因。随后，我们利用247份鹅掌楸属基因型的重测序数据鉴定存在/缺失变异（PAVs），其中包含13779个核心基因和18179个可变基因。为进一步评估PAV的应用价值，我们开展了全基因组关联分析（GWAS），以将杂交鹅掌楸的基因PAV与生长性状关联起来，包括树高（H）、胸径（DBH）、主干高（CBH）和冠长比（CLR）。该方法鉴定出14个与上述生长性状相关的候选基因。此外，基因PAVs似乎是生长性状杂种优势的主要贡献因素——在比较强、弱杂交组合的叶片、嫩梢和韧皮部组织时，表现出显性表达模式。同时，我们鉴定出两个关键候选基因Litul.02G164100和Litul.01G057400，它们通过在强杂交组合的叶片和嫩梢组织中表现出高亲本表达模式，似乎能驱动杂种优势。总而言之，本研究扩展了鹅掌楸属的基因组数据集，鉴定了与生长性状相关的候选基因，并为杂交鹅掌楸的杂种优势机制提供了见解。这些发现为鹅掌楸属的分子育种和功能基因组学研究提供了宝贵的遗传资源。