State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands.
Genome Biol. 2024 Aug 27;25(1):231. doi: 10.1186/s13059-024-03370-z.
Polyploidy is widely recognized as a significant evolutionary force in the plant kingdom, contributing to the diversification of plants. One of the notable features of allopolyploidy is the occurrence of homoeologous exchange (HE) events between the subgenomes, causing changes in genomic composition, gene expression, and phenotypic variations. However, the role of HE in plant adaptation and domestication remains unclear.
Here we analyze the whole-genome resequencing data from Brassica napus accessions representing the different morphotypes and ecotypes, to investigate the role of HE in domestication. Our findings demonstrate frequent occurrence of HEs in Brassica napus, with substantial HE patterns shared across populations, indicating their potential role in promoting crop domestication. HE events are asymmetric, with the A genome more frequently replacing C genome segments. These events show a preference for specific genomic regions and vary among populations. We also identify candidate genes in HE regions specific to certain populations, which likely contribute to flowering-time diversification across diverse morphotypes and ecotypes. In addition, we assemble a new genome of a swede accession, confirming the HE signals on the genome and their potential involvement in root tuber development. By analyzing HE in another allopolyploid species, Brassica juncea, we characterize a potential broader role of HE in allopolyploid crop domestication.
Our results provide novel insights into the domestication of polyploid Brassica species and highlight homoeologous exchange as a crucial mechanism for generating variations that are selected for crop improvement in polyploid species.
多倍体被广泛认为是植物界的一种重要进化力量，促进了植物的多样化。异源多倍体的一个显著特征是亚基因组之间同源重组（HE）事件的发生，导致基因组组成、基因表达和表型变异的变化。然而，HE 在植物适应和驯化中的作用仍不清楚。
在这里，我们分析了代表不同形态和生态型的甘蓝型油菜品系的全基因组重测序数据，以研究 HE 在驯化中的作用。我们的研究结果表明，HE 在甘蓝型油菜中频繁发生，种群间存在大量的 HE 模式，表明它们在促进作物驯化中的潜在作用。HE 事件是不对称的，A 基因组更频繁地取代 C 基因组片段。这些事件表现出对特定基因组区域的偏好，并且在种群间存在差异。我们还在特定种群的 HE 区域中鉴定了候选基因，这些基因可能有助于不同形态和生态型的开花时间多样化。此外，我们组装了一个瑞典芜菁品系的新基因组，证实了基因组上的 HE 信号及其在根状茎发育中的潜在参与。通过分析另一个异源多倍体物种芸薹属的 HE，我们描绘了 HE 在异源多倍体作物驯化中的潜在更广泛作用。
我们的研究结果为多倍体甘蓝型油菜物种的驯化提供了新的见解，并强调了同源重组作为在多倍体物种中产生被选择用于作物改良的变异的关键机制的作用。
