Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361104, China.
School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China.
Plant Cell Rep. 2023 Sep;42(9):1473-1485. doi: 10.1007/s00299-023-03042-5. Epub 2023 Jul 30.
This study provided important insights into the genetic architecture of variations in A. thaliana leaf ionome in a cell-type-specific manner. The functional interpretation of traits associated variants by expression quantitative trait loci (eQTL) analysis is usually performed in bulk tissue samples. While the regulation of gene expression is context-dependent, such as cell-type-specific manner. In this study, we estimated cell-type abundances from 728 bulk tissue samples using single-cell RNA-sequencing dataset, and performed cis-eQTL mapping to identify cell-type-interaction eQTL (cis-eQTLs(ci)) in A. thaliana. Also, we performed Genome-wide association studies (GWAS) analyses for 999 accessions to identify the genetic basis of variations in A. thaliana leaf ionome. As a result, a total of 5,664 unique eQTL genes and 15,038 unique cis-eQTLs(ci) were significant. The majority (62.83%) of cis-eQTLs(ci) were cell-type-specific eQTLs. Using colocalization, we uncovered one interested gene AT2G25590 in Phloem cell, encoding a kind of plant Tudor-like protein with possible chromatin-associated functions, which colocalized with the most significant cis-eQTL(ci) of a Mo-related locus (Chr2:10,908,806:A:C; P = 3.27 × 10). Furthermore, we prioritized eight target genes associated with AT2G25590, which were previously reported in regulating the concentration of Mo element in A. thaliana. This study revealed the genetic regulation of ionomic variations and provided a foundation for further studies on molecular mechanisms of genetic variants controlling the A. thaliana ionome.
这项研究提供了重要的见解，了解拟南芥叶片离子组在细胞类型特异性方式上的遗传结构。通过表达数量性状位点 (eQTL) 分析对与性状相关的变体进行功能解释通常在批量组织样本中进行。虽然基因表达的调控是上下文相关的，例如细胞类型特异性。在这项研究中，我们使用单细胞 RNA 测序数据集从 728 个批量组织样本中估计细胞类型丰度，并进行顺式 eQTL 作图，以鉴定拟南芥中的细胞类型相互作用 eQTL (cis-eQTLs(ci))。此外，我们对 999 个品系进行全基因组关联研究 (GWAS) 分析，以鉴定拟南芥叶片离子组变异的遗传基础。结果，总共鉴定出 5664 个独特的 eQTL 基因和 15038 个独特的 cis-eQTLs(ci) 是显著的。大多数 (62.83%) cis-eQTLs(ci) 是细胞类型特异性的 eQTL。通过共定位，我们在韧皮部细胞中发现了一个感兴趣的基因 AT2G25590，它编码一种植物 Tudor 样蛋白，具有可能与染色质相关的功能，该基因与 Mo 相关基因座的最显著 cis-eQTL(ci) 共定位 (Chr2:10,908,806:A:C; P=3.27×10)。此外，我们优先考虑了与 AT2G25590 相关的八个靶基因，这些基因之前在调节拟南芥中 Mo 元素浓度方面有报道。这项研究揭示了离子组变异的遗传调控，并为进一步研究遗传变异控制拟南芥离子组的分子机制提供了基础。
