Background Gene expression is potentially an important heritable quantitative trait that mediates between genetic variation and higher-level complex phenotypes through time and condition-dependent regulatory interactions. Increasing quantities of high-throughput DNA and RNA sequencing and standardization of research populations has resulted in the accumulation of overlapping -omics data allowing for deeper investigation into the genomic structure and conditional stability of gene expression traits. Therefore, we sought to explore both the genomic and condition-specific characteristics of gene expression heritability within the context of chromosomal structure, using a diverse, 84-line, Oryza sativa (rice) population under optimal and salt-stressed conditions. Results Heritability was estimated for the 84 genotypes with common tools and an approach using biological gene expression replicates similar to a twin study in humans. Overall, 5,936 genes were found to have heritable expression regardless of condition and 1,377 genes were found to have heritable expression only during salt stress. These genes with salt-specific heritable expression are enriched for functional terms associated with response to stimulus and transcription factor activity. Additionally, we discovered that highly and lowly expressed genes, and genes with heritable expression are distributed differently along the chromosomes in patterns that follow previously identified chromosomal conformation capture (Hi-C) A/B chromatin compartments. Furthermore, multiple genomic hot-spots enriched for genes with salt-specific heritability were identified on chromosomes 1, 4, 6, and 8. These hotspots were found to contain genes functionally enriched for transcriptional regulation and overlaps with a previously identified major QTL for salt-tolerance in rice. Conclusions Investigating the heritability of traits, and in-particular gene expression traits, is important towards a basic understanding of how regulatory networks behave across a population. Additionally, heritable gene expression architecture can be used for further exploration of gene-trait relationships, assist in interpretation and analysis of eQTLs, used as priors for approaches seeking to identification of potential biomarkers, or used in genomic selection modules with potential applications in plant breeding. This work provides insights into patterns of expression and spatial patterns at the chromosomal level.

中文翻译：

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水稻基因组盐胁迫遗传基因表达的染色体特征

背景基因表达潜在地是重要的可遗传定量特征，其通过时间和条件依赖性调节相互作用介导遗传变异和更高水平的复杂表型之间。高通量DNA和RNA测序的数量不断增加以及研究人群的标准化，导致了重叠的组学数据的积累，从而可以更深入地研究基因表达特征的基因组结构和条件稳定性。因此，我们试图在最佳和盐胁迫条件下，使用多样化的84系水稻品种，在染色体结构的背景下探索基因表达遗传力的基因组和条件特异性特征。结果使用通用工具评估了84种基因型的遗传力，并且使用生物学基因表达的方法与人类的双胞胎研究相似。总体而言，发现5936个基因在任何条件下均具有可遗传表达，并且仅在盐胁迫期间发现1377个基因具有可遗传表达。这些具有盐特​​异性可遗传表达的基因富含与对刺激和转录因子活性的反应相关的功能性术语。此外，我们发现高表达和低表达的基因以及具有可遗传表达的基因在染色体上的分布方式不同，这些模式遵循先前确定的染色体构象捕获（Hi-C）A / B染色质区室。此外，在1号，4号，6号和8号染色体上鉴定了多个富含盐特异性遗传力基因的基因组热点。发现这些热点包含功能丰富的转录调控基因，并与先前鉴定的主要耐盐QTL重叠在米饭中。结论研究性状的遗传性，尤其是基因表达性状，对于基本了解调节网络在整个种群中的行为方式非常重要。此外，可遗传的基因表达架构可用于进一步探索基因-性状关系，协助解释和分析eQTL，用作寻找潜在生物标志物的先验方法，或用于植物育种中潜在应用的基因组选择模块。