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. Therefore, we sought to explore both the genomic and condition-specific characteristics of gene expression heritability within the context of chromosomal structure. Heritability was estimated for biological gene expression using a diverse, 84-line, Oryza sativa (rice) population under optimal and salt-stressed conditions. Overall, 5936 genes were found to have heritable expression regardless of condition and 1377 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 high-throughput 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. Investigating the heritability of traits, and in-particular gene expression traits, is important towards developing a basic understanding of how regulatory networks behave across a population. This work provides insights into spatial patterns of heritable gene expression at the chromosomal level.

中文翻译：

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水稻基因组中盐胁迫遗传基因表达的染色体特征

基因表达可能是一种重要的可遗传数量性状，它通过时间和条件依赖性调节相互作用在遗传变异和更高级的复杂表型之间进行调节。因此，我们试图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。在最佳和盐胁迫条件下，使用多样化的 84 系水稻（水稻）种群估计生物基因表达的遗传力。总体而言，发现 5936 个基因无论条件如何都具有遗传表达，并且发现 1377 个基因仅在盐胁迫下具有遗传表达。这些具有盐特​​异性遗传表达的基因丰富了与刺激反应和转录因子活性相关的功能术语。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高通量染色体构象捕获 (Hi-C) A/B 染色质区室。此外，在 1、4、6 和 8 号染色体上鉴定了富含具有盐特异性遗传力的基因的多个基因组热点。发现这些热点包含功能丰富的转录调控基因，并与先前鉴定的盐的主要 QTL 重叠水稻的耐性。研究性状的遗传性，特别是基因表达性状，对于基本了解调控网络如何在人群中发挥作用非常重要。