Mapping regulatory variants controlling gene expression in drought response and tolerance in maize
Mapping regulatory variants controlling gene expression in drought response and tolerance in maize
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DOI：
10.1186/s13059-020-02069-1
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发表时间：
2020-07-06
期刊：
影响因子：
12.3
通讯作者：
Qin, Feng
中科院分区：
文献类型：
--
作者：
Liu, Shengxue;Li, Cuiping;Qin, Feng
背景基因表达是细胞应答的关键决定因素。基因表达的自然变异将遗传变异与表型改变联系起来。干旱是全球农作物生产的主要环境威胁，鉴定干旱胁迫下调控基因表达的变异体对抗旱基因的鉴定具有重要价值。结果对224份玉米种质进行了627次RNA-seq分析，共检测到73 573个eQTLs，涉及约3万个表达基因，具有高密度的全基因组单核苷酸多态性，反映了干旱胁迫下基因表达的全面动态遗传结构。揭示了组成型或干旱动态调控基因表达的调控变体。针对转录因子编码基因的动态调控变异，构建了一个反映转录因子及其靶基因层次的干旱响应网络。此外，通过孟德尔随机化分析，97个基因由于其表达变异而优先与耐旱性相关。脱落酸8 '-羟化酶是植物耐旱性的负调控基因。结论本研究揭示了遗传变异对干旱反应中基因表达动态的影响，使我们能够更好地理解远端和近端遗传效应对基因表达和表型可塑性的作用。优先干旱相关基因可以作为功能研究或等位基因挖掘的直接目标。
Background Gene expression is a key determinant of cellular response. Natural variation in gene expression bridges genetic variation to phenotypic alteration. Identification of the regulatory variants controlling the gene expression in response to drought, a major environmental threat of crop production worldwide, is of great value for drought-tolerant gene identification. Results A total of 627 RNA-seq analyses are performed for 224 maize accessions which represent a wide genetic diversity under three water regimes; 73,573 eQTLs are detected for about 30,000 expressing genes with high-density genome-wide single nucleotide polymorphisms, reflecting a comprehensive and dynamic genetic architecture of gene expression in response to drought. The regulatory variants controlling the gene expression constitutively or drought-dynamically are unraveled. Focusing on dynamic regulatory variants resolved to genes encoding transcription factors, a drought-responsive network reflecting a hierarchy of transcription factors and their target genes is built. Moreover, 97 genes are prioritized to associate with drought tolerance due to their expression variations through the Mendelian randomization analysis. One of the candidate genes,Abscisic acid 8 '-hydroxylase, is verified to play a negative role in plant drought tolerance. Conclusions This study unravels the effects of genetic variants on gene expression dynamics in drought response which allows us to better understand the role of distal and proximal genetic effects on gene expression and phenotypic plasticity. The prioritized drought-associated genes may serve as direct targets for functional investigation or allelic mining.