Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA.
Department of Horticulture, University of Minnesota, Saint Paul, MN, 55108, USA.
Genome Biol. 2022 Nov 7;23(1):234. doi: 10.1186/s13059-022-02807-7.
Many plant species exhibit genetic variation for coping with environmental stress. However, there are still limited approaches to effectively uncover the genomic region that regulates distinct responsive patterns of the gene across multiple varieties within the same species under abiotic stress.
By analyzing the transcriptomes of more than 100 maize inbreds, we reveal many cis- and trans-acting eQTLs that influence the expression response to heat stress. The cis-acting eQTLs in response to heat stress are identified in genes with differential responses to heat stress between genotypes as well as genes that are only expressed under heat stress. The cis-acting variants for heat stress-responsive expression likely result from distinct promoter activities, and the differential heat responses of the alleles are confirmed for selected genes using transient expression assays. Global footprinting of transcription factor binding is performed in control and heat stress conditions to document regions with heat-enriched transcription factor binding occupancies.
Footprints enriched near proximal regions of characterized heat-responsive genes in a large association panel can be utilized for prioritizing functional genomic regions that regulate genotype-specific responses under heat stress.
许多植物物种表现出遗传变异，以应对环境压力。然而，在非生物胁迫下，对于如何有效地揭示同一物种内多个品种中调节基因不同响应模式的基因组区域，仍然存在有限的方法。
通过分析 100 多个玉米自交系的转录组，我们揭示了许多顺式和反式作用的 eQTLs，它们影响基因对热胁迫的表达响应。对热应激的顺式作用 eQTLs在基因型间热应激响应差异的基因以及仅在热应激下表达的基因中被鉴定出来。对热应激反应表达的顺式作用变体可能源于不同的启动子活性，并且使用瞬时表达测定法证实了所选基因的等位基因的不同热反应。在对照和热应激条件下进行转录因子结合的全局足迹分析，以记录富含热转录因子结合占据的区域。
在大型关联面板中，在特征性热响应基因的近端区域附近富集的足迹可用于优先考虑功能基因组区域，这些区域在热胁迫下调节基因型特异性响应。
