Identifying candidate genes and patterns of heat-stress response in rice using a genome-wide association study and transcriptome analyses

Yang, Yingxue; Zhang, Chao; Zhu, De; He, Huiying; Wei, Zhaoran; Yuan, Qiaoling; Li, Xiaoxia; Gao, Xu; Zhang, Bin; Gao, Hongsheng; Wang, Bo; Cao, Shuaimin; Wang, Tianyi; Li, Yuhua; Yu, Xiaoman; Guo, Longbiao; Hu, Guanjing; Qian, Qian; Shang, Lianguang

doi:10.1016/j.cj.2022.02.011

Cited by 21 publications

(19 citation statements)

References 56 publications

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“…S2). These results suggest that AS and transcription regulation function independently under HTS, which is the case for Arabidopsis [62], tea [31], and rice [63].…”

Section: Discussionmentioning

confidence: 76%

Transcriptomic and alternative splicing analyses provide insights into the roles of exogenous salicylic acid ameliorating waxy maize seedling growth under heat stress

Guo

Wang

et al. 2022

BMC Plant Biol

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Background Salicylic acid (SA) is a phytohormone which works to regulate the abiotic stress response of plants. However, the molecular mechanism by which SA mediates heat tolerance in waxy maize (Zea mays L. sinsensis Kulesh) remains unknown. Results Two varieties of waxy maize seedlings, heat-tolerant ‘Yunuo7’ (Y7) and heat-sensitive ‘Suyunuo5’ (S5), were pretreated with SA prior to heat stress (HTS). After treatment, physiological and transcriptomic changes were analyzed. Compared with HTS, the exogenous application of SA enhanced the shoot dry weight, the activities of antioxidant enzymes (e.g., SOD, POD, CAT and APX), and the concentration of endogenous phytohormones (e.g., SA, ABA, IAA, GA3), while decreased the MDA content. Transcriptome analysis showed that the number of differentially expressed genes (DEGs) identified in the control (CK) vs HTS and HTS vs HTS + SA comparisons were more in S5 than in Y7. HTS induced the downregulation of genes involved in photosynthesis and the upregulation of genes encoding heat shock transcription factors (HSFs) and heat shock proteins (HSPs). Compared with HTS, SA pretreatment reversed the expression of 5 photosynthesis-related genes, 26 phytohormone-related genes, and all genes encoding HSFs and HSPs in S5. Furthermore, the number of alternative splicing (AS) events increased under HTS treatment for both varieties, while decreased under SA pretreatment of S5. Differentially spliced genes (DSGs) showed little overlap with DEGs, and DEGs and DSGs differed significantly in functional enrichment. Conclusions Physiological and transcriptional together indicated that HTS and SA pretreatment had a greater effect on S5 than Y7. Additionally, it appears that transcriptional regulation and AS work synergistically to enhance thermotolerance in heat-sensitive waxy maize. Our study revealed the regulatory effects and underlying molecular mechanisms of SA on waxy maize seedling under HTS.

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“…S2). These results suggest that AS and transcription regulation function independently under HTS, which is the case for Arabidopsis [62], tea [31], and rice [63].…”

Section: Discussionmentioning

confidence: 76%

Transcriptomic and alternative splicing analyses provide insights into the roles of exogenous salicylic acid ameliorating waxy maize seedling growth under heat stress

Guo

Wang

et al. 2022

BMC Plant Biol

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“…There were 4,943 differential TF footprints located in putative promoter regions (-2,000bp from the TSS per gene) and another 1,486 located within gene regions. The differential TF footprints included more regions with increased accessibility in heat stress (11,140) compared to regions with reduced accessibility in heat stress compared to controls (2,652). The regions with increased MOAseq coverage in heat stress compared to control might reflect increased binding or occupancy of transcription factors activated by heat stress.…”

Section: Changes In Chromatin Structure Associated With Heat Responsi...mentioning

confidence: 99%

“…Transcriptome profiling in plants has identified many genes that exhibit altered transcript abundance in response to abiotic stress [7][8][9][10][11] . The heat-shock factor (HSF) transcription factors (TFs) are activated in response to heat stress 12 and can regulate the expression level of many genes through interactions with cis-acting elements.…”

Section: Introductionmentioning

confidence: 99%

Mapping Responsive Genomic Elements to Heat Stress in a Maize Diversity Panel

Liang

Myers

Petrella

et al. 2022

Preprint

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Many plant species exhibit genetic variation for tolerating environmental stress. A transcriptome investigation of over 100 maize inbreds revealed many cis- and trans-acting eQTLs that influence the expression response to heat stress. The cis-acting eQTL 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 were confirmed for selected genes using transient expression assays. Global foot-printing of transcription factor binding was 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 regulatory regions that regulate genotype-specific responses under heat stress.

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“…Transcriptome profiling in plants has identified many genes that exhibit altered transcript abundance in response to abiotic stress [7][8][9][10][11]. The heat shock factor (HSF) transcription factors (TFs) are activated in response to heat stress [12] and can regulate the…”

Section: Introductionmentioning

confidence: 99%

“…Severe heat stress events during reproductive periods can result in major changes in the seed set [3,4]. Heat stress events at earlier vegetative stages can result in leaf senescence and reduced growth rate [5,6].Transcriptome profiling in plants has identified many genes that exhibit altered transcript abundance in response to abiotic stress [7][8][9][10][11]. The heat shock factor (HSF) transcription factors (TFs) are activated in response to heat stress [12] and can regulate the…”

mentioning

confidence: 99%

Mapping responsive genomic elements to heat stress in a maize diversity panel

et al. 2022

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Background 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. Results 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. Conclusions 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.

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Identifying candidate genes and patterns of heat-stress response in rice using a genome-wide association study and transcriptome analyses

Cited by 21 publications

References 56 publications

Transcriptomic and alternative splicing analyses provide insights into the roles of exogenous salicylic acid ameliorating waxy maize seedling growth under heat stress

Transcriptomic and alternative splicing analyses provide insights into the roles of exogenous salicylic acid ameliorating waxy maize seedling growth under heat stress

Mapping Responsive Genomic Elements to Heat Stress in a Maize Diversity Panel

Mapping responsive genomic elements to heat stress in a maize diversity panel

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