A novel TIR-NBS-LRR gene regulates immune response to Phytophthora root rot in soybean

Zhou, Li; Deng, Sushuang; Xuan, Huidong; Fan, Xing‐Xing; Sun, Ruidong; Zhao, Jinming; Wang, Rui; Guo, Na

doi:10.1016/j.cj.2022.03.003

Cited by 18 publications

(12 citation statements)

References 40 publications

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“…In Colfax, among the genes near or containing up-regulated DE TEs, a significantly up-regulated gene ( Glyma.16G135200 ) exhibited an association with an up-regulated LTR/ Copia element (ID 371175) (Figure 4e; Dataset S1). This gene encodes a Toll/interleukin-1-receptors (TIR)-NBS-LRR (TNL) protein (Swiderski et al, 2009), renowned for its regulatory role as a R protein in immune responses to Phytophthora sojae in soybean (Zhou et al, 2022). Additionally, in Colfax, among the DEGs with down-regulated DE TEs, three harbored DNA/ CACTA elements within their coding regions (Dataset S4).…”

Section: Resultsmentioning

confidence: 99%

“…Of particular interest was the up-regulated TE (LTR/ Copia ) located closely downstream of the significantly up-regulated TNL gene ( Glyma.16G135200 ), which showed a similar gene expression pattern to the TE (Figure 4e; Dataset S1). Recently, a TNL was newly identified in soybean, demonstrating resistance against Phytophthora root rot (Zhou et al, 2022), and has been shown to increase JA- and SA-mediated disease resistance. Our finding suggests a potential role for this TE as a cis -regulatory element, modulating the expression of the TNL gene in defense responses to the pathogen in Colfax.…”

Section: Discussionmentioning

confidence: 99%

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Transcriptomic and epigenetic responses shed light on soybean resistance toPhytophthora sansomeana

Lee,

DiBiase,

Liu

et al. 2024

Preprint

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Phytophthora root rot caused by oomycete pathogens in the Phytophthora genus poses a significant threat to soybean productivity. While resistance mechanisms againstPhytophthora sojaehave been extensively studied in soybean, the molecular basis underlying immune responses toPhytophthora sansomeanaremains unclear. We investigated transcriptomic and epigenetic responses of two resistant (Colfax and NE2701) and two susceptible (Williams 82 and Senaki) soybean lines at four time points (2, 4, 8, and 16 hours post inoculation, hpi) afterP. sansomeanainoculation. Comparative transcriptomic analyses revealed a greater number of differentially expressed genes (DEGs) upon pathogen inoculation in resistant lines, particularly at 8 and 16 hpi, predominantly associated with ethylene and reactive oxygen species-mediated defense pathways. Moreover, DE transposons were predominantly up-regulated after inoculation and enriched near genes in Colfax. A long non-coding RNA (lncRNA) within the mapped region of the resistance gene exhibited exclusive up-regulation in the resistant lines after inoculation, potentially regulating two flanking LURP-one-related genes. Furthermore, DNA methylation analysis revealed increased CHH methylation levels in lncRNAs after inoculation, with delayed responses in Colfax compared to Williams 82. Overall, our results provide comprehensive insights into soybean responses toP. sansomeana, highlighting potential roles of lncRNAs and epigenetic regulation in plant defense.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Transcriptomic and epigenetic responses shed light on soybean resistance toPhytophthora sansomeana

Lee,

DiBiase,

Liu

et al. 2024

Preprint

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“…To date, several miRNAs from different plant species have been documented to participate in plant defense against a variety of Phytophthora spp. [ 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 ]. Although phytophthora blight disease frequently causes heavy losses to global pepper production, our knowledge on the regulatory networks of miRNAs and their target genes in pepper’s defense against P. capsici is still limited.…”

Section: Discussionmentioning

confidence: 99%

Integrative Transcriptome Analysis of mRNA and miRNA in Pepper’s Response to Phytophthora capsici Infection

Li,

Wang,

Guo

et al. 2024

Biology

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Phytophthora blight of pepper is a notorious disease caused by the oomycete pathogen Phytophthora capsici, which poses a great threat to global pepper production. MicroRNA (miRNA) is a class of non-coding small RNAs that regulate gene expressions by altering the translation efficiency or stability of targeted mRNAs, which play important roles in the regulation of a plant’s response to pathogens. Herein, time-series mRNA-seq libraries and small RNA-seq libraries were constructed using pepper roots from the resistant line CM334 and the susceptible line EC01 inoculated with P. capsici at 0, 6, 24, and 48 h post-inoculation, respectively. For mRNA-seq analysis, a total of 2159 and 2971 differentially expressed genes (DEGs) were identified in CM334 and EC01, respectively. For miRNA-seq analysis, 491 pepper miRNAs were identified, including 330 known miRNAs and 161 novel miRNAs. Among them, 69 and 88 differentially expressed miRNAs (DEMs) were identified in CM334 and EC01, respectively. Examination of DEMs and their targets revealed 22 regulatory networks, predominantly featuring up-regulated miRNAs corresponding to down-regulated target genes. Notably, these DEM-DEG regulatory networks exhibited significant overlap between CM334 and EC01, suggesting that they might contribute to pepper’s basal defense against P. capsici. Furthermore, five selected DEMs (miR166, miR1171, miR395, miR530 and miRN2) and their target genes underwent qRT-PCR validation, confirming a consistent negative correlation in the expression patterns of miRNAs and their targets. This comprehensive analysis provides novel insights into the regulatory networks of miRNAs and their targets, offering valuable contributions to our understanding of pepper’s defense mechanisms against P. capsici.

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“…NLR were identified as candidate resistant genes for several soybean diseases caused by bacterial, fungal, oomycete and virus [29][30][31][32][33][34][35][36] . Some of these NLR genes have been functionally validated 31,37,38 . Furthermore, genomic regions identified by genome-wide association studies (GWAS) and related to resistance against several soybean diseases were enriched in LRR-RLK and NLR 39 .…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of soybean transcriptional profiles reveals defense mechanisms involved in resistance againstDiaporthe caulivora

Mena

Reboledo

Stewart

et al. 2023

Preprint

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Soybean stem canker (SSC) caused by the fungal pathogen Diaporthe caulivora is an important disease affecting soybean production. However, limited information related to the molecular mechanisms underlying soybean resistance to Diaporthe species is available. In the present work, the defense responses to D. caulivora in two contrasting soybean genotypes were analyzed. We showed that Genesis 5601 is more resistant to fungal infection than Williams, evidenced by significantly smaller lesion length, reduced disease severity and pathogen biomass. Transcriptional profiling was performed in untreated plants and in D. caulivora-inoculated and control-treated tissues at 8 and 48 hours post inoculation (hpi). In total, 2.322 and 1.855 genes were differentially expressed in Genesis 5601 and Williams, respectively. Interestingly, Genesis 5601 exhibited a significantly higher number of upregulated genes compared to Williams at 8 hpi, 1.028 versus 434 genes. Resistance to D. caulivora was associated with defense activation through transcriptional reprogramming mediating perception of the pathogen by receptors, biosynthesis of phenylpropanoids, hormones, small heat shock proteins and pathogenesis related (PR) genes. These findings provide novel insights into soybean defense molecular mechanisms used to control D. caulivora, and generate a foundation for development of resistant SSC varieties within soybean breeding programs.

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A novel TIR-NBS-LRR gene regulates immune response to Phytophthora root rot in soybean

Cited by 18 publications

References 40 publications

Transcriptomic and epigenetic responses shed light on soybean resistance toPhytophthora sansomeana

Transcriptomic and epigenetic responses shed light on soybean resistance toPhytophthora sansomeana

Integrative Transcriptome Analysis of mRNA and miRNA in Pepper’s Response to Phytophthora capsici Infection

Comparative analysis of soybean transcriptional profiles reveals defense mechanisms involved in resistance againstDiaporthe caulivora

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