Patterns of Sequence and Expression Diversification Associate Members of the PADRE Gene Family With Response to Fungal Pathogens

Didelon, Marie; Khafif, Mehdi; Godiard, Laurence; Barbacci, Adelin; Raffaele, Sylvain

doi:10.3389/fgene.2020.00491

Cited by 12 publications

(8 citation statements)

References 89 publications

(118 reference statements)

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“…Recent studies revealed that DUF4228 genes were involved in abiotic stress response and cadmium tolerance. Analysis of AtDUF4228 gene expression under a variety of stress treatments and co-expression network analysis of DUF4228 genes in different species of plants showed that several DUF4228 genes may play a synergistic role in plant defense (Didelon et al, 2020). These results suggest that members of the DUF4228 family may respond to abiotic stresses in soybean.…”

Section: Introductionmentioning

confidence: 85%

Genome-Wide Analysis of the DUF4228 Family in Soybean and Functional Identification of GmDUF4228–70 in Response to Drought and Salt Stresses

Leng

Li²,

Chen

et al. 2021

Front. Plant Sci.

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Domain of unknown function 4228 (DUF4228) proteins are a class of proteins widely found in plants, playing an important role in response to abiotic stresses. However, studies on the DUF4228 family in soybean (Glycine max L.) are sparse. In this study, we identified a total of 81 DUF4228 genes in soybean genome, named systematically based on their chromosome distributions. Results showed that these genes were unevenly distributed on the 20 chromosomes of soybean. The predicted soybean DUF4228 proteins were identified in three groups (Groups I–III) based on a maximum likelihood phylogenetic tree. Genetic structure analysis showed that most of the GmDUF4228 genes contained no introns. Expression profiling showed that GmDUF4228 genes were widely expressed in different organs and tissues in soybean. RNA-seq data were used to characterize the expression profiles of GmDUF4228 genes under the treatments of drought and salt stresses, with nine genes showing significant up-regulation under both drought and salt stress further functionally verified by promoter (cis-acting elements) analysis and quantitative real-time PCR (qRT-PCR). Due to its upregulation under drought and salt stresses based on both RNA-seq and qRT-PCR analyses, GmDUF4228-70 was selected for further functional analysis in transgenic plants. Under drought stress, the degree of leaf curling and wilting of the GmDUF4228-70-overexpressing (GmDUF4228-70-OE) line was lower than that of the empty vector (EV) line. GmDUF4228-70-OE lines also showed increased proline content, relative water content (RWC), and chlorophyll content, and decreased contents of malondialdehyde (MDA), H2O2, and O2–. Under salt stress, the changes in phenotypic and physiological indicators of transgenic plants were the same as those under drought stress. In addition, overexpression of the GmDUF4228-70 gene promoted the expression of marker genes under both drought and salt stresses. Taken together, the results indicated that GmDUF4228 genes play important roles in response to abiotic stresses in soybean.

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Section: Introductionmentioning

confidence: 85%

Genome-Wide Analysis of the DUF4228 Family in Soybean and Functional Identification of GmDUF4228–70 in Response to Drought and Salt Stresses

Leng

Li²,

Chen

et al. 2021

Front. Plant Sci.

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show abstract

“…Current studies illustrated that the DUF4228 genes had been involved in cadmium tolerance and abiotic stress indication. Analysis of the AtDUF4228 gene expression under the various co-expression networks of the DUF4228 gene family and stress treatments in various plant species indicated the synergistic role of DUF4228 genes in plant immune response (Didelon et al, 2020). These obtaining results proposed that DUF4228 gene family may also associate with abiotic stress response in soybean.…”

Section: Introductionmentioning

confidence: 83%

Identification and Expression Analysis of DUF4228 Domain Containing (DDP) Genes in Potato Under Abiotic and Phytohormone Stress

Sharif

Zaynab

Khan

et al. 2021

Preprint

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DUF4228 (Domain of unknown function 4228) proteins are widely distributed in plants and performed a vital role in abiotic stress response. In potato (Solanum tuberosum), the study of the DUF4228 gene family is sparse. To understant the role of DUF4228 in potato a comprehensive genome-wide analysis was carried out in potato genome. Further, the StDUAF4228 genes relative expression was also evaluated in various plant tissues. In the present study identified 31 StDUF4228 genes were clustered into six groups. The promoter analysis of StDUF4228 revealed various cis-acting regulatory components response to abiotic and phytohormones stresses. Under selection pressure, gene duplication also showed various positive and purifying selections in StDUF4228 genes. Expression profiling indicated that StDUF4228 genes were broadly expressed in various tissues and organs in potato. Moreover, the StDUF4228 genes profiles expression was characterized through RNA-sequence analysis data under salt and heat treatments. In potato, StDUF4228-4, StDUF4228-14, StDUF4228-21, and StDUF4228-30 represented a high expression under salt and heat stress.Furthermore, 23 genes under IAA treatment and 18 under ABA treatment, showed that IAA and ABA played a vital role in stresses. The RT-qPCR and expression profilling exhibited high expression in root tissues. Moreover multiple miRNA target StDUF4228 genes in potato.These expression results provide primary reference data and functional analysis data for other commercial crops.

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“…According to this analysis, eight of the 96 genes were biotic-stimulus-responsive ( Table 6 ). These genes are involved in the resistance responses to bacterial or fungal diseases ( Mobley et al., 1999 ; Clay et al., 2009 ; Li et al., 2019 ; Depuydt and Vandepoele, 2021 ) and microbe-associated molecular patterns ( Park et al., 2015 ; Didelon et al., 2020 ). Since these genes were also speculated to play a role in defense responses against invading pathogens in cabbage, we designated them as candidate genes associated with black rot resistance in the BR155 line.…”

Section: Discussionmentioning

confidence: 99%

A GBS-based genetic linkage map and quantitative trait loci (QTL) associated with resistance to Xanthomonas campestris pv. campestris race 1 identified in Brassica oleracea

Choi

Lim

et al. 2023

Front. Plant Sci.

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The production of Brassica oleracea, an important vegetable crop, is severely affected by black rot disease caused by the bacterial pathogen Xanthomonas campestris pv. campestris. Resistance to race 1, the most virulent and widespread race in B. oleracea, is under quantitative control; therefore, identifying the genes and genetic markers associated with resistance is crucial for developing resistant cultivars. Quantitative trait locus (QTL) analysis of resistance in the F2 population developed by crossing the resistant parent BR155 with the susceptible parent SC31 was performed. Sequence GBS approach was used to develop a genetic linkage map. The map contained 7,940 single nucleotide polymorphism markers consisting of nine linkage groups spanning 675.64 cM with an average marker distance of 0.66 cM. The F2:3 population (N = 126) was evaluated for resistance to black rot disease in summer (2020), fall (2020), and spring (2021). QTL analysis, using a genetic map and phenotyping data, identified seven QTLs with LOD values between 2.10 and 4.27. The major QTL, qCaBR1, was an area of overlap between the two QTLs identified in the 2nd and 3rd trials located at C06. Among the genes located in the major QTL interval, 96 genes had annotation results, and eight were found to respond to biotic stimuli. We compared the expression patterns of eight candidate genes in susceptible (SC31) and resistant (BR155) lines using qRT-PCR and observed their early and transient increases or suppression in response to Xanthomonas campestris pv. campestris inoculation. These results support the involvement of the eight candidate genes in black rot resistance. The findings of this study will contribute towards marker-assisted selection, additionally the functional analysis of candidate genes may elucidate the molecular mechanisms underlying black rot resistance in B. oleracea.

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Patterns of Sequence and Expression Diversification Associate Members of the PADRE Gene Family With Response to Fungal Pathogens

Cited by 12 publications

References 89 publications

Genome-Wide Analysis of the DUF4228 Family in Soybean and Functional Identification of GmDUF4228–70 in Response to Drought and Salt Stresses

Genome-Wide Analysis of the DUF4228 Family in Soybean and Functional Identification of GmDUF4228–70 in Response to Drought and Salt Stresses

Identification and Expression Analysis of DUF4228 Domain Containing (DDP) Genes in Potato Under Abiotic and Phytohormone Stress

A GBS-based genetic linkage map and quantitative trait loci (QTL) associated with resistance to Xanthomonas campestris pv. campestris race 1 identified in Brassica oleracea

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