Genome-wide identification, phylogeny and expression analysis of the SPL gene family and its important role in salt stress in Medicago sativa L.

He, Fei; Long, Ruicai; Wei, Chunxue; Zhang, Yunxiu; Li, Mingna; Yang, Qingchuan; Wang, Zhen; Chen, Lin

doi:10.1186/s12870-022-03678-7

Cited by 12 publications

(3 citation statements)

References 57 publications

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“…MEME (Multiple Em for Motif Elicitation) tool (5.4.1 version, https://meme-suite.org/meme/tools/meme ) [ 59 ] was employed for the analysis of conserved motifs from DREB proteins in G. barbadense , G. hirsutum , G. arboreum , and G. raimondii . The phylogenetic trees and conserved motifs were integrated by using TBtools software.…”

Section: Methodsmentioning

confidence: 99%

Genome-wide identification and expression analysis of DREB family genes in cotton

Song

Wang

et al. 2023

BMC Plant Biol

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Background Dehydration responsive element-binding (DREB) transcription factors are widely present in plants, and involve in signalling transduction, plant growth and development, and stress response. DREB genes have been characterized in multiple species. However, only a few DREB genes have been studied in cotton, one of the most important fibre crops. Herein, the genome‑wide identification, phylogeny, and expression analysis of DREB family genes are performed in diploid and tetraploid cotton species. Results In total, 193, 183, 80, and 79 putative genes containing the AP2 domain were identified using bioinformatics approaches in G. barbadense, G. hirsutum, G. arboretum, and G. raimondii, respectively. Phylogenetic analysis showed that based on the categorization of Arabidopsis DREB genes, 535 DREB genes were divided into six subgroups (A1–A6) by using MEGA 7.0. The identified DREB genes were distributed unevenly across 13/26 chromosomes of A and/or D genomes. Synteny and collinearity analysis confirmed that during the evolution, the whole genome duplications, segmental duplications, and/or tandem duplications occurred in cotton DREB genes, and then DREB gene family was further expanded. Further, the evolutionary trees with conserved motifs, cis-acting elements, and gene structure of cotton DREB gene family were predicted, and these results suggested that DREB genes might be involved in the hormone and abiotic stresses responses. The subcellular localization showed that in four cotton species, DREB proteins were predominantly located in the nucleus. Further, the analysis of DREB gene expression was carried out by real-time quantitative PCR, confirming that the identified DREB genes of cotton were involved in response to early salinity and osmotic stress. Conclusions Collectively, our results presented a comprehensive and systematic understanding in the evolution of cotton DREB genes, and demonstrated the potential roles of DREB family genes in stress and hormone response.

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Section: Methodsmentioning

confidence: 99%

Genome-wide identification and expression analysis of DREB family genes in cotton

Song

Wang

et al. 2023

BMC Plant Biol

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“…Multiple studies have proven that squamosa promoter-binding-like protein (SPL) can regulate salt tolerance in many plants, such as apple [ 9 ], alfalfa ( Medicago sativa L.) [ 72 ], and tamarisk ( Tamarix chinensis ) [ 57 ]. Recent research showed that silencing CaSBP12 in pepper ( Capsicum annuum ) enhances tolerance to salt stress and reduces ROS accumulation [ 73 ].…”

Section: Discussionmentioning

confidence: 99%

Integration of mRNA and miRNA Analysis Reveals the Post-Transcriptional Regulation of Salt Stress Response in Hemerocallis fulva

Zhou

Gao

Zhao

2023

IJMS

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MicroRNAs (miRNAs) belong to non-coding small RNAs which have been shown to take a regulatory function at the posttranscriptional level in plant growth development and response to abiotic stress. Hemerocallis fulva is an herbaceous perennial plant with fleshy roots, wide distribution, and strong adaptability. However, salt stress is one of the most serious abiotic stresses to limit the growth and production of Hemerocallis fulva. To identify the miRNAs and their targets involved in the salt stress resistance, the salt-tolerant H. fulva with and without NaCl treatment were used as materials, and the expression differences of miRNAs–mRNAs related to salt-tolerance were explored and the cleavage sites between miRNAs and targets were also identified by using degradome sequencing technology. In this study, twenty and three significantly differential expression miRNAs (p-value < 0.05) were identified in the roots and leaves of H. fulva separately. Additionally, 12,691 and 1538 differentially expressed genes (DEGs) were also obtained, respectively, in roots and leaves. Moreover, 222 target genes of 61 family miRNAs were validated by degradome sequencing. Among the DE miRNAs, 29 pairs of miRNA targets displayed negatively correlated expression profiles. The qRT-PCR results also showed that the trends of miRNA and DEG expression were consistent with those of RNA-seq. A gene ontology (GO) enrichment analysis of these targets revealed that the calcium ion pathway, oxidative defense response, microtubule cytoskeleton organization, and DNA binding transcription factor responded to NaCl stress. Five miRNAs, miR156, miR160, miR393, miR166, and miR396, and several hub genes, squamosa promoter-binding-like protein (SPL), auxin response factor 12 (ARF), transport inhibitor response 1-like protein (TIR1), calmodulin-like proteins (CML), and growth-regulating factor 4 (GRF4), might play central roles in the regulation of NaCl-responsive genes. These results indicate that non-coding small RNAs and their target genes that are related to phytohormone signaling, Ca2+ signaling, and oxidative defense signaling pathways are involved in H. fulva’s response to NaCl stress.

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“…Overexpression of Vitis pseudoreticulata VpSBP16 could enhance the scavenging ability of ROS to enhance the salt tolerance and drought tolerance of grapes (Hou et al 2018 ). In addition, 3 differentially expressed MsSPLs ( MsSPL17 , MsSPL23 and MsSPL36 ) were found in Medicago sativa under salt stress, which provided comprehensive information for the mechanism underlying salt tolerance improvement in M. sativa (He et al 2022b ).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification, stress- and hormone-responsive expression characteristics, and regulatory pattern analysis of Scutellaria baicalensis SbSPLs

Wu,

Zhao,

et al. 2024

Plant Mol Biol

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SQUAMOSA PROMOTER BINDING PROTEIN-LIKEs (SPLs) encode plant-specific transcription factors that regulate plant growth and development, stress response, and metabolite accumulation. However, there is limited information on Scutellaria baicalensis SPLs. In this study, 14 SbSPLs were identified and divided into 8 groups based on phylogenetic relationships. SbSPLs in the same group had similar structures. Abscisic acid-responsive (ABRE) and MYB binding site (MBS) cis-acting elements were found in the promoters of 8 and 6 SbSPLs. Segmental duplications and transposable duplications were the main causes of SbSPL expansion. Expression analysis based on transcriptional profiling showed that SbSPL1, SbSPL10, and SbSPL13 were highly expressed in roots, stems, and flowers, respectively. Expression analysis based on quantitative real-time polymerase chain reaction (RT‒qPCR) showed that most SbSPLs responded to low temperature, drought, abscisic acid (ABA) and salicylic acid (SA), among which the expression levels of SbSPL7/9/10/12 were significantly upregulated in response to abiotic stress. These results indicate that SbSPLs are involved in the growth, development and stress response of S. baicalensis. In addition, 8 Sba-miR156/157 s were identified, and SbSPL1-5 was a potential target of Sba-miR156/157 s. The results of target gene prediction and coexpression analysis together indicated that SbSPLs may be involved in the regulation of L-phenylalanine (L-Phe), lignin and jasmonic acid (JA) biosynthesis. In summary, the identification and characterization of the SbSPL gene family lays the foundation for functional research and provides a reference for improved breeding of S. baicalensis stress resistance and quality traits.

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Genome-wide identification, phylogeny and expression analysis of the SPL gene family and its important role in salt stress in Medicago sativa L.

Cited by 12 publications

References 57 publications

Genome-wide identification and expression analysis of DREB family genes in cotton

Genome-wide identification and expression analysis of DREB family genes in cotton

Integration of mRNA and miRNA Analysis Reveals the Post-Transcriptional Regulation of Salt Stress Response in Hemerocallis fulva

Genome-wide identification, stress- and hormone-responsive expression characteristics, and regulatory pattern analysis of Scutellaria baicalensis SbSPLs

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