Late embryogenesis abundant (LEA) gene family in <i>Salvia miltiorrhiza</i>: identification, expression analysis, and response to drought stress

Chen, Juan; Li, Na; Wang, Xiaoyu; Meng, Xue; Cui, Xiaomin; Chen, Zhiyong; Ren, Hui; Ma, Jing; Líu, Hao

doi:10.1080/15592324.2021.1891769

Cited by 16 publications

(13 citation statements)

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“…In our study, HMM model and BLAST were used to search for PnoLEA gene family in the genome database of P. notoginseng, and consequently 61 PnoLEA genes were identified (Table 1). The numbers of PnoLEA genes identified in P. notoginseng are consistent with the ones in S. miltiorrhiza [11], but is less than the ones in wheat [43] and poplar (Populus simonii) [44]. The number of LEA gene family members showed significant differences among species, and this may be related to the ploidy of the species and the expansion of the gene family.…”

Section: Molecular Characteristics Of Pnolea Genesmentioning

confidence: 51%

“…For example, the expression of most LEA genes showed different tissue-specificity in maize [2]. The SmLEA genes of Salvia miltiorrhiza are specifically expressed in distinct tissues, and most of them are up regulated when Salvia miltiorrhiza is under drought conditions [11]. LEA proteins are generally classified into eight subfamilies based on the similarity of sequences and specific conserved domains, including LEA_1, LEA_2, LEA_3, LEA_4, LEA_5, LEA_6, dehydrin (DHN) and seed maturation protein (SMP) [12].…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide identification and characterization of members of the LEA gene family in Panax notoginseng and their transcriptional responses to dehydration of recalcitrant seeds

Jia

Wang

et al. 2023

BMC Genomics

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Background Late embryogenesis abundant (LEA) proteins play an important role in dehydration process of seed maturation. The seeds of Panax notoginseng (Burkill) F. H. Chen are typically characterized with the recalcitrance and are highly sensitive to dehydration. However, it is not very well known about the role of LEA proteins in response to dehydration stress in P. notoginseng seeds. We will perform a genome-wide analysis of the LEA gene family and their transcriptional responses to dehydration stress in recalcitrant P. notoginseng seeds. Results In this study, 61 LEA genes were identified from the P. notoginseng genome, and they were renamed as PnoLEA. The PnoLEA genes were classified into seven subfamilies based on the phylogenetic relationships, gene structure and conserved domains. The PnoLEA genes family showed relatively few introns and was highly conserved. Unexpectedly, the LEA_6 subfamily was not found, and the LEA_2 subfamily contained 46 (75.4%) members. Within 19 pairs of fragment duplication events, among them 17 pairs were LEA_2 subfamily. In addition, the expression of the PnoLEA genes was obviously induced under dehydration stress, but the germination rate of P. notoginseng seeds decreased as the dehydration time prolonged. Conclusions We found that the lack of the LEA_6 subfamily, the expansion of the LEA_2 subfamily and low transcriptional levels of most PnoLEA genes might be implicated in the recalcitrant formation of P. notoginseng seeds. LEA proteins are essential in the response to dehydration stress in recalcitrant seeds, but the protective effect of LEA protein is not efficient. These results could improve our understanding of the function of LEA proteins in the response of dehydration stress and their contributions to the formation of seed recalcitrance.

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Section: Molecular Characteristics Of Pnolea Genesmentioning

confidence: 51%

Section: Introductionmentioning

confidence: 99%

Genome-wide identification and characterization of members of the LEA gene family in Panax notoginseng and their transcriptional responses to dehydration of recalcitrant seeds

Jia

Wang

et al. 2023

BMC Genomics

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“…Histone acetylation is essential in the cell cycle and in response to abiotic stress (light, heat, UVB, sugar, salt, and wound) and hormonal change (salicylic, ethylene, abscisic acid and auxin) ( Jiang et al., 2020 ). Histone acetyltransferase genes previously discovered in rice ( Liu et al., 2012 ), Triticum aestivum ( Gao et al., 2021 ), and Arabidopsis thaliana ( Pandey et al., 2002 ) (Solyc02g077970.2.1) belong to the LEA protein family which are connected with salinity and water stress signaling and have been reported in many plants like Vigna glabrescens ( Singh et al., 2022 ), cotton ( Magwanga et al., 2018 ), Salvia miltiorrhiza ( Chen et al., 2021 ), and Triticum aestivum ( Liu et al., 2019 ). The presence of AP2 domain was detected in one member (Solyc03g044300.2.1) that contributed to transcriptional regulation and responded to stresses as found in wheat ( Magar et al., 2022 ) and castor bean ( Xu et al., 2013 ).…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification, comprehensive characterization of transcription factors, cis-regulatory elements, protein homology, and protein interaction network of DREB gene family in Solanum lycopersicum

et al. 2022

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Tomato is a drought-sensitive crop which has high susceptibility to adverse climatic changes. Dehydration-responsive element-binding (DREB) are significant plant transcription factors that have a vital role in regulating plant abiotic stress tolerance by networking with DRE/CRT cis-regulatory elements in response to stresses. In this study, bioinformatics analysis was performed to conduct the genome-wide identification and characterization of DREB genes and promoter elements in Solanum lycopersicum. In genome-wide coverage, 58 SlDREB genes were discovered on 12 chromosomes that justified the criteria of the presence of AP2 domain as conserved motifs. Intron–exon organization and motif analysis showed consistency with phylogenetic analysis and confirmed the absence of the A3 class, thus dividing the SlDREB genes into five categories. Gene expansion was observed through tandem duplication and segmental duplication gene events in SlDREB genes. Ka/Ks values were calculated in ortholog pairs that indicated divergence time and occurrence of purification selection during the evolutionary period. Synteny analysis demonstrated that 32 out of 58 and 47 out of 58 SlDREB genes were orthologs to Arabidopsis and Solanum tuberosum, respectively. Subcellular localization predicted that SlDREB genes were present in the nucleus and performed primary functions in DNA binding to regulate the transcriptional processes according to gene ontology. Cis-acting regulatory element analysis revealed the presence of 103 motifs in 2.5-kbp upstream promoter sequences of 58 SlDREB genes. Five representative SlDREB proteins were selected from the resultant DREB subgroups for 3D protein modeling through the Phyre2 server. All models confirmed about 90% residues in the favorable region through Ramachandran plot analysis. Moreover, active catalytic sites and occurrence in disorder regions indicated the structural and functional flexibility of SlDREB proteins. Protein association networks through STRING software suggested the potential interactors that belong to different gene families and are involved in regulating similar functional and biological processes. Transcriptome data analysis has revealed that the SlDREB gene family is engaged in defense response against drought and heat stress conditions in tomato. Overall, this comprehensive research reveals the identification and characterization of SlDREB genes that provide potential knowledge for improving abiotic stress tolerance in tomato.

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“…These drought-induced proteins are divided in functional proteins and regulatory proteins. We found a relevant protective protein named Late embryogenesis abundant (LEA) (Chen et al, 2021) (Phvul.011G001700) only in the RS Motilonia using the SNP marker S11_140976, in other legume of importance such as Vigna sp. has been reported up regulation of some genes grouped like LEA in heat stress tolerant genotypes (Singh et al, 2022).…”

Section: Metabolic Pathways As Response Mechanism To Drought and High...mentioning

confidence: 99%

Multi-environment Genome Wide Association Studies of Yield Traits in Common Bean (Phaseolus vulgaris L.) × Tepary Bean (P. acutifolius A. Gray) Interspecific Advanced Lines at the Humid and Dry Colombian Caribbean Subregions

López-Hernández

Burbano-Erazo

León-Pacheco

et al. 2022

Preprint

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Genome Wide Associations Studies GWAS are a powerful strategy for the exploration adaptive genetic variation to drought stress in advanced lines in common bean with interspecific genotypes, yet they still lack behind in the use of arid multi-environments as the subregions of the Colombian Caribbean. In order to bridge this gap, we couple an advanced genotypes panel integrated with Common Bean (Phaseolus vulgaris L.) x Tepary Bean (P. acutifolius A. Gray) interspecific lines with GWAS algorithms to identify novel sources of drought tolerance across the subregions of Colombian Caribbean. One of the most important challenges in agriculture is to achieve food security in environments vulnerable to climate change which worsens with the passing of the years. The common bean, a key product of the food basket of vulnerable regions of the Caribbean is affected by the reduction in yield under drought stress. A total of 87 advanced accessions with interspecific lines were genotyped by sequencing (GBS), leading to the discovery of 15,645 single-nucleotide polymorphism (SNP) markers. Five yield traits were developed for each accession and inputted in GWAS algorithms (i.e. FarmCPU, and BLINK) to identify putative associated loci in drought stress. Best-fit models revealed 47 significantly associated alleles distributed in all 11 common bean chromosomes. Flanking candidate genes were identified using 1-kb genomic windows centered in each associated SNP marker. A pathways enriched analysis was carried out using the mapped output in the GWAS step for each yield traits indices. Some of these genes were directly linked to response mechanisms of drought stress to level morphological, physiological, metabolic, signal transduction, and fatty acid and phospholipid metabolism. This work offers putative associated loci for marker-assisted and genomic selection for drought tolerance in common bean. It also demonstrates that it is feasible to identify genome-wide associations with an interspecific panel of genotypes and modern GWAS algorithms in multiples environments.

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Late embryogenesis abundant (LEA) gene family in Salvia miltiorrhiza: identification, expression analysis, and response to drought stress

Cited by 16 publications

References 52 publications

Genome-wide identification and characterization of members of the LEA gene family in Panax notoginseng and their transcriptional responses to dehydration of recalcitrant seeds

Genome-wide identification and characterization of members of the LEA gene family in Panax notoginseng and their transcriptional responses to dehydration of recalcitrant seeds

Genome-wide identification, comprehensive characterization of transcription factors, cis-regulatory elements, protein homology, and protein interaction network of DREB gene family in Solanum lycopersicum

Multi-environment Genome Wide Association Studies of Yield Traits in Common Bean (Phaseolus vulgaris L.) × Tepary Bean (P. acutifolius A. Gray) Interspecific Advanced Lines at the Humid and Dry Colombian Caribbean Subregions

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