Characterization of the LBD gene family in Brachypodium: a phylogenetic and transcriptional study

Gombos, Magdolna; Zombori, Zoltán; Szécsényi, Mária; Sándor, Györgyi; Kovács, Hajnalka; Györgyey, János

doi:10.1007/s00299-016-2057-0

Cited by 21 publications

(17 citation statements)

References 72 publications

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“…RNA isolation was performed as described (Gombos, 2017). First-strand cDNA synthesis of 2 mg of total RNA in a final volume of 20 mL was carried out with RevertAid M-MuLV Reverse Transcriptase (Fermentas), using random hexamers.…”

Section: Real Time Quantitative Rt-pcrmentioning

confidence: 99%

Proline Accumulation Is Regulated by Transcription Factors Associated with Phosphate Starvation

et al. 2017

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ORCID ID: 0000-0002-9163-9875 (L.S.).Pro accumulation in plants is a well-documented physiological response to osmotic stress caused by drought or salinity. In Arabidopsis (Arabidopsis thaliana), the stress and ABA-induced D1-PYRROLINE-5-CARBOXYLATE SYNTHETASE1 (P5CS1) gene was previously shown to control Pro biosynthesis in such adverse conditions. To identify regulatory factors that control the transcription of P5CS1, Y1H screens were performed with a genomic fragment of P5CS1, containing 1.2-kB promoter and 0.8-kb transcribed regions. The myeloblastosis (MYB)-type transcription factors PHOSPHATE STARVATION RESPONSE1 (PHR1) and PHR1-LIKE1 (PHL1) were identified to bind to P5CS1 regulatory sequences in the first intron, which carries a conserved PHR1-binding site (P1BS) motif. Binding of PHR1 and PHL1 factors to P1BS was confirmed by Y1H, electrophoretic mobility assay and chromatin immunoprecipitation. Phosphate starvation led to gradual increase in Pro content in wild-type Arabidopsis plants as well as transcriptional activation of P5CS1 and PRO DEHYDROGENASE2 genes. Induction of P5CS1 transcription and Pro accumulation during phosphate deficiency was considerably reduced by phr1 and phl1 mutations and was impaired in the ABA-deficient aba2-3 and ABA-insensitive abi4-1 mutants. Growth and viability of phr1phl1 double mutant was significantly reduced in phosphate-depleted medium, while growth was only marginally affected in the aba2-3 mutants, suggesting that ABA is implicated in growth retardation in such nutritional stress. Our results reveal a previously unknown link between Pro metabolism and phosphate nutrition and show that Pro biosynthesis is target of cross talk between ABA signaling and regulation of phosphate homeostasis through PHR1-and PHL1-mediated transcriptional activation of the P5CS1 gene.

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Section: Real Time Quantitative Rt-pcrmentioning

confidence: 99%

Proline Accumulation Is Regulated by Transcription Factors Associated with Phosphate Starvation

et al. 2017

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“…The latera organ boundaries domain (LBD) transcription factor family promotes lateral root or shoot formation and lateral growth [37]. MdLBD3, a gene homologous to AtLBD3/AtLBD9, is induced by exogenous cytokinin [38].…”

Section: Discussionmentioning

confidence: 99%

Development and validation of functional markers from Dw1 and Dw2 loci to accurately predict apple rootstock dwarfing ability

Yang

Shen²,

Liu

et al. 2020

Preprint

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Background: ‘M9’ is a widely used apple dwarfing rootstock due to the outstanding effects on both precocity and vigorous control. Two quantitative trait loci (QTLs), Dw1 and Dw2 , for the dwarfing effect were previously mapped on ‘M9’, but the genetic variations that underpin the dwarfing ability have not been elucidated to date. Result: By using ‘Red Fuji’ trees grafted on 1123 hybrids from ‘ M alus baccata ’ × ‘M9’, the intervals of Dw1 and Dw2 were narrowed down. MdLBD3 and MdARF6 were predicted as potential candidate genes from Dw1 , while MdG3OX3 was a possible candidate gene from Dw2 . An 11 bp deletion at -339 bp upstream of the transcription start site (TSS) of MdLBD3 generated a new cis-element binding site with MdWRKY2 and caused increased expression of MdLBD3 . Coincidently, a ten bp deletion at -278 bp upstream of the TSS of MdG3OX3 created an additional binding site of MdABI5 , leading to higher expression of MdG3OX3 . At -954 bp of the MdARF6 promoter, a 14 bp insertion destroyed the binding ability by MdABI5 and reduced MdARF6 expression. The genotype effects of these insertion and deletions as diagnostic markers on dwarfing traits (tree height, trunk diameter, and canopy width) were estimated in 108 F1 hybrids. The genomic predicted genetic values (GEGV) were calculated by adding up the genotype effects of the three markers and the population mean phenotype. The GEGV of the dwarfing traits exhibited high correlation coefficients of 0.93, 0.94, and 0.93 in terms of tree height, trunk diameter, and canopy width for the observed phenotype values, respectively. The predictability of GEGV was validated in 64 Malus accessions. Conclusion : The development of the three functional markers, Ld/Li, Ad/Ai, and Gd/Gi, ensures the accurate genomic assisted prediction of dwarfing ability in apple rootstock breeding. The data also suggested that ABA, auxin, GA, and zeatin signals may be involved in the regulation of apple rootstock dwarfing mechanism.

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“…Numerous LBD genes are expressed at the adaxial base of plant lateral organs, they genes play critical roles in lateral organ development during a plant's growth [8][9] . To date, a variety of LBD gene family have been successfully identified and investigated in some plants, including Arabidopsis thaliana, rice, poplar, tomato, Malus, Medicago truncatula, maize, pepper, Nicotiana tobacco and Brachypodium, which contains 43,35,57,46,58,56,44,45, 98 and 28 LBD genes, respectively 4,[10][11][12][13][14][15][16][17][18][19] . What is more, several members of the LBD family have been functionally identified in different species.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide Analysis of LBD (LATERAL ORGAN BOUNDARIES Domain) Gene Family in Brassica rapa

Huang

Liu

Zhang

2018

Braz. arch. biol. technol.

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LOB (lateral organ boundaries)-domain proteins define a family of plant-specific transcription factors involved in developmental process from embryogenesis to seed production. They play a crucial role in shaping the plant architecture through coordinating cell fate at meristem to organ boundaries. Identification of LBD genes from Brassica rapa genome, and analysis of phylogeny，gene structure, chromosome location, phylogenetic and tissue expression pattern analysis of LBD family genes in Chinese cabbage will be useful to the functions identification of plant LBD genes. Based on Brassica rapa genome database and bioinformatic method, Chinese cabbage LBD family genes were identified and the genes were sequenced. A phylogenetic tree was created using the MEGA5 program. Gene structure and chromosomes location were done by MapDraw, GSDS and Clustal X. Expression pattern of LBD genes at different development stages was analyzed based on RNA-seq. A total of 62 LBD genes were identified and could be classified into two classes and four subclasses according to the gene structure and conserved domain phylogeny relationship. Distribution mapping showed that the predicted LBDs were unevenly localized on all the 10 chromosomes, suggesting that they have an extensive distribution on the Brassica rapa chromosomes. Most of the LBD genes had differential expression pattern and showed highly diverse tissue-specific expression and functional diversity. To our knowledge, this is the first report of a genome wide analysis of the Brassica rapa LBD gene family, which would provide valuable information for understanding the classification and putative functions of the gene family.

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Characterization of the LBD gene family in Brachypodium: a phylogenetic and transcriptional study

Cited by 21 publications

References 72 publications

Proline Accumulation Is Regulated by Transcription Factors Associated with Phosphate Starvation

Proline Accumulation Is Regulated by Transcription Factors Associated with Phosphate Starvation

Development and validation of functional markers from Dw1 and Dw2 loci to accurately predict apple rootstock dwarfing ability

Genome-wide Analysis of LBD (LATERAL ORGAN BOUNDARIES Domain) Gene Family in Brassica rapa

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