A comprehensive analysis of the B3 superfamily identifies tissue-specific and stress-responsive genes in chickpea (Cicer arietinum L.)

Verma, Subodh; Bhatia, Sabhyata

doi:10.1007/s13205-019-1875-5

Cited by 17 publications

(18 citation statements)

References 71 publications

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“…B3s have various functions in regulating the development of root, seed and flower, abiotic stresses responses and involving in hormone signaling pathways [ 9 , 14 ]. Genome-wide characterization and expression analysis of B3s were investigated in some plants, and discovered a lot of meaningful information [ 10 , 17 , 36 , 37 ]. In this study, a total of 57 AcB3s were identified by a comprehensive genome-wide analysis.…”

Section: Discussionmentioning

confidence: 99%

“…In A. thaliana , ABI3 (one B3 domain), HSI (one B3 domain and zf-CW domain), ARF (one B3 domain, auxin response factor, and AUX/IAA domain), RAV (one B3 domain and AP2 domain), and REM (two B3 domains) are characterized by having different typical domains [ 15 ]. Each subgroup of B3s plays diverse roles in plant growth, development, and stress responses [ 16 , 17 ]. For example, ARFs have the functions in the development of flowers and leaves, vascular tissue differentiation and root initiation [ 18 , 19 ].…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide characterization and expression profiling of B3 superfamily during ethylene-induced flowering in pineapple (Ananas comosus L.)

Ruan

Chen

et al. 2021

BMC Genomics

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Background The B3 superfamily (B3s) represents a class of large plant-specific transcription factors, which play diverse roles in plant growth and development process including flowering induction. However, identification and functional surveys of B3 superfamily have not been reported in ethylene-induced pineapple flowering (Ananas comosus). Results 57 B3 genes containing B3 domain were identified and phylogenetically classified into five subfamilies. Chromosomal localization analysis revealed that 54 of 57 AcB3s were located on 21 Linkage Groups (LG). Collinearity analysis demonstrated that the segmental duplication was the main event in the evolution of B3 gene superfamily, and most of them were under purifying selection. The analysis of cis-element composition suggested that most of these genes may have function in response to abscisic acid, ethylene, MeJA, light, and abiotic stress. qRT-PCR analysis of 40 AcB3s containing ethylene responsive elements exhibited that the expression levels of 35 genes were up-regulated within 1 d after ethephon treatment and some were highly expressed in flower bud differentiation period in stem apex, such as Aco012003, Aco019552 and Aco014401. Conclusion This study provides a basic information of AcB3s and clues for involvement of some AcB3s in ethylene-induced flowering in pineapple.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-wide characterization and expression profiling of B3 superfamily during ethylene-induced flowering in pineapple (Ananas comosus L.)

Ruan

Chen

et al. 2021

BMC Genomics

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“…To investigate the potential regulatory role of B3 genes, we analysed promoters which were 2000bp in length before ATG, The cis-elements related to plant hormones were showed in Fig 6. There were 42,26,40,28,35,15 AcB3 genes promoters had cis-elements related to abscisic acid, auxin, ethylene, gibberellin, methyl jasmonate and salicylic acid, respectively. Aco009528 and Aco000403 didn't contain these 6 plant hormone related elements.…”

Section: Cis-acting Elements and Gene Ontology Analysis Of B3 Genesmentioning

confidence: 99%

“…B3s had various functions include regulating on root, seed and flower development, responses of organisms to abiotic stresses, involving in hormone signaling pathways [7,12]. Genome-wide characterization and expression analyses about B3 superfamily had been investigated in some plants [8,15,[45][46]. In this study, a comprehensive genome-wide analysis of the AcB3 superfamily in pineapple was performed for the first time and 57 AcB3 genes were identified.…”

Section: Characterization and Structure Of The Pineapple B3 Genes Supmentioning

confidence: 99%

“…In Arabidopsis thaliana, ABI3 (one B3 domain), HIS (one B3 domain and zf-CW domain), ARF (one B3 domain, auxin response factor and AUX/IAA domain), RAV (one B3 domain and AP2 domain) and REM (two B3 domains) have different typical domains [13]. The B3 superfamily plays an important role in plant growth and development as well as stress response [14][15]. ARFs have the function in development of flowers and leaves, vascular tissue differentiation and root initiation [16][17].…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide characterization and expression profiling of B3 superfamily during flower induction stage in pineapple (Ananas comosus L.)

Ruan¹,

Chen²,

Hu³

et al. 2020

Preprint

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The B3 superfamily is a plant-specific family, which involves in growth and development process. By now, the identification of B3 superfamily in pineapple ( Ananas comosus ) has not reported. In this study, 57 B3 genes were identified and further phylogenetically classified into five subfamilies, all genes contained B3 domain. Chromosomal localization analysis revealed that 54 of 57 AcB3 genes were located on 21 chromosomes. Collinearity analysis indicated that the segmental duplication was the main event in the evolution of B3 gene superfamily and most of them were under purifying selection. Moreover, there were 7 and 39 pairs of orthologous B3s were identified between pineapple and Arabidopsis or rice, respectively, which indicated the closer genetic relationship between pineapple and rice. Most genes had cis -element of abscisic acid, ethylene, MeJA, light, and abiotic stress. qRT-PCR showed that the expression level of most AcB3 genes were up-regulated within 1 d after ethephon treatment and expressed high level in flower bud differentiation period in stem apex. This study provide a comprehensive understanding of AcB3s and a basis for future molecular studies of ethephon induced pineapple flowering.

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Identification of loci controlling timing of stem elongation in red clover using genotyping by sequencing of pooled phenotypic extremes

et al. 2022

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Main conclusion Through selective genotyping of pooled phenotypic extremes, we identified a number of loci and candidate genes putatively controlling timing of stem elongation in red clover. Abstract We have identified candidate genes controlling the timing of stem elongation prior to flowering in red clover (Trifolium pratense L.). This trait is of ecological and agronomic significance, as it affects fitness, competitivity, climate adaptation, forage and seed yield, and forage quality. We genotyped replicate pools of phenotypically extreme individuals (early and late-elongating) within cultivar Lea using genotyping-by-sequencing in pools (pool-GBS). After calling and filtering SNPs and GBS locus haplotype polymorphisms, we estimated allele frequencies and searched for markers with significantly different allele frequencies in the two phenotypic groups using BayeScan, an FST-based test utilizing replicate pools, and a test based on error variance of replicate pools. Of the three methods, BayeScan was the least stringent, and the error variance-based test the most stringent. Fifteen significant markers were identified in common by all three tests. The candidate genes flanking the markers include genes with potential roles in the vernalization, autonomous, and photoperiod regulation of floral transition, hormonal regulation of stem elongation, and cell growth. These results provide a first insight into the potential genes and mechanisms controlling transition to stem elongation in a perennial legume, which lays a foundation for further functional studies of the genetic determinants regulating this important trait.

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A comprehensive analysis of the B3 superfamily identifies tissue-specific and stress-responsive genes in chickpea (Cicer arietinum L.)

Cited by 17 publications

References 71 publications

Genome-wide characterization and expression profiling of B3 superfamily during ethylene-induced flowering in pineapple (Ananas comosus L.)

Genome-wide characterization and expression profiling of B3 superfamily during ethylene-induced flowering in pineapple (Ananas comosus L.)

Genome-wide characterization and expression profiling of B3 superfamily during flower induction stage in pineapple (Ananas comosus L.)

Identification of loci controlling timing of stem elongation in red clover using genotyping by sequencing of pooled phenotypic extremes

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