Genome‐wide analysis of <scp>MIKC</scp>‐type <scp>MADS</scp>‐box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization

Schilling, Susanne; Kennedy, Alice; Pan, Sirui; Jermiin, Lars S.; Melzer, Rainer

doi:10.1111/nph.16122

Cited by 229 publications

(238 citation statements)

References 133 publications

(226 reference statements)

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“…To provide additional context to gene function, we performed a BLASTP search using each annotated gene as a query against the NCBI NR database of proteins. We also added additional annotation information for genes encoding members of different transcription factor families [67], MIKC subclass members of the MADS-box gene family [68] and of the FT-like gene family [63]. Full information of the annotations associated with each differentially expressed gene are provided in Additional file 2.…”

Section: Methodsmentioning

confidence: 99%

Effect ofphyBandphyCloss-of-function mutations on the wheat transcriptome under short and long day photoperiods

Kippes

VanGessel

Hamilton

et al. 2020

Preprint

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25Background: Photoperiod signals provide important cues by which plants regulate their growth 26 and development in response to predictable seasonal changes. Phytochromes, a family of red and 27 far-red light receptors, play critical roles in regulating flowering time in response to changing 28 photoperiods. A previous study showed that loss-of-function mutations in either PHYB or PHYC 29 result in large delays in heading time and in the differential regulation of a large number of genes 30 in wheat plants grown in an inductive long day (LD) photoperiod. 31 Results:We found that under non-inductive short-day (SD) photoperiods, phyB-null and phyC-32 null mutants were taller, had a reduced number of tillers, longer and wider leaves, and headed 33 later than wild-type plants. Unexpectedly, both mutants flowered earlier in SD than LD, the 34 inverse response to that of wild-type plants. We observed a larger number of differentially 35 expressed genes between mutants and wild-type under SD than under LD, and in both cases, the 36 number was larger for phyB than for phyC. We identified subsets of differentially expressed and 37 alternatively spliced genes that were specifically regulated by PHYB and PHYC in either SD or 38 LD photoperiods, and a smaller set of genes that were regulated in both photoperiods. We 39 observed significantly higher transcript levels of the flowering promoting genes VRN-A1, PPD-40 B1 and GIGANTEA in the phy-null mutants in SD than in LD, which suggests that they could 41 contribute to the earlier flowering of the phy-null mutants in SD than in LD. 42 Conclusions: Our study revealed an unexpected reversion of the wheat LD plants into SD plants 43in the phyB-null and phyC-null mutants and identified candidate genes potentially involved in 44 this phenomenon. Our RNA-seq data provides insight into light signaling pathways in inductive 45 and non-inductive photoperiods and a set of candidate genes to dissect the underlying 46 developmental regulatory networks in wheat. 47 Keywords: Wheat, heading date, phytochrome, FT1, FT2, FT3, PPD1, VRN1. 48 Background 49As sessile organisms, plants must be able to respond to fluctuations in their environment to 50 maximize their reproductive success. To achieve this, plants have evolved a series of regulatory 51 mechanisms to ensure that critical stages of their development coincide with optimal 52 environmental conditions. One important determinant of reproductive success is flowering time, 53 which is strongly influenced by seasonal changes in photoperiod and temperature [1]. In cereal 54 crops, these cues are fundamental to ensure the plant does not flower too early, to prevent 55 exposure of sensitive reproductive tissues to late-spring frosts, or too late, so as to minimize 56 exposure to damaging high temperatures during grain filling [2]. There is a direct link between 57 reproductive success and grain production, so characterizing the regulatory networks underlying 58 flowering time is critical to support the development of resilient crop varieties, ...

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Section: Methodsmentioning

confidence: 99%

Effect ofphyBandphyCloss-of-function mutations on the wheat transcriptome under short and long day photoperiods

Kippes

VanGessel

Hamilton

et al. 2020

Preprint

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“…The MADS-box transcription factors analysed here using the proposed nomenclature of (Schilling et al, 2020), which are different from those we have described previously (Dixon et al, 2018b).…”

Section: Rna Extraction and Expression Analysismentioning

confidence: 97%

Step-wise increases inFT1expression regulate seasonal progression of flowering in wheat (Triticum aestivumL.)

Gauley

Boden

2020

Preprint

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ABSTRACTFlowering is regulated by genes that respond to changing daylengths and temperature, which have been well-studied using controlled conditions; however, the molecular processes underpinning flowering in nature remain poorly understood. Here, we investigate the genetic pathways that coordinate flowering and inflorescence development of wheat as daylengths extend naturally in the field, using lines that contain variant alleles for the key photoperiod gene, Photoperiod-1 (Ppd-1). We found flowering involves a step-wise increase in the expression of FLOWERING LOCUS T1 (FT1), which initiates under day-neutral conditions of early spring. The incremental rise in FT1 expression is overridden in plants that contain a photoperiod-insensitive allele of Ppd-1, which hastens the completion of spikelet development and accelerates flowering time. The accelerated inflorescence development of photoperiod-insensitive lines is promoted by advanced seasonal expression of floral meristem identity genes. The completion of spikelet formation is promoted by FLOWERING LOCUS T2, which regulates spikelet number and is activated by Ppd-1. In wheat, flowering under natural photoperiods is regulated by step-wise increases in the expression of FT1, which responds dynamically to extending daylengths to promote early inflorescence development. This research provides a strong foundation to improve yield potential by fine-tuning the photoperiod-dependent control of inflorescence development.

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“…4). The result suggested that fifty of the predicted JcMADS genes were expressed in at least one of the organs examined, while thirteen (JcMADS04, 11,17,20,21,22,28,30,31,35,43,45 and 57) were not expressed in any of these tissues. Of the 50 JcMADS genes for which expression was detected, two (JcMADS03 and 53) were highly expressed across all the tissues sampled, ten (JcMADS09, 10,16,19,23,40,41,42, 56 and 58) were expressed only in seeds, thirteen (JcMADS01, 02, 05, 08, 13,29,34,40,44,51,55,60, and 63) exhibited highest expression in seeds, four (JcMADS24, 36, 48 and 49) preferred to be expressed in roots, and one (JcMADS32) was most strongly expressed in the stem cortex.…”

Section: Expression Profile Of Jcmads Genes Under Non-stressed Growthmentioning

confidence: 98%

Genome-wide analysis of Jatropha curcas MADS-box gene family and functional characterization of the JcMADS40 gene in transgenic rice

Tang

Wang

Bao

et al. 2020

Preprint

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Background: Physic nut (Jatropha curcas), a non-edible oilseed plant, is among the most promising alternative energy sources because of its high seed oil content, rapid growth and extensive adaptability. Proteins encoded by MADS-box genes are important transcription factors involved in the regulation of plant growth, seed development and responses to abiotic stress. However, there has been no in-depth research on the MADS-box genes and their roles in physic nut. Results: In the present study, 63 MADS-box genes (JcMADSs) were identified in the physic nut genome, and classed into five groups (MIKCC, Mα, Mβ, Mγ, MIKC*) based on phylogenetic comparison with Arabidopsis homologs. Expression profile analysis based on RNA-seq suggested that many JcMADS genes were expressed most strongly in seeds, and seven of them responded in leaves to at least one abiotic stressor (drought and/or salinity) at one or more time points. Transient expression analysis and a transactivation assay indicated that JcMADS40 is a nucleus-localized transcriptional activator. Plants overexpressing JcMADS40 did not show altered plant growth, but the overexpressing plants did exhibit reductions in grain size, grain length, grain width, 1000-seed weight and yield per plant. Further data on the reduced grain size in JcMADS40-overexpressing plants supported the putative role of JcMADS genes in seed development. Conclusions: This study will be useful in understanding the involvement of MADS-box genes in growth and development in addition to their functions in abiotic stress resistance, and will ultimately form the basis for functional characterization and the exploitation of candidate genes for the genetic engineering of physic nut.

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Genome‐wide analysis of MIKC‐type MADS‐box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization

Cited by 229 publications

References 133 publications

Effect ofphyBandphyCloss-of-function mutations on the wheat transcriptome under short and long day photoperiods

Effect ofphyBandphyCloss-of-function mutations on the wheat transcriptome under short and long day photoperiods

Step-wise increases inFT1expression regulate seasonal progression of flowering in wheat (Triticum aestivumL.)

Genome-wide analysis of Jatropha curcas MADS-box gene family and functional characterization of the JcMADS40 gene in transgenic rice

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