MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress

Arora, Rita; Agarwal, Pinky; Ray, Subhasree; Singh, Ashok Kumar; Singh, Vijay Pal; Tyagi, Akhilesh K.; Kapoor, Sanjay

doi:10.1186/1471-2164-8-242

Cited by 516 publications

(609 citation statements)

References 74 publications

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“…Arabidopsis SEP3 directly represses AGL24 and SVP expression (Kaufmann et al, 2009). In contrast, we find that OsMADS1 can directly activate OsMADS55 in panicles with developing florets, consistent with the coexpression of these genes in developing panicles (Arora et al, 2007). Furthermore, overexpression phenotypes for OsMADS1, OsMADS22, and OsMADS55 share some characteristics like short panicle branches and spikelets with empty glumes transformed to lemmalike organs (Prasad et al, 2001;Sentoku et al, 2005;Lee et al, 2008).…”

Section: Osmads1 Promotes Fm Identity and Its Maintenancementioning

confidence: 44%

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RiceLHS1/OsMADS1Controls Floret Meristem Specification by Coordinated Regulation of Transcription Factors and Hormone Signaling Pathways

2013

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SEPALLATA (SEP) MADS box transcription factors mediate floral development in association with other regulators. Mutants in five rice (Oryza sativa) SEP genes suggest both redundant and unique functions in panicle branching and floret development. LEAFY HULL STERILE1/OsMADS1, from a grass-specific subgroup of LOFSEP genes, is required for specifying a single floret on the spikelet meristem and for floret organ development, but its downstream mechanisms are unknown. Here, key pathways and directly modulated targets of OsMADS1 were deduced from expression analysis after its knockdown and induction in developing florets and by studying its chromatin occupancy at downstream genes. The negative regulation of OsMADS34, another LOFSEP gene, and activation of OsMADS55, a SHORT VEGETATIVE PHASE-like floret meristem identity gene, show its role in facilitating the spikelet-to-floret meristem transition. Direct regulation of other transcription factor genes like OsHB4 (a class III homeodomain Leu zipper member), OsBLH1 (a BEL1-like homeodomain member), OsKANADI2, OsKANADI4, and OsETTIN2 show its role in meristem maintenance, determinacy, and lateral organ development. We found that the OsMADS1 targets OsETTIN1 and OsETTIN2 redundantly ensure carpel differentiation. The multiple effects of OsMADS1 in promoting auxin transport, signaling, and auxin-dependent expression and its direct repression of three cytokinin A-type response regulators show its role in balancing meristem growth, lateral organ differentiation, and determinacy. Overall, we show that OsMADS1 integrates transcriptional and signaling pathways to promote rice floret specification and development.Patterning an angiosperm flower requires the combined and individual functions of class A, B, C, D, and E MADS box transcription factors (Krizek and Fletcher, 2005;Thompson and Hake, 2009). In Arabidopsis (Arabidopsis thaliana), the class E activity is conferred by four redundant proteins, SEPALLATA1 (SEP1), SEP2, SEP3, and SEP4, that are cofactors in complexes with other MADS box factors that determine floral organ identities and meristem determinacy (Pelaz et al., 2000). Studies on loss-and gain-of-function mutants in SEP genes together with protein interaction analyses point to their pivotal role in mediating interactions among other floral organ-patterning genes (Honma and Goto, 2001;Ditta et al., 2004;Immink et al., 2009). The largely shared functions of Arabidopsis SEP genes differ from observations that homologs in other plants often have discrete roles in floral development (Malcomber and Kellogg, 2005), but the molecular mechanism underlying their species-specific roles is not well studied. In addition to the ABCDE class of organ fate regulators, a number of hormone signaling pathways influence floral transition, organ numbers, fertility, and floral meristem (FM) determinacy. Dynamic interactions are reported between transcription factors and specific hormone signaling factors during the establishment of Arabidopsis FMs (Sessions et al., 1997;Leibfried et al., ...

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Section: Osmads1 Promotes Fm Identity and Its Maintenancementioning

confidence: 44%

“…The rice genome encodes three SHORT VEGETATIVE PHASE (SVP)-like genes: OsMADS22, OsMADS55, and OsMADS47 (Arora et al, 2007;Lee et al, 2008). Among these, we detect decreased expression of OsMADS22 and OsMADS55 but not of OsMADS47 in OsMADS1-RNAi panicles ( Fig.…”

Section: Loss-of-function Phenotypesmentioning

confidence: 78%

RiceLHS1/OsMADS1Controls Floret Meristem Specification by Coordinated Regulation of Transcription Factors and Hormone Signaling Pathways

2013

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“…3a and Supplementary Table 16). The transcription factor genes that are homologs of OsMADS1, OsMADS2, OsMADS3 and OsMADS14 in rice 30 were determined to be involved in floral meristem identity (FMI), which converts the vegetative meristem to a flowering fate. However, the genes employed in typical flowering promotion pathways (such as those in the photoperiod, gibberellins, ambient-temperature or lightquality pathways) and floral pathway integrator (FPI) genes 31,32 were not highly expressed in these floral tissues in bamboo.…”

Section: E T T E R Smentioning

confidence: 99%

The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla)

et al. 2013

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l e t t e r sBamboo represents the only major lineage of grasses that is native to forests and is one of the most important nontimber forest products in the world. However, no species in the Bambusoideae subfamily has been sequenced. Here, we report a high-quality draft genome sequence of moso bamboo (P. heterocycla var. pubescens). The 2.05-Gb assembly covers 95% of the genomic region. Gene prediction modeling identified 31,987 genes, most of which are supported by cDNA and deep RNA sequencing data. Analyses of clustered gene families and gene collinearity show that bamboo underwent whole-genome duplication 7-12 million years ago. Identification of gene families that are key in cell wall biosynthesis suggests that the whole-genome duplication event generated more gene duplicates involved in bamboo shoot development. RNA sequencing analysis of bamboo flowering tissues suggests a potential connection between droughtresponsive and flowering genes.Bamboo is one of the most important non-timber forest products in the world. About 2.5 billion people depend economically on bamboo, and international trade in bamboo amounts to over 2.5 billion US dollars per year 1 . Bamboo has a rather striking life history, characterized by a prolonged vegetative phase lasting decades before flowering, thereby inhibiting genetic improvement. Recent genomic studies in bamboo have included genome-wide full-length cDNA sequencing 2 , chloroplast genome sequencing 3 , identification of syntenic genes between bamboo and other grasses 4 and phylogenetic analysis of Bambusoideae subspecies 5 . Fifty-nine simple sequence repeat markers from rice and sugarcane were used in the genetic diversity analyses of 23 bamboo species 6 , and 2 species-specific sequence-characterized amplified region markers were developed in the identification of different bamboo species 7 .Here, we report the draft genome of moso bamboo, a large woody bamboo that has ecological, economic and cultural value in Asia and accounts for ~70% of the total bamboo growth area. Comparative genome-wide analyses of bamboo to other grass species, including rice, maize and sorghum, yielded new genetic insights into the rapid and marked phenotypic and ecological divergence of bamboo and closely related grasses.The moso bamboo genome contains 24 pairs of chromosomes 8 (2n = 48) and is characteristic of a diploid (Supplementary Fig. 1a). We conducted a flow cytometry analysis and estimated that it had a genome size of 2.075 Gb (2C = 4.24 pg; Supplementary Fig. 1b), which was very close to that estimated in a previous report 9 .Because it is difficult to generate an inbred line of moso bamboo, owing to its infrequent sexual reproduction and the long periods of time between flowering intervals, we selected five plants from a single individual rhizome of the moso bamboo ecotype (P. heterocycla var. pubescens) and performed whole-genome shotgun sequencing. We generated 295 Gb of raw sequence data (approximately 147-fold coverage), including Illumina short reads and 10,327 pairs of BAC end ...

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“…More interestingly, another C-function gene, DROOPING LEAF (DL), orthologous to Arabidopsis gene, CRABS CLAW (CRC), encoding a YABBY domain protein in rice has been identified, playing roles in carpel specification, floral meristem determinacy and the antagonistic function with class B genes [23]. Rice has diverse SEP-like genes, with at least five members in the genome [24]. Currently, OsMADS1 (also called LEAFY HULL STERILE1, LHS1) is one of the best-characterized SEP-like genes in rice, which has been shown to be required for determining the identity of the lemma/palea and the meristem of inner floral organs [25][26][27][28][29].…”

Section: Introductionmentioning

confidence: 99%

The AGL6-like gene OsMADS6 regulates floral organ and meristem identities in rice

et al. 2009

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Although AGAMOUS-LIKE6 (AGL6) MADS-box genes are ancient with wide distributions in gymnosperms and angiosperms, their functions remain poorly understood. Here, we show the biological role of the AGL6-like gene, OsMADS6, in specifying floral organ and meristem identities in rice (Oryza sativa L.). OsMADS6 was strongly expressed in the floral meristem at early stages. Subsequently, OsMADS6 transcripts were mainly detectable in paleas, lodicules, carpels and the integument of ovule, as well as in the receptacle. Compared to wild type plants, osmads6 mutants displayed altered palea identity, extra glume-like or mosaic organs, abnormal carpel development and loss of floral meristem determinacy. Strikingly, mutation of a SEPALLATA (SEP)-like gene, OsMADS1 (LHS1), enhanced the defect of osmads6 flowers, and no inner floral organs or glume-like structures were observed in whorls 2 and 3 of osmads1-z osmads6-1 flowers. Furthermore, the osmads1-z osmads6-1 double mutants developed severely indeterminate floral meristems. Our finding, therefore, suggests that the ancient OsMADS6 gene is able to specify "floral state" by determining floral organ and meristem identities in monocot crop rice together with OsMADS1.

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MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress

Cited by 516 publications

References 74 publications

RiceLHS1/OsMADS1Controls Floret Meristem Specification by Coordinated Regulation of Transcription Factors and Hormone Signaling Pathways

RiceLHS1/OsMADS1Controls Floret Meristem Specification by Coordinated Regulation of Transcription Factors and Hormone Signaling Pathways

The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla)

The AGL6-like gene OsMADS6 regulates floral organ and meristem identities in rice

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