Identification of rhizome-specific genes by genome-wide differential expression Analysis in Oryza longistaminata

Hu, Fengyi; Wang, Di; Zhao, Xiuqin; Zhang, Ting; Sun, Hai‐Xi; Zhu, Linghua; Zhang, Fan; Li, Lijuan; Li, Qiong; Tao, Dayun; Fu, Binying; Li, Zhikang

doi:10.1186/1471-2229-11-18

Cited by 72 publications

(76 citation statements)

References 72 publications

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“…Additionally, five of the unisequences corresponding to known rhizome-specific expressed genes (Hu et al 2011), comprising genes encoding betaine-aldehyde dehydrogenase (Os04g0464200), SL-TPS/P (Os05g0518600), naringenin-chalcone synthase (Os10g0472900), protein kinase domain-containing protein (Os01g0655500), and one hypothetical protein (Os07g0588800), were also colocalized to the regions of Rhz3, QRn5, QRn10, QRl1, and QRl7, respectively. The unisequences reported in this study will be a useful resource for gene discovery in O. longistaminata, especially of genes involved in rhizome formation and development.…”

Section: Ssr Analysismentioning

confidence: 93%

“…Hu et al (2003) reported that the rhizome phenotype in O. longistaminata is controlled by two dominant complementary genes, Rhz2 and Rhz3, located on chromosomes 3 and 4. Furthermore, Hu et al (2011) identified rhizome-specific genes by genomewide differential expression analysis in O. longistaminata and suggested a complex gene regulatory network underlies rhizome development and growth.…”

Section: Introductionmentioning

confidence: 98%

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Analysis of ESTs from a Normalized cDNA Library of the Rhizome Tip of Oryza longistaminata

Zhang

et al. 2011

J. Plant Biol.

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Oryza longistaminata, a perennial wild rice species with an AA genome, is characterized by the presence of rhizomatous stems. The rhizomatous trait in rice was previously shown to be quantitatively controlled by many genes, but the molecular mechanism related to rhizome development is still unknown. In the present study, expressed sequence tags (ESTs) generated from rhizome tips of O. longistaminata were collected and analyzed. A total of 10,283 complimentary deoxyribunucleic acid clones were randomly sequenced, which generated 10,136 raw sequences, and finally, 4,419 unisequences with diverse functional categories were generated. These unisequences were mapped onto the Oryza sativa genome, which revealed that 4,285 (96.97%) and 4,151 (93.94%) of the unisequences were alignable to the japonica and indica genomic sequences, respectively, with >80% sequence identity. Additionally, 41 unisequences showed four typical types of alternative splicing patterns. More than 600 simple sequence repeats were identified in these unisequences. A subset of unisequences were physically colocalized onto rhizome-related quantitative trait locus intervals in rice and sorghum, and one gene, OLRR1, was further confirmed to be enriched in the rhizome tip and young leaf by real-time polymerase chain reaction and in situ hybridization. Unisequences reported in this study provide valuable data for molecular dissection of the rhizomatous growth habit in O. longistaminata.

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Section: Ssr Analysismentioning

confidence: 93%

Section: Introductionmentioning

confidence: 98%

Analysis of ESTs from a Normalized cDNA Library of the Rhizome Tip of Oryza longistaminata

Zhang

et al. 2011

J. Plant Biol.

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“…Propagation through rhizomes makes the plant (in this case, the clone) potentially immortal. Hu et al (2011) have shown that the initiation and development of the rhizomatous trait in O. longistaminata are controlled by very complex gene networks involving several plant hormones and regulatory genes. This study has identified several quantitative trait loci, paving the way to the characterization of new genes responsible for this important trait.…”

Section: Roots Of Perennialitymentioning

confidence: 99%

Perennial Roots to Immortality ,

Munné‐Bosch

2014

Plant Physiology

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Maximum lifespan greatly varies among species, and it is not strictly determined; it can change with species evolution. Clonal growth is a major factor governing maximum lifespan. In the plant kingdom, the maximum lifespans described for clonal and nonclonal plants vary by an order of magnitude, with 43,600 and 5,062 years for Lomatia tasmanica and Pinus longaeva, respectively. Nonclonal perennial plants (those plants exclusively using sexual reproduction) also present a huge diversity in maximum lifespans (from a few to thousands of years) and even more interestingly, contrasting differences in aging patterns. Some plants show a clear physiological deterioration with aging, whereas others do not. Indeed, some plants can even improve their physiological performance as they age (a phenomenon called negative senescence). This diversity in aging patterns responds to species-specific life history traits and mechanisms evolved by each species to adapt to its habitat. Particularities of roots in perennial plants, such as meristem indeterminacy, modular growth, stress resistance, and patterns of senescence, are crucial in establishing perenniality and understanding adaptation of perennial plants to their habitats. Here, the key role of roots for perennial plant longevity will be discussed, taking into account current knowledge and highlighting additional aspects that still require investigation.

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“…Within this experiment, the authors found that rhizome formation was a key but not the only factor that controlled winter survival, again providing indirect evidence that many aspects of dormancy and winter-survival can be separated. More recently, other researchers have begun the task of dissecting the genes and co-expressed gene sets that might control rhizomatousness in monocots [85][86][87][88][89]. These studies have identified transcripts for several genes including transcription factors that are selectively enriched in rhizomes relative to shoots.…”

Section: Molecular Studies On Rhizomatousness In Grassesmentioning

confidence: 99%

Senescence, dormancy and tillering in perennial C4 grasses

2014

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a b s t r a c tPerennial, temperate, C 4 grasses, such as switchgrass and miscanthus have been tabbed as sources of herbaceous biomass for the production of green fuels and chemicals based on a number of positive agronomic traits. Although there is important literature on the management of these species for biomass production on marginal lands, numerous aspects of their biology are as yet unexplored at the molecular level. Perenniality, a key agronomic trait, is a function of plant dormancy and winter survival of the belowground parts of the plants. These include the crowns, rhizomes and meristems that will produce tillers. Maintaining meristem viability is critical for the continued survival of the plants. Plant tillers emerge from the dormant crown and rhizome meristems at the start of the growing period in the spring, progress through a phase of vegetative growth, followed by flowering and eventually undergo senescence. There is nutrient mobilization from the aerial portions of the plant to the crowns and rhizomes during tiller senescence. Signals arising from the shoots and from the environment can be expected to be integrated as the plants enter into dormancy. Plant senescence and dormancy have been well studied in several dicot species and offer a potential framework to understand these processes in temperate C 4 perennial grasses. The availability of latitudinally adapted populations for switchgrass presents an opportunity to dissect molecular mechanisms that can impact senescence, dormancy and winter survival. Given the large increase in genomic and other resources for switchgrass, it is anticipated that projected molecular studies with switchgrass will have a broader impact on related species.

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Identification of rhizome-specific genes by genome-wide differential expression Analysis in Oryza longistaminata

Cited by 72 publications

References 72 publications

Analysis of ESTs from a Normalized cDNA Library of the Rhizome Tip of Oryza longistaminata

Analysis of ESTs from a Normalized cDNA Library of the Rhizome Tip of Oryza longistaminata

Perennial Roots to Immortality ,

Senescence, dormancy and tillering in perennial C4 grasses

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