Evolutionary fate of rhizome-specific genes in a non-rhizomatous Sorghum genotype

Jang, Cholsoon; Kamps, Terry L.; Tang, Haibao; Bowers, John E.; Lemke, Cornelia; Paterson, Andrew H.

doi:10.1038/hdy.2008.119

Cited by 32 publications

(38 citation statements)

References 33 publications

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“…In common with O. sativa, O. longistaminata possesses an AA genome. Much effort has been devoted to the identification of the molecular mechanisms underlying the rhizomatous trait in the bamboo Phyllostachys praecox, Sorghum propinquum, and especially O. longistaminata (Ghesquiere 1991;Ghesquiere and Causse 1992;Paterson et al 1995;Maekawa et al 1998;Hu et al 2003;Jang et al 2006Jang et al , 2009Wang et al 2009a). 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.…”

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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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: 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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“…Previously, rhizome-enriched genes have been identified from S. halepense and S. propinquum [15]. Similarity search showed that 383 out of 768 rhizome-enriched genes found in the two Sorghum species have at least one ortholog in Miscanthus ESTs and 171 have orthologs in both leaf and rhizome from the two Miscanthus species.…”

Section: Resultsmentioning

confidence: 99%

“…While no particular category was predominant, the ‘response to stimulus’ (GO:0050896), seemingly related to signals in response to stress, occupies a high portion. Jang et al [15] suggested that the loss of rhizomatousness in S. bicolor might have been caused by changes in gene regulation. Although the 31 genes are not specifically associated with functions and GO categories found in roots or rhizomes, these genes could be primary targets for investigating rhizomatousness in Miscanthus .…”

Section: Resultsmentioning

confidence: 99%

Sequencing of transcriptomes from two Miscanthus species reveals functional specificity in rhizomes, and clarifies evolutionary relationships

et al. 2014

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BackgroundMiscanthus is a promising biomass crop for temperate regions. Despite the increasing interest in this plant, limited sequence information has constrained research into its biology, physiology, and breeding. The whole genome transcriptomes of M. sinensis and M. sacchariflorus presented in this study may provide good resources to understand functional compositions of two important Miscanthus genomes and their evolutionary relationships.ResultsFor M. sinensis, a total of 457,891 and 512,950 expressed sequence tags (ESTs) were produced from leaf and rhizome tissues, respectively, which were assembled into 12,166 contigs and 89,648 singletons for leaf, and 13,170 contigs and 112,138 singletons for rhizome. For M. sacchariflorus, a total of 288,806 and 267,952 ESTs from leaf and rhizome tissues, respectively, were assembled into 8,732 contigs and 66,881 singletons for leaf, and 8,104 contigs and 63,212 singletons for rhizome. Based on the distributions of synonymous nucleotide substitution (Ks), sorghum and Miscanthus diverged about 6.2 million years ago (MYA), Saccharum and Miscanthus diverged 4.6 MYA, and M. sinensis and M. sacchariflorus diverged 1.5 MYA. The pairwise alignment of predicted protein sequences from sorghum-Miscanthus and two Miscanthus species found a total of 43,770 and 35,818 nsSNPs, respectively. The impacts of striking mutations found by nsSNPs were much lower between sorghum and Miscanthus than those between the two Miscanthus species, perhaps as a consequence of the much higher level of gene duplication in Miscanthus and resulting ability to buffer essential functions against disturbance.ConclusionsThe ESTs generated in the present study represent a significant addition to Miscanthus functional genomics resources, permitting us to discover some candidate genes associated with enhanced biomass production. Ks distributions based on orthologous ESTs may serve as a guideline for future research into the evolution of Miscanthus species as well as its close relatives sorghum and Saccharum.

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“…Others have noted that genes associated with tillering in the Poaceae may have some relationship to rhizomes (Jang et al 2006). It is possible that rhizomespecific genes may serve multiple functions for plant growth and development as well as serving regulatory functions (Jang et al 2009). The temperate region sugarcane cultivars showing better production performance are generationally less distance removed from the ancestral S. spontaneum (Tew and Cobill 2008).…”

Section: The Rhizomementioning

confidence: 97%

Sugarcane Underground Organs: Going Deep for Sustainable Production

Matsuoka

Garcia

2011

Tropical Plant Biol.

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Sugarcane breeding has greatly advanced in recent decades, but many aspects of sugarcane physiology are still poorly understood, including the root-shoot relationships that ultimately affect yield. Traditional methods for studying root systems are imprecise due to methodological difficulties of in situ assessment and sampling; this seems especially true for the sugarcane root system. Studies on sugarcane roots lag well behind those on other crops, in part due to the large plant stature and long crop cycle. Commercial sugarcane cultivars are hybrids from crosses mostly between Saccharum officinarum and S. spontaneum made by breeders at the beginning of the last century. These hybrids have a genomic structure composed of 80% S. officinarum, 10% S. spontaneum and 10% recombinants of these two species. S. spontaneum is included in large part for the robustness of its underground organs (root and rhizome). The S. spontaneum genes controlling these characteristics may be lost during recurrent backcrosses with S. officinarum to increase sugar content and yield. Thus, ratooning ability is one of the most desired traits. Ratooning ability comes mainly from the rhizomatousness of S. spontaneum, but this trait has been diluted during the selection process so that the stubble of hybrids does not have rhizomes sensu stricto. In this review, we revisit some basic aspects of the sugarcane root system, mainly from an ecophysiological view, and point out considerations for breeders to consider in designing the architecture of a new sugarcane cultivar that can meet the need for sustainable agricultural production.

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Evolutionary fate of rhizome-specific genes in a non-rhizomatous Sorghum genotype

Cited by 32 publications

References 33 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

Sequencing of transcriptomes from two Miscanthus species reveals functional specificity in rhizomes, and clarifies evolutionary relationships

Sugarcane Underground Organs: Going Deep for Sustainable Production

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