Utility and distribution of conserved noncoding sequences in the grasses

Kaplinsky, Nicholas J.; Braun, David; Penterman, Jon; Goff, Stephen A.; Freeling, Michael

doi:10.1073/pnas.052139599

Cited by 95 publications

(116 citation statements)

References 34 publications

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“…This result supports the notion that comparing large orthologous genomic sequences could quickly extend our knowledge of the molecular basis of transcriptional regulation. Our findings are also in keeping with previous observations that CNSs are often found upstream of transcription factors (28) and are shorter and less conserved in plants than in animals (29)(30)(31).…”

Section: Discussionsupporting

confidence: 93%

Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize

Salvi

Sponza

Morgante

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

533

459

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Central America (1), natural genetic variations in flowering time enabled early Native Americans to select maize adapted to a range of latitudes and lengths of growing seasons, including the very short summer season typical of the eastern Canadian region of Quebec. Under such conditions, early flowering allows seed to mature before the onset of frost. Flowering time is also a key trait of improved drought tolerance. Indeed, it has been shown that a single day of drought during flowering can decrease yield by as much as 8% (2). One way to address such losses is to develop and grow cultivars characterized by a short cycle and able to flower before predictable drought episodes.The genetic variability available for maize breeding is essentially quantitative; i.e., it involves allelic variation at different quantitative trait loci (QTLs), which are influenced by environmental effects. Although a large body of mapping information on QTLs is available for flowering time (3), relatively little is known about the molecular basis of QTLs, with only one gene, Dwarf8, correlated thus far with quantitative effects (4, 5). Furthermore, a few mutants for flowering time have been described (6, 7), two of which, id1 (8) and dlf1 (9), have been cloned. Our results (i) show that the allelic variation responsible for the major flowering-time QTL, Vegetative to generative transition 1 (Vgt1) (10, 11) on chromosome 8, is confined to an Ϸ2-kb intergenic region upstream of an Ap2-like flowering-time gene, (ii) identify maize-sorghum-rice evolutionarily conserved noncoding sequences (CNSs) within Vgt1, and (iii) support a cisacting transcription-regulatory role for Vgt1. ResultsPositional Cloning of Vgt1. Previous work (12) mapped Vgt1 to a 1.3-cM region (Fig. 1A) on bin 8.05, based on a mapping population derived from the cross N28 ϫ C22-4. The strain C22-4 is nearly isogenic to N28 and carries the early Vgt1 allele in an Ϸ7-cM introgression originating from the early maize variety Gaspé Flint. By using standard positional cloning, Vgt1 was confined to an Ϸ2-kb region (Fig. 1 B-D). Sequence annotation of the original BAC clone and the corresponding sequences derived from N28 and Gaspé Flint genetic backgrounds showed that Vgt1 is apparently noncoding and is located Ϸ70 kb (61-76 kb, depending on the genetic background) upstream of an Ap2-like gene identified here as ZmRap2.7. This gene is orthologous to Rap2.7 (also known as TOE1), a transcription factor that regulates flowering time in Arabidopsis (13,14). No other genes were annotated between Vgt1 and ZmRap2.7. Pseudogenes due to transduplication events mediated by nonautonomous helitron elements (15) were observed in N28 and other genetic backgrounds but not in Gaspé Flint (data not shown). Within the Vgt1 region, the contrasting QTL alleles showed 29 SNPs and insertion/deletion-type polymorphisms (Indels) and one 143-bp insertion into the Gaspé Flint allele of a Mite transposon belonging to the Tourist (16) family [ Fig. 4 Lower and supporting information (SI) Fig. 5].Association M...

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Section: Discussionsupporting

confidence: 93%

Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize

Salvi

Sponza

Morgante

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

533

459

View full text Add to dashboard Cite

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“…If the activity of the sorghum promoter was delayed in maize, then this would imply that changes had occurred in the cis-regulatory region of ra1 in sorghum, opening the door to experiments to determine the exact molecular basis of the change in cis-regulation. A starting point, which has been used in both animals and plants, would be to compare the regulatory regions of ra1 from different species to identify conserved noncoding sequences potentially important in function Kaplinsky et al, 2002).…”

Section: Changes In How Transcription Factors Are Regulatedmentioning

confidence: 99%

Branching Out: The ramosa Pathway and the Evolution of Grass Inflorescence Morphology

McSteen

2006

Plant Cell

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“…These evolutionary conserved motifs are then hypothesized to be potential functional elements. This method, called phylogenetic footprinting (53), has successfully been used to identify a limited number of regulatory regions in vertebrates (54,55) and plants (56,57). More sophisticated comparative approaches are starting to combine computational prediction and laboratory validation of regulatory networks.…”

Section: Evolution Of Biological Networkmentioning

confidence: 99%

Genomes, phylogeny, and evolutionary systems biology

Medina

2005

Proc. Natl. Acad. Sci. U.S.A.

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With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics, and computer science are now known as systems biology. Here, I present an overview, with an emphasis on eukaryotes, of how the postgenomics era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.postgenomics ͉ eukaryotic genomics ͉ network evolution Systems biology is in the eye of the beholder.Leroy Hood O nly in the last decade have we had access to nearly complete genomes of a diversity of organisms allowing for large-scale comparative analysis. The access to this immense amount of data is providing profound insight into the tree of life at all levels of divergence ( Fig. 1 A). It is thus not surprising that understanding phylogenetic relationships is a prevalent research goal among not only evolutionary biologists but also all scientists interested in the organization and function of the genome. New genome sequences and analysis methods are helping improve our understanding of phylogeny, and at the same time improved phylogenies and phylogenetic theory are generating a better understanding of genome evolution. Currently however, the level of genome sequencing for different branches of the tree of life is far from equivalent. Prokaryotic genome projects are abundant, mainly due to their small genome sizes, with Ͼ200 genomes already published and at least 500 currently in progress (www. genomesonline.org). In contrast, Ͻ300 eukaryotic genomes are either finished or in progress (www.genomesonline.org). Nevertheless, these data are starting to have a major impact on our understanding of eukaryotic evolution.These new genomic data have informed our understanding of phylogenetic relationships, and the emerging consensus topologies are adding new insight to the small subunit ribosomal RNA phylogenies. For example, the topology of the ribosomal eukaryotic tree has been recently redrawn with the use of genomic signatures that place the root of all eukaryotic life between two newly uncovered major clades, Unikonts and Bikonts (Fig. 1 A). Unikonts, which contain the heterotrophic groups Opisthokonta and the Amebozoa, share a derived three-gene fusion of enzymeencoding genes in the pyrimidine synthesis pathway (1), whereas Bikonts, which contain the remaining eukaryotic clades, share another derived gene fusion between dihydrofolate reductase and thymidine synthase (2). All photosynthetic groups of primary and secondary plastid symbiotic origins are now thought to be within the Bikonts. Although the animal, fungal, and plant lineages are the most widely represented in terms of genome initiatives (Fig. 1 B-D), it is significant that multiple protistan genome projects have also been initiated by th...

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Utility and distribution of conserved noncoding sequences in the grasses

Cited by 95 publications

References 34 publications

Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize

Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize

Branching Out: The ramosa Pathway and the Evolution of Grass Inflorescence Morphology

Genomes, phylogeny, and evolutionary systems biology

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