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Gramene: a growing plant comparative genomics resource.

Liang C, Jaiswal P, Hebbard C, Avraham S, Buckler ES, Casstevens T, Hurwitz B, McCouch S, Ni J, Pujar A, Ravenscroft D, Ren L, Spooner W, Tecle I, Thomason J, Tung CW, Wei X, Yap I, Youens-Clark K, Ware D, Stein L - Nucleic Acids Res. (2007)

Bottom Line: Since our last NAR publication 2 years ago, we have updated these data types to include new datasets and new connections among them.Completely new features include rice pathways for functional annotation of rice genes; genetic diversity data from rice, maize and wheat to show genetic variations among different germplasms; large-scale genome comparisons among Oryza sativa and its wild relatives for evolutionary studies; and the creation of orthologous gene sets and phylogenetic trees among rice, Arabidopsis thaliana, maize, poplar and several animal species (for reference purpose).We have significantly improved the web interface in order to provide a more user-friendly browsing experience, including a dropdown navigation menu system, unified web page for markers, genes, QTLs and proteins, and enhanced quick search functions.

View Article: PubMed Central - PubMed

Affiliation: Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.

ABSTRACT
Gramene (www.gramene.org) is a curated resource for genetic, genomic and comparative genomics data for the major crop species, including rice, maize, wheat and many other plant (mainly grass) species. Gramene is an open-source project. All data and software are freely downloadable through the ftp site (ftp.gramene.org/pub/gramene) and available for use without restriction. Gramene's core data types include genome assembly and annotations, other DNA/mRNA sequences, genetic and physical maps/markers, genes, quantitative trait loci (QTLs), proteins, ontologies, literature and comparative mappings. Since our last NAR publication 2 years ago, we have updated these data types to include new datasets and new connections among them. Completely new features include rice pathways for functional annotation of rice genes; genetic diversity data from rice, maize and wheat to show genetic variations among different germplasms; large-scale genome comparisons among Oryza sativa and its wild relatives for evolutionary studies; and the creation of orthologous gene sets and phylogenetic trees among rice, Arabidopsis thaliana, maize, poplar and several animal species (for reference purpose). We have significantly improved the web interface in order to provide a more user-friendly browsing experience, including a dropdown navigation menu system, unified web page for markers, genes, QTLs and proteins, and enhanced quick search functions.

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A syntenic region showing related QTLs and genes between rice and maize in CMap. Please refer to CMap tutorial (http://www.gramene.org/tutorials/cmap.html) on how to construct this comparative map view. The maize chromosomes 3 and 8 contain big syntenic regions (including inversions) with rice chromosome 1 as evidenced in Ensembl synteny view http://tinyurl.com/2sl55k. The QTLs are shown in blue and genes in green. The rice markers are shown on the right side of the chromosome, where the markers in red are those also mapped on the maize map. There are many plant height QTLs in rice and maize mapped in this region (PTHT, in blue ovate—the names were enlarged for better viewing). The rice PTHT QTLs are probably contributed by the sd1 gene (McCouch et al., unpublished data), but the maize PTHT QTLs have not been characterized regarding the underlying genes. Note that several maize height genes, d12, d*-N394 and d*-N282 (in brown ovate) are also mapped in the region. Based on the syntenic view, we can expect that the sd1 orthologs in maize will be able to be identified after the maize genome sequence is completed, and they will likely contribute to some of these maize PTHT QTLs.
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Figure 2: A syntenic region showing related QTLs and genes between rice and maize in CMap. Please refer to CMap tutorial (http://www.gramene.org/tutorials/cmap.html) on how to construct this comparative map view. The maize chromosomes 3 and 8 contain big syntenic regions (including inversions) with rice chromosome 1 as evidenced in Ensembl synteny view http://tinyurl.com/2sl55k. The QTLs are shown in blue and genes in green. The rice markers are shown on the right side of the chromosome, where the markers in red are those also mapped on the maize map. There are many plant height QTLs in rice and maize mapped in this region (PTHT, in blue ovate—the names were enlarged for better viewing). The rice PTHT QTLs are probably contributed by the sd1 gene (McCouch et al., unpublished data), but the maize PTHT QTLs have not been characterized regarding the underlying genes. Note that several maize height genes, d12, d*-N394 and d*-N282 (in brown ovate) are also mapped in the region. Based on the syntenic view, we can expect that the sd1 orthologs in maize will be able to be identified after the maize genome sequence is completed, and they will likely contribute to some of these maize PTHT QTLs.

Mentions: CMap, the comparative mapping tool used in Maps module, allows arbitrary sets of maps to be aligned in order to show the relationships among them. There are currently more than 200 different map sets from 26 species in CMap. The most significant of these are the reference rice genome, now known as the ‘Rice Gramene Annotated Nipponbare Sequence’ map, as well as a large series of QTL maps. The inclusion of the latter allows researchers to follow a trait mapped via a QTL to the rice genomic sequence, and from there to maps of other species. For example, Figure 2 shows a typical application of CMap in comparative genomic studies around the rice sd1 gene.Figure 2.


Gramene: a growing plant comparative genomics resource.

Liang C, Jaiswal P, Hebbard C, Avraham S, Buckler ES, Casstevens T, Hurwitz B, McCouch S, Ni J, Pujar A, Ravenscroft D, Ren L, Spooner W, Tecle I, Thomason J, Tung CW, Wei X, Yap I, Youens-Clark K, Ware D, Stein L - Nucleic Acids Res. (2007)

A syntenic region showing related QTLs and genes between rice and maize in CMap. Please refer to CMap tutorial (http://www.gramene.org/tutorials/cmap.html) on how to construct this comparative map view. The maize chromosomes 3 and 8 contain big syntenic regions (including inversions) with rice chromosome 1 as evidenced in Ensembl synteny view http://tinyurl.com/2sl55k. The QTLs are shown in blue and genes in green. The rice markers are shown on the right side of the chromosome, where the markers in red are those also mapped on the maize map. There are many plant height QTLs in rice and maize mapped in this region (PTHT, in blue ovate—the names were enlarged for better viewing). The rice PTHT QTLs are probably contributed by the sd1 gene (McCouch et al., unpublished data), but the maize PTHT QTLs have not been characterized regarding the underlying genes. Note that several maize height genes, d12, d*-N394 and d*-N282 (in brown ovate) are also mapped in the region. Based on the syntenic view, we can expect that the sd1 orthologs in maize will be able to be identified after the maize genome sequence is completed, and they will likely contribute to some of these maize PTHT QTLs.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238951&req=5

Figure 2: A syntenic region showing related QTLs and genes between rice and maize in CMap. Please refer to CMap tutorial (http://www.gramene.org/tutorials/cmap.html) on how to construct this comparative map view. The maize chromosomes 3 and 8 contain big syntenic regions (including inversions) with rice chromosome 1 as evidenced in Ensembl synteny view http://tinyurl.com/2sl55k. The QTLs are shown in blue and genes in green. The rice markers are shown on the right side of the chromosome, where the markers in red are those also mapped on the maize map. There are many plant height QTLs in rice and maize mapped in this region (PTHT, in blue ovate—the names were enlarged for better viewing). The rice PTHT QTLs are probably contributed by the sd1 gene (McCouch et al., unpublished data), but the maize PTHT QTLs have not been characterized regarding the underlying genes. Note that several maize height genes, d12, d*-N394 and d*-N282 (in brown ovate) are also mapped in the region. Based on the syntenic view, we can expect that the sd1 orthologs in maize will be able to be identified after the maize genome sequence is completed, and they will likely contribute to some of these maize PTHT QTLs.
Mentions: CMap, the comparative mapping tool used in Maps module, allows arbitrary sets of maps to be aligned in order to show the relationships among them. There are currently more than 200 different map sets from 26 species in CMap. The most significant of these are the reference rice genome, now known as the ‘Rice Gramene Annotated Nipponbare Sequence’ map, as well as a large series of QTL maps. The inclusion of the latter allows researchers to follow a trait mapped via a QTL to the rice genomic sequence, and from there to maps of other species. For example, Figure 2 shows a typical application of CMap in comparative genomic studies around the rice sd1 gene.Figure 2.

Bottom Line: Since our last NAR publication 2 years ago, we have updated these data types to include new datasets and new connections among them.Completely new features include rice pathways for functional annotation of rice genes; genetic diversity data from rice, maize and wheat to show genetic variations among different germplasms; large-scale genome comparisons among Oryza sativa and its wild relatives for evolutionary studies; and the creation of orthologous gene sets and phylogenetic trees among rice, Arabidopsis thaliana, maize, poplar and several animal species (for reference purpose).We have significantly improved the web interface in order to provide a more user-friendly browsing experience, including a dropdown navigation menu system, unified web page for markers, genes, QTLs and proteins, and enhanced quick search functions.

View Article: PubMed Central - PubMed

Affiliation: Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.

ABSTRACT
Gramene (www.gramene.org) is a curated resource for genetic, genomic and comparative genomics data for the major crop species, including rice, maize, wheat and many other plant (mainly grass) species. Gramene is an open-source project. All data and software are freely downloadable through the ftp site (ftp.gramene.org/pub/gramene) and available for use without restriction. Gramene's core data types include genome assembly and annotations, other DNA/mRNA sequences, genetic and physical maps/markers, genes, quantitative trait loci (QTLs), proteins, ontologies, literature and comparative mappings. Since our last NAR publication 2 years ago, we have updated these data types to include new datasets and new connections among them. Completely new features include rice pathways for functional annotation of rice genes; genetic diversity data from rice, maize and wheat to show genetic variations among different germplasms; large-scale genome comparisons among Oryza sativa and its wild relatives for evolutionary studies; and the creation of orthologous gene sets and phylogenetic trees among rice, Arabidopsis thaliana, maize, poplar and several animal species (for reference purpose). We have significantly improved the web interface in order to provide a more user-friendly browsing experience, including a dropdown navigation menu system, unified web page for markers, genes, QTLs and proteins, and enhanced quick search functions.

Show MeSH
Related in: MedlinePlus