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Linking rice, Arabidopsis and the grasses to explore natural genetic variation
Support: NSF Plant Genome Award # 0110004 (2001-2004)
Personnel:
Susan McCouch PI
Ray Wu Co-PI
Project Website:
http://ricegenomics.plbr.cornell.edu/index.html
ABTRACT:
To date, the map-based cloning and characterization of genes from crop species has largely been limited to monogenic traits, such as those providing disease resistance, that are controlled by single genes causing clear phenotypic effects. Most agronomically-important traits, such as yield and yield components, however, are polygenic traits controlled by multiple genes and influenced by the environment. Over the past decade, the application of molecular markers and genetic linkage maps has allowed specific regions of the genome controlling polygenic traits, called quantitative trait loci (QTLs), to be identified in all of the major crop species. In spite of the wealth of positional information for these regions, however, few genes underlying quantitative traits have actually been cloned. As a result, many questions concerning the nature and function of these genes, as well as the molecular mechanisms behind the genetic variation of agronomically-important traits, remain unanswered.
The genes underlying QTLs derived from a wild rice ancestor (O. rufipogon) that are associated with natural variation for flowering time, grain weight, and plant height in elite cultivated material will be identified and characterized. Three QTLs that map to rice chromosome 1, one of the first rice chromosomes to be completely sequenced, will be targeted. The specific objectives are to fine-map major QTLs for flowering time, grain weight, and plant height, then to isolate candidate genes that are located within those regions and, finally, to demonstrate phenotypic complementation via transformation with genes underlying the QTLs. The sequence variation from orthologs of the genes underlying the target QTLs in wild and cultivated Oryza, other grasses, and Arabidopsis will be compared to gain an evolutionary perspective and insight into functionally-important conserved domains. This work will generate significant new information about the identity and functional significance of genes associated with agronomically-important traits in the grasses and will test a multi-faceted strategy for rapid identification of genes underlying QTLs when genomic sequence is available in the target region.
Objectives:
The overall objective of this proposal is to clone and characterize genes associated with agronomically-significant genetic variation in flowering time, seed size, and plant height in rice. Once the genes are cloned, alleles at these loci from wild and cultivated Oryza will be compared with each other and with putative orthologs in other plant species to determine how changes in nucleotide sequence affect gene function in a biochemical and organismal context. A multi-faceted approach will be used to take advantage of the functional genomics tools now available, extensive QTL mapping information and nearly-isogenic lines developed for these QTLs, as well as knowledge of genes and pathways controlling these traits in Arabidopsis, the grasses, and other species. If this project is successful, we will apply this information to productively broaden the genetic base of cultivated crop plants and establish a deeper understanding of gene and genome evolution in the grasses and all higher plants.
The specific objectives are:
- Fine-map three major QTLs.
To produce high resolution maps of major QTLs for flowering time, plant height, and seed size located on chromosome 1 using mapping populations developed from existing nearly-isogenic lines (NILs) and SSR and SNP markers developed from available rice genomic sequence of these regions.
- Identify positional-candidate genes.
To identify and isolate positional-candidate genes from O. rufipogon cDNA and genomic libraries using predicted ORFs in genomic sequence (based on #1 above), and information about genes associated with flowering time, plant height, and seed development from Arabidopsis and other species.
- Confirm cloning of the genes underlying the QTLs.
To confirm the cloning of the genes underlying the QTLs via transformation and complementation analysis. This will be accomplished by transforming the recurrent parent genome with O. rufipogon QTL candidate alleles cloned and characterized in #1-2) above. In addition, sequence variation from natural alleles at orthologous loci identified in wild and cultivated Oryza, the grasses, and Arabidopsis will be analyzed to better understand the functional significance of these loci in an evolutionary perspective.
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