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Title: Positional Cloning of qSD7-1, a Dormancy Locus Associated with Red Pericarp Color in Weedy Rice

item Foley, Michael
item Horvath, David
item Anderson, James

Submitted to: American Society of Plant Biologists Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 6/15/2007
Publication Date: 7/1/2007
Citation: Gu, X., Foley, M.E., Horvath, D.P., Anderson, J.V. 2007. Positional cloning of qSD7-1, a dormancy locus associated with red pericarp color in weedy rice. [Abstract]. Plant Biology & Botany 2007 Program & Abstract Book. P29016. p. 182.

Interpretive Summary:

Technical Abstract: Seed dormancy has been associated with red pericarp color in cereal crops for about a century. However, it remains unknown if the association arises from pleiotropy or linkage. We identified a dormancy locus (i.e., qSD7-1) in the genomic region containing the red pericarp color gene Rc in weedy rice (Oryza sativa L.) accessions. Populations with about 10,000 individuals segregating for a few centiMorgans only over the qSD7-1 to Rc region were generated to clone and characterize the dormancy gene. Molecular markers developed based on the Nipponbare genomic sequence were used to identify rare recombinants for the target region. The genomic region for the locus Os07g11020 or Rc locus has been cloned from the wild and mutant parents and sequence comparisons identified 18 point mutations, including single nucleotide polymorphisms, insertions, and deletions within the 6445-base pair (bp) region. We obtained one red pericarp colored intragenic recombinant, in which the 5'- and 3'-end crossovers occurred in two successive generations. Sequence analysis confirmed that the 5' and 3' crossovers occurred between 2441 and 3206 bp and 5185 and 5395 bp, respectively, indicating that a segment of about 2,000 bp between the two crossovers plays a key role in maintaining the red pericarp color function during the evolution. We are using a progeny testing technique to evaluate seed dormancy for this intragenic recombinant and other rare recombinants. The experimental results and isogenic lines obtained from this research will allow us to unambiguously conclude if qSD7-1 and Rc belong to the same or different loci and to further characterize the dormancy locus for gene structure and expression profile in the model system.