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Developing molecular markers to enable selection against chalk in rice

Project ID:
CIM/2006/176: Developing molecular markers to enable selection against chalk in rice
Collaborating Countries:
Philippines
Commissioned Organisation:
International Rice Research Institute, Philippines
Project Leader
Dr Melissa Fitzgerald
Phone: 63 2 5805600
Fax: 63 2 5805699
Email: m.fitzgerald@cgiar.org
Collaborating Institutions:
  • NSW Department of Primary Industries, Australia
Project Budget:
$998,960
Project Duration:
01/05/2007 - 31/05/2012
ACIAR Research Program Manager
Dr Paul Fox
Project Overview

Chalkiness in rice occurs during grain development and no breeding program has been yet overcome it. It occurs in high temperatures during grain filling. Earlier research found that tropical germplasm (tropical japonica and indica) is more chalk-prone than temperate japonica germplasm. Therefore, to protect food security in developing countries where tropical rice is the staple, as well as the security of the world rice supply, it is imperative to resolve the genetic/physiological difference for low chalk between temperate and tropical germplasm. This project will build on earlier work to gain more insight into the genetic mechanisms of low-chalk in temperate lines and how to incorporate traits that will result in reduction of chalk in tropical breeds.

Project Progress Reports
Year One

Three sets of introgression lines with a total of 750 lines were provided from a joint IRRI China research project, along with linkage maps. These were planted in the dry season of 2007, and were found to be very mixed. During the growing season, off-type plants were removed in an attempt to achieve uniformity in each plot. Grain was harvested for chalk measurements from several plants in the plot, 10 panicles were randomly selected from the plot for DNA extraction, and a single plant was selected for replanting to ensure the plots were pure in the next season. A plot was generated from each of those single plants in the wet season, panicles were collected to relate panicle architecture to chalk, and grain was collected for measuring chalk. Chalk values vary across the spectrum from quite translucent all the way to very chalky. For some lines, the chalk value was similar for both the wet and dry season; for the rest, the chalk values were higher in the dry season. No lines gave lower chalk in the dry season than in the wet season. When attempting to use the chalk data and the linkage map to find genetic regions that associate with chalk, we discovered that the samples were not just individually mixed, but there were many inconsistencies in the populations. We were therefore unable to associate genotype with phenotype. We have two options: sort out the problem or create our own genetic map. We have opted for the latter. Despite the issues with the labelling of the populations, we have two seasons of data and excellent segregation, independent of grain shape, for both chalk and panicle architecture, and we are creating a minimal genetic map using 40 SSR markers. We intend to use that map and the phenotype data to select a subset of the 750 lines for growing in the glasshouse in the second year and for carrying out detailed phenotyping. SNP markers will be added to the framework SSR map.