Molecular Marker Assisted
Rice Improvement - 2010



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Project Leader and Principle Investigators

Thomas Tai, research geneticist, USDA-ARS, Dept of Plant Sciences, UC Davis




The overall objective of this project is to integrate molecular genetics with conventional breeding methods to develop improved germplasm for the California rice industry.

Primary emphasis is on the development of molecular DNA markers that can be used to predict the presence or absence of traits of interest, such as disease resistance, cold tolerance, and grain quality. Use of these markers is intended to accelerate the selection process and to streamline the breeding of improved varieties.

Basic genetic studies have resulted in the identification of DNA markers for many important traits. Genes underlying traits for yield, fertility, grain size, grain quality, and others have been identified. The objective of 2010 research was to examine genes present in California rice varieties to determine their usefulness for improving yield, quality, stress tolerance, or to assist in the breeding process. In addition, work was performed to enhance knowledge of the genetic basis for key traits and the development of genetic materials to assist in California breeding programs.

Yield-related genes

Genes that contribute significantly to yield are being isolated and characterized. Some of these genes impact yield by directly affecting grain number (Gn1a gene), grain size (GW2 and GW5 genes), or heading date and plant shape (Ghd7 gene). Studies have shown that some higher yielding varieties have specific versions of these genes.

The objective of research in 2010 was to expand the assessment of gene-specific DNA markers identified in 2009 and to determine which versions of these genes are present in California varieties and breeding materials. Calrose (ancestral variety), S-102 (short grain), M-206 (medium grain), and L-202 (long grain) were chosen as representative varieties for study.

The Gn1a gene encodes a protein that influences the development of reproductive organs in rice plants and thus has the potential to impact grain yield. Results indicate that the high yielding version of Gn1a is present in some but not all California varieties.

The GW2 gene is associated with grain size. Sequencing of this gene from Calrose, S-102, M-206, and L-202 indicates that they do not have the version of the GW2 gene that might result in larger grains. This finding suggests that introduction of this gene from other sources might be useful for breeding of larger grains.

Rice grain size (width and weight) has also been reported to be influenced by the GW5 gene. Out of 45 California cultivars examined, 12 have the version of this gene associated with wider rice grains, including all the short grain varieties except S-301. Since the version of GW5 associated with increased grain width is already present in California varieties and breeding materials, new introductions are not needed.

In 2011 geneticists plan to take a larger-scale approach to characterizing genetic markers with high-capacity DNA sequencing technology that will improve the efficiency and cost-effectiveness of this research.

Additionally, DNA markers developed to distinguish Japanese varieties are being employed in cooperation with Japanese colleagues. This may provide another powerful platform for highly detailed DNA fingerprinting of California varieties and breeding lines.

Trait genetics

In addition to extending the molecular analysis of gene markers, genetic studies involving important traits continued or were initiated in cooperation with rice breeders:

Stem rot resistance—Advanced backcross inbred lines developed at the Rice Experiment Station were obtained for use in DNA fingerprinting by sequencing in coordination with efforts of RES scientists to identify resistance genes.

Blanking tolerance—Several varieties identified at the International Rice Research Institute in the Philippines and breeding programs in Japan were obtained and seed was produced for use in 2011 studies to examine both blanking and seedling cold tolerance. Additionally, 102 lines from the USDA rice germplasm collection that were grown in the 2009 UC Davis nursery were planted again in the 2010 nursery to examine heading date and fertility.

Population development

Work continues on the genetic analysis of important traits for California rice production, including the development and seed increase of genetic materials for genetic studies and as potential donors of useful traits.

Several genetic mapping populations are currently under development for analysis of milling quality. Other collections of cultivars, germplasm, and breeding lines will be analyzed for milling yield and quality, stem rot resistance, and blanking tolerance.


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