This ongoing project integrates advanced techniques in molecular biology with conventional plant breeding methods to develop improved rice germplasm for use in new varieties adapted for the California environment. Molecular markers are the primary tool used in this work.  Progress on cold tolerance, grain quality, disease resistance and other areas is reported below.

Cold Tolerance

Fine genetic mapping for cold-induced yellowing and stunting of seedlings resulted in the identification of several candidate genes that may confer cold tolerance during the seedling stage of development. These candidate genes will be tested to determine which is involved in the tolerance trait. Strategies for increasing the cold tolerance of rice grown in California will be developed based on the findings. A set of 483 recombinant lines, previously characterized with DNA markers, was planted in the UC Davis and Biggs nurseries for assessment of heading date and fertility. Information gathered from field testing will be used to identify lines for analysis of tolerance to low temperature-induced blanking.

Grain Quality

The “waxy” gene is associated with the enzyme that greatly contributes to the amylose (starch) content in rice grains. Approximately 1,000 lines were assessed for the waxy marker in long grain materials from the Rice Experiment Station.

Stem Rot

The primary objective of stem rot-related genetics research is to identify DNA markers linked to disease resistance that exists in the wild species Oryza rufipogon and to transfer these traits into California varieties with marker-assisted selection. 

In 2006 approximately 150 recombinant lines derived from a long-grain cross were advanced. These lines will be examined to determine if they will be useful in mapping genes that are associated with tolerance to stem rot, which appears to be derived from several genes. If successful this will facilitate identification of DNA markers for more efficient development of tolerant varieties.

In 2006, 45 isolates of stem rot were characterized to determine their genetic relationships. Fourteen of these isolates were selected for analysis of traits such as growth on complex media, sclerotia production, fungicide sensitivity and other factors involved in this disease’s prevalence in nature. Four isolates were selected for further analysis of  virulence (i.e., degree of disease-causing ability). Crosses of these isolates were made for further characterization and the development of a genetic map of stem rot. The objective of this work is to identify stem rot genes that are important for infection and disease development. These genes and their products may be targets for novel control strategies.

Blast Resistance

A project in collaboration with the plant pathologist at the Rice Experiment Station was begun to extract and analyze DNA from 13 rice lines carrying various blast resistance genes and the susceptible line M-206. The objective is to identify DNA markers that may be used to verify the transfer of blast resistance genes into M-206 via a backcrossing strategy applied by the RES.

Semidwarf 1 Trait

All the varieties released by the RES were examined in 2006 using markers for the Semidwarf 1 gene. Most modern California varieties possess the semidwarf trait, which results in high-yielding varieties with reduced plant height. The most common genetic sources of this trait in California rice are the varieties IR8 and Calrose76. This analysis was able to clarify the origin of the semidwarf trait in all the varieties released by the RES.  Whether one source of the semidwarf trait confers an agronomic advantage over another is unknown and may be useful to determine in future studies.