Genetics for Rice Improvement, 2019


Thomas Tai, research geneticist, USDA-ARS Crops Pathology and Genetics Research Unit, Dept. of Plant Sciences, UC Davis

The overall goal of this project is to employ trait and DNA-based genetic screens to identify and characterize novel rice germplasm to advance the understanding of agronomic performance and grain quality for incorporation into breeding programs for the California rice industry.

Primary emphasis is on screening rice populations generated by traditional mutagenesis for new traits that improve the value of the rice crop and reduce production costs. This is achieved by directly screening plant materials for traits of interest and by identifying changes in the DNA sequence of genes that may result in the expression of these traits. Specific targets currently include reduced uptake and/or localization of arsenic in milled rice grains and resistance or tolerance of rice plants to select herbicides.

The traditional approach to mutant populations is to conduct screens that identify new characteristics of interest. Examples of this “forward” genetics approach in rice include the identification of the semidwarf trait, conditional male sterility, and herbicide tolerance.

“Reverse” genetics is a complementary approach for exploiting mutant populations. This strategy requires prior knowledge of the genes that are responsible for the target traits. These genes are used to screen the DNA from mutant populations to identify mutated versions that may result in the expression of novel characteristics.

In 2019, the primary focus of this project was the continued characterization of rice mutants identified through reverse genetic screens of genes encoding silicon/arsenic transporters. Although several objectives were established for 2019 work, the federal government shutdown in the early part of the year, coupled with critical staff vacancies, necessitated research to focus primarily on evaluating arsenic and silicon content in mutant lines.

Rice mutants were evaluated for tolerance to the herbicide carfentrazone (Shark). The temperate japonica Nipponbare and Kitaake lines were the most tolerant, followed by the Southern variety Sabine. This photo shows response of Kitaake and a mutant line at two different rates.
A second year of total arsenic and silicon content analysis of field-grown mutants carrying mutations in the Lsi1and Lsi2 metalloid transport genes and the arsenic sequestration transporter gene OsABCC1 was completed.

Results of the content analysis from UC Davis and Rice Experiment Station field locations were generally consistent for straw total silicon but differed from the previous analysis of UC Davis-grown lines with regard to lines exhibiting higher total silicon.

Mutant line NM-4903 continued to exhibit high total silicon in straw and reduced total arsenic in grain at the UC Davis location, but these effects were not observed at RES. This difference warrants further investigations.

Several lines have been identified for further study and preliminary evaluation of traits that may be influenced by reduced or increased silicon, such as resistance to diseases and insect pests. In a preliminary trial at the RES stem rot nursery performed by Dr. Teresa De Leon, some metalloid uptake and sequestration mutants and mutants with reduced or altered cuticle (leaf surface) wax were evaluated and were found to possibly play a role in tolerance or susceptibility to stem rot. Visual ratings of experimental lines in 2019 suggest that two mutants, NM-E2244 and SAB-1558.1, may be highly tolerant to stem rot. Both silicon and cuticle wax have been implicated in providing protection to terrestrial plants against a wide variety of environmental stresses. Thus, further screening is warranted.

Conditions for evaluating specific mutants and mutant populations for herbicide tolerance are being established and will be pursued in 2020.