Location: Crops Pathology and Genetics Research2012 Annual Report
1a. Objectives (from AD-416):
Overall objective is to integrate molecular genetic approaches and conventional breeding methods to develop improved germplasm for the California rice industry.
1b. Approach (from AD-416):
Single nucleotide polymorphisms (SNPs) will be identified by sequencing reduce representation libraries of selected rice germplasm in conjunction with computational genomics. SNP markers identified in this manner will be used to assess genetic diversity and map traits of interest where possible. SNPs developed and validated by Japanese researchers will also be employed to determine the utility of these markers in analyzing California rice germplasm. Transcriptomes of various tissues and developmental stages of selected rice germplasm will be characterized by sequencing to identify genes of interest and potentially useful markers. In addition, rice plants undergoing various stresses (e.g. low temperature, stem rot disease) will also be characterized using this method which will facilitate identification of rice genes involved in responses to these stresses and, in the case of stem rot disease, fungal genes that are induced during infection and spread of the pathogen.
3. Progress Report:
The goal of this project is to develop tools and resources for improving rice varieties for California, which contributes directly to objective 2 of the in-house project. The emphasis is on developing DNA markers to predict the presence of traits such as cold tolerance, disease resistance, and grain quality and to develop rice populations (mapping and mutant). The markers will accelerate breeding of improved varieties. The mapping and mutant populations will facilitate gene discovery and characterization and may provide useful germplasm for future variety development by public breeding programs. Progress has been made in three areas to date: 1) Single nucleotide polymorphism (SNP) marker genotyping: we have employed next-generation sequencing to identify and genotype SNP markers. These markers allow the highest level of resolution in distinguishing the most closely-related varieties such as those found in the California breeding programs. DNA libraries from about 45 important California varieties have been sequenced, SNPs have been identified, additional data analyses are being performed and a manuscript is in preparation; 2) Population development: A recombinant inbred line (RIL) mapping population derived from a cross between California varieties M-203 and M-206 was advanced to the F6 generation. This population is segregating for various grain quality characteristics. Induced mutagenesis of the California variety M-204 was performed using gamma-irradiation and sodium azide as mutagenic agents. Data on the response of M-204 to each of these agents were collected along with M2 seeds; and 3) Cold tolerance evaluation: Diverse rice germplasm accessions from the USDA-ARS collection were evaluated for seedling and reproductive stage cold tolerance using molecular, physiological and visual methods.