Location: Crops Pathology and Genetics Research2011 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 are employing next-generation sequencing to identify and genotype SNP markers. These markers allow the highest level of resolution in distinguishing between the most closely-related varieties such as those found in the California breeding programs. DNA libraries from about 45 important California varieties have been prepared for sequencing which will be completed by December 2011 (end of this project period); 2) Population development: Mapping populations derived from California varieties differing in various grain quality characteristics are being advanced to develop recombinant inbred line populations. Populations are in the F4 and F5 generations. Induced mutagenesis of the California variety M-204 has been performed and data are being collected on the response to various mutagenic treatments. Mutant populations (M2 generation seed) will be harvested by December 2011; and 3) Cold tolerance evaluation: Diverse rice germplasm accessions from the USDA-ARS collection are undergoing evaluation for seedling and reproductive stage cold tolerance. Evaluation methods include molecular, physiological and visual methods.