Location: Crops Pathology and Genetics Research2012 Annual Report
1a. Objectives (from AD-416):
1)SNP marker discovery and genotyping using next-generation sequencing platforms, 2)development and trait evaluation of genetic mapping and mutant populations, 3)Transcriptome sequencing in rice to identify genes and markers of interest for stress tolerance, disease resistance, grain quality, and yield.
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. 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 cold stress during the reproductive stage of growth will be characterized using this method which will facilitate identification of rice genes involved in responses to this stress. Development of genetic mapping and mutant populations will consist of generation advance through single-seed descent. Screening populations for agronomic traits of interest will be performed in consultation and conjunction with Rice Experiment Station breeders.
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: The M-203/M-206 recombinant inbred line (RIL) mapping population (F6 generation) was planted at the Rice Experiment Station for evaluation and seed increase. Additional replicates of this population were planted in Davis. The S-301/M-206 RIL population was advanced to the F6 generation and the M-204/S-301 and S-301/M-204 RIL populations were advanced to the F5 generation. In addition, the Rice Experiment Station provided F1 seed of various crosses (>100) which were planted to generate F2 for development of additional mapping populations. M-204 mutants (M2 generation) were planted for phenotyping and generation of M3 seeds; and 3) Cold tolerance evaluation: Reproductive tolerance of two short duration varieties (Kitaake and 29Lu1) was evaluated in the growth chamber to test the suitability of this method of assessment. Several cold tolerant (vegetative and reproductive) varieties have been planted for genetic crosses to be completed by the end of 2012. Advanced backcross lines having the major seedling cold tolerance QTLs (qCTS4 and 12) separately and in combination have been developed and are being evaluated on a small scale while seeds are being increase for field-based evaluation.