Location: Crops Pathology and Genetics Research
2013 Annual Report
1)Next-generation genotyping of rice germplasm: We have employed next-generation sequencing to identify and genotype single-nucleotide polymorphism (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, a manuscript describing the results of this study has been published;.
2)Sequencing of expressed rice genes from California varieties: Using an approach called exome sequencing, we have characterized a number of California varieties. Sequences representing the expressed regions of the genome (i.e. exome) of rice were identified by our cooperators and used to generate DNA probes for capturing these regions via solution-based hybridization with rice genomic DNA. Target (i.e. captured) sequences were subjected to short read DNA sequencing using an Illumina sequencing platform. These sequences are under analysis. A manuscript describing the rice exome sequencing approach used is in preparation;.
3)Development and screening of rice populations for genetic analysis of agriculturally important traits: A recombinant inbred line (RIL) mapping population derived from a cross between California varieties M-203 and M-206 is being advanced to the F7 generation and phenotypic analysis of the RILs for milling quality, seedling vigor, reproductive cold tolerance, and other important traits is underway. Additional genetic mapping populations under development include recombinant inbred lines of the following crosses: M-204/S-301 (F5:6 generation), S-301/M-204 (F5:6), and Calmochi-101/94Y561 (F2:3). Induced mutants (M2 generation) derived from the chemical mutagenesis (3 mM sodium azide) of the California variety M-204 were planted for creation of a reverse genetics resource and will be available for screening via Targeting of Induced Local Lesions in Genomes (TILLING) by sequencing. These M2 plants will also be subjected to heat stress during grain filling in order to identify mutants that may be tolerant to heat-induced grain chalkiness. M3 seeds harvested from sibling M2’s of this M-204 mutant population have been planted for generation advance (i.e. development of fixed mutant lines) and the M4 seeds will be harvested at the end of 2013 (or early 2014). M2 and M3 seeds of the M-204 mutants are currently being screened for enhanced tolerance to abiotic stresses and for altered grain quality traits. Due to the low mutation densities observed from exome sequencing of the M-204 mutant populations derived from gamma-irradiation (350 and 400 Grays) and 1 mM sodium azide mutagenesis, these populations are not being used currently.