Location: Crops Pathology and Genetics Research
Project Number: 2032-21000-027-010-T
Project Type: Trust Fund Cooperative Agreement
Start Date: Jan 1, 2025
End Date: Dec 31, 2025
Objective:
The overall goals of this project are to employ genetic and pre-breeding approaches to identify genes controlling traits important for grain quality and agronomic performance in California rice and to incorporate these genes and/or rice germplasm carrying those genes into genetic resources that are useful to the breeding programs serving the California rice industry. Emphasis will be placed on grain quality (i.e., milling yield and stability), yield, and herbicide tolerance. Genetic mapping, reverse genetics (including gene editing technology), forward genetics, and DNA sequence analyses will be employed to identify, locate, and isolate genes of interest (i.e., gene discovery). Pre-breeding will be conducted concurrently through the development of genetic resources from the gene discovery activities. Specific objectives are: 1) Mapping population development and characterization; 2) Allele mining of RES varieties; and 3) Screening remnant mutant populations for herbicide resistance.
Approach:
1) Mapping population development and characterization: An augmented randomized complete block design will be employed to grow out and evaluate 200-250 recombinant inbred rice lines (F7 generation) at the UC Davis Row Crops Facility. Each block will contain unique F7 mapping population lines plus a set of checks or controls which will include the two parents of the population and 2-4 additional varieties. The set of checks will be replicated in each block. Standard row crop field practices modified for rice production will be employed. Rice trait evaluations will be conducted in the field (e.g., height, heading date) and remote sensing by drone-based spectral imaging will be used to collect additional information. Pure seed increases will also be performed in well-spaced single rows of each of the lines to produce a breeder's seed source and leaf tissue will be collected and DNA extracted for genotyping to confirm purity of the lines. Larger grow outs of the parental lines and up to 10 selected F7 lines will be used to generate milling yield curves to evaluate the milling yield and stability of the lines.
2) Allele mining of RES varieties: One ancestral germplasm (Terso) and 5 RES varieties (M-401, M-203, M-206, M-105, and M-211) will be subjected to whole genome sequencing (minimum of 30X coverage) and sequence data will be processed and analyzed to identify allelic variants in genes responsible for grain quality (e.g., starch metabolism) and agronomic performance (e.g., heading date, stature).
3) Screening remnant mutant populations for herbicide resistance: Remnant mutant population lines derived from various temperate and tropical japonica rice varieties using chemical and physical mutagenesis will be grown in the field and screened with the herbicide clethodim at the 3-6 leaf stages to look for tolerant lines. Any survivors will be transferred to the greenhouse to produce seeds for subsequent re-testing.