Location: Crops Pathology and Genetics Research
2025 Annual Report
Objectives
Objective 1: Characterize novel traits and mutations in rice affecting grain quality, yield, and climate resiliency.
Sub-objective 1.A: Characterize endosperm mutant phenotypes and their underlying mutations to determine their potential for non-table rice uses.
Sub-objective 1.B: Determine the role of cuticular waxes and silicon in the response of rice plants to their environment.
Objective 2: Expand select genetic resources for elucidating agriculturally important processes, e.g., climate resilience, and improving rice germplasm.
Sub-objective 2.A: Generate and make publicly available germplasm from mutants previously identified by forward and reverse genetics.
Sub-objective 2.B: Develop and make publicly available rice mutant populations for genetics and breeding.
Approach
Objective 1: Genetic crosses of two mutant-derived rice lines will be performed to generate germplasm and provide materials for trait evaluations and gene expression studies. Sequencing-based strategies will be used to identify the causal mutations in both rice lines. Seed amplification and field-based phenotyping using a randomized complete block design will be conducted to facilitate evaluation including grain and agronomic traits. Physicochemical tests and assays specific to characterization of brewing properties will be conducted on the grains of the germplasm developed from genetic crosses. Established statistical methods will be employed to determine the significance of any trait differences observed between rice lines. The same methods and strategies will be used for developing genetic materials and identifying causal mutations in cuticle wax deficient mutants. Field and greenhouse-based assays will be used to evaluate the performance of and collect data from these wax deficient mutants in response to abiotic and biotic stresses. Statistical analyses of trait data will be conducted to determine the significance of any differences observed between mutant lines in response to environmental conditions.
Objective 2: Previously identified rice mutants will be genetically crossed to their wild type progenitor varieties to remove or minimize the presence of mutations unrelated to the mutant traits of interest. Seeds from the resulting mutants lines will be increased and deposited into ARS rice gene banks for distribution to the research community. Mutant populations derived from three rice varieties (Kitaake, Sabine, and Nipponbare) will be grown in the field for seed increase and trait evaluations using an augmented randomized complete block design. Seeds and trait data, including digital documentation of visible mutant phenotypes, will be deposited in ARS rice gene banks for distribution to interested researchers. More detailed phenotypic or trait evaluations will be conducted on fixed mutant lines derived from the variety Kitaake. Data will also be obtained from sequencing a small subset of the Kitaake rice mutants and used to assess the number of mutations in this population.
Progress Report
This report documents progress for project 2032-21000-027-000D, Leveraging Rice Mutant Resources for Trait Discovery, Analysis, and Germplasm Enhancement. The overall goal is to identify novel mutations and traits to further our understanding of grain quality and productivity in rice and to develop novel genetic resources for breeding new, climate-resilient varieties. This research builds on work involving the generation of rice mutant populations and the subsequent identification of novel gene mutations and mutant phenotypes. The two main objectives are: 1) characterize novel traits and mutations affecting rice grain quality, productivity, and climate resiliency; and 2) transfer useful rice mutants and populations to the U.S. rice germplasm collections.
In support of Objective 1, research continued on characterizing rice grain mutants exhibiting an opaque, non-waxy endosperm trait and germplasm from those mutants. Work focused on the hollow core grain mutant KDS-1830C and K7352, a line derived from the mutants KDS- 2173A and KDS-1852. This involved evaluation of grain quality attributes of materials generated in the field in FY24 and the grow out of more materials in FY25 for analysis in FY26. Work is underway to determine morphological, physico-chemical, and sake brewing-specific characteristics of KDS-1830C and K7352 in comparison to California medium grain and Japanese sake brewing varieties. Lines from genetic crosses between KDS-1830C and its wildtype variety Kitaake and the California variety M-103 were planted in the field in FY25 and are being evaluated. These materials will be used for Objective 1 experiments and in support of Objective 2. Work to characterize K7352 lines also continued. Forty-five lines developed from the original K7352 lines and grown in the field in FY24 were planted in FY25 for more preliminary trait evaluations, seed increase for grain analysis, and generation advancement. Research on cuticular wax-deficient and altered silicon mutants continued. Analysis of bulked segregant sequencing data obtained in FY22 identified a missense mutation in a candidate gene for the wax-deficient mutant SAB-1558. This gene encodes a wax biosynthesis enzyme. Confirmation of this mutation and characterization of SAB-1558 continues in collaboration with researchers in Daejeon, South Korea. Work to identify the mutations for several wax-deficient mutants (SAB-7-17A, 11-39A, 6-1A, and 1064.2) using bulked-segregant sequencing approach continued in FY25. Results from field-based evaluations of SAB-1558, 7-17A, and 11-39A mutants planted under aerobic field conditions in Davis, California, in FY24 are being analyzed. In FY25, SAB-1558 and an advanced line developed by crossing the wax-deficient mutant KDS-2249D and its wildtype Kitaake were grown in a flooded paddy conditions at Biggs, California, along with their respective wildtypes Sabine and Kitaake for evaluation of performance. Due to conditions in FY24, the evaluation of field performance of three mutants (NM-E1746, NM-3403, and NM-3380) carrying mutations in the Low Silicon 1 transporter gene was not feasible and there were insufficient personnel to conduct these experiments in FY25. In collaboration with researchers at Louisiana State University in Baton Rouge, Louisiana, research on characterizing these silicon mutants in response to insect herbivory continued. In FY25, whole genome sequencing of the low silicon mutants and wildtype Nipponbare used for insect studies was conducted by the Louisiana State University collaborators and analysis of the data are underway.
In support of Objective 2, research was conducted to expand selected genetic resources for rice researchers and breeders. Genetic crossing of previously identified mutants affecting grain quality, cuticular wax content, metalloid accumulation and other traits to the wildtype varieties from which they were derived continued to produce lines with reduced background mutations. Seeds from mutants and backcrosses are being produced for submission to an ARS rice genebank. Endosperm mutants noted in Objective 1, mutants with altered gel temperature (KDS-1623B and KDS-1824B), cuticular wax deficient mutants (SAB-1558, 6-1A, 7-17A, 11-39A, KDS-2249D, and others), and low silicon mutants (NM-E1746, NM-3403, and NM-3380) are being prepared for submission in FY25 and FY26. In FY25, Kitaake M9 seeds from the FY24 harvest (105 lines) were planted by direct seeding in an augmented randomized complete block design for seed increase and evaluations including agronomic performance traits and multispectral imaging. Data collection on plant morphology, development, yield, and seed morphology will be conducted in FY25 and FY26. Evaluation of Kitaake M9 and M8 lines grown in FY24 continues and included elemental analysis of straw samples from M9 (n=252) and M8 (n=140) in FY25. Analysis of the results is underway. M10 seeds produced from M9 lines in FY24 and FY25 will be submitted to an ARS rice genebank. Sabine and Nipponbare mutant populations were not planted in FY25 due to a critical vacancy.
Accomplishments