Progress 10/01/23 to 09/30/24
Outputs
PROGRESS REPORT Objectives (from AD-416): 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 (from AD-416): 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. This report documents progress for project 2032-21000-027-000D, "Leveraging Rice Mutant Resources for Trait Discovery, Analysis, and Germplasm Enhancement" and continues research from project 2032-21000-023- 000D, "Evaluation and Utilization of Novel Genetic Variation in Rice for the Enhancement of Agronomic Performance and Grain Quality". The overall goal of this project 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 previous 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, ARS scientists in Davis, California, conducted research on the genetic analysis of rice grain mutants exhibiting an opaque, non-waxy endosperm trait (KDS-1830C, KDS-1661A, KDS-1852, KDS- 2173A, and NE-334.1). Work to confirm and characterize the KDS-1830C mutant gene was completed. This mutant has an internal central cavity that develops in the endosperm and a candidate gene was identified. In FY24, other research groups reported the identification of the same gene, OsLESV, based on the characterization of similar rice mutants, thus confirming that mutations affecting the function of this gene result in the formation of a central cavity (hollow core) in the endosperm of the rice grain. The KDS-1830C grain mutant differs somewhat than those reported by the other groups, likely due to the differences in the mutations. Work to determine the usefulness of this grain mutant is underway. Plants from genetic crosses between various grain mutants as well as with their respective wild types were planted in the field and are being evaluated. These genetic materials will be used for Objective 1 experiments and in support of Objective 2. Work to characterize K7352 lines derived from a genetic cross between the grain mutant lines KDS- 2173A and KDS-1852 continued. Several lines developed from the original K7352 lines were planted in the field for agronomic trait evaluations, seed increase for grain analysis, and generation advancement for germplasm development. Selected K7352 lines are being crossed to the wildtype variety Kitaake. 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 are underway in collaboration with researchers in Daejeon, South Korea. Experiments to identify the mutations for wax-deficient mutants SAB-7-17A and 11-39A and to characterize the nature of the wax-deficient trait in these mutants continue. The approach used to identify the SAB-1558 gene is now being employed for these mutants. The SAB-1558, 7-17A, and 11-39A mutants were planted in the field along with the wildtype parent Sabine using a randomized complete block design (RCBD) and agronomic performance traits will be evaluated. To investigate the effects of reduced silicon on field performance, three mutants (NM-E1746, NM-3403, and NM-3380) carrying mutations in the Low Silicon 1 transporter gene were also planted using a RCBD. Data are being collected on plant morphology (height, leaf shape, leaf angle), development (flowering time, tiller number), yield (panicle number and morphology, fertility, grain weight), and seed morphology (dimensions, hull color and appearance). In collaboration with researchers at Louisiana State University in Baton Rouge, Louisiana, research on characterizing these silicon mutants in response to insect herbivory continued. Spodoptera frugiperda Smith, the fall armyworm, was used as a model insect in greenhouse experiments, and the biomechanical and biochemical mechanisms of plant defense were investigated. Lines with reduced silicon showed much lower constitutive resistance to the fall armyworm, although silicon deficiency did not compromise the ability of rice to mount an induced response. Constitutive and armyworm-induced levels of volatiles, phenolics, proteinase inhibitors, and silicon are under investigation, as is gene expression following armyworm feeding. In a small-plot field study, infestations of rice water weevils, an early season pest, did not differ between Nipponbare and the mutants. In support of Objective 2, ARS scientists conducted research to expand selected genetic resources for the elucidation of agriculturally important processes and improvement of rice germplasm. 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 was continued to produce lines with reduced background mutations. Seeds from mutants with at least one round of backcrossing are being produced for submission to the 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, and KDS-2249D), and low silicon mutants (NM-E1746, NM-3403, and NM-3380) are being made publicly available. In FY24, Kitaake M9 (252 lines) and Sabine M5 (300 lines) were planted by direct seeding for seed increase and evaluations including agronomic performance traits and multispectral imaging. Data are being collected on plant morphology (height, leaf shape, leaf angle), development (flowering time, tiller number), yield (panicle number and morphology, fertility, grain weight), and seed morphology (dimensions, hull color and appearance). Seeds from these two populations will be submitted to an ARS rice genebank. Kitaake M8 (508 lines) were planted for generation advance and seed increase for FY25 field planting. All mutant populations were planted using an augmented randomized completed block design with various wildtype varieties serving as controls to facilitate trait evaluations. In FY24, seeds of the Nipponbare TILLING M3 population were obtained from an ARS rice genebank in Stuttgart, Arkansas, as seeds used in FY23 field plantings did not germinate. A set of 50 lines was planted to evaluate germination. Sufficient germination was observed to warrant planting the alternate seed source of the Nipponbare TILLING M3 population in the field in FY25. Artificial Intelligence (AI)/Machine Learning (ML) Neither artificial intelligence (AI) or machine learning (ML) methods were used for this project during FY 2024. ACCOMPLISHMENTS 01 Identification of a mutation underlying a novel cuticular wax-deficient mutant in rice. Cuticular waxes are a major part of the outermost protective barrier in land plants. These waxes help prevent uncontrolled loss of water and gases, and also, interact with microbes and insects. ARS researchers at Davis, California, have identified a missense mutation underlying a novel cuticular wax mutant which alters interaction of the leaf surfaces with water. This is an important step in analysis of gene function and the development of a genetic resource to study the impact of altered cuticular waxes on the response of rice to abiotic and biotic stressors.
Impacts
(N/A)
Publications
- Wang, Z., Wang, Y., Kasuga, T., Hassler, H., Lopez-Giraldez, F., Dong, C., Yarden, O., Townsend, J. 2023. Origins of lineage-specific elements via gene duplication, relocation, and regional rearrangement in Neurospora crassa. Molecular Ecology. https://doi.org/10.1111/mec.17168.
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