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ARS Home » Pacific West Area » Albany, California » Plant Gene Expression Center » Research » Research Project #434411

Research Project: Conserved Genes and Signaling Networks that Control Environmental Responses of C4 Grain Crops

Location: Plant Gene Expression Center

2019 Annual Report

The long-term goal of this project is to identify genetic pathways useful for adaptation of crop plants to stressful and/or novel environmental conditions. This project investigates two aspects of post-transcriptional regulation associated with the plant circadian clock, namely regulation of protein activity via protein-protein interactions and control over alternative splicing of transcripts. Based on previous knowledge, these mechanisms are predicted to be associated with key plant signaling networks governing responses to temperature signals. Specifically, during the next five years we will focus on the following objectives. Objective 1: Dissect the circadian clock regulatory network underlying time to maturity at the genetic and molecular levels, particularly in C4 crops including maize and sorghum. • Subobjective 1A: Investigate whether SbG1 contributes to the timing of maturity in sorghum. (Harmon) • Subobjective 1B: Investigate the effect of sbgi mutants on expression of flowering time and circadian clock genes. (Harmon) • Subobjective 1C: Identify protein partners of SbGI and ZmGI proteins. (Harmon) Objective 2: Establish the relationship between alternative transcript splicing and the circadian clock control responses to heat and cold at the genetic and molecular level in C4 crops including maize and sorghum. • Subobjective 2A: Define the impact of sic mutants on low temperature-sensitive alternative splicing within the Arabidopsis transcriptome. (Harmon) • Subobjective 2B: Test whether specific clock-associated splice variants occurring in sic-3 alter circadian clock responses to temperature cues. (Harmon) Objective 3: Identify genetic variation in circadian clock genes to enhance agronomic performance in the field for maize and sorghum in response to temperature variation and/or change in latitude. • Subobjective 3A: Test whether GI genes contribute to yield in maize and sorghum under field conditions with sustained suboptimal temperatures.

Objective 1 will study flowering time, leaf senescence, and time to maturity in SbGI mutants. Flowering time will be days from sowing to boot stage and days from sowing to anthesis/stigma exertion. Leaf senescence will be scored visually from flowering until harvest maturity. Time to maturity will be days to hard dough stage in maturing seeds. Also, expression of flowering time and circadian clock genes will be compared between sbgi mutant and normal plants to test if SbGI contributes to regulation of these genes. Quantitative polymerase chain reaction will be used to determine relative transcript levels in leaves of plants exposed to short or long day photoperiods. Proteins interacting with the SbGI and ZmGI proteins will be identified through testing of candidate proteins and large-scale library screening with yeast two-hybrid. Objective 2 will identify splice variants accumulating at low temperature in the reference sic-3 allele but not wild type plants by RNA sequencing (RNA-seq). All alternative splicing events from circadian clock genes significantly changed in sic-3 according to RNA-seq will be validated with reverse transcription-polymerase chain reaction. In addition, experiments will test whether splice variants of circadian clock transcripts found in sic-3 impair circadian clock function at low temperatures. Two complementary transgenic approaches will be used: 1) ectopic overexpression of a splice variant in wild type plants, which tests whether high levels of a specific splice variant interfere with clock function, and 2) silencing of splice variant expression in sic-3, which tests whether removal of a splice variant suppresses circadian clock defects in this mutant. Objective 3 will test whether GI genes participate in response pathways required for optimal plant growth and yield under high and low temperatures. SbGI and ZmGI mutants will be tested for flowering time, as in Objective 1, and yield-associated traits, including total dry matter (weight of panicle/ear before threshing), grain yield (total seed weight per panicle/ear) and 100 seed weight. Harvest index also will be calculated as the ratio of grain yield to total dry matter. Different temperature conditions will be provided by growing plants at Gill tract in Albany, California, a comparatively cool site, and at University of California, Davis, a comparatively hot site. This objective will also determine whether SIC genes contribute to low temperature tolerance of maize and sorghum. sic mutants will be tested for low temperature sensitivity during germination by calculating percent germination at 26°C, 22°C, 16°C, and 12°C. Also, mutant plants will be evaluated for the flowering time, maturity, and yield traits as described above. If available gi or sic mutations do not sufficiently reduce gene function, CRISPR-Cas9 genome editing can be used to generate mutant alleles. If conditions at the Albany and Davis fields are too severe to score traits, greenhouse space is available for these studies.

Progress Report
Researchers in Albany, California, continued work on a project with the goal of improved crop plant productivity under stressful environmental conditions. The approach is to study genes in grain crops needed for resistance to stressful temperatures and genes controlling environmentally-sensitive plant developmental transitions relevant to grain production. In support of Objective 1, work continued on verifying sorghum lines with mutations in the GIGANTEA gene. Work also continued on developing experimental reagents and growth conditions for future experiments to test high temperature stress tolerance and flowering time responses of these mutant lines. In support of Objective 2, work continued on the Arabidopsis sickle-3 mutant to understand why this mutation renders plants more sensitive to low temperature conditions. Transcriptome-wide RNA sequencing (RNA-seq) revealed significant alterations in the levels and structure of messenger RNA (mRNA) in mutant plants exposed to low temperature conditions. The scope of mRNA changes in the sickle-3 mutant was more extensive than previously known. While further work is needed, the SICKLE gene appears to be required for maintenance of fundamental gene expression processes when plants experience low temperature conditions. Under Objective 3, work continued on investigating SICKLE gene function in maize and sorghum. Mutagenized plant populations were grown out and individuals with mutations in orthologs of the SICKLE gene were identified. Mutant plants discovered here were backcrossed to normal plants to prepare for future experiments.

1. Plant resistance to the adverse consequences of low temperature requires the SICKLE gene to maintain fundamental gene expression-associated processes. Low temperatures alter plant growth and development. Understanding genetic mechanisms plants use to deliberately alter their behavior in response to temperature conditions is important for expansion of crop plant growth range and season. Researchers at Albany, California, have identified extensive reconfiguration of gene expression-associated processes under cold temperatures when the SICKLE gene is mutated in the well characterized plant, Arabidopsis thaliana, which is a stand-in for crop plants. Therefore, plants require the SICKLE gene to maintain fundamental gene expression processes under low temperature conditions. The knowledge gained from this study is translatable to grain and specialty crop plants. These findings will inform breeders and scientists working to develop crop lines that can be planted earlier in the year or in regions where low temperatures currently interfere with crop production.

Review Publications
Basso, M.F., Ferreira, P.G., Kobayashi, A.K., Harmon, F.G., Nepomuceno, A.L., Molinari, H.C., Grossi-de-Sa, M.F. 2019. MicroRNAs and new biotechnological tools for its modulation and improving stress tolerance in plants. Plant Biotechnology Journal. 17(8):1482-1500.