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ARS Home » Midwest Area » Columbia, Missouri » Plant Genetics Research » Research » Research Project #434241

Research Project: Genetic and Physiological Mechanisms Underlying Complex Agronomic Traits in Grain Crops

Location: Plant Genetics Research

2018 Annual Report

Objective 1: Identify genetic and physiological mechanisms controlling growth under drought in maize, wheat, and related species. • Sub-objective 1.1: Characterize the genetic regulation of maize root growth responses to soil water-deficit stress. • Sub-objective 1.2: Determine the roles of plant hormones abscisic acid (ABA) and gibberellins (GA) in the regulation of wheat root responses to water deficit. • Sub-objective 1.3: Characterize the genetic networks that link transcription factor expression and metabolism central to cellular protection during dehydration in a C4 resurrection grass. Objective 2: Characterize corn for natural rootworm resistance, rootworm larvae for Bt tolerance, and artificial diets for improved understanding of rootworm biology and management. • Sub-objective 2.1: Systematically screen exotic and Germplasm Enhancement of Maize (GEM) germplasm, identify potential sources of western corn rootworm (WCR) resistance, verify resistance, and move into adapted germplasm. • Sub-objective 2.2: Characterize heritability and other traits of rootworm larvae with Bt tolerance. • Sub-objective 2.3: Evaluate northern corn rootworm (NCR) development on larval Diabrotica diets and develop a diet toxicity assay for NCR. Objective 3: Identify genetic and physiological mechanisms governing response to artificial selection in cereals and related species. • Sub-objective 3.1: Develop an experimental evolution maize population to characterize adaptation to selective pressures at the genomic level in maize and related species. • Sub-objective 3.2: Quantify the importance of epistasis with novel Epistasis Mapping Populations. • Sub-objective 3.3: Develop, implement, and validate statistical methods to better understand traits controlled by multiple genes acting in concert. Objective 4: Develop and characterize germplasm to elucidate the genetic mechanisms underlying nutritional and food traits in maize. • Sub-objective 4.1: Screen and develop maize germplasm for traits important in food-grade corn. Objective 5: Identify genetic and physiological mechanisms underlying maize adaptation to the environment to enhance its productivity. • Sub-objective 5.1: Develop and evaluate germplasm segregating for adaptation to high elevation. • Sub-objective 5.2: Evaluate diverse maize hybrids in multi-location trials as part of the Genomes To Fields Genotype x Environment Project.

Conduct genome-wide association analysis of water-stress root growth using high-throughput maize root phenotyping to link transcription factor (TF) expression with root growth phenotypes under stress. Characterize water deficit growth and hormone responses in wheat roots, and interrogate the gene expression profiles (RNAseq) for the root growth zone. Use chromatin immunoprecipitation-sequencing to establish the role of transcription and TF targets in the response of both wheat and maize roots to water deficits. Develop gene network maps for dehydration TFs in the resurrection grass Sporobolus stapfianus. Evaluate 75 new sources of maize germplasm each year for resistance to Western Corn Rootworm (WCR) larval feeding in replicated field trials. Develop an artificial diet for Northern Corn Rootworm (NCR) and conduct toxicity assays for all available Bt proteins. Expose NCR populations to current industry Bt corn in plant assays and measure the effect on insect development. Evaluate the inheritance of Bt resistance in WCR. Conduct five cycles of selection for high and low plant height in the Shoepeg maize landrace population, followed by genotyping and selection mapping. Phenotype an Epistasis Mapping Population and conduct statistical tests for epistatic effects. Screen 100 heirloom maize varieties for adaptation to the southern Corn Belt and make selections based on agronomic performance and kernel composition traits. Create and release modified open pollinated varieties with improved performance and food characteristics. Conduct quantitative trait locus (QTL) mapping of traits related to highland adaptation in maize populations grown at low, mid, and high elevations. Compare QTLs identified in a Mexican and South American germplasm. Identify candidate genes based on traits related to adaptation and fitness at varying elevation. Participate in multi-location yield trials to evaluate diverse maize hybrids across the US.

Progress Report
We completed the construction of “Rootbot” our high-throughput root phenotyping robot that is the foundation of both our genetic approaches to understanding water deficit stress induced changes in root growth in maize (Sub-objective 1.1) and for our hormonal studies on root growth regulation under water deficit stress in wheat (Sub-objective 1.1). We are currently putting the robot through working trials to establish standard operating protocols and ensure reliable outcomes. We have identified contrasting genotypes of wheat for both the growth response of the root and hormonal contents. Mutant wheat lines have been tested also and contrasting pairs have been chosen for further analysis. We have obtained cloned maize transcription factor coding sequences for all of the transcription factors genes identified as differentially expressed in roots in response to a water deficit stress. We are currently initiating the construction of the necessary tools to progress with the proposed DAP-Seq analysis of transcription factor target genes for maize. We have identified possible dehydration induced transcription factor targets from the resurrection grass Sporobolus stapfianus and we will initiate the cloning of the requisite coding sequences for DAP-Seq analyses. We have completed transcriptome sequencing (exome) for regions of the nodal root growth zone from both lab and field grown for both of our targeted maize lines (sub-ordinate project 5070-21000-038-09R). The data has been compiled and initial analyses performed and we are in the process of assessing the transcriptomes for hypothesis generation. Objective 2: This year, rather than screening a random set of 50 to 100 germplasm lines, we evaluated resistance to corn rootworm feeding the full 282 Association Panel of maize inbred lines that have been fully sequenced. Data collection was just recently completed and is still being compiled. We created a “removal of selection colony” derived from our Cry34/35Ab1-resistant colony. After six generations without feeding on Cry34/35Ab1-expressing corn, the colony was less resistant to Cry34/35Ab1-expressing corn than its parent colony that continued to be reared on Cry34/35Ab1-expressing corn. This is the first instance of possible fitness costs to any Bt toxins targeting the western corn rootworm. We completed the baseline susceptibility studies of the Brookings, SD Northern corn rootworm colony to each of the current Bt toxins targeting rootworms. This colony was susceptible to all current Bt corn lines. Objective 3: No progress to report, SY left ARS in March 2018. Objective 4: We have screened a large collection of landraces from the U.S. and around the world, and planted a food corn trial with three replicates of 60 landraces in both Missouri and North Carolina in summer 2018. Pollinations are underway in order to produce grain for compositional analysis, as well as data collection for an array of plant traits. After harvest, an array of ear and kernel phenotypes will also be collected. Additional landraces are in the nursery for seed increase and inclusion in subsequent trials. Objective 5: We completed the seed increase of F2:3 populations derived from crosses of highland by lowland landraces from both Mexico and South America. The final population sizes are 384 F2:3 families for the Mexican population, and 300 families for the South American population. Both populations were planted in Puerto Vallarta in winter 2017-18 in two replicates each, and plant phenotypes (male and female maturity, plant and ear height, tassel length and number tassel branches) were collected. Ear and kernel data collection (number of ears, total kernel mass per plant, and fifty kernel mass) is underway. We are participating in the G2F trial in summer 2018 by growing 1600 2-row yield plots comprised of three different experiments in two replicates each. At present, only 80% of the hybrids have flowered, and despite the hot and dry conditions in Missouri, the plants look healthy indicating we will have a successful season.

1. Rootbot: A high-throughput automatic platform for root growth phenotyping. Drought (water deficit stress) threatens the food security of not just for the U.S. but globally. Drought tolerance is a very complex trait, influenced by genetic, physiological, and environmental factors. However, it is clear that root traits have a major impact on drought tolerance in agronomic crops but our understanding of roots is limited, even more so when drought is factored in. ARS researchers in Columbia, Missouri have developed a low-cost robotic system to directly observe roots in soil and to measure the growth rate response under both ideal and water-deficit conditions. The robot, referred to as “RootBot” was designed to be placed in a controlled environment and to allow for roots to develop normally in the dark and in soil. This technology has broad applications for use in multiple crops and with varying soil treatments aside from water deficit stress. The platform will allow for the rapid assessments of root traits for breeding efforts to improve drought tolerance in all major crops.

Review Publications
Huynh, M.P., Meihls, L.N., Hibbard, B.E., Lapointe, S.L., Niedz, R.P., Ludwick, D.C., Coudron, T.A. 2017. Diet improvement for western corn rootworm (Coleoptera: Chrysomelidae) larvae. PLoS One. 12(11):e0187997.
Ludwick, D.C., Meihls, L.N., Huynh, M.P., Pereira, A.E., French, B.W., Coudron, T.A., Hibbard, B.E. 2018. A new artificial diet for western corn rootworm larvae is compatible with and detects resistance to all current Bt toxins. Scientific Reports. 8:5379.
Vanous, A., Gardner, C.A., Blanco, M., Martin-Schwarze, A., Lipka, A.E., Flint Garcia, S.A., Bohn, M., Edwards, J.W., Lübberstedt, T. 2018. Association mapping of flowering and height traits in Germplasm Enhancement of Maize doubled haploid (GEM-DH) lines. The Plant Genome. 11(2):170083.