Effects of Sustainable Soil Management on Gene Expression in Maize

EPA Grant Number: FP917229
Title: Effects of Sustainable Soil Management on Gene Expression in Maize
Investigators: Roach, Erika Danielle
Institution: Pennsylvania State University
EPA Project Officer: Lee, Sonja
Project Period: September 1, 2010 through August 31, 2012
Project Amount: $74,000
RFA: STAR Graduate Fellowships (2010) RFA Text |  Recipients Lists
Research Category: Academic Fellowships , Fellowship - Science & Technology for Sustainability: Green Engineering/Building/Chemistry/Materials


Project Objectives: 1. Determine the effect of a hairy vetch cover crop, no-tillage, and their interaction on soil and crop health and expression of a candidate group of genes in maize. 2. Be able to use gene expression results to help explain observed plant and soil health and quality results. 3. Determine how gene expression changes are manifested in protein level changes.

Developing sustainable agricultural systems will lead to solutions to environmental issues associated with conventional agriculture. I will examine the expression of candidate genes in maize grown in sustainable agricultural systems and conventional agricultural systems. If gene expression in corn changes to promote crop health and vitality as a result of sustainable farming methods, farmers, scientists, and extension agents will be provided with incentive to implement sustainable methods.


The field trial is a split-plot in a randomized complete block design. The main plots are cover crop (hairy vetch) versus no cover crop, and the sub-plots are no-tillage versus moldboard/disk/harrow tillage. Plant parameters I will measure include plant emergence regularly during the first 6 weeks after planting; plant population at 3 weeks after planting; plant height at 4 and 8 weeks after planting and at maturity; leaf carbon and nitrogen content at V6, silking, and grain fill stages; chlorophyll content at V6 and bi-weekly after V6; leaf area index at V6 and bi-weekly after V6; plant moisture content at V6, silking, and grain fill stages; and grain yield upon harvest of maize for grain. I will also score each plot regularly during the season to determine presence and extent of pests and disease infestation. Soil parameters I will measure include bulk density in the first month after planting and after harvest; surface soil moisture weekly; organic carbon and total soil nitrogen content once at the beginning of the season; active carbon and nitrate content monthly for the first 3 months after planting; available P, K, Ca, Mg, pH, and cation exchange capacity one time at the beginning of the season; aggregate stability at V6 and after harvest; soil temperature hourly with data loggers; and earthworm population one time at the beginning of the season. Gene expression analysis that I will conduct includes sampling leaves during V6, silking, and grain fill stages from the ear leaf or youngest fully developed leaf in V6. These samples will be frozen in liquid nitrogen and used for subsequent gene expression analysis, protein analysis, and carbon and nitrogen content evaluation. Gene expression analysis will be conducted initially only on samples taken during V6 stage to get a general idea of expected results while maintaining a manageable sample size. Candidate genes were chosen based on predicted environmental differences between treatments as well as results from similar research done studying gene expression in tomatoes planted in hairy vetch residue compared to no cover. In analyzing gene expression in my plant samples, I will isolate total RNA, synthesize cDNA, and conduct reverse transcriptase PCR and real-time PCR using primers designed specifically for the genes of interest. Objective 2: Plant and soil measurements will be compared to the results of the gene and protein expression analysis. Statistical analysis will be performed using analysis of variance (ANOVA) and other statistical tools. Objective 3: I will work with Dr. Autar Mattoo at the USDA ARS in Beltsville, MD, to study expression of proteins in plant samples in order to determine if gene expression differences are also manifested in protein expression differences.

Expected Results:

I expect to see changes in gene expression due to environmental changes experienced by maize growing in different treatments. I expect to see higher expression of cold tolerance genes early in the season in maize growing in no-tillage and in fields with a cover crop mulch due to cooler soil temperatures experienced in these treatments. I expect to see higher expression of drought tolerance genes in maize grown in fields without a cover crop and in fields with tillage. This is due to higher temperatures and lower soil moisture associated with these treatments. I expect to see higher expression of nitrogen-responsive genes in fields with a hairy vetch cover crop due to the high levels of nitrogen supplied to the soil as hairy vetch breaks down. I expect to see the greatest difference early in the season before side-dress fertilization and later in the season when hairy vetch has had time to fully break down. I also expect to see higher expression of nitrogen-responsive genes in tilled fields with hairy vetch early in the season because tillage helps accelerate the breakdown of hairy vetch. I expect to see higher expression of nitrogen-responsive genes in no-tillage fields with hairy vetch later in the season when the hairy vetch on the tilled fields has broken down almost completely and the vetch mulch remains on the no-tillage fields to further provide nutrients. I expect to see genes associated with senescence expressed at lower levels in fields treated with hairy vetch mulch and no-tillage. This prediction is based on results of similar research in tomatoes grown in hairy vetch mulch. For the same reason, I expect to see higher expression of genes associated with defense against pests and disease in maize grown in no-tillage and with a hairy vetch cover crop. I expect to see results that indicate improved soil quality in fields treated with a hairy vetch cover crop and no-tillage. I expect to see higher presence of pest and disease issues in plants grown with a cover crop in no-tillage early in the season but I expect this difference to not be manifested in yield differences.

Potential to Further Environmental/Human Health Protection
This study will supply novel information about how sustainable soil management practices affect crops grown for profit. This information will enable scientists to better understand the phenotypic changes in crops observed in sustainable systems. The results of this study can be used to better understand the fundamental mechanisms of sustainable agriculture. By providing sustainable agriculture with a stronger justification, wider implementation will likely follow. Conventional agricultural systems can contribute to environmental degradation such as air and water pollution, soil structure and health depletion, erosion, and reduction of natural biodiversity. The movement toward more sustainable systems will become increasingly important when considering the growing world population and rising importance of environmental stewardship. Cover crops benefit the health of the soil in which they are grown and the health of crops grown after. Cover crops supply nutrients to the following crop, provide organic matter to improve soil quality, and supply mulch to improve soil physical and biological properties. Legumes help to fix atmospheric nitrogen for the following crop. Hairy vetch fixes high levels of atmospheric nitrogen, has vigorous growth, fits well into diverse cropping rotations, has low fertility needs, and is winter hardy. Cover crop root systems assist in soil erosion prevention, retrieve available nutrients in the soil after a cash crop, and help to prevent runoff of agricultural chemicals over the winter. Erosion is a major cause of soil and crop quality depletion in much of the cropland in the United States. Using a no-till farming system not only helps in erosion control, it helps maintain soil aggregate and overall structure and helps maintain crop residue and organic matter on the soil surface. This research would help scientists, extension agents, and farmers better understand the effects of sustainable soil and crop management techniques on gene expression in a widely grown crop. Uncovering genetic explanations for negative and positive phenotypes resulting from use of cover crops or no-tillage could assist in the negation of negative responses and the enhancement of positive responses. The end result of this research would be to provide further incentive for farmers to implement environmentally sustainable farm management techniques and for scholars and extension agents to have a scientific basis to further promote their use.

Supplemental Keywords:

sustainable agriculture, cover crops, no-tillage, gene expression, hairy vetch,

Progress and Final Reports:

  • 2011
  • Final