Performing Department
Plant Pathology
Non Technical Summary
Agricultural systems must become more sustainable while also increasing productivity in changing climates. Improved crop varieties are our best tool to combat these challenges, but it is difficult to simultaneously breed for these contrasting goals. Moreover, while plant breeding has traditionally focused on improving yield and quality of the specific crop being bred, all crops are grown within integrated agricultural systems. Thus, it is imperative that breeding programs consider the consequences of crop varieties not only on their own yield, but also their impacts on other crops in the rotation scheme - in other words, good varieties should also be good companions to other crops in the system. We propose to investigate the soil and rhizosphere microbiome of oat as a potential breeding tool, since these communities play key roles for crop plants, including nutrient acquisition, drought resistance, and suppression of soil-borne disease, and because plants can leave a legacy in soil microbial communities that harms or benefits the next plant grown in that soil. Specifically, we propose to test what, if any, aspects of oat root and soil microbiomes are under genetic control by the host plant, how these microbial community aspects related to yield and quality breeding targets, and finally, whether oat genotypes can be used to improve soil microbial communities for the next crop species in the rotation system.
Animal Health Component
0%
Research Effort Categories
Basic
75%
Applied
(N/A)
Developmental
25%
Goals / Objectives
Our overarching goal in this project is to investigate the soil and rhizosphere microbiome of oat as a potential breeding tool in order to improve nutrient acquisition, drought resistance, and suppression of soil-borne disease for oat crops, as well as develop oat varieties that leave behind positive legacies in soil microbial communities forthe next plant grown in that soil.Our specific objectives are:Determine whether genetic variation exists within elite oat genotypes for control of root-associated microbial communities, and how this interacts with environments to affect oat yield and quality.Determine whether a specific root fungal endophyte, Periconia macrospinosa, found in high abundance in oat roots and varying among genotypes, can provide greater yield, quality, and abiotic stress tolerance to oats.Determine whether oat genotypes differ in their ability to cultivate soil microbial communities beneficial to themselves and other crop species included in rotation schemes.
Project Methods
Objective 1:Determine whether genetic variation exists within elite oat genotypes for control of root-associated microbial communities, and how this interacts with environments to affect oat yield and quality.We have sampled rhizosphere tissue from 16 oat genotypes, sown reciprocally at six sites in five different states and one Canadian province (WI, SD, IL, IA, NY, and Manitoba, CA), with three replications per site.We will extract genomic DNA from root tissue using commercial kits, amplify the prokaryotic 16S and fungal ITS2 rRNA genes, and sequence the amplicons using Illumina Miseq technology.Additionally, we will use a large mapping population generated by co-PI Gutierrez's group to evaluate a broader diversity of oat genotypes in their ability to differentially recruit beneficial microbial communities. A set of 320 advanced oat inbred lines will be evaluated in each of two locations in an augmented alpha experimental design with three replications in Madison and Arlington. Grain yield, test weight, and grain quality, as well as disease resistance, plant lodging, plant height, and other agronomic traits were evaluated.Root tissue from each plot in the Madison location will be sampled in 2019, for a total of 960 root samples. Genomic DNA from root tissue will be extracted, and the 16S and ITS2 rRNA amplified, sequenced, and processed as described above.A genome-wide association mapping (GWAS) approach will be used to map the microbial community quantitative trait loci (QTL). Standard GWAS mixed models approaches will be used correcting for population structure and genetic relatedness among genotypes. Multi-trait models will be used to evaluate the relationship of the "microbial" QTL to QTL for correlated traits such as test weight and disease resistance. This will allow us to have a first approximation at the oat genomic regions responsible for microbial community recruitment.Objective 2:Determine whether a specific root fungal endophyte, Periconia macrospinosa, found in high abundance in oat roots and varying among genotypes, can provide greater yield, quality, and abiotic stress tolerance to oats.In order to test the specific impact of P. macrospinosa, we will perform a series of inoculation studies in which oat genotypes that show high or low rates of colonization by this species in field plots are grown in controlled conditions with or without the endophyte, in a variety of abiotic stress contexts. We will grow eight oat genotypes, and each genotype will be grown without inoculation, or inoculated with one of 4 isolated P. macrospinosa strains. This inoculation treatment will be factorially crossed with two drought treatments (well-watered vs. water-stressed) and three nitrogen treatments (no added N, mineral N fertilizer, or equivalent N addition via sterilized compost, to provide a source of complex organic N). In total this will create 8x5x2x3 = 240 combinations, with three replicate pots per combination (for a total of 720 pots). Based on the growth and seed set of the oat plants, we will determine 1) whether oat yield and test weight are higher in inoculated vs. non-inoculated treatments, 2) if this effect is only evident under certain drought or nutrient stress conditions, indicating a specific benefit under particular stresses, 3) if oat genotypes differ in the benefits they receive from this endophyte. Of particular interest is whether the oat genotypes that show the highest colonization in field settings also show the strongest growth benefits in controlled settings.Objective 3.Determine whether oat genotypes differ in their ability to cultivate soil microbial communities beneficial to themselves and other crop species included in rotation schemes.Genetic variation among oat genotypes in the specific microbial populations promoted or suppressed in their root-zone and bulk soil may lead to legacies that effect their own growth and/or the growth of the next crop grown in that soil. To assess this, we will utilize a plant-soil feedback approach. Using the field plots at the West Madison Agricultural Research Station, we will take soil samples from three replicate plots from each of eight genotypes (chosen from the larger set to show the greatest divergence in microbiome structure). We will use the field soil to inoculate greenhouse pots (5% living field soil to 95% common, sterilized background soil), and reciprocally plant each genotype into each soil. Since 95% of the pot will be filled with a common, sterilized soil, we ensure that abiotic soil conditions are the same across all experimental pots, and any differences in plant growth across pots must be attributed to the different microbial communities used to initiate the microbial communities in the pot. We will cross the eight different soil microbial community inocula, along with a sterilized soil control, with a suite of oat genotypes (the same ones used to condition the field plots), as well as three other crop species often grown in rotation with oats in Wisconsin (corn, soybean, and potato) that represent three different plant families.