Recipient Organization
PENNSYLVANIA STATE UNIVERSITY
208 MUELLER LABORATORY
UNIVERSITY PARK,PA 16802
Performing Department
Plant Science
Non Technical Summary
Global agriculture faces the complex challenge of delivering more for less: population growth will increase demand; current rates of fertilizer and agrochemical use will not be sustainable as limited natural resources become exhausted and the environmental costs associated with their use continue to rise; climate change will reduce both the area of high quality agricultural land and the length of the useful growing season. Although these are daunting prospects, there is every reason to be optimistic that significant improvements can be made to our agricultural systems, including enhancing the efficiency of the crop plants themselves. The broader crop gene pool (traditional varieties, crop wild-relatives, orphan and under-utilized crop species) is adapted to a wide range of resource-poor environments and low-input management systems. To date, mainstream breeding efforts have focused on high-input, high-density systems, leaving much of this potential untapped. The emergence of agriculture and the domestication of plant and animal species are among the defining events of the last 10,000 years of human history. The latest genomics technologies have the capacity to generate an unprecedented level of understanding of these processes and the rich diversity of crop varieties and agronomic practices present in the world today. Such understanding will be vital in our efforts to generate more efficient crops and cropping systems for a sustainable future agriculture.The root system is the primary connection of the plant to the environment and fundamental to the efficient use of water and soil nutrients. This project will further efforts to generate resource efficient crops by advancing our knowledge of root system function in maize (corn) and sorghum. Maize is the cornerstone of US agriculture, providing raw material in the form of starch, oil, protein and biofuel, while supporting further agricultural activities such as dairy and beef industries. Sorghum is a close relative of maize that is of African origin and displays good tolerance to heat, drought and nutrient-poor soils, and that is finding increasing importance in US agriculture. Across the global pool of maize and sorghum varieties (modern breeding material, traditional landrace varieties, and wild-relatives), root systems are highly diverse - in architecture and anatomy, in the molecular machinery of resource acquisition, in the compounds they secrete to the environment, and in their symbiotic interactions with other organisms. Using novel genomics data and custom generated genetic-mapping resources, this project will explore the genetic basis of this functional diversity and evaluate the ecological implications of the root system for plant adaptation to different soil and resource environments. Within the context of an internationally competitive academic research program, this project will generate resources, data and publications available to the research community, while providing extensive opportunities for undergraduate, graduate and postgraduate training. This project will fall within the wider strategic aims of the PSU Huck Plant Institute Root Biology Center collaborative network.
Animal Health Component
30%
Research Effort Categories
Basic
70%
Applied
30%
Developmental
(N/A)
Goals / Objectives
1. Estimation of genotype-trait associations for root traits in maize and sorghum; generation of predictive polygenic models a) Curation of existing trait and genotype datasets b) Generation of novel sorghum root architecture/anatomy data c) Generation of novel maize/sorghum mycorrhiza response data 2. Exploration of genotype-environment/root-environment associations a) Application of polygenic trait prediction models to global maize/sorghum diversity b) Identification of environment/root trait correlations 3. Evaluate models in context of i) landrace/wild-relative diversity; ii) diverse agronomic scenarios a) Characterization of novel maize landrace-derived inbred families4. Mechanistic study of selected candidate variation a) Functional analysis of the Pho1 family of phosphorus transporters/sensors in maize and sorghum
Project Methods
1. Estimation of genotype-trait associations for root traits in maize and sorghum. Generation of predictive polygenic models.a) Curation of existing trait and genotype datasets (primarily maize root architecture/anatomy)We will collate and link pre-selected phenotypic, environmental and genomic data sets (Genetic datasets:SEED landrace GBS (maize)(Romero Navarro et al., 2017);(Gates et al., 2019);Global resequencing (sorghum)(Lasky et al., 2015; Bellis et al., 2019);Wisconsin diversity panel (maize)(Mazaheri et al., 2019);Sorghum association panel (sorghum)(Shakoor et al., 2016);Andosol landrace maize WGS (Sawers and Rellan-Alvarez, unpublished). Funcrional datasets: Root architecture and anatomy (Lynch);Seed element composition (maize)(Fikas et al., 2019);Seed element composition (sorghum)(Shakoor et al., 2016);Mycorrhizal response (sorghum) Sawers et al., unpublished. Environmental datasets:Bioclimhttps://www.worldclim.org/bioclim;Phenology-weighted climatic variables (maize)(Gates et al., 2019);Accession-linked climatic variables (sorghum)(Lasky et al., 2015; Bellis et al., 2019);Global soil modelshttps://soilgrids.org;Scaled P-retention prediction doi.org/10.5281/zenodo.1233213).Beyond the benefits of hosting different types of data in the same place, we will anchor all genomic information to the same genome reference and same gene-model annotation. While we anticipate that much will be possible by cross-referencing, re-mapping, and imputation, there may be good reason to generate additional genetic data - for instance, where (re-)genotyping of a panel that has been used for phenotypic evaluation would facilitate extrapolation to larger population genetic data sets. We will look to facilitate collective study of the two crops, leveraging understanding of their shared history and the relationship between their genomes.b) Generation of novel sorghum root architecture/anatomy dataTo investigate environmental correlations with root anatomy, we will evaluate a well-defined sorghum association panel (Shakoor et al., 2016) using a high-throughput laser ablation tomography (LAT) platform developed by PSU researchers (Figure 2. Saengwilai et al., 2014; York et al., 2015). In collaboration with Stephen Kresovich (Clemson), we will perform root sampling at a site in North Carolina, during Summer 2020. On site, we will dig up a predetermined sample of plants and collect their roots (whorls 2-4) for laser ablation. We will investigate the relationship between environmental factors at the site of origin and root anatomy.c) Generation of novel maize/sorghum mycorrhiza response dataWe will evaluate mycorrhizal response in a well characterized maize association panel (Mazaheri et al., 2019) using a small-pot greenhouse-based system. Young plants will be evaluated for biomass production and mineral accumulation, with or without inoculation with mycorrhizal fungi. We will use both microscopy and molecular methods to estimate mycorrhizal colonization. We will address the hypothesis that more stressful environments promote stronger mutualism, looking to link mycorrhizal symbiosis with specific environments. We will explore the impact of domestication and improvement on mycorrhizal response.2. Exploration of genotype-environment/root-environment associations.a) Application of polygenic trait prediction models to global maize/sorghum diversityWe will use standard genome wide association scans to identify SNPs linked with root architecture/anatomical traits and mycorrhizal responsiveness, using both existing data and data generated inthis project. Polygenic models generated from well-characterized diversity panels will be used to extrapolate phenotypic predictions to broader genotyped maize and sorghum diversity.b) Isolation of environment/root trait correlationsWe will use explore trait correlations (e.g. the relationship between root anatomy and mycorrhizal symbiosis) and trait-environment correlations. We will cross-reference the results of whole genome scans of environment-genotype relationships with phenotypic trait hits. In addition to identification of single-gene candidates, we will explore global relationships between environmental DNA variant candidates and specific traits. This approach will reveal the potential adaptive significance of trait variation with respect to different environmental gradients (e.g. precipitation, temperature, soil chemistry).3. Evaluation of models in context of i) landrace/wild-relative diversity; ii) diverse agronomic scenariosa) Characterization of novel maize landrace-derived inbred familiesOur approach requires the ability to infer root system functionality across global diversity using genetic models based on direct observation of relatively small samples.Heterogeneous, outbred landrace maize populations are difficult to work with and lack the genetic uniformity required for meaningful fine-scale evaluation. To address thisproblem, we are using conventional breeding techniques to introduce fragments of exotic maize diversity into a temperate inbred background. We willgenerate a collection of ~750 BC1S4 families derived from ~250 distinct donors, sourced from across the Americas. This material will be genotyped and evaluated during years 2-4 of this project. Evaluation will include both greenhouse and field components, taking in selected root traits, as well as an evaluation of mycorrhizal symbiosis, along with overall plant performance and ionomic profiling of both vegetative tissue and grain. Availability of this unique resource will be a key component of future external funding applications, and will provide opportunity for collaboration and impact beyond the immediate project.4. Mechanistic study of selected candidate variation.We will provide functional follow-up of a specific family of gene leads identified on the basis of prior knowledge in other plant systems and through the results of preliminary genotype-environment scans. It is anticipated that the activities in Goals 1-3 will identify additional candidates, a small number of which will also be selected for functional study and further follow-up.a) Functional analysis of the Pho1 family of phosphorus transporters/sensors in maize and sorghumThe plant Pho1 genes encode a key family of phosphorus transporters/sensors that have been shown to play a role in the distribution of phosphorus within the plant and in signaling events impacting phosphorus homeostasis. Significantly, partial loss of function alleles of Pho1 in Arabidopsis have been linked to increased phosphate use efficiency.We have previously characterized the Pho1 gene families of maize and sorghum (Salazar-Vidal et al., 2016) and initiated a program of targeted mutagenesis using both endogenous transposon resources and CRISPR gene editing. We will advance the phenotypic characterization of this material, in both greenhouse and field experiments, allowing us to define the role of Pho1 genes, and to address the degree of specialization and overlap between family members.Comparative study of maize and sorghum orthologs of Arabidopsis Pho1 provides an opportunity to study functional divergence in the context of plant nutrient signaling.Phenotypic evaluation will extend preliminary observations indicating impacts of the mutations of root-architecture, plant growth, global transcriptomes and patterns of phosphorus/protein/carbohydrate accumulation in the vegetative parts of the plant and the grain. Although we have several endogenous transposon alleles available, CRISPR material will be needed to provide a complete view of the gene family, and to extend the work to sorghum. This material is in development and is projected to be available for characterization by year 3 of this project. In parallel, we will work through conventional crossing to generate the double and higher-order mutant combinations required to obtain a better understanding of the gene family.