Recipient Organization
SOUTH DAKOTA STATE UNIVERSITY
PO BOX 2275A
BROOKINGS,SD 57007
Performing Department
Plant Science
Non Technical Summary
The purpose of this project is to increase our knowledge at the genomic level of plants, microbes, and animals of potential agricultural significance. With the development of new DNA sequencing technologies and computing approaches it is possible and economical to use these approaches to guide utilization, improvement, and conservation of genetics resources of plants, animals, and microbes in diverse areas. For example, these technologies can be used in plant breeding to improve growth and nutrient content, in food safety to characterize new strains of food borne pathogens, and in the development of new microbial strains for bioprocessing.We plan to use genomics approaches to study how plants adapt their environment. As one example we are very interested in the adaptation of perennial plants to yearly cycles of changing temperatures and light in relation to survival, growth, and productivity. Genomic approaches allow us to examine the expression of all the genes in an organism at one time. Examination of multiple samples correlated with physiological and morphological changes will help to better understand how perennial plants adapt to annual cycles, and how they might adapt to a warming climate.The SDSU Genomics Sequencing Facility has contributed to multiple projects from soil sciences to basic molecular cell biology. The facility works with each researcher to optimize their experimental approach and maximize the data obtained per each dollar. The facility works with each researcher to address datelines for manuscripts, and grant
Animal Health Component
40%
Research Effort Categories
Basic
20%
Applied
40%
Developmental
40%
Goals / Objectives
The long-term goal of this project is to apply genomic tools to study environmental adaptation of plants, animals, and microbes of agricultural significance. Crops of interest include wheat, oats and perennial grasses. The first two are food and feed crops of special interest for South Dakota. Both crops are in need of additional efforts in the area of applied genetics to substantially increase yields and profitability. Perennial grasses present potential opportunities for biofuel production and to introduce diversity in the cropping systems, especially in marginal areas such those affected by high salinity. Animals of interest include cattle and bison, which are the primary large ruminants raised in pasture and feedlot settings. Microbes relevant to this project include those that are pathogenic and symbiotic with plants and animals, and those of interest to the food and bioprocessing industries.ObjectivesObjective 1. Application of genetic and genomic tools to study plant-microbe interactions. Objective 2. Study the genetic mechanisms of environmental adaptation of plants, animals, and microbes to changing environmental conditions.Objective 3. Manage the Genomics Sequencing Facility and facilitate the application of next generation sequencing technologies in other research projects.
Project Methods
ApproachObjective 1. Application of genetic and genomic tools to study plant-microbe interactions. The focus of this objective is to understand how plants of agronomical interest, such as wheat, oats, and others, interact with different microbes resulting in detrimental or beneficial relationships. We will study the genetics in the host plant that control these interactions, making use of different types of mapping populations derived from materials with diverse phenotypes. When possible we will use existing populations that may be already genotyped. The populations will be studied in field or/and greenhouse trials. If the genotypes are not available, the population will be genotyped using different molecular markers depending on the species in question. One of the marker platforms we plan to use will be genotyping by sequencing. For the purpose of detecting marker-trait associations, imputation of missing data in the diversity panel will be performed in several ways, using both the marker order from the genetic linkage map and also testing un-ordered marker imputation algorithms applied previously to wheat and other species.We will also study the changes in the microbial communities in the individual plants and their close environment. This will help us understand plant-microbe interactions at the ecological level. For this we will use genomic approaches tailored to the identification and quantification of the different members in the microbial communities.Objective 2. Study the genetic mechanisms of environmental adaptation of plants, animals, and microbes to changing environmental conditions. The foci of this objective are plants, animals, and microbes of interest to the agricultural, food, and bioprocessing industries. We will make use of three approaches: 1) global gene expression analysis, 2) genome sequencing, and 3) amplicon based and whole genome metagenomic and metatranscriptomic analysis.Global gene expression characterization of selected individuals. We plan to use 3-5 biological replicates per treatment (ie, growth condition) following any applicable standards such as the MIAME standard. Samples from each individual plant/plant/microbe will be harvested and flash frozen in liquid nitrogen and stored at -80°C and processed and sequenced at SDSU Genomics Sequencing facility. The goal is to sequence an adequate number of reads to generate quantitative gene expression information and allow for the identification of potential new transcript splicing. Sequenced reads will be quality filtered using the default filtering parameters of the Illumina platform to eliminate low quality and shorter ones. The RNA sequences will be aligned to genomes of related species if available. If no genome is available, we will develop a de novo transcriptome assembly to use as a reference. Genome sequencing will be used to characterize new plants, animals or bacterial strains. Depending on the sample nature and the coverage needed, we will use different combination of sequencing technologies. As an example, in the case of microbial strains of interest to the food industry, genome characterization may lead to identifying novel antimicrobial resistance genes impacting sanitation practices. Objective 3. Manage the Genomics Sequencing Facility and facilitate the application of next generation sequencing technologies in other research projects.Genome sequencing and analysis. We will take advantage of the equipment at the SDSU Genomics Sequencing Facility to sequence complete genomes in the case of bacteria and other microbes with smaller genomes using a combination of Oxford nanopore long reads and Illumina short reads. Projects we expect to contribute include plant and animal gene expression (ie cattle, mice, wheat and grapes), bacterial genomes sequencing, Genome assemblies will be carried out in the SDSU HPC Cluster with software such as FLYE or CANU. To annotate these genomes we will use de novo gene prediction software for bacterial genomes and RNAseq data based programs (i.e., AUGUSTUS) for larger eukaryotic genomes.