Location: Soybean/maize Germplasm, Pathology, and Genetics Research
2018 Annual Report
Objectives
Objective 1: Efficiently and effectively acquire soybean genetic resources, maintain their safety, genetic integrity, health and viability, and distribute them and associated information worldwide.
Objective 2: Develop more effective germplasm maintenance, evaluation, and characterization methods, and apply them to priority soybean genetic resources. Record and disseminate evaluation and characterization data via GRIN-Global and other data sources.
Sub-objective 2a. Evaluate annual accessions for basic agronomic, descriptive and seed composition traits.
Sub-objective 2b. Conserve, regenerate, and distribute genetic resources and associated information.
Objective 3: Develop improved germplasm with increased yield by utilizing exotic soybean (Glycine max), wild soybean (Glycine soja) and wild perennial Glycine species; identify important introgressed genomic regions; and determine the impact of the introgressions.
Sub-objective 3a. Develop improved germplasm with increased yield using exotic and wild soybean, and identify integrated exotic DNA.
Sub-objective 3b. Identify important introgressed genomic regions associated with yield.
Sub-objective 3c. Understand the causes of genetic instability as seen in some mutants, as well as in some G. tomentella-derived lines that reverted from 2n=42 to 2n=40 chromosomes, that produce diversity in qualitative and quantitative traits.
Objective 4: Use appropriate genomic methods, including mapping and gene expression data, to identify genetic regions conferring quantitative defense to soybean pathogens and pests, discover useful genes, and work with breeders to deploy them in suitable germplasm.
Sub-objective 4a. Use GWAS, whole genome sequence assembly, and RNA-Seq to identify candidate defense-associated loci and genes to enhance resistance to S. sclerotiorum, rust, and the red-banded stink bug.
Sub-objective 4b. Verify candidate gene functions and usefulness of molecular markers related to defense-associated loci.
Approach
We will continue to expand the holdings of the USDA Soybean Germplasm Collection and optimize maintenance procedures. We will collect data on descriptive and agronomic traits, including photographs, and submit to GRIN-Global to facilitate the use of the Collection. High quality seeds will be maintained and distributed. We will use available breeding, genetic, and genomic tools to exploit the diversity of the Collection to increase seed yield and improved disease or pest resistance. Exotic accessions not in the commercially used gene pool will be used to develop high yielding experimental lines and populations to expand the genetic base of soybean production in the U.S. and identify new alleles from exotic germplasm that increase seed yield. Select lines derived from wide-crosses will be sequence analyzed to determine if genomic sections of the wild relative have been introgressed into the G. max genome. Genome-wide association mapping and analysis of gene expression data will assist in identification of candidate defense-associated genes, and the genes will be isolated for functional study.
Progress Report
Distributed 10,274 seed lots from 6,103 accessions from the USDA Soybean Germplasm Collection in response to 226 requests from 159 individuals. There were 198 domestic requests (88% of the total) with a total of 7,488 seed packets representing 4,717 accessions sent to 134 researchers from 31 states. There were 2,786 seed packets of 2,616 accessions in 28 orders sent to 25 scientists in 19 countries. Six requests were made for 66 seed packets of 61 perennial Glycine accessions. Sent backup seeds of 133 accessions to the National Center for Genetic Resources Preservation (NCGRP) and 331 accessions for storage in the Svalbard Arctic Seed Vault. 99% of the collection is backed up at NCGRP and 89% is backed up at the Svalbard Arctic Seed Vault.
Continued DNA extractions from the remaining soybean accessions that have yet to be genotyped by the 50k single nucleotide polymorphism arrays. DNA was extracted from about 650 plants, which is about half of what is needed. We plan to finish all 1400 by the end of the FY18 fiscal year.
Plants from two mutant lines were collected in the fall of 2017, and leaf tissue stored -80C. Seed from these plants were sown in May 2018 with 41 subline rows coming from seed of 41 individual plants on one line, and 23 subline rows coming from seed of 23 individual plants of another line. Phenotyping these plants during the 2018 growing season, it is clear that at least one subline of each 2017 line is producing plants of varying phenotypes. DNA from these individual plants were collected, as well as the DNA from the progenitor lines and the wild type plants.
ARS scientists identified 10 fosmid clones spanning the Rpp1 region in two rust resistant lines, as well as an Rpp1 dominant susceptible line. Sequencing these DNA regions should provide insight into the cause of the dominant susceptibility, as well as probable identification of Rpp1.
Tested five constructs related to interfering oxalate accumulation in Sclerotinia infected tissue and expressed them transiently in Nicotiana benthamiana. However, no effect was noticed on these plants when inoculated with Sclerotinia. Transformed these constructs stably into Arabidopsis and will challenge the F2 progeny of these plants later in 2018.
Extracted high molecular weight DNA of one of the G. max by G. tomentella 2n=40 derived line and its parent, Dwight. The DNAs were sequenced as synthetic long reads, which was sufficient to assemble draft genome sequences for each line. The assemblies are being validated, and once validated, the two genomes will be compared to each other to try to identify if any G. tomentella DNA introgressed into G. max.
Sequenced the genomes of two public soybean varieties, Emgopa316 and IAC100, using synthetic long-read technologies. Both Emgopa316 and IAC100 were used in Sclerotinia GWAS studies of Sclerotinia stem rot resistance and showed enhanced resistance to the disease. IAC100 is also reported to have partial resistance to stink bug feeding and enhanced quantitative resistance to soybean rust.
Accomplishments
1. Sequenced and assembled draft genomes of the soybean variety Dwight and a line derived from a cross of Dwight by Glycine tomentella, a wild perennial relative of soybean. Soybean’s wild perennial relatives have genes for yield, disease resistance and other desirable traits not present in cultivated soybean. Previous work developed new genetic materials from crosses of soybean and G. tomentella. Some of the offspring produced had new phenotypes such as enhanced disease resistance, increased yield, and changes in seed coat texture. To verify the success of the crosses, ARS researchers at Urbana, Illinois, in cooperation with researchers at the University of Illinois, sequenced and assembled the genomes of the recurrent parent (Dwight) and one of the offspring. This successful whole genome sequencing will allow comparisons to determine which regions, if any, of the G. tomentella genome have been incorporated into the offspring. This information will be useful to scientists interested in enhancing the agronomic performance and diversity of crops through wide crossing.
