2013 Annual Report
1a.Objectives (from AD-416):
1. Strategically expand the USDA Soybean Germplasm Collection, conserve and distribute available genetic diversity in genus Glycine, and evaluate genetic resources in the collection. 2. Develop experimental lines derived from exotic germplasm with high yield and/or modified seed composition and map the loci associated with these traits. 3. Elucidate genetic mechanisms of resistance to sudden death syndrome, white mold, and soybean rust in diverse soybean germplasm.
1b.Approach (from AD-416):
Identify genes associated with defense to various pathogens such as Fusarium solani, Sclerotinia sclerotiorum, and Phakopsora pachyrhizi by comparing genomic mRNA levels between resistant and susceptible lines. Candidate genes related to defense will be characterized by functional molecular studies and will be located on the physical map to determine if gene is from a region of the genome associated with any known QTLs for resistance to the specific disease. Analyze soybean interactions with Sclerotinia by analyzing effects of oxalic acid on soybean. Examine physiological conditions that might enhance soybean susceptibility to rust disease caused by Phakopsora pachyrhizi. Strategically expand the USDA Soybean Germplasm Collection to better represent the diversity of the genus Glycine. Conserve, evaluate and distribute available genetic diversity in genus Glycine. Develop experimental lines derived from exotic germplasm with high yield, high protein concentration and/or high oil concentration. Map and confirm quantitative trait loci for yield, and protein and oil concentration with the positive allele coming from exotic germplasm.
We distributed 193,000 seed samples from the USDA Soybean Germplasm Collection and grew 9757 plots to replace seeds in the Collection. We sent 3329 back-up samples to the National Center for Genetic Resources Preservation and 13,457 accessions to the Svalbard Arctic Seed Vault. We released 4 high yielding germplasm lines derived from 9 exotic accessions. LG004-6000 significantly exceeded the yield of the best check in the USDA Uniform IV test for two consecutive years. We made available to commercial soybean breeders 1234 high yielding experimental lines derived from over 50 exotic soybean accessions. We did general field evaluations for 1214 germplasm accessions. We identified soybean lines with differential responses to increased ozone concentration. The most sensitive lines had yield decreases of 14% while the less sensitive lines declined only 5%. Increase CO2 concentration increased yield in some varieties by as much as 24% and some varieties showed no yield increases. We identified accessions that are resistant to Asian soybean rust and genetically mapped the resistance in two accessions. We established a core collection of 1685 accessions for the G. max accessions using both qualitative and quantitative data. We identified and mapped the location of three chromosomal regions where the genes from exotic germplasm increased yield.
We determined small RNA production in response to several pathogens. We analyzed soybean response to Sclerotinia sclerotiorum and its main virulence factor oxalic acid (OA) with transcriptomic studies involving purified OA, a transgenic soybean that degrades OA, and an OA mutant. We identified over 2000 genes that were either increased or decreased in response to Sclerotinia and/or OA. The gene expression patterns support that OA is affecting physiology related to iron, benefitting the pathogen by providing for its iron needs, and affecting the plant's ability to defend against the pathogen. Several genes were selected as being candidate defense-associated genes. These defense-associated genes were selected for studies involving the reduction of the expression of these genes by RNA interference (RNAi) or Virus Induced Gene Silencing (VIGS). We generated RNAi transgenics that reduce expression of 3 candidate defense genes, and preliminary studies indicate that all three of these genes are providing enhanced defense. We designed at least 20 VIGS constructs, however we were not able to obtain clear results with the VIGS system for our studies.
We identified candidates for Rpp1 and rpp5, genes providing resistance to certain isolates of soybean rust. We designed VIGS constructs to silence these candidates, but again, VIGS results were not clear. One of the genes selected as a candidate defense gene was a 14-3-3, and we showed that this gene is also involved in establishing nodulation, as soybean roots transformed with a construct that silences the gene were severely inhibited in nodule formation. This work was published.
We continued to improve our soybean gene expression database, allowing us and the public researchers to cross compare how soybean genes responded to different pathogens and other treatments.