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ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » Research » Research Project #434493

Research Project: Genetic and Genomic Characterization of Soybean and Other Legumes

Location: Corn Insects and Crop Genetics Research

2018 Annual Report

Objective 1: Identify and characterize genes, markers, and molecular networks contributing to yield, resistance to pathogens, and nutrient stress tolerance in soybean and other legumes, and work with researchers to use the information in crop improvement by conventional breeding and gene editing technology. Sub-objective 1.A. Identify and characterize legume gene expression and epigenetic networks that control nutrient homeostasis, generating information for improving resistance or tolerance to abiotic stress. Sub-objective 1.B. Identify and characterize soybean disease resistance loci and defense gene expression and epigenetic networks, generating information for improving resistance or tolerance to pathogens that cause economic loss in soybeans.

The United States leads world soybean production, contributing over 40 billion dollars to the economy in 2014. However, nutrient, disease and pest stresses limit agricultural production. The overarching goal of this project is to provide data and resources that will increase soybean (Glycine max (L.) Merrill) production by mitigating losses due to abiotic and biotic stresses. To study nutrient deficiency we will use iron deficiency chlorosis as a model. To study disease resistance responses we will use a variety of pathogens including Phakopsora pachyrhizi (Asian soybean rust), Phialophora gregata (brown stem rot), Phytophthora sojae (Phytophthora rot), and the insect pest Aphisglycines (soybean aphid). Regulation of abiotic and biotic stress responses requires constant signaling, likely controlled by gene expression and epigenetic changes. Further, a single stress exposure likely primes subsequent plant stress responses. To characterize the genes and networks involved in these responses we will couple RNA-seq, Methyl-seq and Virus Induced Gene Silencing. Finally, we will use RNA-seq data to characterize resistance loci and downstream defense responses. Successful completion of this project will result in genes, gene networks and validated markers that can be used to breed soybean germplasm with durable resistance to abiotic and biotic stress. This project will provide valuable resources to public and private soybean breeders, scientists and growers.

Progress Report
Characterizing novel gene networks regulating tolerance to iron deficiency chlorosis. In plants, iron deficiency chlorosis causes a reduction in photosynthesis, interveinal yellowing of the leaves and reduced yield. In previous work, ARS and Iowa State University scientists demonstrated that a region on soybean chromosome 3 previously associated with iron deficiency tolerance was actually made up four distinct regions. To understand how these regions contribute to iron deficiency tolerance, we identified 16 soybean lines with different combinations of these regions and different levels of iron deficiency tolerance. We then conducted whole genome expression analyses (RNA-seq) of root and shoots grown in iron sufficient and deficient conditions for all 16 lines. Analysis of this large and complex data set is ongoing. In addition, we are developing virus-induced gene silencing constructs to target candidate genes within each of these genetic blocks. Understanding how genes in these regions interact will lead to the development of soybean lines with improved tolerance while preserving yield. Investigating gene expression changes in response to micro- and macro- nutrient deficiencies in soybean. Iron is an essential micronutrient for plants, involved in multiple physiological processes including photosynthesis and electron transport. However, environmental conditions can render iron insoluble and unavailable for plant use. Phosphorous, in its orthophosphate form, is one of the most rate-limiting nutrients in agricultural production. Like iron, phosphate is often plentiful in the soils, but slow diffusion and high fixation rates within the soils leaves little available for plant use. Understanding nutrient uptake and utilization in crops is critical to improving agricultural systems. We conducted genome-wide expression analyses (RNA-seq) of soybean shoots and roots exposed to multiple nutrient stress exposures of the same nutrient stress and mixed stress exposure. Analysis of this data set is ongoing. In addition, we have combined these data with historical mapping data to identify candidate genes for virus induced gene silencing. Understanding the molecular underpinnings of these responses in crop species could have major implications in improving stress tolerance and preserving yield. Identification and characterization of plant proteins targeted by Phakopsora pachyrhizi, the cause of Asian soybean rust. Outbreaks of Asian Soybean Rust have been reported in all major soybean-producing countries, with yield losses as high as 80%. Only a handful of disease resistance loci have been identified within the soybean germplasm collection. Previously, ARS scientists used a combination of map-based cloning, gene expression analyses, and whole genome expression analyses to identify a candidate gene for Resistance to Phakopsora pachyrhizi 1 (Rpp1). Unlike other Rpp genes, Rpp1 contained a novel integrated ubiquitin-like protease (ULP) domain. It is hypothesized that integrated domains, which are copies of real plant proteins, act as bait to catch pathogen effectors. This suggests the pathogen effectors target actual ULPs to cause disease. To test this hypothesis, ARS scientists have developed virus induced gene silencing constructs for ten ULPs in the soybean genome. These constructs will be tested to see if silencing the corresponding genes alters infection by P. pachyrhizi. In addition, since ULPs are known to regulate flowering time in other plant species, the constructs will also be tested to examine their effect of flowering time. Identifying markers and genes linked to Asian soybean rust resistance will help in developing improved soybean germplasm with enhanced disease resistance.