Seth L. Naeve

Phenotypic and genomic analyses of a fast neutron mutant population resource in soybean

Mutagenized populations have become indispensable resources for introducing variation and studying gene function in plant genomics research. In this study, fast neutron (FN) radiation was used to induce deletion mutations in the soybean (Glycine max) genome. Approximately 120,000 soybean seeds were exposed to FN radiation doses of up to 32 Gray units to develop over 23,000 independent M2 lines. Here, we demonstrate the utility of this population for phenotypic screening and associated genomic characterization of striking and agronomically important traits. Plant variation was cataloged for seed composition, maturity, morphology, pigmentation, and nodulation traits. Mutants that showed significant increases or decreases in seed protein and oil content across multiple generations and environments were identified. The application of comparative genomic hybridization (CGH) to lesion-induced mutants for deletion mapping was validated on a midoleate x-ray mutant, M23, with a known FAD2-1A (for fatty acid desaturase) gene deletion. Using CGH, a subset of mutants was characterized, revealing deletion regions and candidate genes associated with phenotypes of interest. Exome resequencing and sequencing of PCR products confirmed FN-induced deletions detected by CGH. Beyond characterization of soybean FN mutants, this study demonstrates the utility of CGH, exome sequence capture, and next-generation sequencing approaches for analyses of mutant plant genomes. We present this FN mutant soybean population as a valuable public resource for future genetic screens and functional genomics research.

Iron deficiency of soybean in the North Central U.S. and associated soil properties

Abstract Despite extensive research and variety screening efforts, iron deficiency chlorosis is a common, yield-limiting condition for soybean [Glycine max (L.) Merr.] grown in areas with high pH, calcareous soils. In the North Central U.S., total land area where soybean is grown on high pH soils is approximately 1.8 million ha, with iron deficiency responsible for an estimated loss in soybean grain production of 340,000 Mg at a value of

Genome Resilience and Prevalence of Segmental Duplications Following Fast Neutron Irradiation of Soybean

820 million per annum. This is a significant increase in the extent of iron deficiency problems relative to the past because of an expansion of soybean production in the region. Soil properties associated with iron deficiency in this region compared to adjacent areas without iron deficiency include greater soil moisture content and concentrations of soluble salts, carbonates, and DTPA-Cr, and lesser concentrations of DTPA-Fe, Mn, Ni, and Cd. Iron deficiency occurs due to multiple stresses and not simply to limited available iron. Biotic and management factors such as pests and diseases, symbiotic nitrogen fixation, seeding rate, and herbicide application also interact with iron deficiency in the field. There is a need to better match varieties to the specific soil and environmental conditions to which they are adapted.

Differential accumulation of Soybean seed storage protein subunits in response to sulfur and nitrogen nutritional sources

Fast neutron radiation has been used as a mutagen to develop extensive mutant collections. However, the genome-wide structural consequences of fast neutron radiation are not well understood. Here, we examine the genome-wide structural variants observed among 264 soybean [Glycine max (L.) Merrill] plants sampled from a large fast neutron-mutagenized population. While deletion rates were similar to previous reports, surprisingly high rates of segmental duplication were also found throughout the genome. Duplication coverage extended across entire chromosomes and often prevailed at chromosome ends. High-throughput resequencing analysis of selected mutants resolved specific chromosomal events, including the rearrangement junctions for a large deletion, a tandem duplication, and a translocation. Genetic mapping associated a large deletion on chromosome 10 with a quantitative change in seed composition for one mutant. A tandem duplication event, located on chromosome 17 in a second mutant, was found to cosegregate with a short petiole mutant phenotype, and thus may serve as an example of a morphological change attributable to a DNA copy number gain. Overall, this study provides insight into the resilience of the soybean genome, the patterns of structural variation resulting from fast neutron mutagenesis, and the utility of fast neutron-irradiated mutants as a source of novel genetic losses and gains.

An induced chromosomal translocation in soybean disrupts a KASI ortholog and is associated with a high-sucrose and low-oil seed phenotype

Abstract Soybean (Glycine max [L.] Merr.) seed storage proteins consist of subunits that differ in amino acid profile, the β-subunit of 7S protein being essentially devoid of the S-containing amino acids, methionine and cysteine. Our objective was to examine the interaction of N and S nutrition on the relative abundance of these storage protein subunits in soybean seed. ‘Kenwood’ soybean was grown in hydroponic culture, and during vegetative growth (V2–R4.5) N was provided as 5 mM KNO3 to plants grown under sulfur-deficient (0.004 raM Na2SO4) or sulfur-sufficient (0.4 mM Na2S04) conditions. During seed fill (R4.5–R7) N was supplied as 5 mM KNO3 or 2.5 mM urea. Each N group was given S treatments of 1) no sulfur, 2) 0.4mM Na2SO4, 3) 0.2 mM L-cystine, or 4) 0.4 mM L-methionine. Effects on seed protein quality of S deficiency during vegetative growth were essentially overcome by supplying sulfate as late as R4.5. Total protein and seed storage protein were increased with urea as N source, but urea also increased the β-subunit. Provision of reduced S as methionine essentially suppressed β-subunit production, but cystine did not, suggesting that cystine did not influence methionine level in the seed. We also report the accumulation of two as yet unreported proteins which occur at extremes of S nutrition : (1) a putative β-subunit of 7S protein occurring in the embryonic axis under S-deficiency ; and (2) a ca. 14kD protein in cotyledon tissue under provision of L-methionine. Though S and N did interact to a limited extent to influence seed protein composition, major effects were from S or N acting individually.

Determination of isoflavone (genistein and daidzein) concentration of soybean seed as affected by environment and management inputs

Mutagenesis is a useful tool in many crop species to induce heritable genetic variability for trait improvement and gene discovery. In this study, forward screening of a soybean fast neutron (FN) mutant population identified an individual that produced seed with nearly twice the amount of sucrose (8.1% on dry matter basis) and less than half the amount of oil (8.5% on dry matter basis) as compared to wild type. Bulked segregant analysis (BSA), comparative genomic hybridization, and genome resequencing were used to associate the seed composition phenotype with a reciprocal translocation between chromosomes 8 and 13. In a backcross population, the translocation perfectly cosegregated with the seed composition phenotype and exhibited non-Mendelian segregation patterns. We hypothesize that the translocation is responsible for the altered seed composition by disrupting a β-ketoacyl-[acyl carrier protein] synthase 1 (KASI) ortholog. KASI is a core fatty acid synthesis enzyme that is involved in the conversion of sucrose into oil in developing seeds. This finding may lead to new research directions for developing soybean cultivars with modified carbohydrate and oil seed composition.

Spatial Characterization of Soybean Yield and Quality (Amino Acids, Oil, and Protein) for United States

BACKGROUND Isoflavones, such as genistein and daidzein, are produced in soybean seed [Glycine max (L.) Merr.] and may be associated with health benefits in the human diet. More research is required to determine the effect of agronomic soybean treatments on isoflavone concentration. In this study from 2012 to 2014 at Michigan State University and Breckenridge locations, we have evaluated agronomic input management systems which are marketed to increase or protect potential soybean grain yield, including: nitrogen fertilization, herbicide-defoliant, foliar applied fertilizer, a biological-based foliar application, foliar applied fungicide, foliar applied insecticide, a seed applied fungicide, and a maximized seed treatment that included fungicide and insecticide as well as an inoculant and lipo-chitooligosaccharide nodulation promoter, for their effect on soybean seed genistein and daidzein concentrations. RESULTS Paired comparisons were made between treatments receiving a designated management input and those without the input. Year and location had a significant effect on isoflavone concentrations. Agronomic management inputs impacted soybean seed daidzein concentrations in 15 of 48 field observations and genistein concentrations in 11 of 48 observations. CONCLUSION The research supports findings that soybean seed isoflavone levels exhibit a location specific response, and the temporal variability experienced between years appears to influence changes in soybean isoflavone levels more than location.

Soybean Seed Yield Was Not Influenced by Foliar Applications of Sugar

Continued economic relevancy of soybean is a function of seed quality. The objectives of this study were to: (i) assess the spatial association between soybean yield and quality across major US soybean producing regions, (ii) investigate the relationship between protein, oil, and yield with amino acids (AAs) composition, and (iii) study interrelationship among essential AAs in soybean seed. Data from soybean testing programs conducted across 14 US states from 2012 to 2016 period (n = 35,101 data points) were analyzed. Results indicate that for each Mg ha−1 yield increase, protein yield increased by 0.35 Mg protein ha−1 and oil yield improved by 0.20 Mg oil ha−1. Essential AA concentrations exhibit a spatial autocorrelation and there was a negative relationship between concentration of AA, protein, and oil, with latitude. There was a positive interrelationship with different degree of strength among all AAs, and the correlation between Isoleucine and Valine was the strongest (r = 0.93) followed by the correlation among Arginine, Leucine, Lysine, and Threonine (0.71 < r < 0.88). We concluded that the variability in genotype (G) x management (M) x environment (E) across latitudes influencing yield also affected soybean quality; AA, protein, and oil content in a similar manner.

Genetic Improvement of U.S. Soybean in Maturity Groups II, III, and IV

Branden Furseth, Graduate Student, and Vince M. Davis, Assistant Professor, Department of Agronomy, University of Wisconsin, Madison, WI 53706; Shaun N. Casteel, Assistant Professor, Department of Agronomy, West Lafayette, IN 47907; Seth L. Naeve, Associate Professor, Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108; and Shawn P. Conley, Associate Professor, Department of Agronomy, University of Wisconsin, Madison, WI 53706