David Grant

Iowa State University | ISU

Seeds, especially those of certain grasses and legumes, provide the majority of the protein and carbohydrates for much of the world’s population. Therefore, improvements in seed quality and yield are important drivers for the development of new crop varieties to feed a growing population. Quantitative Trait Loci (QTL) have been identified for many...

We report characteristics of soybean genetic diversity and structure from the resequencing of 481 diverse soybean accessions, comprising 52 wild ( Glycine soja ) selections and 429 cultivated ( Glycine max ) varieties (landraces and elites). This data was used to identify 7.8 million SNPs, to predict SNP effects relative to genic regions, and to id...

SoyBase, a USDA genetic and genomics database, holds professionally curated soybean genetic and genomic data, which is integrated and made accessible to researchers and breeders. The site holds several reference genome assemblies, as well as genetic maps, thousands of mapped traits, expression and epigenetic data, pedigree information, and extensiv...

Brassica napus L. represents a potential plant feedstock for the sustainable production of hydrotreated renewable fuels needed to support carbon-based energy production. However, to increase the use of plant-derived oils for energy needs, breeding efforts are required to optimize the amount and profile of fatty acids (FAs) contained in the oil extr...

As sequencing prices drop, genomic data accumulates-seemingly at a steadily increasing pace. Most genomic data potentially have value beyond the initial purpose-but only if shared with the scientific community. This, of course, is often easier said than done. Some of the challenges in sharing genomic data include data volume (raw file sizes and num...

The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require datamanagement plans for publicly funded research. Furthermore, the value of data increases exponentially when they are pr...

SoyBase, the USDA-ARS soybean genetics and genomics database, provides a comprehensive collection of data, analysis tools, and links to external resources of interest to soybean researchers. The SoyBase home page (https://soybase.org) contains the SoyBase Toolbox which provides quick access to a search of the SoyBase database or the SoyCyc metaboli...

In soybean, variegated flowers can be caused by somatic excision of the CACTA-type transposable element Tgm9 from Intron 2 of the DFR2 gene encoding dihydroflavonol-4-reduc-tase of the anthocyanin pigment biosynthetic pathway. DFR2 was mapped to the W4 locus, where the allele containing Tgm9 was termed w4-m. In this study we have demonstrated that...

Identification of a germinal revertant from a progeny row of a single mutable T322 (w4-m) plant. Approximately 150 progeny of a mutable plant identified in an earlier experiment were grown in a 15-foot long plot to locate a germinal revertant with only purple flowers. (PPTX)

Transposon display of two selected progenies from each of six independent plants carrying variegated flowers. A single progeny row was grown from each of the six independent mutable plants harvested in 2014. From each row, two plants were selected for transposon display: (i) one plant with only green stem; (ii) the other plant with only purple stem...

Flow diagram of the transposon display procedure. Adaptor has 5’ extended strand with no binding site for primers AP1 (Adaptor Primer 1) or AP2 (Adaptor Primer 2). Binding site for AP1 or AP2 can only be generated by transposon specific primers (TransR1 or TransR2). Exposed 3’ end of the adaptor is blocked by amino group to prevent extension. Uniqu...

List of primers used in this investigation. (DOCX)

Tgm9 caused the insertion mutation in the GmMER3 gene of the mer3 mutant. Transposon insertion sequence from the GmMER3 gene was amplified by conducting long-range PCR and compared to both Tgm9 and Tgmt*, the two highly similar transposons characterized from soybean. A) The orientation of the Tgm9 insertion in the MER3 gene and primers used for nes...

Exon and intron sequences of the soybean genome. (DOCX)

Tgm9 insertion sites in 105 independent mutants. (XLSX)

The allotetraploid species Brassica napus L. is a global crop of major economic importance, providing canola oil (seed) and vegetables for human consumption and fodder and meal for livestock feed. Characterizing the genetic diversity present in the extant germplasm pool of B. napus is fundamental to better conserve, manage and utilize the genetic r...

Quantitative trait loci (QTL) analysis is often the starting point for dissecting underlying genetic mechanisms of complex traits. To make use of the many QTL mapping studies in legumes, methods are needed for integrating QTLs from various studies within a species. We describe the approaches used in public databases for soybean (soybase.org), commo...

Industrial rapeseed (Brassica napus L.) is an annual crop whose seeds produce high levels of erucic acid. The non-edible oil can be used as a sustainable source of hydrotreated renewable jet (HRJ) fuel, motivating strategies to increase the domestic production of industrial rapeseed oil. In part, increased production can be achieved by introducing...

One of the central principles of biology is the concept that an organism’s genotype interacts with the environment to produce the observable characteristics, or phenotype. Understanding this interaction is a core goal of modern biology, and enables development of organisms with commercially useful characteristics through modern breeding programs. A...

The Crop Ontology (CO) of the Generation Challenge Program (GCP) (http://cropontology.org/) currently contains eleven crop-specific ontologies and has been developed for the Integrated Breeding Platform (IBP) (https://www.integratedbreeding.net/) by several CGIAR centers. The CO provides validated trait names used by crop communities of practice (C...

Soybean researchers and breeders have access to many bioinformatic resources via several on-line research tools. Two of those resources are SoyBase and the Legume Information System (LIS). Together, these websites provide access to genetic maps, genome sequences, genes, locations of Quantitative Trait Loci (QTL), metabolic pathways, descriptions of...

Soybean is a model for the legume research community because of its importance as a crop, densely populated genetic maps, and the availability of a genome sequence. Even though a whole-genome shotgun sequence and bacterial artificial chromosome (BAC) libraries are available, a high-resolution, chromosome-based physical map linked to the sequence as...

Transposable elements (TEs) can affect the structure of genomes through their acquisition and transposition of novel DNA sequences. The 134-bp repetitive elements, Lep1, are conserved non-autonomous Helitrons in lepidopteran genomes that have characteristic 5'-CT and 3'-CTAY nucleotide termini, a 3'-terminal hairpin structure, a 5'- and 3'-subtermi...

With the advent of high-throughput sequencing, the availability of genomic sequence for comparative genomics is increasing exponentially. Numerous completed plant genome sequences enable characterization of patterns of the retention and evolution of genes within gene families due to multiple polyploidy events, gene loss and fractionation, and diffe...

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 uni...

Studies have indicated that exon and intron size and intergenic distance are correlated with gene expression levels and expression breadth. Previous reports on these correlations in plants and animals have been conflicting. In this study, next-generation sequence data, which has been shown to be more sensitive than previous expression profiling tec...

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Near-isogenic lines (NILs) are valuable genetic resources for many crop species, including soybean (Glycine max). The development of new molecular platforms promises to accelerate the mapping of genetic introgressions in these materials. Here, we compare some existing and emerging methodologies for genetic introgression mapping: single-feature poly...

Previous work has established a genomic signature based on relative counts of the 16 possible dinucleotides. Until now, it has been generally accepted that the dinucleotide signature is characteristic of a genome and is relatively homogeneous across a genome. However, we found some local regions of the soybean genome with a signature differing wide...

Next generation sequencing is transforming our understanding of transcriptomes. It can determine the expression level of transcripts with a dynamic range of over six orders of magnitude from multiple tissues, developmental stages or conditions. Patterns of gene expression provide insight into functions of genes with unknown annotation. The RNA Seq-...

Seed specific gene expression. Genes with high gene expression specific to seed development.

Transcriptionally active genes from all predicted gene models. List of gene models from all the predicted gene models that were transcriptionally active. A gene model was considered transcriptionally active if the sum of the raw counts that mapped to the model in one or more tissues was greater than 1.

Hierarchical clustering of genes significantly expressed in underground tissues. Hierarchical clustering dendrogram of genes with significant expression in underground tissues.

Heatmap of highest expressed genes. This figure is the actual output from the heatmap.2 R command. Each cell in heatmap for the highest expressed genes contains the name of the gene model.

Transcriptionally active genes from the highly-confident gene models. List of gene models from the highly-confident gene models that were transcriptionally active. A gene model was considered transcriptionally active if the sum of the raw counts that mapped to the model in one or more tissues was greater than 1.

Raw short read sequence count data. Raw short read sequence count data after our filtering criteria (see methods) but before normalization for every predicted gene model in 14 tissues.

Genes significantly expressed in underground tissues. List of gene models for which there was as significant change in gene expression in one of the underground tissues (root and nodule) over all other tissues in this study.

All genes annotated with lipoxygenase activity. List of gene models from all predicted models that have a GOslim annotation of lipoxygenase activity.

Heatmap of legume specific genes. This figure is the actual output from the heatmap.2 R command. Each cell in the heatmap for the legume specific genes contains the name of the gene model.

Genes significantly expressed in seed tissues. List of gene models for which there was as significant change in gene expression in one of the seed tissues (seed 10-DAF, seed 14-DAF, seed 21-DAF, seed 25-DAF, seed 28-DAF, seed 35-DAF and seed 42-DAF) over all other tissues in this study.

Interval matching script. Script to perform interval matching of short read sequence intervals after lignment with GSNAP and predicted gene models (Glyma1.01 genome assembly).

Transposable elements are the most abundant components of all characterized genomes of higher eukaryotes. It has been documented that these elements not only contribute to the shaping and reshaping of their host genomes, but also play significant roles in regulating gene expression, altering gene function, and creating new genes. Thus, complete ide...

Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromoso...

Background: Next generation sequencing is transforming our understanding of transcriptomes. It can determine the expression level of transcripts with a dynamic range of over six orders of magnitude from multiple tissues, developmental stages or conditions. Patterns of gene expression provide insight into functions of genes with unknown annotation....

SoyBase, the USDA-ARS soybean genetic database, is a comprehensive repository for professionally curated genetics, genomics and related data resources for soybean. SoyBase contains the most current genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. The quantitative trait loci (QTL) represent more than 1...

Soybeans grown in the upper Midwestern United States often suffer from iron deficiency chlorosis, which results in yield loss at the end of the season. To better understand the effect of iron availability on soybean yield, we identified genes in two near isogenic lines with changes in expression patterns when plants were grown in iron sufficient an...

Background SSWAP (Simple Semantic Web Architecture and Protocol; pronounced "swap") is an architecture, protocol, and platform for using reasoning to semantically integrate heterogeneous disparate data and services on the web. SSWAP was developed as a hybrid semantic web services technology to overcome limitations found in both pure web service tec...

Differentially expressed genes in the Clark genotype comparing plants grown in iron sufficient and iron deficient conditions. A table of differentially expressed genes in the Clark genotype comparing plants grown in iron sufficient and iron deficient conditions including the identified fold changes and gene annotations.

Differentially expressed transcripts in the IsoClark genotype between plants grown in iron sufficient and iron deficient conditions. A table of differentially expressed genes in the IsoClark genotype comparing plants grown in iron sufficient and iron deficient conditions including the identified fold changes and gene annotations.

Identified and annotated SFPs between two NILs Soybean Genome Chip consensus sequences. A table identifying the Affymetrix probes containing a SFP between the Clark and IsoClark genotypes. The data also identifies the chromosome containing the identified SFP and the annotation of the gene containing the SFP.

Differentially Expressed Genes in Clusters identified in the IsoClark genotype with a sliding window of 1,000,000 bases. A table of differentially expressed genes in the IsoClark genotype illustrating the identified gene clusters using a sliding window of 1,000,000 bases, their chromosomal location, and gene annotation.

Primer sequences used for semi quantitative real time RT-PCR. A table listing the Affymetrix probe IDs and the associated forward and reverse sequences of the primers used in the semi quantitative real time RT-PCR.

Differentially Expressed Genes between Clark and IsoClark genotypes grown under Iron Deficient Conditions. A table of differentially expressed genes between Clark and IsoClark genotypes grown under iron deficient conditions including the identified fold changes and gene annotations.

Differentially Expressed Genes in Clusters identified in the Clark genotype with a sliding window of 1,000,000 bases. A table of differentially expressed genes in the Clark genotype illustrating the identified gene clusters using a sliding window of 1,000,000 bases, their chromosomal location, and gene annotation.