David Grant

Molecular characterization of iron deficiency chlorosis in soybean

Abstract Iron deficiency chlorosis (IDC) of soybean occurs on calcareous soils when a cultivar is unable to utilize the iron (Fe) in the soil. The objectives of this study were to map gene(s) for Fe chlorosis resistance in two Glycine max x G. max populations, and to evaluate the use of marker‐assisted selection in breeding for improved Fe chlorosis resistance in soybean. Chlorosis symptoms were evaluated by visual scores and spectrometric chlorophyll determinations at the V4 stage (third trifoliate leaf fully developed) in each of two years. Ninety restriction fragment length polymorphism (RFLP) and 10 simple sequence repeat (SSR) markers in the Pride B216 x A15 population, and 82 RFLP, 14 SSR and one morphological (hilum color) markers in the Anoka × A7 population were used to map quantitative trait loci (QTL) affecting IDC. In the Pride population, 120 random F2 plants were used, 92 were used in the Anoka population. In the Pride population, QTL with minor effects were detected in three linkage groups for visual scores, and for chlorophyll concentration, for a total of five different linkage groups for both traits, indicating a polygene mechanisms for IDC. In the Anoka population, two QTL were each mapped for visual scores and chlorophyll concentration. One of the QTL had major effect and was mapped in the same interval of linkage group N using both visual scores and chlorophyll concentrations, verifying that one major gene is involved in segregation for IDC in this population. Different genetic linkage groups in soybean have been identified by letters, and as such will be used throughout the paper. Two QTL on linkage groups I and N were common to the Pride and Anoka populations and were considered for use in marker‐assisted selection. A thorough analysis conducted in both populations, however, indicated the impossibility of using these markers for marker‐assisted selection. In no cases were both of the QTL‐flanking markers present in one population also present in the other population. On the basis of these results we concluded the markers identified in this study can not be used in marker‐assisted selection because of a general lack of common markers between the two populations.

Mobilizing the Genome of Lepidoptera through Novel Sequence Gains and End Creation by Non-autonomous Lep1 Helitrons

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′-subterminal inverted repeat (SIR), and integrations that occur between AT or TT nucleotides. Lep1 Helitrons have acquired and propagated sequences downstream of their 3′-CTAY termini that are 57–344-bp in length and have termini composed of a 3′-CTRR preceded by a 3′-hairpin structure and a region complementary to the 5′-SIR (3′-SIRb). Features of both the Lep1 Helitron and multiple acquired sequences indicate that secondary structures at the 3′-terminus may have a role in rolling circle replication or genome integration mechanisms, and are a prerequisite for novel end creation by Helitron-like TEs. The preferential integration of Lep1 Helitrons in proximity to gene-coding regions results in the creation of genetic novelty that is shown to impact gene structure and function through the introduction of novel exon sequence (exon shuffling). These findings are important in understanding the structural requirements of genomic DNA sequences that are acquired and transposed by Helitron-like TEs.

SoyBase: A Comprehensive Database for Soybean Genetic and Genomic Data

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 metabolic pathways database, access to the data download page, a genome sequence BLAST tool, and direct links to the genetic and sequence maps. An extensive navigation menu and site description provides facile access to all sections of SoyBase. Comprehensive information for a number of data types is available at SoyBase including the current genetic maps, the soybean reference genome sequence with tracks covering genetic markers, genome organization, gene annotation and expression, and gene knockout mutants. SoyBase includes an extensive RNA-Seq gene atlas and innovative tools for identifying fast neutron-induced mutants. SoyBase is an actively curated database, with new data regularly being incorporated, including additions to the controlled vocabularies (ontologies) for soybean growth, development and phenotypic traits, soybean genes, and quantitative trait loci. New “omics” tools enable sophisticated queries on lists of genes. These features are all accessed using intuitive interfaces and are linked together wherever possible.