Potential Use of Perennial Sunflower to Reduce Blackbird Damage to Sunflower

Wildlife Conservation Sunflower Plots (WCSP) have shown potential to reduce blackbird (Icteridae) damage in commercial sunflower. Also known as lure, decoy, or trap crops, WCSP are strategically placed food plots that provide an easily available and proximate food source that entices blackbirds away from valuable commercial crops. By providing an alternative food source, WCSP reduce direct damage to commercial fields, while also lowering indirect costs that producers incur attempting to prevent blackbird damage. However, cost inefficiencies have deterred widespread use of WCSP. Cost-benefit ratios of using WCSP would be greatly improved if a perennial sunflower were used instead of the annual types currently available. Perennial sunflower would reduce seed cost and planting cost, and perhaps lower opportunity costs, if able to thrive on poorer quality soils. In the near-term, scientists are focused on producing a perennial sunflower sufficiently productive to replace annualWCSP plantings. In 2013, scientists from the University of Minnesota, USDA-Agricultural Research Service, and USDAWildlife Services National Wildlife Research Center evaluated a test plot of an open-pollinated variety of perennial sunflower resulting from genetic crossing of a domesticated annual species (Helianthus annuus) and a perennial wild species (H. tuberosus). Here, we report on results from the 2013 field test and discuss the outlook for development of perennial sunflower, which would help lessen damage to commercial sunflower when used in WCSP; provide a pesticide-free food source for beneficial insects, such as honey bees; help stabilize highly erodible lands near wetlands; and provide year-round habitat for wildlife. Lastly, we provide an initial strategy for using perennial sunflower to reduce blackbird damage in commercial sunflower

Potential Use of Perennial Sunflower to Reduce Blackbird Damage to Sunflower

Wildlife Conservation Sunflower Plots (WCSP) have shown potential to reduce blackbird (Icteridae) damage in commercial sunflower. Also known as lure, decoy, or trap crops, WCSP are strategically placed food plots that provide an easily available and proximate food source that entices blackbirds away from valuable commercial crops. By providing an alternative food source, WCSP reduce direct damage to commercial fields, while also lowering indirect costs that producers incur attempting to prevent blackbird damage. However, cost inefficiencies have deterred widespread use of WCSP. Cost-benefit ratios of using WCSP would be greatly improved if a perennial sunflower were used instead of the annual types currently available. Perennial sunflower would reduce seed cost and planting cost, and perhaps lower opportunity costs, if able to thrive on poorer quality soils. In the near-term, scientists are focused on producing a perennial sunflower sufficiently productive to replace annualWCSP plantings. In 2013, scientists from the University of Minnesota, USDA-Agricultural Research Service, and USDAWildlife Services National Wildlife Research Center evaluated a test plot of an open-pollinated variety of perennial sunflower resulting from genetic crossing of a domesticated annual species (Helianthus annuus) and a perennial wild species (H. tuberosus). Here, we report on results from the 2013 field test and discuss the outlook for development of perennial sunflower, which would help lessen damage to commercial sunflower when used in WCSP; provide a pesticide-free food source for beneficial insects, such as honey bees; help stabilize highly erodible lands near wetlands; and provide year-round habitat for wildlife. Lastly, we provide an initial strategy for using perennial sunflower to reduce blackbird damage in commercial sunflower

Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis

<p>Abstract</p> <p>Background</p> <p>Heterosis is the superior performance of F₁hybrid progeny relative to the parental phenotypes. Maize exhibits heterosis for a wide range of traits, however the magnitude of heterosis is highly variable depending on the choice of parents and the trait(s) measured. We have used expression profiling to determine whether the level, or types, of non-additive gene expression vary in maize hybrids with different levels of genetic diversity or heterosis.</p> <p>Results</p> <p>We observed that the distributions of better parent heterosis among a series of 25 maize hybrids generally do not exhibit significant correlations between different traits. Expression profiling analyses for six of these hybrids, chosen to represent diversity in genotypes and heterosis responses, revealed a correlation between genetic diversity and transcriptional variation. The majority of differentially expressed genes in each of the six different hybrids exhibited additive expression patterns, and ~25% exhibited statistically significant non-additive expression profiles. Among the non-additive profiles, ~80% exhibited hybrid expression levels between the parental levels, ~20% exhibited hybrid expression levels at the parental levels and ~1% exhibited hybrid levels outside the parental range.</p> <p>Conclusion</p> <p>We have found that maize inbred genetic diversity is correlated with transcriptional variation. However, sampling of seedling tissues indicated that the frequencies of additive and non-additive expression patterns are very similar across a range of hybrid lines. These findings suggest that heterosis is probably not a consequence of higher levels of additive or non-additive expression, but may be related to transcriptional variation between parents. The lack of correlation between better parent heterosis levels for different traits suggests that transcriptional diversity at specific sets of genes may influence heterosis for different traits.</p

Dissecting the Genetic Basis of Local Adaptation in Soybean

Soybean (Glycine max) is the most widely grown oilseed in the world and is an important source of protein for both humans and livestock. Soybean is widely adapted to both temperate and tropical regions, but a changing climate demands a better understanding of adaptation to specific environmental conditions. Here, we explore genetic variation in a collection of 3,012 georeferenced, locally adapted landraces from a broad geographical range to help elucidate the genetic basis of local adaptation. We used geographic origin, environmental data and dense genome-wide SNP data to perform an environmental association analysis and discover loci displaying steep gradients in allele frequency across geographical distance and between landrace and modern cultivars. Our combined application of methods in environmental association mapping and detection of selection targets provide a better understanding of how geography and selection may have shaped genetic variation among soybean landraces. Moreover, we identified several important candidate genes related to drought and heat stress, and revealed important genomic regions possibly involved in the geographic divergence of soybean

Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes

Abstract Background Previous studies exploring sequence variation in the model legume, Medicago truncatula, relied on mapping short reads to a single reference. However, read-mapping approaches are inadequate to examine large, diverse gene families or to probe variation in repeat-rich or highly divergent genome regions. De novo sequencing and assembly of M. truncatula genomes enables near-comprehensive discovery of structural variants (SVs), analysis of rapidly evolving gene families, and ultimately, construction of a pan-genome. Results Genome-wide synteny based on 15 de novo M. truncatula assemblies effectively detected different types of SVs indicating that as much as 22% of the genome is involved in large structural changes, altogether affecting 28% of gene models. A total of 63 million base pairs (Mbp) of novel sequence was discovered, expanding the reference genome space for Medicago by 16%. Pan-genome analysis revealed that 42% (180 Mbp) of genomic sequences is missing in one or more accession, while examination of de novo annotated genes identified 67% (50,700) of all ortholog groups as dispensable – estimates comparable to recent studies in rice, maize and soybean. Rapidly evolving gene families typically associated with biotic interactions and stress response were found to be enriched in the accession-specific gene pool. The nucleotide-binding site leucine-rich repeat (NBS-LRR) family, in particular, harbors the highest level of nucleotide diversity, large effect single nucleotide change, protein diversity, and presence/absence variation. However, the leucine-rich repeat (LRR) and heat shock gene families are disproportionately affected by large effect single nucleotide changes and even higher levels of copy number variation. Conclusions Analysis of multiple M. truncatula genomes illustrates the value of de novo assemblies to discover and describe structural variation, something that is often under-estimated when using read-mapping approaches. Comparisons among the de novo assemblies also indicate that different large gene families differ in the architecture of their structural variation

A Roadmap for Functional Structural Variants in the Soybean Genome

Gene structural variation (SV) has recently emerged as a key genetic mechanism underlying several important phenotypic traits in crop species. We screened a panel of 41 soybean (Glycine max) accessions serving as parents in a soybean nested association mapping population for deletions and duplications in more than 53,000 gene models. Array hybridization and whole genome resequencing methods were used as complementary technologies to identify SV in 1528 genes, or approximately 2.8%, of the soybean gene models. Although SV occurs throughout the genome, SV enrichment was noted in families of biotic defense response genes. Among accessions, SV was nearly eightfold less frequent for gene models that have retained paralogs since the last whole genome duplication event, compared with genes that have not retained paralogs. Increases in gene copy number, similar to that described at the Rhg1 resistance locus, account for approximately one-fourth of the genic SV events. This assessment of soybean SV occurrence presents a target list of genes potentially responsible for rapidly evolving and/or adaptive traits

Development of mPing-based activation tags for crop insertional mutagenesis

Modern plant breeding increasingly relies on genomic information to guide crop improvement. Although some genes are characterized, additional tools are needed to effectively identify and characterize genes associated with crop traits. To address this need, the mPing element from rice was modified to serve as an activation tag to induce expression of nearby genes. Embedding promoter sequences in mPing resulted in a decrease in overall transposition rate; however, this effect was negated by using a hyperactive version of mPing called mmPing20. Transgenic soybean events carrying mPing-based activation tags and the appropriate transposase expression cassettes showed evidence of transposition. Expression analysis of a line that contained a heritable insertion of the mmPing20F activation tag indicated that the activation tag induced overexpression of the nearby soybean genes. This represents a significant advance in gene discovery technology as activation tags have the potential to induce more phenotypes than the original mPing element, improving the overall effectiveness of the mutagenesis system

A Roadmap for Functional Structural Variants in the Soybean Genome

Gene structural variation (SV) has recently emerged as a key genetic mechanism underlying several important phenotypic traits in crop species. We screened a panel of 41 soybean (Glycine max) accessions serving as parents in a soybean nested association mapping population for deletions and duplications in more than 53,000 gene models. Array hybridization and whole genome resequencing methods were used as complementary technologies to identify SV in 1528 genes, or approximately 2.8%, of the soybean gene models. Although SV occurs throughout the genome, SV enrichment was noted in families of biotic defense response genes. Among accessions, SV was nearly eightfold less frequent for gene models that have retained paralogs since the last whole genome duplication event, compared with genes that have not retained paralogs. Increases in gene copy number, similar to that described at the Rhg1 resistance locus, account for approximately one-fourth of the genic SV events. This assessment of soybean SV occurrence presents a target list of genes potentially responsible for rapidly evolving and/or adaptive traits

Genetic Architecture of Soybean Yield and Agronomic Traits

Soybean is the world’s leading source of vegetable protein and demand for its seed continues to grow. Breeders have successfully increased soybean yield, but the genetic architecture of yield and key agronomic traits is poorly understood. We developed a 40-mating soybean nested association mapping (NAM) population of 5,600 inbred lines that were characterized by single nucleotide polymorphism (SNP) markers and six agronomic traits in field trials in 22 environments. Analysis of the yield, agronomic, and SNP data revealed 23 significant marker-trait associations for yield, 19 for maturity, 15 for plant height, 17 for plant lodging, and 29 for seed mass. A higher frequency of estimated positive yield alleles was evident from elite founder parents than from exotic founders, although unique desirable alleles from the exotic group were identified, demonstrating the value of expanding the genetic base of US soybean breeding