Importance of genetic architecture in marker selection decisions for genomic prediction.

We demonstrate potential for improved multi-environment genomic prediction accuracy using structural variant markers. However, the degree of observed improvement is highly dependent on the genetic architecture of the trait. Breeders commonly use genetic markers to predict the performance of untested individuals as a way to improve the efficiency of breeding programs.

Linking genetic and environmental factors through marker effect networks to understand trait plasticity.

Understanding how plants adapt to specific environmental changes and identifying genetic markers associated with phenotypic plasticity can help breeders develop plant varieties adapted to a rapidly changing climate. Here, we propose the use of marker effect networks as a novel method to identify markers associated with environmental adaptability. These marker effect networks are built by adapting commonly used software for building gene coexpression networks with marker effects across growth environments as the input data into the networks.

Evaluation of Corn Germplasm Accessions for Resistance to , Causal Agent of Goss's Bacterial Wilt and Leaf Blight.

Goss's bacterial wilt and leaf blight of corn (), caused by , is a reemerging disease in the Midwestern United States. From 2011 to 2013, field studies and a greenhouse study were conducted to assess the University of Illinois maize inbred collection for putative sources of resistance to Goss's bacterial wilt and leaf blight. This inbred collection consisted of over 2,000 diverse inbred corn lines that have been collected from all over the world.

Multiple Maize Reference Genomes Impact the Identification of Variants by Genome-Wide Association Study in a Diverse Inbred Panel.

Use of a single reference genome for genome-wide association studies (GWAS) limits the gene space represented to that of a single accession. This limitation can complicate identification and characterization of genes located within presence-absence variations (PAVs). In this study, we present the draft de novo genome assembly of 'PHJ89', an 'Oh43'-type inbred line of maize ( L.

Foliar Glyphosate Treatment Alters Transcript and Hormone Profiles in Crown Buds of Leafy Spurge and Induces Dwarfed and Bushy Phenotypes throughout its Perennial Lifecycle.

Leafy spurge ( L.) is an invasive weed of North America and its perennial nature attributed to underground adventitious buds (UABs) that undergo seasonal cycles of para-, endo-, and ecodormancy. Recommended rates of glyphosate (∼1 kg ha) destroy aboveground shoots but plants still regenerate vegetatively; therefore, it is considered glyphosate-tolerant.

Wild emmer genome architecture and diversity elucidate wheat evolution and domestication.

Wheat ( spp.) is one of the founder crops that likely drove the Neolithic transition to sedentary agrarian societies in the Fertile Crescent more than 10,000 years ago. Identifying genetic modifications underlying wheat's domestication requires knowledge about the genome of its allo-tetraploid progenitor, wild emmer ( ssp.

Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize.

Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production of high-yielding hybrids, we generated a draft genome assembly of the inbred line PH207 to complement and compare with the existing B73 reference sequence. B73 is a founder of the Stiff Stalk germplasm pool, while PH207 is a founder of Iodent germplasm, both of which have contributed substantially to the production of temperate commercial maize and are combined to make heterotic hybrids.

Glyphosate's impact on vegetative growth in leafy spurge identifies molecular processes and hormone cross-talk associated with increased branching.

Background: Leafy spurge (Euphorbia esula) is a perennial weed that is considered glyphosate tolerant, which is partially attributed to escape through establishment of new vegetative shoots from an abundance of underground adventitious buds. Leafy spurge plants treated with sub-lethal concentrations of foliar-applied glyphosate produce new vegetative shoots with reduced main stem elongation and increased branching. Processes associated with the glyphosate-induced phenotype were determined by RNAseq using aerial shoots derived from crown buds of glyphosate-treated and -untreated plants.

High-resolution genetic mapping of maize pan-genome sequence anchors.

In addition to single-nucleotide polymorphisms, structural variation is abundant in many plant genomes. The structural variation across a species can be represented by a 'pan-genome', which is essential to fully understand the genetic control of phenotypes. However, the pan-genome's complexity hinders its accurate assembly via sequence alignment.

Halomonas sulfidaeris-dominated microbial community inhabits a 1.8 km-deep subsurface Cambrian Sandstone reservoir.

A low-diversity microbial community, dominated by the γ-proteobacterium Halomonas sulfidaeris, was detected in samples of warm saline formation porewater collected from the Cambrian Mt. Simon Sandstone in the Illinois Basin of the North American Midcontinent (1.8 km/5872 ft burial depth, 50°C, pH 8, 181 bars pressure).

Auxin and ABA act as central regulators of developmental networks associated with paradormancy in Canada thistle (Cirsium arvense).

Dormancy in underground vegetative buds of Canada thistle, an herbaceous perennial weed, allows escape from current control methods and contributes to its invasive nature. In this study, ~65 % of root sections obtained from greenhouse propagated Canada thistle produced new vegetative shoots by 14 days post-sectioning. RNA samples obtained from sectioned roots incubated 0, 24, 48, and 72 h at 25°C under 16:8 h light-dark conditions were used to construct four MID-tagged cDNA libraries.

Development and annotation of perennial Triticeae ESTs and SSR markers.

Triticeae contains hundreds of species of both annual and perennial types. Although substantial genomic tools are available for annual Triticeae cereals such as wheat and barley, the perennial Triticeae lack sufficient genomic resources for genetic mapping or diversity research. To increase the amount of sequence information available in the perennial Triticeae, three expressed sequence tag (EST) libraries were developed and annotated for Pseudoroegneria spicata, a mixture of both Elymus wawawaiensis and E.

Characterization of an 18,166 EST dataset for cassava (Manihot esculenta Crantz) enriched for drought-responsive genes.

Cassava (Manihot esculenta Crantz) is a staple food for over 600 million people in the tropics and subtropics and is increasingly used as an industrial crop for starch production. Cassava has a high growth rate under optimal conditions but also performs well in drought-prone areas and on marginal soils. To increase the tools for understanding and manipulating drought tolerance in cassava, we generated expressed sequence tags (ESTs) from normalized cDNA libraries prepared from dehydration-stressed and control well-watered tissues.