Genetics, not environment, contributed to winter wheat yield gains in Ontario, Canada.

Changes in entries' market classes and genetic improvements within classes-not environmental changes-enhanced yields over thirty-one years of wheat trials. Correlations between yields and ancestries drove genomic prediction accuracies. Increasing crop yields is important for enhancing farmers' livelihoods, meeting market demands, and reducing the environmental impact of agriculture.

Patterns of stability and change in the maize genome: a case study of small RNA transcriptomes in two recombinant inbred lines and their progenitors.

Small RNAs (sRNAs) are epigenetic regulators of eukaryotic genes and transposable elements (TEs). Diverse sRNA expression patterns exist within a species, but how this diversity arises is not well understood. To provide a window into the dynamics of maize sRNA patterning, sRNA and mRNA transcriptomes were examined in two related recombinant inbred lines (RILs) and their inbred parents.

The Induction of the Isoflavone Biosynthesis Pathway Is Associated with Resistance to Common Bacterial Blight in L.

infects common bean ( L.) causing the disease common bacterial blight (CBB). The aim of this study was to investigate the molecular and metabolic mechanisms underlying CBB resistance in .

Introgressed DNA within a near-isogenic line displays lower levels of 24nt sRNA expression than the homologous region from the recurrent parent.

Near-isogenic lines (NILs) are classical genetic tools used to dissect the actions of an allele when placed in a uniform genetic background. Although the goal of NIL creation is to examine the effects of a single allele in isolation, DNA linked to the allele is invariably retained and can confound any allele-specific effects. In addition to genetic variation, highly polymorphic species such as will contain introgressed polymorphisms encompassing transposable elements (TEs) and the -acting small RNA (sRNA) that represses them.

The effects of crop attributes, selection, and recombination on Canadian bread wheat molecular variation.

Cultivated germplasm provides an opportunity to investigate how crop agronomic traits, selection for major genes, and differences in crossing-over rates drive patterns of allelic variation. To identify how these factors correlated with allelic variation within a collection of cultivated bread wheat (Triticum aestivum L.), we generated genotypes for 388 accessions grown in Canada over the past 170 yr using filtered single nucleotide polymorphism (SNP) calls from an Illumina Wheat iSelect 90K SNP-array.

Zea mays RNA-seq estimated transcript abundances are strongly affected by read mapping bias.

Background: Genetic variation for gene expression is a source of phenotypic variation for natural and agricultural species. The common approach to map and to quantify gene expression from genetically distinct individuals is to assign their RNA-seq reads to a single reference genome. However, RNA-seq reads from alleles dissimilar to this reference genome may fail to map correctly, causing transcript levels to be underestimated.

The neonicotinoid insecticide thiamethoxam enhances expression of stress-response genes in in an environmentally specific pattern.

Recent studies indicate that thiamethoxam (TMX), a neonicotinoid insecticide, can affect plant responses to environmental stressors, such as neighboring weeds. The molecular mechanisms behind both stable and environmentally specific responses to TMX likely involve genes related to defense and stress responses. We investigated the effect of a TMX seed treatment on global gene expression in maize coleoptiles both under normal conditions and under low ratio red to far-red (R:FR) light stress induced by the presence of neighboring plants.

Genomic regions associated with important seed quality traits in food-grade soybeans.

Background: The production of soy-based food products requires specific physical and chemical characteristics of the soybean seed. Identification of quantitative trait loci (QTL) associated with value-added traits, such as seed weight, seed protein and sucrose concentration, could accelerate the development of competitive high-protein soybean cultivars for the food-grade market through marker-assisted selection (MAS). The objectives of this study were to identify and validate QTL associated with these value-added traits in two high-protein recombinant inbred line (RIL) populations.

Evidence for the Accumulation of Nonsynonymous Mutations and Favorable Pleiotropic Alleles During Wheat Breeding.

Plant breeding leads to the genetic improvement of target traits by selecting a small number of genotypes from among typically large numbers of candidate genotypes after careful evaluation. In this study, we first investigated how mutations at conserved nucleotide sites normally viewed as deleterious, such as nonsynonymous sites, accumulated in a wheat, , breeding lineage. By comparing a 150 year old ancestral and modern cultivar, we found recent nucleotide polymorphisms altered amino acids and occurred within conserved genes at frequencies expected in the absence of purifying selection.

Shared and genetically distinct Zea mays transcriptome responses to ongoing and past low temperature exposure.

Background: Cold temperatures and their alleviation affect many plant traits including the abundance of protein coding gene transcripts. Transcript level changes that occur in response to cold temperatures and their alleviation are shared or vary across genotypes. In this study we identify individual transcripts and groups of functionally related transcripts that consistently respond to cold and its alleviation.

Distinct gene networks modulate floral induction of autonomous maize and photoperiod-dependent teosinte.

Temperate maize was domesticated from its tropical ancestor, teosinte. Whereas temperate maize is an autonomous day-neutral plant, teosinte is an obligate short-day plant that requires uninterrupted long nights to induce flowering. Leaf-derived florigenic signals trigger reproductive growth in both teosinte and temperate maize.

Proanthocyanidin accumulation and transcriptional responses in the seed coat of cranberry beans (Phaseolus vulgaris L.) with different susceptibility to postharvest darkening.

Background: Edible dry beans (Phaseolus vulgaris L.) that darken during postharvest storage are graded lower and are less marketable than their non-darkened counterparts. Seed coat darkening in susceptible genotypes is dependent upon the availability of proanthocyanidins, and their subsequent oxidation to reactive quinones.

Changes in light quality alter physiological responses of soybean to thiamethoxam.

The interaction between neighboring weed-induced far-red enriched light and thiamethoxam can significantly alter soybean seedling morphology, nodulation, isoflavone levels, UV-absorbing phenolics, and carbon and nitrogen content. Neonicotinoid insecticides that are widely used on major crop plants can enhance plant growth and yield. Although the underlying mechanism of this enhanced growth and yield is not clear, recent studies suggest that neonicotinoids such as thiamethoxam (TMX) may exert their effects at least in part via signals that involve salicylic acid (SA) and jasmonic acid (JA).

Brevis plant1, a putative inositol polyphosphate 5-phosphatase, is required for internode elongation in maize.

In maize (Zea mays L.), as in other grass species, stem elongation occurs during growth and most noticeably upon the transition to flowering. Genes that reduce stem elongation have been important to reduce stem breakage, or lodging.

Maize (Zea mays) seeds can detect above-ground weeds; thiamethoxam alters the view.

Background: Far red light is known to penetrate soil and delay seed germination. Thiamethoxam as a seed treatment has been observed to enhance seed germination. No previous work has explored the effect of thiamethoxam on the physiological response of buried maize seed when germinating in the presence of above-ground weeds.

Regulatory motifs identified from a maize developmental coexpression network.

Transcriptional control is an important determinant of plant development, and distinct modules of coordinated genes characterize the maize developmental transcriptome. Upstream regulatory sequences are often the primary factors that control gene expression pattern and abundance. Here, we identify 244 regulatory motifs that are significantly enriched within 24 gene expression modules previously constructed from transcript abundances of 34,876 Zea mays (maize) gene models from embryogenesis to senescence.

Current perspectives and the future of domestication studies.

It is difficult to overstate the cultural and biological impacts that the domestication of plants and animals has had on our species. Fundamental questions regarding where, when, and how many times domestication took place have been of primary interest within a wide range of academic disciplines. Within the last two decades, the advent of new archaeological and genetic techniques has revolutionized our understanding of the pattern and process of domestication and agricultural origins that led to our modern way of life.

Beyond the single gene: How epistasis and gene-by-environment effects influence crop domestication.

Domestication is a multifaceted evolutionary process, involving changes in individual genes, genetic interactions, and emergent phenotypes. There has been extensive discussion of the phenotypic characteristics of plant domestication, and recent research has started to identify the specific genes and mutational mechanisms that control domestication traits. However, there is an apparent disconnect between the simple genetic architecture described for many crop domestication traits, which should facilitate rapid phenotypic change under selection, and the slow rate of change reported from the archeobotanical record.

Thiamethoxam as a seed treatment alters the physiological response of maize (Zea mays) seedlings to neighbouring weeds.

Background: Thiamethoxam is a broad-spectrum neonicotinoid insecticide that, when applied to seed, has been observed to enhance seedling vigour under environmental stress conditions. Stress created by the presence of neighbouring weeds is known to trigger the accumulation of hydrogen peroxide (H2 O2 ) in maize seedling tissue. No previous work has explored the effect of thiamethoxam as a seed treatment on the physiological response of maize seedlings emerging in the presence of neighbouring weeds.

Evidence for selection on gene expression in cultivated rice (Oryza sativa).

Artificial selection has been used throughout plant domestication and breeding to develop crops that are adapted to diverse environments. Here, we investigate whether gene regulatory changes have been widespread targets of lineage-specific selection in cultivated lines Minghui 63 and Zhenshan 97 of rice, Oryza sativa. A line experiencing positive selection for either an increase or a decrease in genes' transcript abundances is expected to have an overabundance of expression quantitative trait locus (eQTL) alleles that increase or decrease those genes' expression, respectively.

High throughput RNA sequencing of a hybrid maize and its parents shows different mechanisms responsive to nitrogen limitation.

Background: Development of crop varieties with high nitrogen use efficiency (NUE) is crucial for minimizing N loss, reducing environmental pollution and decreasing input cost. Maize is one of the most important crops cultivated worldwide and its productivity is closely linked to the amount of fertilizer used. A survey of the transcriptomes of shoot and root tissues of a maize hybrid line and its two parental inbred lines grown under sufficient and limiting N conditions by mRNA-Seq has been conducted to have a better understanding of how different maize genotypes respond to N limitation.

Nitrogen transporter and assimilation genes exhibit developmental stage-selective expression in maize (Zea mays L.) associated with distinct cis-acting promoter motifs.

Nitrogen is considered the most limiting nutrient for maize (Zea mays L.), but there is limited understanding of the regulation of nitrogen-related genes during maize development. An Affymetrix 82K maize array was used to analyze the expression of ≤ 46 unique nitrogen uptake and assimilation probes in 50 maize tissues from seedling emergence to 31 d after pollination.

Protein-coding cis-natural antisense transcripts have high and broad expression in Arabidopsis.

Pairs of genes within eukaryotic genomes are often located on opposite DNA strands such that transcription generates cis-natural sense antisense transcripts (cis-NATs). This orientation of genes has been associated with the biogenesis of splice variants and natural antisense small RNAs. Here, in an analysis of currently available data, we report that within Arabidopsis (Arabidopsis thaliana), protein-coding cis-NATs are also characterized by high abundance, high coexpression, and broad expression.