Genome-wide association analysis of stalk biomass and anatomical traits in maize.

BackgroundMaize stover is an important source of crop residues and a promising sustainable energy source in the United States. Stalk is the main component of stover, representing about half of stover dry weight. Characterization of genetic determinants of stalk traits provide a foundation to optimize maize stover as a biofuel feedstock. We investigated maize natural genetic variation in genome-wide association studies (GWAS) to detect candidate genes associated with traits related to stalk biomass (stalk diameter and plant height) and stalk anatomy (rind thickness, vascular bundle density and area).ResultsUsing a panel of 942 diverse inbred lines, 899,784 RNA-Seq derived single nucleotide polymorphism (SNP) markers were identified. Stalk traits were measured on 800 members of the panel in replicated field trials across years. GWAS revealed 16 candidate genes associated with four stalk traits. Most of the detected candidate genes were involved in fundamental cellular functions, such as regulation of gene expression and cell cycle progression. Two of the regulatory genes (Zmm22 and an ortholog of Fpa) that were associated with plant height were previously shown to be involved in regulating the vegetative to floral transition. The association of Zmm22 with plant height was confirmed using a transgenic approach. Transgenic lines with increased expression of Zmm22 showed a significant decrease in plant height as well as tassel branch number, indicating a pleiotropic effect of Zmm22.ConclusionSubstantial heritable variation was observed in the association panel for stalk traits, indicating a large potential for improving useful stalk traits in breeding programs. Genome-wide association analyses detected several candidate genes associated with multiple traits, suggesting common regulatory elements underlie various stalk traits. Results of this study provide insights into the genetic control of maize stalk anatomy and biomass

The effect of artificial selection on phenotypic plasticity in maize

Remarkable productivity has been achieved in crop species through artificial selection and adaptation to modern agronomic practices. Whether intensive selection has changed the ability of improved cultivars to maintain high productivity across variable environments is unknown. Understanding the genetic control of phenotypic plasticity and genotype by environment (G × E) interaction will enhance crop performance predictions across diverse environments. Here we use data generated from the Genomes to Fields (G2F) Maize G × E project to assess the effect of selection on G × E variation and characterize polymorphisms associated with plasticity. Genomic regions putatively selected during modern temperate maize breeding explain less variability for yield G × E than unselected regions, indicating that improvement by breeding may have reduced G × E of modern temperate cultivars. Trends in genomic position of variants associated with stability reveal fewer genic associations and enrichment of variants 0–5000 base pairs upstream of genes, hypothetically due to control of plasticity by short-range regulatory elements

Consensus Recommendations for the Use of Automated Insulin Delivery (AID) Technologies in Clinical Practice

International audienceThe significant and growing global prevalence of diabetes continues to challenge people with diabetes (PwD), healthcare providers and payers. While maintaining near-normal glucose levels has been shown to prevent or delay the progression of the long-term complications of diabetes, a significant proportion of PwD are not attaining their glycemic goals. During the past six years, we have seen tremendous advances in automated insulin delivery (AID) technologies. Numerous randomized controlled trials and real-world studies have shown that the use of AID systems is safe and effective in helping PwD achieve their long-term glycemic goals while reducing hypoglycemia risk. Thus, AID systems have recently become an integral part of diabetes management. However, recommendations for using AID systems in clinical settings have been lacking. Such guided recommendations are critical for AID success and acceptance. All clinicians working with PwD need to become familiar with the available systems in order to eliminate disparities in diabetes quality of care. This report provides much-needed guidance for clinicians who are interested in utilizing AIDs and presents a comprehensive listing of the evidence payers should consider when determining eligibility criteria for AID insurance coverage

Springer Lab UAV Maize Phenotyping Project at UMN StPaul: 2018 and 2019

Files include digital elevation models for all flights of our maize field in the summer of 2018 and 2019, the plot boundary shapefiles, information on each plot including planting date and density and stand counts, yield data for all plots, and weather station data for both summers. More detailed info can be found in the readme file.This dataset provides a valuable resource for evaluating the utility of unmanned aerial vehicles to collect phenotypic data in agricultural fields. Many flights throughout the growing season of a maize experiment were conducted and this dataset includes digital elevation models generated from images within these flights, the plot boundary shapefiles for plot identification, plant height values extracted following Tirado et al., 2019 procedure, hand measurement height values conducted following flights, and yield data for each plot. This maize experiment consisted of twelve hybrids planted at three different planting densities (low, medium and high) and two planting dates (early and late) across two years and therefore provides a valuable resource for evaluating how temporal data collected from UAVs can aid in assessing plant productivity. It can also be utilized to develop and test different protocols for plant height extraction from DEMs at different growth stages as the hand measurements can be used to test the accuracy.N

Opportunities and challenges in phenotyping row crops using drone‐based RGB imaging

Abstract Developing the resilient crops of the future will require access to a broad set of tools. While advances in sequencing and marker technologies have facilitated marker‐trait associations and the ability to predict the phenotype of an individual from its genotypic information, other tools such as high‐throughput phenotyping are still in their infancy. Advances in sensors, aeronautics, and computing have enabled progress. Here, we review current platforms and sensors available for top‐down field phenotyping with a focus on unoccupied aerial vehicles (UAVs) and red, green, blue sensors. We also review the ability and effectiveness of extracting traits from images captured using combinations of these platforms and sensors. Improvements in trait standardization and extraction software are expected to increase the use of high‐throughput phenotyping in the coming years and further facilitate crop improvement

Tandem Duplicate Genes in Maize Are Abundant and Date to Two Distinct Periods of Time

Tandem duplicate genes are proximally duplicated and as such occur in similar genomic neighborhoods. Using the maize B73 and PH207 de novo genome assemblies, we identified thousands of tandem gene duplicates that account for ∼10% of the annotated genes. These tandem duplicates have a bimodal distribution of ages, which coincide with ancient allopolyploidization and more recent domestication. Tandem duplicates are smaller on average and have a higher probability of containing LTR elements than other genes, suggesting origins in nonhomologous recombination. Within relatively recent tandem duplicate genes, ∼26% appear to be undergoing degeneration or divergence in function from the ancestral copy. Our results show that tandem duplicates are abundant in maize, arose in bursts throughout maize evolutionary history under multiple potential mechanisms, and may provide a substrate for novel phenotypic variation

Genetic Fine-Mapping of a Quantitative Trait Locus (QTL) Associated with Embryogenic Tissue Culture Response and Plant Regeneration Ability in Maize (Zea mays L.)

Embryogenic and regenerable tissue cultures are widely utilized in plant transformation, clonal propagation, and biological research applications. Germplasm utilized in those applications are limited, however, due to genotype-dependent culture response. The goal of this study was to identify genomic regions controlling embryogenic and regenerable tissue culture response in the globally important crop, maize ( L.), toward the long-term objective of developing approaches for genotype-independent plant genetic engineering and clonal propagation systems. An inbred maize line, WCIC2, nearly-isogenic to reference inbred B73, was developed by phenotypic selection and molecular marker analysis. WCIC2 has over 50x increase in tissue culture response relative to the recurrent parent, B73. This line was used to genetically fine-map a region on chromosome 3 controlling embryogenic and regenerable tissue culture response to a 23.9 Mb region. WCIC2 and derivatives will be useful materials to enable maize research in a genetic background similar to B73, and our genetic mapping results will advance research to identify causal genes controlling somatic embryo formation and plant regeneration in maize

Supplemental Material for Kono et al., 2018

<div>Figure S1. Weighted pairwise similarity distribution for adjacent genes in B73 and PH207. Solid lines are from all pairs of adjacent genes in the genome and the dashed lines are from pairs of adjacent genes defined as tandem duplicates from raw CoGe output. Green line at 0.3 marks the threshold used to define tandem duplicate genes for downstream analysis.</div><div><br></div><div>Figure S2. Tandem duplicate gene cassette identification. Similarity heatmap on right shows an example tandem duplicate gene cassette in which the off-diagonal heat (yellow) shows high similarity among genes within the cassette. </div><div><br></div><div>Figure S3. Distribution of orthologous group sizes as defined by OrthoFinder. Grey box (size 10 to 75) indicates orthogroups that were used in downstream PAML analysis.</div><div><br></div><div>Figure S4. Example marked input tree for PAML relative rates analysis. Orthologous groups were defined using OrthoFinder.</div><div><br></div><div>Figure S5. Number of intervening genes in tandem duplicate gene cluster. Genes that are directly adjacent have an intervening gene number of zero.</div><div><br></div><div>Figure S6. Genomic locations of maize tandem duplicates for all chromosomes in B73. Purple ticks show tandem duplications. Black line shows gene density, dark grey line shows RNA transposable element density, light grey line shows DNA transposable elements per Mb. Subgenome 1 is shown in green shading and subgenome 2 is shown in blue shading.</div><div><br></div><div>Figure S7. Distance to nearest transposable element (upstream or downstream) for B73 tandem duplicate genes. </div><div><br></div><div>Table S1. Species, assembly versions, annotation versions, and data sources for the grass species used for orthologue identification.</div><div><br></div><div>Table S2. Summary of maize tandem duplicates in B73 and PH207. Cluster number is a generic number given to each tandem duplicate cluster. Duplicates in B73 are from the version 4 assembly and duplicates in PH207 are from the version 1 assembly. Shared duplicates are contained in the syntenic portion of both B73 and PH207 and private duplicates are in the syntenic portion of only one genome, and non-syntenic duplicates are in non co-orthologous blocks relative to rice and/or sorghum. Estimated date of tandem duplicates was determined based on substitution rates relative to sorghum.</div

Whole transcriptome profiling of maize during early somatic embryogenesis reveals altered expression of stress factors and embryogenesis-related genes.

Embryogenic tissue culture systems are utilized in propagation and genetic engineering of crop plants, but applications are limited by genotype-dependent culture response. To date, few genes necessary for embryogenic callus formation have been identified or characterized. The goal of this research was to enhance our understanding of gene expression during maize embryogenic tissue culture initiation. In this study, we highlight the expression of candidate genes that have been previously regarded in the literature as having important roles in somatic embryogenesis. We utilized RNA based sequencing (RNA-seq) to characterize the transcriptome of immature embryo explants of the highly embryogenic and regenerable maize genotype A188 at 0, 24, 36, 48, and 72 hours after placement of explants on tissue culture initiation medium. Genes annotated as functioning in stress response, such as glutathione-S-transferases and germin-like proteins, and genes involved with hormone transport, such as PINFORMED, increased in expression over 8-fold in the study. Maize genes with high sequence similarity to genes previously described in the initiation of embryogenic cultures, such as transcription factors BABY BOOM, LEAFY COTYLEDON, and AGAMOUS, and important receptor-like kinases such as SOMATIC EMBRYOGENESIS RECEPTOR LIKE KINASES and CLAVATA, were also expressed in this time course study. By combining results from whole genome transcriptome analysis with an in depth review of key genes that play a role in the onset of embryogenesis, we propose a model of coordinated expression of somatic embryogenesis-related genes, providing an improved understanding of genomic factors involved in the early steps of embryogenic culture initiation in maize and other plant species