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Additional file 1. Supplementary Figures S1-S32.

Additional file 12. Review history.

Root architectural phenes have heritable and plastic responses, and genetic loci associated with stress and environmental plasticity are distinct from loci controlling phenotypic expression in water-stress and well-watered conditions., Root phenotypes regulate soil resource acquisition; however, their genetic control and phenotypic plasticity are poorly understood. We hypothesized that the responses of root architectural phenes to water deficit (stress plasticity) and different environments (environmental plasticity) are under genetic control and that these loci are distinct. Root architectural phenes were phenotyped in the field using a large maize association panel with and without water deficit stress for three seasons in Arizona and without water deficit stress for four seasons in South Africa. All root phenes were plastic and varied in their plastic response. We identified candidate genes associated with stress and environmental plasticity and candidate genes associated with phenes in well-watered conditions in South Africa and in well-watered and water-stress conditions in Arizona. Few candidate genes for plasticity overlapped with those for phenes expressed under each condition. Our results suggest that phenotypic plasticity is highly quantitative, and plasticity loci are distinct from loci that control phene expression in stress and non-stress, which poses a challenge for breeding programs. To make these loci more accessible to the wider research community, we developed a public online resource that will allow for further experimental validation towards understanding the genetic control underlying phenotypic plasticity.

Q-Q plots assessing the fitness of K model for GWAS of stalk traits. (PPTX 1508 kb)

Manhattan plot of GWAS result for vascular bundle area. (PPTX 294 kb)

Gel electrophoresis showing sqPCR results of a sample of transgenic lines (T) and non-transgenic siblings (C). (PPTX 226 kb)

LD plots of genomic regions containing significant SNPs and adjacent candidate genes. Significant SNPs are shown in red boxes. Each LD block contains all of the SNPs within a specific gene. (PPTX 4069 kb)

Correlation between flowering time and stalk traits. Spearman correlation was calculated between BLUP values. (PDF 354 kb)

The U.S. has long played a leading role in developing advanced agricultural technology. We must continue to develop novel approaches to increase the production of food, fiber and fuel while protecting our natural resources and ensuring an economically vibrant agriculture sector. The Genomes to Fields (G2F) Initiative strives to take advantage of new technologies to improve the productivity and stability of maize. In particular, this initiative seeks to connect advances in our understanding of crop genomes with new robotics, high-throughput sensing technologies, and other data gathering devices to understand how plant traits are influenced by genetics and the environment with a long-term aim of developing crops that will exhibit sustainable enhanced productivity across diverse sets of environments and years.In January 2018, G2F hosted a meeting in Ames, Iowa to consider trajectories for research in field-based phenotyping and how best to support those trajectories, and informing USDA NIFA and other federal agencies of our findings and conclusions. For four years, a distributed network of G2F field sites and public-sector collaborators has been generating the data needed to develop predictive models. Generating a vibrant community of researchers from diverse disciplines including the breadth of the plant sciences (e.g., genetics, agronomy, physiology, modeling, and breeding), engineering, computational sciences, and climatology is critical to the full success of the initiative. Many topics were discussed over the course of the three-day workshop, but four themes emerged as areas ripe for focused effort in the coming years: (1) support for ongoing community experiments; (2) development and use of field sensors and plant imaging platforms, (3) creation of data management, sharing, and analytics platforms especially for making effective use of large scale image sets, and (4) engaging additional scientific disciplines in G2F and training the next generation of agricultural scientists. It was suggested that these topics were of interest to advance not only the goals of the G2F initiative, but also the field of predictive plant phenomics more generally. The group supported the idea to enhance coordination efforts across all four themes by designating and/or creating a number of (5) High-Intensity Phenotyping Sites (HIPS) where individualized research areas and local expertise could develop alongside intentional, coordinated linkages focused on advancing topics within the four shared themes. While community experiments are necessarily extensive, these HIPS experiments can be embedded within the G2F testing network and allow for more intensive investigation and development of predictive phenomics tools. Tools and learnings from the HIPS could then be deployed more broadly.

Additional file 2. Genotypes selected to evaluate the relationship between k and germination. Table of genotype, swelling category, swelling coefficient, and germination metrics

Additional file 1. Information about inbred lines used for the seed source and diallel experiments. Table of genotypes, pedigrees, year of kernel production

Additional file 1. Figure 1. Molecular characterization of the mu1013391 insertion in Zmccr1. A) Scale diagram of the ZmCCR1 locus GRMZM2G131205, Chr1: 211567137..211573211. Black and white boxes represent exons and untranslated regions, respectively, while lines indicate introns. Shown is the location of the Uniform Mu insertion mu1013391 (triangle) in seed lots UFMu00732 (Zmccr 1a) and UFMu01379 (Zmccr 1b) along with relative primer locations (arrows). B) Shown are agarose gel-electrophoresed PCR products indicating either the presence (primers T1 + R1, 375 bp) or absence (primers F1 + R1, 537 bp) of the mu1013391 insertion in either plants homozygous for the mu1013391 insertion (Zmccr 1a and 1b) or wild-type W22. (C) Agarose gel-electrophoresed PCR products semi-quantitatively amplified from reverse-transcribed first-strand cDNA from plants either homozygous for the mu1013391 insertion (Zmccr 1a and 1b) or WT B73 (primers F2 + R2, ~408 bp). Note that the Zmccr 1a and 1b PCR products appear larger than that of WT B73 due to a 12-bp insertion. GAPDH was used as a loading control (224 bp). NT = no template. Figure 2. Raw DFRC data. A) GC-MS chromatograms of coniferyl dihydro-ferulate (G-DHFA) conjugates from wild-type and ccr1 Maize plants, and the Arabidopsis ccr1 mutant, irx4; the highlighted region the position of the trans isomer. The asterisks indicate the sinapyl dihydro-p-coumarate peaks (cis and trans) in the maize samples that also have this MRM transition, but elute at different retention times. B) The GC-MS chromatograms of sinapyl dihydro-ferulate (S-DHFA) conjugates from Maize and Arabidopsis samples. The first highlighted peak is cis-S-DHFA and the second is trans-S-DHFA. Note that the peaks shown are from the molecular ion minus ketene (CH2=C=O); this can come from the acetate on either end of the conjugate (as shown by the dotted bond).

Additional file 1. List of parameters accepted by TIPS, their default values, and descriptions.

Panicum virgatum L. (switchgrass) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuel feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype, composed of tetraploid and octoploid accessions, and a southern lowland ecotype, composed of primarily tetraploid accessions. We employed high-coverage exome capture sequencing (~2.4 Tb) to genotype 537 individuals from 45 upland and 21 lowland populations. From these data, we identified ~27 million single-nucleotide polymorphisms (SNPs), of which 1 590 653 high-confidence SNPs were used in downstream analyses of diversity within and between the populations. From the 66 populations, we identified five primary population groups within the upland and lowland ecotypes, a result that was further supported through genetic distance analysis. We identified conserved, ecotype-restricted, non-synonymous SNPs that are predicted to affect the protein function of CONSTANS (CO) and EARLY HEADING DATE 1 (EHD1), key genes involved in flowering, which may contribute to the phenotypic differences between the two ecotypes. We also identified, relative to the near-reference Kanlow population, 17 228 genes present in more copies than in the reference genome (up-CNVs), 112 630 genes present in fewer copies than in the reference genome (down-CNVs) and 14 430 presence/absence variants (PAVs), affecting a total of 9979 genes, including two upland-specific CNV clusters. In total, 45 719 genes were affected by an SNP, CNV, or PAV across the panel, providing a firm foundation to identify functional variation associated with phenotypic traits of interest for biofuel feedstock production.

Heterosis is the increase in vigor that is observed in progenies of matings of diverse individuals from different species, isolated populations, or selected strains within species or populations. Heterosis has been of immense economic value in agriculture and has important implications regarding the fitness and fecundity of individuals in natural populations. Genetic models based on complementation of deleterious alleles, especially in the context of linkage and epistasis, are consistent with many observed manifestations of heterosis. The search for the genes and alleles that underlie heterosis, as well as for broader allele-independent, genomewide mechanisms, has encompassed many species and systems. Common themes across these studies indicate that sequence diversity is necessary but not sufficient to produce heterotic phenotypes, and that the molecular pathways that produce heterosis involve chromatin modification, transcriptional control, translation and protein processing, and interactions between and within developmental and biochemical pathways. Taken together, there are many and diverse molecular mechanisms that translate DNA into phenotype, and it is the combination of all these mechanisms across many genes that produce heterosis in complex traits.

Recombinant inbred lines developed from the maize (Zea mays ssp. mays) inbreds B73 and Mo17 have been widely used to discover quantitative trait loci controlling a wide variety of phenotypic traits and as a resource to produce high-resolution genetic maps. These two parents were used to produce a set of near-isogenic lines (NILs) with small regions of introgression into both backgrounds. A novel array-based genotyping platform was used to score genotypes of over 7,000 loci in 100 NILs with B73 as the recurrent parent and 50 NILs with Mo17 as the recurrent parent. This population contains introgressions that cover the majority of the maize genome. The set of NILs displayed an excess of residual heterozygosity relative to the amount expected based on their pedigrees, and this excess residual heterozygosity is enriched in the low-recombination regions near the centromeres. The genotyping platform provided the ability to survey copy number variants that exist in more copies in Mo17 than in B73. The majority of these Mo17-specific duplications are located in unlinked positions throughout the genome. The utility of this population for the discovery and validation of quantitative trait loci was assessed through analysis of plant height variation.

A large-scale functional genomics project was initiated to study the function of chromatin-related genes in maize (Zea mays). Transgenic lines containing short gene segments in inverted repeat orientation designed to reduce expression of target genes by RNA interference (RNAi) were isolated, propagated, and analyzed in a variety of assays. Analysis of the selectable marker expression over multiple generations revealed that most transgenes were transmitted faithfully, whereas some displayed reduced transmission or transgene silencing. A range of target-gene silencing efficiencies, from nondetectable silencing to nearly complete silencing, was revealed by semiquantitative reverse transcription-PCR analysis of transcript abundance for the target gene. In some cases, the RNAi construct was able to cause a reduction in the steady-state RNA levels of not only the target gene, but also another closely related gene. Correlation of silencing efficiency with expression level of the target gene and sequence features of the inverted repeat did not reveal any factors capable of predicting the silencing success of a particular RNAi-inducing construct. The frequencies of success of this large-scale project in maize, together with parameters for optimization at various steps, should serve as a useful framework for designing future RNAi-based functional genomics projects in crop plants.

The covalent modification of eukaryotic DNA by methylation of the 5' carbon of cytosine residues is frequently associated with transcriptional silencing. In mammals, a potential mechanism for transducing DNA methylation patterns into altered transcription levels occurs via binding of methyl-CpG-binding domain (MBD) proteins. Mammalian MBD-containing proteins bind specifically to methylated DNA and recruit chromatin-modifying complexes containing histone deacetylase activities. Sequence similarity searches reveal the presence of multiple proteins in plants containing a putative MBD. Outside of the MBD itself, there is no sequence relationship between plant and mammalian MBD proteins. The plant MBD proteins can be divided into eight classes based on sequence similarity and phylogenetic analyses of sequences obtained from two complete genomes (rice [Oryza sativa] and Arabidopsis [Arabidopsis thaliana]) and from maize (Zea mays). Two classes of MBD proteins are only represented in dicot species. The striking divergence of plant and animal MBD-containing proteins is in stark contrast to the amino acid conservation of DNA methyltransferases across plants, animals, and fungi. This observation suggests the possibility that while plants and mammals have retained similar mechanisms for the establishment and maintenance of DNA methylation patterns, they may have evolved distinct mechanisms for the interpretation of these patterns.