Genetic characterization of the Cy transposable element system at the Bz locus of Zea mays L.

The unstable bz-rcy allele arose by the insertion of a receptor element, rcy, into the Bz locus of a single gamete from the TEL population. Mutability of bz-rcy is controlled by the independently segregating regulatory element Cy (Cycler). In the absence of Cy, bz-rcy conditions a stable bronze aleurone. In the presence of Cy, bz-rcy conditions many small fully colored spots on a bronze background. These two elements, rcy and Cy, were previously undescribed;Genetic tests have established a relationship between Cy and the Mutator system. Cy is not functionally homologous to any of the non-Mutator transposable element systems;The number of genetically active Cy elements in a plant can increase or decrease via Cy transposition;Nonresponsive derivatives of bz-rcy have been isolated. A model has been established to explain the loss of the distal markers C and Sh coincident with the origin of some of these derivatives;The original isolate of bz-rcy often generates derivative alleles (states) that condition altered spotting patterns, e.g., reduced numbers of spots and/or larger and smaller spots, that reflect alterations in the frequency and timing of rcy excisions from bz-rcy. In contrast to receptors of the Ac and En(Spm) systems, which undergo changes of state only in the presence of the appropriate regulatory element, bz-rcy can undergo changes of state in the absence of an active Cy;Cy changes of state occur less frequently than those of bz-rcy. States of Cy have been isolated that induce reduced rates (but not altered timing) of rcy excision from bz-rcy. Many of the Cy states show progressive loss of function over succeeding generations;Many bz-rcy states and some Cy states have the ability to revert to fine-high spotting (cycling). Cycling is developmentally regulated and occurs only in the presence of Cy. A model has been proposed which evokes a form of reversible DNA modification to explain the cycling phenomenon and the origin of bz-rcy states in the absence of Cy;Of 47 diverse maize lines assayed, only two sources were found to contain strong Cy elements, i.e., Mutator-related stocks and the TEL population. Of the remaining lines, six, contained weak Cy elements and the rest lacked genetically detectable Cy elements

Harnessing Phenotypic Plasticity to Improve Maize Yields

Plants can produce different phenotypes when exposed to different environments. Understanding the genetic basis of these plastic responses is crucial for crop breeding efforts. We discuss two recent studies that suggest that yield plasticity in maize has been under selection but is controlled by different genes than yield

tGBS® genotyping-by-sequencing enables reliable genotyping of heterozygous loci

Conventional genotyping-by-sequencing (cGBS) strategies suffer from high rates of missing data and genotyping errors, particularly at heterozygous sites. tGBS® genotyping-by-sequencing is a novel method of genome reduction that employs two restriction enzymes to generate overhangs in opposite orientations to which (single-strand) oligos rather than (double-stranded) adaptors are ligated. This strategy ensures that only doubledigested fragments are amplified and sequenced. The use of oligos avoids the necessity of preparing adaptors and the problems associated with inter-adaptor annealing/ligation. Hence, the tGBS protocol simplifies the preparation of high-quality GBS sequencing libraries. During polymerase chain reaction (PCR) amplification, selective nucleotides included at the 3\u27-end of the PCR primers result in additional genome reduction as compared to cGBS. By adjusting the number of selective bases, different numbers of genomic sites are targeted for sequencing. Therefore, for equivalent amounts of sequencing, more reads per site are available for SNP calling. Hence, as compared to cGBS, tGBS delivers higher SNP calling accuracy (\u3e97–99%), even at heterozygous sites, less missing data per marker across a population of samples, and an enhanced ability to genotype rare alleles. tGBS is particularly well suited for genomic selection, which often requires the ability to genotype populations of individuals that are heterozygous at many loci

A high-throughput, field-based phenotyping technology for tall biomass crops

Recent advances in omics technologies have not been accompanied by equally efficient, cost-effective and accurate phenotyping methods required to dissect the genetic architecture of complex traits. Even though high-throughput phenotyping platforms have been developed for controlled environments, field-based aerial and ground technologies have only been designed and deployed for short stature crops. Therefore, we developed and tested Phenobot 1.0, an auto-steered and self-propelled field-based high-throughput phenotyping platform for tall dense canopy crops, such as sorghum (Sorghum bicolor L. Moench). Phenobot 1.0 was equipped with laterally positioned and vertically stacked stereo RGB cameras. Images collected from 307 diverse sorghum lines were reconstructed in 3D for feature extraction. User interfaces were developed and multiple algorithms were evaluated for their accuracy in estimating plant height and stem diameter. Tested feature extraction methods included: i) User-interactive Individual Plant Height Extraction based on dense stereo 3D reconstruction (UsIn-PHe); ii) Automatic Hedge-based Plant Height Extraction (Auto-PHe) based on dense stereo 3D reconstruction; iii) User-interactive Dense Stereo Matching Stem Diameter Extraction (DenS-Di); and iv) User-interactive Image Patch Stereo Matching Stem Diameter Extraction (IPaS-Di). Comparative genome-wide association analysis and ground-truth validation demonstrated that both UsIn-PHe and Auto-PHe were accurate methods to estimate plant height while Auto-PHe had the additional advantage of being a completely automated process. For stem diameter, IPaS-Di generated the most accurate estimates of this biomass-related architectural trait. In summary, our technology was proven robust to obtain ground-based high-throughput plant architecture parameters of sorghum, a tall and densely planted crop species

The Genetics, Pathology, and Molecular Biology of T-Cytoplasm Male Sterility in Maize

This chapter reviews the genetics, pathology, and molecular biology of T-cytoplasm male sterility in maize. The chapter discusses the role of cytoplasmic male sterility systems in facilitating the production of hybrid seeds. The effects of widespread planting of T-cytoplasm maize on the severe 1970 epidemic and effect of a mitochondria1 gene on disease susceptibility and male sterility are discussed. It also discusses the involvement of nuclear cytoplasmic interactions in restoration of cms-T, the perspectives of cms-T researchers, and future directions. In cms-T plants, male sterility is associated with premature breakdown of the mitochondria-rich, tapetal cell layer of the anther; this layer is crucial to pollen production because it supplies nutrients to the developing microspores. In many species, cms is associated with the expression of novel open-reading frames in the mitochondrial genome. The studies provided a foundation for further research that resulted in the cloning of the T-urf13 and Rf2 genes from maize and the ChPKSl gene from C. heterostrophus, and the generation of models for the topology of urf13 in the inner mitochondrial membrane, Rfl-mediated processing of T-urfl3 transcripts, and the evolution of toxin biosynthesis in C. heterostrophus and M. zeae-maydis

An Interdisciplinary Graduate Course for Engineers, Plant Scientists, and Data Scientists in the Area of Predictive Plant Phenomics

This paper describes the development and first offering of a new graduate course entitled Fundamentals of Predictive Plant Phenomics, which is part of a recently awarded National Science Foundation Graduate Research Traineeship (NRT) award to Iowa State University. The focus of this particular NRT award is to train engineering, plant science, and data science graduate students in the area of predictive plant phenomics (P3), with the goal to develop researchers who can design and construct crops with desired traits to meet the needs of a growing population and that can thrive in a changing environment. To meet this goal, the P3 NRT program will train next generation crop scientists to have broad technical skillsets as well as strong soft skills in communication and collaboration. A companion paper (Dickerson et al., 2017) provides an overview of the P3 NRT program, whereas this paper focuses on a new course developed as part of the P3 NRT. One of the challenges associated with providing the students in the P3 NRT program with the needed multidisciplinary skills to thrive is to ensure that all students have a common knowledge base in engineering, plant sciences, and data sciences, no matter their background. The goal is to get all students communicating in the same language. The course Fundamentals of Predictive Plant Phenomics was developed to meet this challenge. The course planning took nearly one year and incorporated input from faculty with various disciplinary backgrounds. The actual course is coordinated by an engineering faculty member and taught through a series of guest lecturers covering various plant science, data science, and engineering topics over a 15-week period. In addition to the three 50-minute lectures per week, a 3-hour laboratory each week provides an experiential learning opportunity where students can apply the knowledge they learn in the lectures. The first offering of this course occurred in fall 2016, with 16 enrolled students, 7 from engineering disciplines, and 9 from plant and data science programs. Lessons learned from the first offering of this course are summarized in this paper. The course is providing the needed background so students can develop a successful research topic in the area of predictive plant phenomics and communicate with others in this broad multidisciplinary field. Because the course is a leveling or survey of three disciplines, and each student has a good background in at least one of the three, it has been challenging to keep all students interested and engaged for all lectures (but not labs). To address this challenge, expanding the application of Inquiry-Based Learning approaches during the lecture period in future years is proposed