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Breeding Maize Maternal Haploid Inducers, Henrique Uliana Trentin, Ursula K. Frei, Thomas Lubberstedt 2020 Iowa State University

Breeding Maize Maternal Haploid Inducers, Henrique Uliana Trentin, Ursula K. Frei, Thomas Lubberstedt

Agronomy Publications

Maize doubled haploid (DH) lines are usually created in vivo, through crosses with maternal haploid inducers. These inducers have the inherent ability of generating seeds with haploid embryos when used to pollinate other genotypes. The resulting haploid plants are treated with a doubling agent and self-pollinated, producing completely homozygous seeds. This rapid method of inbred line production reduces the length of breeding cycles and, consequently, increases genetic gain. Such advantages explain the wide adoption of this technique by large, well-established maize breeding programs. However, a slower rate of adoption was observed in medium to small-scale breeding programs. The high price ...


A Basic Ddradseq Two‐Enzyme Protocol Performs Well With Herbarium And Silica‐Dried Tissues Across Four Genera, Ingrid E. Jordon-Thaden, James B. Beck, Catherine A. Rushworth, Michael D. Windham, Nicolas Diaz, Jason T. Cantley, Christopher T. Martine, Carl J. Rothfels 2020 University of Wisconsin-Madison

A Basic Ddradseq Two‐Enzyme Protocol Performs Well With Herbarium And Silica‐Dried Tissues Across Four Genera, Ingrid E. Jordon-Thaden, James B. Beck, Catherine A. Rushworth, Michael D. Windham, Nicolas Diaz, Jason T. Cantley, Christopher T. Martine, Carl J. Rothfels

Faculty Journal Articles

Premise

The ability to sequence genome‐scale data from herbarium specimens would allow for the economical development of data sets with broad taxonomic and geographic sampling that would otherwise not be possible. Here, we evaluate the utility of a basic double‐digest restriction site–associated DNA sequencing (ddRADseq) protocol using DNAs from four genera extracted from both silica‐dried and herbarium tissue.

Methods

DNAs from Draba, Boechera, Solidago, and Ilex were processed with a ddRADseq protocol. The effects of DNA degradation, taxon, and specimen age were assessed.

Results

Although taxon, preservation method, and specimen age affected data recovery, large phylogenetically ...


Mapping Quantitative Trait Loci Associated With Leaf Rust Resistance In Five Spring Wheat Populations Using Single Nucleotide Polymorphism Markers, Firdissa E. Bokore, Ron E. Knox, Richard D. Cuthbert, Curtis J. Pozniak, Brent D. McCallum, Amidou N’Diaye, Ron M. DePauw, Heather L. Campbell, Catherine Munro, Arti Singh, Colin W. Hiebert, Curt A. McCartney, Andrew G. Sharpe, Asheesh K. Singh, Dean Spaner, D. B. Fowler, Yuefeng Ruan, Samia Berraies, Brad Meyer 2020 Agriculture and Agri-Food Canada

Mapping Quantitative Trait Loci Associated With Leaf Rust Resistance In Five Spring Wheat Populations Using Single Nucleotide Polymorphism Markers, Firdissa E. Bokore, Ron E. Knox, Richard D. Cuthbert, Curtis J. Pozniak, Brent D. Mccallum, Amidou N’Diaye, Ron M. Depauw, Heather L. Campbell, Catherine Munro, Arti Singh, Colin W. Hiebert, Curt A. Mccartney, Andrew G. Sharpe, Asheesh K. Singh, Dean Spaner, D. B. Fowler, Yuefeng Ruan, Samia Berraies, Brad Meyer

Agronomy Publications

Growing resistant wheat (Triticum aestivum L) varieties is an important strategy for the control of leaf rust, caused by Puccinia triticina Eriks. This study sought to identify the chromosomal location and effects of leaf rust resistance loci in five Canadian spring wheat cultivars. The parents and doubled haploid lines of crosses Carberry/AC Cadillac, Carberry/Vesper, Vesper/Lillian, Vesper/Stettler and Stettler/Red Fife were assessed for leaf rust severity and infection response in field nurseries in Canada near Swift Current, SK from 2013 to 2015, Morden, MB from 2015 to 2017 and Brandon, MB in 2016, and in New ...


De Novo Sequencing And Analysis Of Salvia Hispanica Tissue-Specific Transcriptome And Identification Of Genes Involved In Terpenoid Biosynthesis, James Wimberley, Joseph Cahill, Hagop S. Atamian 2020 Chapman University

De Novo Sequencing And Analysis Of Salvia Hispanica Tissue-Specific Transcriptome And Identification Of Genes Involved In Terpenoid Biosynthesis, James Wimberley, Joseph Cahill, Hagop S. Atamian

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Salvia hispanica (commonly known as chia) is gaining popularity worldwide as a healthy food supplement due to its low saturated fatty acid and high polyunsaturated fatty acid content, in addition to being rich in protein, fiber, and antioxidants. Chia leaves contain plethora of secondary metabolites with medicinal properties. In this study, we sequenced chia leaf and root transcriptomes using the Illumina platform. The short reads were assembled into contigs using the Trinity software and annotated against the Uniprot database. The reads were de novo assembled into 103,367 contigs, which represented 92.8% transcriptome completeness and a diverse set of ...


Impact Of Spontaneous Haploid Genome Doubling In Maize Breeding, Nicholas A. Boerman, Ursula K. Frei, Thomas Lubberstedt 2020 Iowa State University

Impact Of Spontaneous Haploid Genome Doubling In Maize Breeding, Nicholas A. Boerman, Ursula K. Frei, Thomas Lubberstedt

Agronomy Publications

Doubled haploid (DH) technology has changed the maize-breeding landscape in recent years. Traditionally, DH production requires the use of chemical doubling agents to induce haploid genome doubling and, subsequently, male fertility. These chemicals can be harmful to humans and the plants themselves, and typically result in a doubling rate of 10%–30%. Spontaneous genome doubling and male fertility of maize haploids, without using chemical doubling agents, have been observed to a limited extent, for nearly 70 years. Rates of spontaneous haploid genome doubling (SHGD) have ranged from less than 5% to greater than 50%. Recently, there has been increased interest ...


Arkansas Cotton Variety Test 2019, F. Bourland, A. Beach, E. Brown, C. Kennedy, L. Martin, B. Robertson 2020 University of Arkansas, Fayetteville

Arkansas Cotton Variety Test 2019, F. Bourland, A. Beach, E. Brown, C. Kennedy, L. Martin, B. Robertson

Research Series

The primary goal of the Arkansas Cotton Variety Test is to provide unbiased data regarding the agronomic performance of cotton varieties and advanced breeding lines in the major cotton-growing areas of Arkansas. This information helps seed companies establish marketing strategies and assists producers in choosing varieties to plant. These annual evaluations will then facilitate the inclusion of new, improved genetic material in Arkansas cotton production. Adaptation of varieties is determined by evaluating the lines at five University of Arkansas System Division of Agriculture research sites (Manila, Keiser, Judd Hill, Marianna, and Rohwer). Entries in the 2019 Arkansas Cotton Variety Test ...


Quantitative Inheritance Of Total Anthocyanin Content In The Tassel Of Small-Ear Waxy Corn (Zea Mays Var. Ceratina), P. Duangpapeng, K. Lertrat, K. Lomthaisong, F. S. Aguilar, M. P. Scott, B. Suriharn 2020 Khon Kaen University

Quantitative Inheritance Of Total Anthocyanin Content In The Tassel Of Small-Ear Waxy Corn (Zea Mays Var. Ceratina), P. Duangpapeng, K. Lertrat, K. Lomthaisong, F. S. Aguilar, M. P. Scott, B. Suriharn

Agronomy Publications

Information on the gene effects governing the inheritance of traits is very important for crop breeding and germplasm management. The objective of this study was to estimate genetic effects for total anthocyanin content in the tassel of small-ear waxy corn. Six generations (P1, P2, F1, F2, BC11, and BC12) were developed from two crosses of small-ear waxy corn (TB1 × TW1 and TC1 × TB3). TB1 and TB3 had purple tassels, and TW1 and TC1 had green tassels. All generations of each cross were evaluated under field conditions in the rainy season of 2017 and the dry season of 2017/2018. Season ...


Evaluation Of The Functional Role Of The Maize Glossy2 And Glossy2-Like Genes In Cuticular Lipid Deposition, Liza Esther Alexander, Yozo Okazaki, Michael A. Schelling, Aeriel Davis, Xiaobin Zheng, Ludmila Rizhsky, Marna D. Yandeau-Nelson, Kazuki Saito, Basil J. Nikolau 2020 Iowa State University

Evaluation Of The Functional Role Of The Maize Glossy2 And Glossy2-Like Genes In Cuticular Lipid Deposition, Liza Esther Alexander, Yozo Okazaki, Michael A. Schelling, Aeriel Davis, Xiaobin Zheng, Ludmila Rizhsky, Marna D. Yandeau-Nelson, Kazuki Saito, Basil J. Nikolau

Genetics, Development and Cell Biology Publications

Plant epidermal cells express unique molecular machinery that juxtapose the assembly of intracellular lipid components and the unique extracellular cuticular lipids that are unidirectionally secreted to plant surfaces. In maize (Zea mays L.), mutations at the glossy2 (gl2) locus affect the deposition of extracellular cuticular lipids. Sequence-based genome scanning identified a novel gl2 homolog in the maize genome, Gl2-like. Sequence homology identifies that both the Gl2-like and Gl2 genes are members of the BAHD superfamily of acyltransferases, with close sequence homology to the Arabidopsis CER2 gene. Transgenic experiments demonstrate that Gl2-like and Gl2 functionally complement the Arabidopsis cer2 mutation, with ...


Transcriptome And Parasitome Analysis Of Beet Cyst Nematode Heterodera Schachtii, Abdelnaser M. Elashry, Samer S. Habash, Paramasivan Vijayapalani, Nahal Brocke-Ahmadinejad, Roman Blümel, Arun Seetharam, Heiko Schoof, Florian M. W. Grundler 2020 University of Bonn

Transcriptome And Parasitome Analysis Of Beet Cyst Nematode Heterodera Schachtii, Abdelnaser M. Elashry, Samer S. Habash, Paramasivan Vijayapalani, Nahal Brocke-Ahmadinejad, Roman Blümel, Arun Seetharam, Heiko Schoof, Florian M. W. Grundler

Office of Biotechnology Publications

Beet cyst nematodes depend on a set of secretory proteins (effectors) for the induction and maintenance of their syncytial feeding sites in plant roots. In order to understand the relationship between the beet cyst nematode H. schachtii and its host, identification of H. schachtii effectors is crucial and to this end, we sequenced a whole animal pre-infective J2-stage transcriptome in addition to pre- and post-infective J2 gland cell transcriptome using Next Generation Sequencing (NGS) and identified a subset of sequences representing putative effectors. Comparison between the transcriptome of H. schachtii and previously reported related cyst nematodes and root-knot nematodes revealed ...


Phenotypic And Genotypic Characterization Of Aroma And Cercospora Janseana Resistance In U.S. Rice, Christopher Keith Addison 2020 Louisiana State University at Baton Rouge

Phenotypic And Genotypic Characterization Of Aroma And Cercospora Janseana Resistance In U.S. Rice, Christopher Keith Addison

LSU Doctoral Dissertations

Rice is a staple food for over one-third of the world’s population. With the increasing population, plant breeders must continue to breed for improved varieties. The utilization of markers to applied breeding program can increase the efficiency of selection for key traits. The targeted traits for this research include grain aroma and resistance to the fungal disease narrow brown leaf spot (Cercospora janseana). Our objective was to characterize SNP diversity across the BADH2 gene in publicly available sequence data of a collection of 2,932 rice varieties was characterized to determine the number of gene haplotypes in O. sativa ...


Mapping Of Qtl For Kernel Abortion Caused By In Vivo Haploid Induction In Maize (Zea Mays L.), Yanzhi Qu, Penghao Wu, Jiaojiao Ren, Zonghua Liu, Jihua Tang, Thomas Lubberstedt, Haochuan Li, Shaojiang Chen 2020 Henan Agricultural University

Mapping Of Qtl For Kernel Abortion Caused By In Vivo Haploid Induction In Maize (Zea Mays L.), Yanzhi Qu, Penghao Wu, Jiaojiao Ren, Zonghua Liu, Jihua Tang, Thomas Lubberstedt, Haochuan Li, Shaojiang Chen

Agronomy Publications

Kernel abortion is common phenomenon in vivo haploid induction and closely linked with haploid induction rate, but little information of kernel abortion is available and its genetic basis still unclear. We used two mapping populations including 186 and 263 F2.3 family lines to analyze the different degree of kernel abortion and identify quantitative trait loci (QTL) responsible for kernel abortion during haploid induction. In total 62 putative QTL, accounting for 3.27–14.70% of the phenotypic variation in kernel abortion traits, were detected across all 10 chromosomes. Ten QTL with over 10% contribution to phenotypic variation were affecting ...


Computer Vision And Machine Learning Enabled Soybean Root Phenotyping Pipeline, Kevin G. Falk, Talukder Z. Jubery, Seyed V. Mirnezami, Kyle A. Parmley, Soumik Sarkar, Arti Singh, Baskar Ganapathysubramanian, Asheesh K. Singh 2020 Iowa State University

Computer Vision And Machine Learning Enabled Soybean Root Phenotyping Pipeline, Kevin G. Falk, Talukder Z. Jubery, Seyed V. Mirnezami, Kyle A. Parmley, Soumik Sarkar, Arti Singh, Baskar Ganapathysubramanian, Asheesh K. Singh

Mechanical Engineering Publications

Background Root system architecture (RSA) traits are of interest for breeding selection; however, measurement of these traits is difficult, resource intensive, and results in large variability. The advent of computer vision and machine learning (ML) enabled trait extraction and measurement has renewed interest in utilizing RSA traits for genetic enhancement to develop more robust and resilient crop cultivars. We developed a mobile, low-cost, and high-resolution root phenotyping system composed of an imaging platform with computer vision and ML based segmentation approach to establish a seamless end-to-end pipeline - from obtaining large quantities of root samples through image based trait processing and ...


Floral Trait Architecture In Crop Sunflower (Helianthus Annuus) Under Drought Conditions, Lauren Segarra 2020 Central Washington University

Floral Trait Architecture In Crop Sunflower (Helianthus Annuus) Under Drought Conditions, Lauren Segarra

All Master's Theses

Longer and more intense droughts are predicted to become more common in the coming century due to anthropogenic climate change. Drought can reduce crop yield and decrease food security. In order to mitigate the negative effects of drought on crop production, it is important to elucidate the underlying mechanisms that promote drought stress resistance in crop plants. Floral traits impact yield, especially in oilseed crops such as sunflower (Helianthus annuus), but their susceptibility to drought stress is understudied. The goal of this study was to describe the floral trait architecture of H. annuus crop lines under drought versus well-watered conditions ...


Dynamics Of Corn Dry Matter Content And Grain Quality After Physiological Maturity, Md Rasel Parvej, Charles R. Hurburgh, H. Mark Hanna, Mark A. Licht 2020 Louisiana State University

Dynamics Of Corn Dry Matter Content And Grain Quality After Physiological Maturity, Md Rasel Parvej, Charles R. Hurburgh, H. Mark Hanna, Mark A. Licht

Agronomy Publications

Delayed corn (Zea mays L.) harvest after physiological maturity (PM) is a universal practice in the U.S. Corn Belt to reduce grain drying cost. However, corn yield is speculated to be lost due to kernel dry matter loss from seed respiration. We evaluated the impact of in‐field dry down on corn dry matter content and grain quality after PM at two locations in Iowa during 2016 and 2017. Each site‐year consisted of two planting dates and three hybrids where ears were collected six to eight times from PM to harvest. Regardless of site‐year and hybrid, grain ...


Genomic Prediction Of Maternal Haploid Induction Rate In Maize, Vinícius Costa Almeida, Henrique Uliana Trentin, Ursula Karoline Frei, Thomas Lubberstedt 2020 Iowa State University

Genomic Prediction Of Maternal Haploid Induction Rate In Maize, Vinícius Costa Almeida, Henrique Uliana Trentin, Ursula Karoline Frei, Thomas Lubberstedt

Agronomy Publications

Genomic prediction (GP) might be an efficient way to improve haploid induction rate (HIR) and to reduce the laborious and time‐consuming task of phenotypic selection for HIR in maize (Zea mays L.). In this study, we evaluated GP accuracies for HIR and other agronomic traits of importance to inducers by independent and cross‐validation. We propose the use of GP for cross prediction and parental selection in the development of new inducer breeding populations. A panel of 159 inducers from Iowa State University (ISU set) was genotyped and phenotyped for HIR and several agronomic traits. The data of an ...


Mapping Of Qtl For Grain Yield Components Based On A Dh Population In Maize, Jiwei Yang, Zonghua Liu, Qiong Chen, Yanzhi Qu, Jihua Tang, Thomas Lubberstedt, Haochuan Li 2020 Henan Agricultural University

Mapping Of Qtl For Grain Yield Components Based On A Dh Population In Maize, Jiwei Yang, Zonghua Liu, Qiong Chen, Yanzhi Qu, Jihua Tang, Thomas Lubberstedt, Haochuan Li

Agronomy Publications

The elite maize hybrid Zhengdan 958 (ZD958), which has high and stable yield and extensive adaptability, is widely grown in China. To elucidate the genetic basis of yield and its related traits in this elite hybrid, a set of doubled haploid (DH) lines derived from ZD958 were evaluated in four different environments at two locations over two years, and a total of 49 quantitative trait loci (QTL) and 24 pairs of epistatic interactions related to yield and yield components were detected. Furthermore, 21 QTL for six investigated phenotypic traits were detected across two different sites. Combining the results of these ...


Complementarity‐Based Selection Strategy For Genomic Selection, Saba Moeinizade, Megan Wellner, Guiping Hu, Lizhi Wang 2020 Iowa State University

Complementarity‐Based Selection Strategy For Genomic Selection, Saba Moeinizade, Megan Wellner, Guiping Hu, Lizhi Wang

Industrial and Manufacturing Systems Engineering Publications

Genomic selection is a technique that breeders use to select plant or animal individuals to mate and produce new generations of species. The conventional selection method is to select individuals that are either observed or predicted to be the best based on the assumption that parents with better phenotypes will produce better offspring. A major limitation of this method is its focus on the short‐term genetic gains at the cost of genetic diversity and long‐term growth potential. Recently, several new genomic selection methods were proposed to maximize the long‐term potential. Along this research direction, we propose a ...


Biological And Cellular Functions Of The Microdomain-Associated Fwl/Cnr Protein Family In Plants, Sandra Thibivilliers, Andrew Farmer, Marc Libault 2020 University of Nebraska-Lincoln

Biological And Cellular Functions Of The Microdomain-Associated Fwl/Cnr Protein Family In Plants, Sandra Thibivilliers, Andrew Farmer, Marc Libault

Faculty Publications from the Center for Plant Science Innovation

Membrane microdomains/nanodomains are sub-compartments of the plasma membrane enriched in sphingolipids and characterized by their unique protein composition. They play important roles in regulating plant development and plant-microbe interactions including mutualistic symbiotic interactions. Several protein families are associated with the microdomain fraction of biological membranes such as flotillins, prohibitins, and remorins. More recently, GmFWL1, a FWL/CNR protein exclusively expressed in the soybean nodule, was functionally characterized as a new microdomain-associated protein. Interestingly, GmFWL1 is homologous to the tomato FW2-2 protein, a major regulator of tomato fruit development. In this review, we summarize the knowledge gained about the biological ...


Semantic Segmentation Of Sorghum Using Hyperspectral Data Identifies Genetic Associations, Chenyong Miao, Alejandro Pages, Zheng Xu, Eric Rodene, Jinliang Yang, James C. Schnable 2020 University of Nebraska - Lincoln

Semantic Segmentation Of Sorghum Using Hyperspectral Data Identifies Genetic Associations, Chenyong Miao, Alejandro Pages, Zheng Xu, Eric Rodene, Jinliang Yang, James C. Schnable

Faculty Publications from the Center for Plant Science Innovation

This study describes the evaluation of a range of approaches to semantic segmentation of hyperspectral images of sorghum plants, classifying each pixel as either nonplant or belonging to one of the three organ types (leaf, stalk, panicle). While many current methods for segmentation focus on separating plant pixels from background, organ-specific segmentation makes it feasible to measure a wider range of plant properties. Manually scored training data for a set of hyperspectral images collected from a sorghum association population was used to train and evaluate a set of supervised classification models. Many algorithms show acceptable accuracy for this classification task ...


Isoseq Transcriptome Assembly Of C3 Panicoid Grasses Provides Tools To Study Evolutionary Change In The Panicoideae, Daniel S. Carvalho, Aime V. Nishimwe, James C. Schnable 2020 University of Nebraska - Lincoln

Isoseq Transcriptome Assembly Of C3 Panicoid Grasses Provides Tools To Study Evolutionary Change In The Panicoideae, Daniel S. Carvalho, Aime V. Nishimwe, James C. Schnable

Faculty Publications from the Center for Plant Science Innovation

The number of plant species with genomic and transcriptomic data has been increasing rapidly. The grasses—Poaceae—have been well represented among species with published reference genomes. However, as a result the genomes of wild grasses are less frequently targeted by sequencing efforts. Sequence data from wild relatives of crop species in the grasses can aid the study of domestication, gene discovery for breeding and crop improvement, and improve our understanding of the evolution of C4 photosynthesis. Here, we used long-read sequencing technology to characterize the transcriptomes of three C3 panicoid grass species: Dichanthelium oligosanthes, Chasmanthium laxum, and ...


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