Robert N. Trigiano

Quantitative trait loci for agronomic and seed quality traits in an F2 and F4:6 soybean population

AbstractMolecular breeding is becoming more practical as better technology emerges. The use of molecular markers in plant breeding for indirect selection of important traits can favorably impact breeding efficiency. The purpose of this research is to identify quantitative trait loci (QTL) on molecular linkage groups (MLG) which are associated with seed protein concentration, seed oil concentration, seed size, plant height, lodging, and maturity, in a population from a cross between the soybean cultivars ‘Essex’ and ‘Williams.’ DNA was extracted from F2 generation soybean leaves and amplified via polymerase chain reaction (PCR) using simple sequence repeat (SSR) markers. Markers that were polymorphic between the parents were analyzed against phenotypic trait data from the F2 and F4:6 generation. For the F2 population, significant additive QTL were Satt540 (MLG M, maturity, r2 = 0.11; height, r2 = 0.04, seed size, r2= 0.06], Satt373 (MLG L, seed size, r2 = 0.04; height, r2 = 0.14), Satt50 (MLG A1, maturity r2 = 0.07), Satt14 (MLG D2, oil, r2 = 0.05), and Satt251 (protein r2 = 0.03, oil, r2 =0.04). Significant dominant QTL for the F2 population were Satt540 (MLG M,height, r2 = 0.04; seed size, r2 = 0.06) and Satt14 (MLG D2, oil, r2 = 0.05). In the F4:6 generation significant additive QTL were Satt239 (MLGI, height, r2 = 0.02 at Knoxville, TN and r2 = 0.03 at Springfield, TN), Satt14 (MLG D2, seed size, r2 = 0.14 at Knoxville, TN), Satt373 (MLG L, protein, r2 = 0.04 at Knoxville, TN) and Satt251 (MLG B1, lodging r2 = 0.04 at Springfield, TN). Averaged over both environments in the F4:6 generation, significant additive QTL were identified as Satt251 (MLG B1, protein, r2 = 0.03), and Satt239 (MLG I, height, r2 = 0.03). The results found in this study indicate that selections based solely on these QTL would produce limited gains (based on low r2 values). Few QTL were detected to be stable across environments. Further research to identify stable QTL over environments is needed to make marker-assisted approaches more widely adopted by soybean breeders.

Towards a More Sustainable Agriculture

Critical Reviews in Plant Sciences is pleased to devote these issues to research in Sustainable Agriculture. The general topic of “sustainability” has been discussed in many regards—from housing to population growth, land usage to the effects of pollution on the environment, and so on. Intertwined among all the issues encompassed by sustainability is that of a sustainable food source, without which global society would certainly crumble. These very timely and thoughtful reports take a careful look at issues confronting conversion of our agricultural base into a truly sustainable model. In particular, organic approaches are mentioned and discussed. But also importantly, uses of the wild landscape as food sources are examined and education of the populace on the needs and methods of sustainability are discussed. Throughout the issue, the authors make a case for the need to achieve more sustainability of our food and fiber supply, as well as the consequences for not doing so. We are especially indebted to Guest Editor Professor Tiziano Gomiero for taking the lead on this project, along with David Pimentel and Maurizio G. Paoletti for their contributions. It is important to note that Professors Pimentel and Paoletti are long-time members of the CRPS editorial board and the Guest Editors’ collective talents can be seen throughout the issue.

Plant Development and Biotechnology

Introduction Dennis J. Gray and Robert N. Trigiano HISTORY OF PLANT TISSUE CULTURE History of Plant Tissue and Cell Culture James D. Caponetti, Dennis J. Gray, and Robert N. Trigiano SUPPORTING METHODOLOGIES Getting Started with Tissue Culture: Media Preparation, Sterile Technique, and Laboratory Equipment Caula A. Beyl Histological Techniques Robert N. Trigiano, Kathleen R. Malueg, Kimberly A. Pickens, Zong-Ming Cheng, and Effin T. Graham Photographic Methods for Plant Cell and Tissue Culture Dennis J. Gray Elements of In Vitro Research Michael E. Compton A Brief Introduction to Plant Anatomy Robert N. Trigiano and Dennis J. Gray Plant Growth Regulators in Plant Tissue Culture and Development Victor P. Gab Software and Databases as Tools for Analyzing Nucleic Acid and Protein Sequences Zhijian T. Li Molecular Approaches to the Study of Plant Development Albrecht G. von Arnim PROPAGATION AND DEVELOPMENT CONCEPTS Shoot Culture Procedures Michael E. Kane Propagation from Nonmeristematic Tissues: Organogenesis Otto J. Schwarz, Anjuna R. Sharma, and Robert M. Beaty Molecular Aspects of In Vitro Shoot Organogenesis Shibo Zhang and Peggy G. Lemaux Propagation from Nonmeristematic Tissues: Nonzygotic Embryogenesis Dennis J. Gray Some Developmental and Molecular Aspects of Somatic Embryogenesis (Nonzygotic Embryogenesis) Andreas Mordhorst, Erika Charbit, and Sacco C. de Vries CROP IMPROVEMENT TECHNIQUES Use of Protoplasts for Plant Improvement Richard E. Veilleux, Michael E. Compton, and James A. Saunders Haploid Cultures Sandra M. Reed Embryo Rescue Sandra M. Reed Genetic Engineering Technologies Zhijian T. Li and Dennis J. Gray Genetically Modified Plant Controversies: Sensational Headlines versus Pragmatic Research Harry A. Richards, Laura C. Hudson, Matthew D. Halfhill, and Charles N. Stewart, Jr. Construction and Use of a Simple Gene Gun for Particle Bombardment Dennis J. Gray, Michael E. Compton, Ernest Hiebert, Chia Min Lin, and Victor P. Gaba A Simple Illumination System for Visualizing Green Fluorescent Protein Dennis J. Gray, Subramanian Jayasankar, and Zhijian T. Li Germplasm Preservation Leigh E. Towill Valuable Secondary Products from In Vitro Culture Mary Ann Lila In Vitro Plant Pathology Subramanian Jayasankar and D. J. Gray SPECIAL TOPICS Variation in Tissue Culture Subramanian Jayasankar Commercial Laboratory Production Gayle R. L. Suttle Indexing for Plant Pathogens Alan C. Cassells and Barbara M. Doyle Entrepreneurship for Biotechnology Ventures: From Bench to Bag David W. Altman

DNA amplification fingerprinting provides evidence that Discula destructiva, the cause of dogwood anthracnose in North America, is an introduced pathogen

DNA amplification fingerprinting was used to characterize 28 isolates of Discula destructiva and three isolates of an undescribed species of Discula. These filamentous fungi cause anthracnose of various species of dogwood (Cornus). Isolates were obtained from throughout the disease range in the eastern and western United States and western Canada and DNA

Plant Pathology Concepts and Laboratory Exercises

Introductory Concepts Plant Pathology and Historical Perspectives, M.T. Windham and A.S. Windham What Is A Disease? M.T. Windham and A.S. Windham Introduction to the Groups of Plant Pathogens, M.T. Windham Groups of Plant Pathogens Plant Pathogenic Viruses, M.A.C. Langham Mechanical Inoculation of Plant Viruses, M.A.C. Langham Plant-Parasitic Nematodes, J.P. Noe Pathogenicity and Isolation of Plant Parasitic Nematodes, J.P. Noe Plant Pathogenic Fungi and Fungal-like Organisms, A. Brooks Gould Slime Molds and Zoosporic Fungi, S.E. Mozley-Standridge, D. Porter, and M.A. Cubeta Laboratory Exercises with Zoosporic Plant Pathogens, M.A. Cubeta, D. Porter, and S.E. Mozley-Standridge Archiascomycete and Hemiascomycete Pathogens, M. L. Daughtrey, K. T. Hodge, and N. Shishkoff The Powdery Mildews, M.L. Daughtrey, K.T. Hodge, and N. Shishkoff Ascomycota: Pyrenomycetes, Discomycetes, and Loculoascomycetes, K.J. Curry and R.E. Baird Deuteromycota: An Artificial Assemblage of Asexually Reproducing Fungi, R.E. Baird Laboratory Exercises with Selected Asexually Reproducing Fungi, R.E. Baird Smut and Rust Diseases, L.J. Littlefield, Y.H. Li, and D. Hensley Basidiomycota: Fleshy Mushrooms and Other Important and Symbiotic Associations, R.E. Baird Oomycota: The Fungi-like Organisms, R.N. Trigiano, M.H. Ament, and K.H. Lamour Laboratory Exercises with the Oomycetes, R.N. Trigiano, R. E. Baird, and S. N. Jeffers Soilborne Plant Pathogens, B.H. Ownley and D. Michael Benson Laboratory Exercises with Soilborne Plant Pathogens, D M. Benson and B.H. Ownley Parasitic Seed Plants, Protozoa, Algae, and Mosses, M.T. Windham and A.S. Windham Abiotic Diseases, A.S. Windham and M.T. Windham Molecular Tools for Studying Plant Pathogens Molecular Tools for Studying Plant Pathogens, T.A. Rinehart, X.W. Wang, and R.N. Trigiano Molecular Techniques Used for Studying Systematics and Phylogeny of Plant Pathogens, R.N. Trigiano, M.H. Ament, S.L. Finley, R.E. DeVries, N.R. Rowland, and G. Caetano-Anolles Plant-Pathogen Interactions Plant-Fungal Interactions at the Molecular Level, R.B. Ferreira, S. Monteiro, R. Freitas, C.N. Santos, Z. Chen, L.M. Batista, J. Duarte, A. Borges, and A.R. Teixeira Testing Blad, a Potent Antifungal Polypeptide, S. Monteiro and R. Boavida Ferreira Detecting and Measuring Extracellular Enzymes Produced by Fungi and Bacteria, R.N. Trigiano and M.H. Ament Host Defenses: A Physical and Physiological Approach, K.D. Gwinn, S.E. Greene, J.F. Green, and D. Trently Disruption of Plant Function, M.B. Riley Epidemiology and Disease Control Plant Disease Epidemiology, K.L. Bowen Host Resistance, J.K. Pataky and M.L. Carson Cultural Control of Plant Diseases, G. Moorman and K.D. Gwinn Chemical Control of Plant Diseases, A.S. Windham and M.T. Windham Biological Control of Plant Pathogens, B.H. Ownley and M.T. Windham Integrated Pest Management, C.A. Hollier and D.E. Hershman Plant Disease Diagnosis, J.M. Mullen Diagnostic Techniques and Media Preparation, J.M. Mullen Special Topics In Vitro Plant Pathology, J. Subramanian and D.J. Gray Proper Use of Compound and Stereo Microscopes, D.T. Webb Appendix 1: Careers In Plant Pathology, A.S. Windham and M.T. Windham Glossary Index

Functional Genomics Analysis of Horseweed (Conyza canadensis) with Special Reference to the Evolution of Non-Target-Site Glyphosate Resistance

Abstract The evolution of glyphosate resistance in weedy species places an environmentally benign herbicide in peril. The first report of a dicot plant with evolved glyphosate resistance was horseweed, which occurred in 2001. Since then, several species have evolved glyphosate resistance and genomic information about nontarget resistance mechanisms in any of them ranges from none to little. Here, we report a study combining iGentifier transcriptome analysis, cDNA sequencing, and a heterologous microarray analysis to explore potential molecular and transcriptomic mechanisms of nontarget glyphosate resistance of horseweed. The results indicate that similar molecular mechanisms might exist for nontarget herbicide resistance across multiple resistant plants from different locations, even though resistance among these resistant plants likely evolved independently and available evidence suggests resistance has evolved at least four separate times. In addition, both the microarray and sequence analyses identified non–target-site resistance candidate genes for follow-on functional genomics analysis. Nomenclature: Glyphosate, horseweed, Conyza canadensis (L.) Cronq. ERICA

Somatic embryogenesis and plantlet regeneration in Cornus florida.

Somatic embryos were initiated from 12 to 15 weeks postanthesis (WPA) zygotic embryos of Cornus florida L. (flowering dogwood) cultured on Murashige-Skoog (MS) or Schenk and Hildebrandt (SH) medium amended with either 3 mg/L 2,4-D or 5 mg/L 2,4-D and 1 mg/L kinetin. White, opaque globular and early cotyledonary stage embryos were formed directly on detached cotyledons from 2 of the 5 trees sampled after 7 weeks of culture. Morphologically mature embryos developed after an additional 4 weeks incubation on medium without growth regulators; however, many of the embryos were fused in pairs along the entire length of the hypocotyl-radicle axis. Indirect embryogenesis was observed from callus cultures initiated from 9 to 15 WPA zygotic embryos. These cultures have continued to produce embryos for 16 months. Many of the embryos formed roots on germination medium, but only 12% formed plantlets and none developed past the first true leaf stage.

Somatic embryogenesis from immature embryos of redbud (Cercis canadensis)

Somatic embryos developed directly from 96 and 110 day post-anthesis Cercis canadensis L. (redbud) zygotic embryos from one of two trees sampled that were explanted onto modified Schenk and Hildebrandt medium amended with either 1, 2, 3 or 5 mg/1 2,4-D in combination with either 7.6 or 12. 6 mM ammonium ion. Although somatic embryogenesis was expressed on most media, the number of explants that produced somatic embryos and the mean number of embryos formed per explant were greatest on media that contained either 2 or 3 mg/1 2,4-D; 12.6 mM ammonium ion inhibited embryogenesis from 96 day post-anthesis explants. Zygotic embryos explanted 117 days after anthesis produced only callus and roots. Somatic embryos that were bottle-shaped or had distinct cotyledons organized roots on germination media, but only one embryo formed a shoot. No additional development occurred. Histological examination of somatic embryos showed that shoot apical meristems were poorly developed.

Comparison of Aflatoxigenic and Nonaflatoxigenic Isolates of Aspergillus flavus using DNA Amplification Fingerprinting Techniques

Aspergillus flavus is a filamentous fungus that produces mycotoxins in many food and feed crops, such as maize (Zea mays L.). Isolates were analyzed for toxin production by nucleic acid profiles in an attempt to differentiate aflatoxigenic from nonaflatoxigenic isolates. A total of 41 aflatoxigenic and 34 nonalfatoxigenic isolates were included in the study. The isolates were evaluated initially using DNA amplification fingerprinting (DAF) without clear resolution of the groups. A weak association of aflatoxigenic isolates was observed, as evidenced by their clustering in 18 of 81 trees recovered from maximum parsimony analysis of binary characters derived from arbitrary signatures from amplification profiles (ASAP) data; nonaflatoxigenic isolates exhibited a pattern of paraphyletic laddering. Up to five markers unambiguously supported the aflatoxigenic isolate grouping, but the presence of alternative conflicting topologies in equally parsimonious trees precluded the observation of meaningful statistical support. With additional markers for genome of A. flavus, this method could be used to resolve toxigenic from nontoxigenic strains. This additional work could resolve aflatoxigenic isolates of A. flavus present on maize plants using ASAP, which would reduce labor intense costs and potentially lead to faster determination of resistant cultivars in breeding efforts.

Molecular phylogeny and DNA amplification fingerprinting of Petunia taxa.

The relationship of five species of Petunia and ten cultivars of the cultivated petunia, Petunia x hybrida, were investigated using DNA-amplification fingerprinting (DAF). Reproducible banding profiles were obtained from P. parodii and P. axillaris DNA from different seed sources. In contrast, other petunias such as P. inflata, P. violacea and P. integrifolia produced variable fingerprints when different plants were examined. However, representative profiles of the variable Petunia taxa were obtained by bulking the leaf tissue from ten different individual plants. Each of ten octamer primers revealed polymorphic loci between taxa. Among a total of 201 bands produced, 146 (73%) loci were polymorphic and distinguished all species and cultivars. Phenetic and cluster analysis using DAF markers separated P. axillaris from P. parodii and distinguished between the violet-flowered species, P. inflata, P. violacea, and P. integrifolia. P. parodii grouped together with the monophyletic set of the ten cultivars of P. x hybrida examined, indicating that it had made a major contribution to the development of these cultivars. Cultivars were distributed within the dendograms by flower color. The results demonstrated the utility of DAF in establishing relationships among closely related species and cultivars of Petunia.