Tuesday, December 20, 2005

Collected Links on Plant Science

Hyperlink to Return to GMO Pundit Main Page

Links to Notes on Plant Science:

General Format for List:


......# Document

Plant Science Journals

........# Crop Science
........# Journal of Agronomy
......# Weed Science
......# The Plant Journal

Overexpression of DWARF4 in the brassinosteroid biosynthetic pathway results in increased vegetative growth and seed yield in Arabidopsis
Sunghwa Choe, Shozo Fujioka, Takahiro Noguchi, Suguru Takatsuto, Shigeo Yoshida and Kenneth A. Feldmann

Plants unable to synthesize or perceive brassinosteroids (BRs) are dwarfs. Arabidopsis dwf4 was shown to be defective in a steroid 22α hydroxylase (CYP90B1) step that is the putative rate-limiting step in the BR biosynthetic pathway. To better understand the role of DWF4 in BR biosynthesis, transgenic Arabidopsis plants ...overexpressing DWF4 (AOD4) were generated... This suggests that it will be possible to control plant growth by engineering DWF4 transcription in plants.
The Plant Journal Volume 26 Page 573 - June 2001 doi:10.1046/j.1365-313x.2001.01055.x Volume 26 Issue 6

Origins, genetic organization and transcription of a family of non-autonomous helitron elements in maize.
Brunner S, Pea G, Rafalski A.

Helitron transposable elements carrying gene fragments were recently discovered in maize. These elements are frequently specific to certain maize lineages. Here
we report evidence supporting the involvement of helitrons in the rapid evolution of the maize genome, in particular in the multiplication of related genic fragments across the genome. We describe a family of four closely related, non-autonomous maize helitrons and their insertion sites at four non-allelic genetic loci across the maize genome: two specific to the B73 inbred, and two to the Mo17 inbred. We propose the phylogeny of this helitron family and provide an approximate timeline of their genomic insertions. One of these elements, the Mo17-specific helitron on chromosome 1 (bin 1.07), is transcriptionally active, probably as a result of insertion in the vicinity of a promoter. Significantly,it produces an alternatively spliced and chimeric transcript joining together genic segments of different chromosomal origin contained within the helitron. This transcript potentially encodes up to four open reading frames. During the course of evolution, transcribed helitrons containing multiple gene fragments may occasionally give rise to new genes with novel biochemical functions by a combinatorial assembly of exons. Thus helitrons not only constantly reshape the genomic organization of maize and profoundly affect its genetic diversity, but also may be involved in the evolution of gene function.

Plant J. 2005 Sep;43(6):799-810.
Brunner S, Pea G, Rafalski A.

Potato lectin: an updated model of a unique chimeric plant protein.

Van Damme EJ, Barre A, Rouge P, Peumans WJ.

Department of Molecular Biotechnology, Ghent University, Coupure Links 653, 9000
Gent, Belgium. ElsJM.Van Damme--AT--UGent.be

A complete cDNA encoding a potato tuber lectin has been identified and sequenced. Based on the deduced amino acid sequence, the still enigmatic molecular structure of the classical chimeric potato lectin could eventually be determined. Basically, the potato lectin consists of two nearly identical chitin-binding modules, built up of two in-tandem arrayed hevein domains that are interconnected by an extensin-like domain of approximately 60 amino acid residues. Although this structure confirms the 'canonical' chimeric nature of the Solanaceae lectins, it differs fundamentally from all previously proposed models. The new insights in the structure are also discussed in view of the physiological role of the Solanaceae lectins.

Plant J. 2004 Jan;37(1):34-45.

Related Links

The tomato lectin consists of two homologous chitin-binding modules separated by an extensin-like linker. [Biochem J. 2003] PMID:14503921

Potato lectin: a modular protein sharing sequence similarities with the extensin family, the hevein lectin family, and snake venom disintegrins
(platelet aggregation inhibitors). [Plant J. 1994] PMID:8054990

Potato lectin: a three-domain glycoprotein with novel hydroxyproline-containing sequences and sequence similarities to wheat-germ
agglutinin. [Int J Biochem Cell Biol. 1996] PMID:9022287

Chitin-binding proteins in potato (Solanum tuberosum L.) tuber. Characterization, immunolocalization and effects of wounding. [Biochem J. 1992]

Regulation of a hevein-like gene in Arabidopsis. [Mol Plant Microbe Interact. 1993] PMID:8118053

Journal of experimental botany.

....# The challenge of improving nitrogen use efficiency in crop plants: towards a more central role for genetic variability and quantitative genetics within integrated approaches

Bertrand Hirel, Jacques Le Gouis, Bertrand Ney and André Gallais, Journal of Experimental Botany 2007 (58(9):2369-2387; doi:10.1093/jxb/erm097), published online on June 7, 2007

In this review, recent developments and future prospects of obtaining a better understanding of the regulation of nitrogen use efficiency in the main crop species cultivated in the world are presented. In these crops, an increased knowledge of the regulatory mechanisms controlling plant nitrogen economy is vital for improving nitrogen use efficiency and for reducing excessive input of fertilizers, while maintaining an acceptable yield. Using plants grown under agronomic conditions at low and high nitrogen fertilization regimes, it is now possible to develop whole-plant physiological studies combined with gene, protein, and metabolite profiling to build up a comprehensive picture depicting the different steps of nitrogen uptake, assimilation, and recycling to the final deposition in the seed. A critical overview is provided on how understanding of the physiological and molecular controls of N assimilation under varying environmental conditions in crops has been improved through the use of combined approaches, mainly based on whole-plant physiology, quantitative genetics, and forward and reverse genetics approaches. Current knowledge and prospects for future agronomic development and application for breeding crops adapted to lower fertilizer input are explored, taking into account the world economic and environmental constraints in the next century.

Research Papers: Nitrogen Nutrition Special Issue:Journal of Experimental Botany 2007 (58(9):

Emilio Fernandez and Aurora Galvan
Inorganic nitrogen assimilation in Chlamydomonas
JXB Advance Access published on June 19, 2007
J. Exp. Bot. 2007 58: 2279-2287; doi:10.1093/jxb/erm106

Ralf R. Mendel
Biology of the molybdenum cofactor
JXB Advance Access published on March 9, 2007
J. Exp. Bot. 2007 58: 2289-2296; doi:10.1093/jxb/erm024

Anthony J. Miller, Xiaorong Fan, Mathilde Orsel, Susan J. Smith, and Darren M. Wells
Nitrate transport and signalling
JXB Advance Access published on May 22, 2007
J. Exp. Bot. 2007 58: 2297-2306; doi:10.1093/jxb/erm066

Francisco M. Cánovas, Concepción Avila, Francisco R. Cantón, Rafael A. Cañas, and Fernando de la Torre
Ammonium assimilation and amino acid metabolism in conifers
JXB Advance Access published on May 8, 2007
J. Exp. Bot. 2007 58: 2307-2318; doi:10.1093/jxb/erm051

Mayumi Tabuchi, Tomomi Abiko, and Tomoyuki Yamaya
Assimilation of ammonium ions and reutilization of nitrogen in rice (Oryza sativa L.)
JXB Advance Access published on March 8, 2007
J. Exp. Bot. 2007 58: 2319-2327; doi:10.1093/jxb/erm016

Hanma Zhang, Honglin Rong, and David Pilbeam
Signalling mechanisms underlying the morphological responses of the root system to nitrogen in Arabidopsis thaliana
JXB Advance Access published on June 19, 2007
J. Exp. Bot. 2007 58: 2329-2338; doi:10.1093/jxb/erm114

Brian G. Forde and Peter J. Lea
Glutamate in plants: metabolism, regulation, and signalling
JXB Advance Access published on June 19, 2007
J. Exp. Bot. 2007 58: 2339-2358; doi:10.1093/jxb/erm121

Rodrigo A. Gutiérrez, Miriam L. Gifford, Chris Poultney, Rongchen Wang, Dennis E. Shasha, Gloria M. Coruzzi, and Nigel M. Crawford
Insights into the genomic nitrate response using genetics and the Sungear Software System
JXB Advance Access published on April 29, 2007
J. Exp. Bot. 2007 58: 2359-2367; doi:10.1093/jxb/erm079

Bertrand Hirel, Jacques Le Gouis, Bertrand Ney, and André Gallais
The challenge of improving nitrogen use efficiency in crop plants: towards a more central role for genetic variability and quantitative genetics within integrated approaches
JXB Advance Access published on June 7, 2007
J. Exp. Bot. 2007 58: 2369-2387; doi:10.1093/jxb/erm097

Current Opinion in Plant Biology.
.....# Natural genetic variation for improving crop quality.
Fernie AR, Tadmor Y, Zamir D.
Curr Opin Plant Biol. 2006 Apr;9(2):196-202. Epub 2006 Feb 15.
Abteilung Willmitzer, Max-Planck-Institut fur Molekulare Pflanzenphysiologie, Am Muhlenberg 1, 14476 Golm, Germany.

The narrow genetic basis of many crops combined with restrictions on the commercial use of genetically modified plants, has led to a surge of interest in exploring natural biodiversity as a source of novel alleles to improve the productivity, adaptation, quality and nutritional value of crops. Genetic methodologies have been applied to natural variation to improve quality aspects
that are associated with the chemical composition of agricultural products. A future challenge in this emerging field is to integrate metabolic, phenotypic and genomic databases to allow a wider view of the plant metabolome and the application of this knowledge within genomics-assisted breeding.

Citizens' Compendium

.......# Agriculture
.......# Crop origins and evolution
......# RNA interference
......# Wheat
......# Plant breeding
......# Classical plant breeding
......# Biotechnology and plant breeding
......# Transgenic plants
......# Barbara McClintock
......# Horizontal gene transfer in plants

Purdue Universty
HORT640 - Metabolic Plant Physiology
......# Links to Useful Plant Related Databases (see next items)

Iowa State University
Integrated Crop Management News-No-Till

Plant breeding at Infography

......# Infography book list

Darwin, C. (1883) The Variation of Animals and Plants under Domestication. 2nd edition, Appleton.

Duvick, D.N. (1996) "Plant Breeding, an Evolutionary Concept." Plant Science 36, 539-48.

Kloppenburg, J.R. (2004) First the Seed: The Political Economy of Plant Biotechnology, 1492-2000. 2nd edition, University of Wisconsin Press.

Murphy, D.J. (2007) Plant Breeding and Biotechnology: Societal Context and the Future of Agriculture. Cambridge University Press.

Simmonds, N., and Smartt, J. (1995) Principles of Crop Improvement. 2nd edition, Blackwell.

Vavilov, N.I. (1935) The Phytogeographical Basis for Plant Breeding, Volume I, Moscow, Origin and Geography of Cultivated Plants. In: Vavilov, N.I., and Love, D. (translator), The Phytogeographical Basis for Plant Breeding, pp. 316-66, Cambridge University Press.

Acquaah, G. (2006) Principles of Plant Genetics and Breeding. Blackwell.

Brown, J. and Caligari, P. (2007) An Introduction to Plant Breeding. Blackwell.

Fernandez-Cornejo, J., et al. (2004) The Seed Industry in U.S. Agriculture: An Exploration of Data and Information on Crop Seed Markets, Regulation, Industry Structure, and Research and Development. Agriculture Information Bulletin Number 786, Resource Economics Division, Economic Research Service, U.S. Department of Agriculture.

Frey, K.J. (1997) National Plant Breeding Study, Volume II, National Plan for Promoting Breeding Programs for Minor Crops in the United States. Special Report 100, Agriculture and Home Economics Experiment Station, Iowa State University.

Gepts, P. (2004) "Crop Domestication as a Long-Term Selection Experiment." Plant Breeding Reviews 24, 1-44.

Graff, G.D., Cullen, S.E., Bradford, K.J., Zilberman, D., and Bennett, A.B. (2003) "The Public-Private Structure of Intellectual Property Ownership in Agricultural Biotechnology." Nature Biotechnology 21, 989-95.

"History of Plant Breeding." Transgenic Crops: An Introduction and Resource Guide, Colorado State University.

Innes, N.L. (1990) "Plant Breeding and Intellectual Property Rights." Paper presented at the Consequences of Intellectual Property at the International Agricultural Research Centers Workshop, ICRISAT Center, Hyderabad, India, 19-21 November, 1990.
Innes, N.L. (1984) "Public and Private Plant Breeding of Horticultural Food Crops in Western Europe." Horticultural Science 19, 803-08.

Jain, H.K., and Kharkwal, M.C., eds. (2004) Plant Breeding: Mendelian to Molecular Approaches. Springer.

Knight, J. (2003) "A Dying Breed." Nature 421, 568-70.

Lindner, R. (2004) "Economic Issues for Plant Breeding -- Public Funding and Private Ownership." Australasian Agribusiness Review 12, Paper 6.

McCouch, S. (2004) "Diversifying Selection in Plant Breeding." PLoS Biology 2(10), e347.

Mendel, G. (1865) "Experiments in Plant Hybridization." MendelWeb.

Murphy, D.J. (2007) People, Plants, and Genes: The Story of Crops and Humanity. Oxford University Press.

Murray, B. (2003) "Hybridization and Plant Breeding." In: Thomas, B., Murphy, D.J., and Murray, B., eds., Encyclopedia of Applied Plant Sciences, pp. 119-25, Elsevier Academic Press.

Palladino, P. (1990) "The Political Economy of Applied Research: Plant Breeding in Great Britain, 1910-1940." Minerva 28, 446-68.

Price, S.C. (1999) "Public and Private Plant Breeding." Nature Biotechnology 17, 938. 47

Schlegel, R.H.J. (2003) Encyclopedic Dictionary of Plant Breeding and Related Subjects. Haworth Press.

Thirtle, C.G., Bottomley, P., Palladino, P., Schimmelpfennig, D., and Townsend, R. (1998) "The Rise and Fall of Public Sector Plant Breeding in the United Kingdom: A Causal Chain Model of Basic and Applied Research and Diffusion." Agricultural Economics 19, 127-43.

Tripp, R., and Byerlee, D. (2000) "Public Plant Breeding in an Era of Privatisation." Natural Resource Perpectives 57, June 2000.

Webster, A. (1989) "Privatisation of Public Sector Research: The Case of a Plant Breeding Institute." Science and Public Policy 16(4), 224-32.

Wehner, T.C. (2005) "History of Plant Breeding." Plant Breeding Methods, North Carolina State University.

Zohary, D., and Hopf, M. (2000) Domestication of Plants in the Old World. 3rd edition, Oxford University Press.

University of Sydney, Plant Pathology
An essay by Angela Moncrieff.

Plants are constantly confronted with a wide variety of potential pathogens within their environment. Nevertheless, the development of disease is the exception rather than the rule, due to the highly efficient nature of the coordinated systems of passive and active defences that have evolved in plants Link to Passive Defenses and Active Defenses. These defences generally limit the host range of a microorganism capable of causing plant disease to the members of a single plant genus or species, and affect all races of a particular pathogen similarly. However, plant disease resistance can also be induced in specific plant cultivars within the host range, or only in response to specific races of pathogen.

The specificity of plant responses to pathogens can be classified into two broad categories. Non-specific resistance (general, non-host or basic resistance) is a response to all races of a particular pathogen, and occurs in all cultivars of a host plant species. In contrast, specific resistance is dependent upon the presence of a particular pathogen race, a particular host plant cultivar, or both. The underlying genetic basis of each type of plant disease resistance differs according to the genetic makeup of both plant and pathogen... continues

University of Illinois Extension
.......# Western corn rootworm feeding behavior on a transgenic hybrid described in detail
June 8, 2006
The Bulletin (No. 11 Article 4)
University of Illinois Extension
Mike Gray

In a recent journal article (Journal of Economic Entomology, June 2006), researchers from the University of Nebraska and Monsanto Company described the feeding behavior of western corn rootworms on a transgenic corn rootworm hybrid (MON 863, Cry3Bb1) and its nontransgenic isoline. The scientists utilized a novel transparent growth medium placed in test tubes in which seedling plants were grown and through which corn rootworm larvae could be observed feeding on root tissue.
Eight days after seedlings were transplanted into the test tubes containing the growth medium, 20 newly hatched larvae were carefully placed into each tube. Three treatments were utilized for the experiment: infested transgenic maize, infested isoline, and uninfested isoline. Each treatment was replicated six times. Observations and collection of data (head-capsule widths, larval weights, and wet-root weights) were made 3, 6, 9, and 12 days following the introduction of larvae into each test tube.
The researchers made the following observations: "Larvae on the roots of the susceptible treatment were actively feeding in one concentrated area, causing severe root injury. Larvae in the resistant treatment exhibited two types of behavior. The first type of behavior was illustrated by larvae with little body movement and visibly reduced abdominal segments (giving them a flattened appearance). The midgut of these lethargic larvae contained visible root tissue, indicating ingestion. Larvae exhibiting the second observed behavior moved actively up and down the root system and were observed to sample maize root hairs with their mandibles or take small bites of the root tissue, never concentrating on one feeding location. These larvae had visibly empty midgets and died, presumably from starvation."
Corn rootworm emergence from fields planted to transgenic corn rootworm hybrids (MON 863, Cry3Bb1) has been reported many times previously. The authors of this paper correctly point out that it is "not entirely clear" how this occurs. Yet some larvae are surviving in fields planted to transgenic rootworm hybrids and emerging as adults in sufficient numbers to warrant scouting of fields for silk clipping in some instances. Much speculation has been used to explain this observation and includes the following: (1) low to moderate dose of MON 863 hybrids; (2) declining titre of Cry3Bb1 in root tissue of some MON 863 hybrids during the growing season; (3) late corn rootworm larval hatch and, thereby, potential exposure to lower concentrations of Cry3Bb1 in root tissue; and (4) corn rootworm larval feeding on alternate grass hosts helping to bridge eventual movement (and survivorship) of later instars to corn roots.
This recent paper by University of Nebraska and Monsanto Company scientists sheds additional light on an intriguing topic and suggests that some western corn rootworm larvae may be able to detect small concentrations of Cry3Bb1 in root tissue, stop feeding, and survive to the next instar. Later instars of corn rootworm larvae are less likely to succumb to the Cry3Bb1 protein expressed in transgenic root tissue. Ultimately, under this scenario, we have adult emergence into producers' fields.
Based on observations in this paper, some first instars consumed enough root tissue to result in death. Are western corn rootworm adults emerging from fields planted to transgenic rootworm hybrids (MON 863) primarily those that exhibit this nonpreference (antixenosis) feeding behavior? Will some larvae also be able to detect Bt proteins expressed in root tissue of other transgenic corn rootworm hybrids (Cry34Ab1/Cry35Ab1, DAS-59122-7), stop feeding, and survive? These and many other questions related to transgenic corn rootworm hybrids will provide fertile research areas for years to come. If you're interested in taking a look at the article, go to the following Entomological Society of America Web site.

Clark, P.L., T.T. Vaughn, L.J. Meinke, J. Molina-Ochoa, and J.E. Foster. 2006. Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae) larval feeding behavior on transgenic maize (MON 863) and its isoline. Journal of Economic Entomology 99(3): 722-727.

Agricultural Production Systems Research Unit. University of Queensland.

......# APSIM was developed to simulate biophysical processes in farming systems, particularly as it relates to the economic and ecological outcomes of management practices in the face of climate risk.

APSIM is structured around plant, soil and management modules. These modules include a diverse range of crops, pastures and trees, soil processes including water balance, N and P transformations, soil pH, erosion and a full range of management controls.
APSIM resulted from a need for tools that provided accurate predictions of crop production in relation to climate, genotype, soil and management factor while addressing the long-term resource management issues.
......# The APSIM SoilWater Module
The SoilWater module is a cascading water balance model that owes much to its precursors in CERES (Jones and Kiniry, 1986) and PERFECT(Littleboy et al , 1992). The algorithms for redistribution of water throughout the soil profile have been inherited from the CERES family of models. The water characteristics of the soil are specified in terms of the lower limit (ll15), drained upper limit (dul) and saturated (sat) volumetric water contents. Water movement is described using separate algorithms for saturated or unsaturated flow. It is notable that redistribution of solutes, such as nitrate- and urea-N, is carried out in this module. Modifications adopted from PERFECT include (i) the effects of surface residues and crop cover on modifying runoff and reducing potential soil evaporation, (ii) small rainfall events are lost as first stage evaporation rather than by the slower process of second stage evaporation, and (iii) specification of the second stage evaporation coefficient (cona) as an input parameter, providing more flexibility for describing differences in long term soil drying due to soil texture and environmental effects. The module is interfaced with the RESIDUE and crop modules so that simulation of the soil water balance responds to change in the status of surface residues and crop cover (via tillage, decomposition and crop growth).

ISAA CropBiotech.Net

......# Improved maize, wheat varieties lower farmers’ risks
04.aug.06 CropBiotech Update

Modern maize and wheat varieties not only increase maximum yields in developing countries but add to farmers’ incomes by assuring more reliable yields than traditional varieties. “By reducing the fluctuations in maize and wheat grain yields, scientists have played a vital role in making modern crop technology attractive, accessible, and beneficial to farmers and consumers around the globe,” says Douglas Gollin, an associate professor of economics in Williams College, Massachusetts, USA.
Gollin analyzed changes in national-level yield stability for wheat and maize across developing countries and related them directly to the diffusion of modern varieties. His study shows that “over the past 40 years, there has actually been a decline in the relative variability of grain yields.” This finding, says Gollin, disproves critics’ views that farmers are exposed to greater risks due to the variability in yield of modern varieties.
The study on “Impacts of international research on inter-temporal yield stability in what and maize: an economic assessment” can be downloaded from

A news feature by John Dixon is available at

Nucleic Acids Res. 2006

Nature Biotechnology
Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72

Azoarcus sp. strain BH72, a mutualistic endophyte of rice and other grasses, is of agrobiotechnological interest because it supplies biologically fixed nitrogen to its host and colonizes plants in remarkably high numbers without eliciting disease symptoms. The complete genome sequence is 4,376,040-bp long and contains 3,992 predicted protein-coding sequences. Genome comparison with the Azoarcus-related soil bacterium strain EbN1 revealed a surprisingly low degree of synteny. Coding sequences involved in the synthesis of surface components potentially important for plant-microbe interactions were more closely related to those of plant-associated bacteria. Strain BH72 appears to be 'disarmed' compared to plant pathogens, having only a few enzymes that degrade plant cell walls; it lacks type III and IV secretion systems, related toxins and an N-acyl homoserine lactones–based communication system. The genome contains remarkably few mobile elements, indicating a low rate of recent gene transfer that is presumably due to adaptation to a stable, low-stress microenvironment.
Nature Biotechnology - 24, 1385 - 1391 (2006)
Andrea Krause, Adarsh Ramakumar, Daniela Bartels, Federico Battistoni, Thomas Bekel, Jens Boch, Melanie Böhm, Frauke Friedrich, Thomas Hurek, Lutz Krause, Burkhard Linke, Alice C McHardy, Abhijit Sarkar, Susanne Schneiker, Arshad Ali Syed, Rudolf Thauer, Frank-Jörg Vorhölter, Stefan Weidner, Alfred Pühler, Barbara Reinhold-Hurek, Olaf Kaiser & Alexander Goesmann

Published online: 22 October 2006; | doi:10.1038/nbt1243
Correspondence should be addressed to Barbara Reinhold-Hurek breinhold--AT--uni-bremen.de

2006. Jan 1;34(Database issue):D717-23.

......# Gramene: a bird's eye view of cereal genomes.

Rice, maize, sorghum, wheat, barley and the other major crop grasses from the family Poaceae (Gramineae) are mankind's most important source of calories and contribute tens of billions of dollars annually to the world economy (FAO 1999, http://www.fao.org; USDA 1997, http://www.usda.gov). Continued improvement of Poaceae crops is necessary in order to continue to feed an ever-growing world population. However, of the major crop grasses, only rice (Oryza sativa), with a
compact genome of approximately 400 Mbp, has been sequenced and annotated. The Gramene database (http://www.gramene.org) takes advantage of the known genetic colinearity (synteny) between rice and the major crop plant genomes to provide maize, sorghum, millet, wheat, oat and barley researchers with the benefits of an annotated genome years before their own species are sequenced. Gramene is a one stop portal for finding curated literature, genetic and genomic datasets related to maps, markers, genes, genomes and quantitative trait loci. The addition of several new tools to Gramene has greatly facilitated the potential for comparative analysis among the grasses and contributes to our understanding of the anatomy, development, environmental responses and the factors influencing agronomic performance of cereal crops. Since the last publication on Gramene database by D. H. Ware, P. Jaiswal, J. Ni, I. V. Yap, X. Pan, K. Y. Clark, L. Teytelman, S. C. Schmidt, W. Zhao, K. Chang et al. [(2002), Plant Physiol., 130, 1606-1613], the database has undergone extensive changes that are described in this publication.
Jaiswal P, Ni J, Yap I, Ware D, Spooner W, Youens-Clark K, Ren L, Liang C, Zhao
W, Ratnapu K, Faga B, Canaran P, Fogleman M, Hebbard C, Avraham S, Schmidt S,Casstevens TM, Buckler ES, Stein L, McCouch S.

Department of Plant Breeding, 240 Emerson Hall, Cornell University, Ithaca, NY
14853, USA.

Australian Journal of Experimental Agriculture

......# Solutions to Salinity in Australia 2005

Agricultural Water Management
Volume 80, Issues 1-3, Pages 1-276 (24 February 2006)
Special Issue on Water Scarcity: Challenges and Opportunities for Crop Science
Edited by Neil C. Turner

Pages 1-3
Neil C. Turner
Water scarcity: Fact or fiction? • ARTICLE
Pages 5-22
Frank R. Rijsberman
Improving agricultural water use efficiency in arid and semiarid areas of China • ARTICLE
Pages 23-40
Xi-Ping Deng, Lun Shan, Heping Zhang and Neil C. Turner
Managing secondary dryland salinity: Options and challenges • ARTICLE
Pages 41-56
David J. Pannell and Michael A. Ewing

See Also

Causes of dryland salinity

Salt, mainly sodium chloride, occurs naturally at high levels in the subsoils of most Australian agricultural land. Some of the salts in the landscape have been released from weathering rocks (particularly marine sediments) (National Land and Water Resources Audit 2001), but most have been carried inland from the oceans on prevailing winds and deposited in small amounts (20-200 kg/ha/year) with rainfall and dust (Hingston and Gailitis 1976). Over tens of thousands of years, it has accumulated in sub-soils and in Western Australia, for example, it is commonly measured at levels between 100 and 15,000 tonnes per ha (McFarlane and George 1992).

Prior to European settlement, groundwater tables in Australia were in long-term equilibrium. In agricultural regions, settlers cleared most of the native vegetation and replaced it with annual crop and pasture species, which allow a larger proportion of rainfall to remain unused by plants and to enter the groundwater (George et al. 1997; Walker et al. 1999). As a result, groundwater tables have risen, bringing dissolved accumulated salt to the surface (Anonymous 1996). Patterns and rates of groundwater change vary widely but most bores show a rising trend, except where they have already reached the surface or during periods of low rainfall. Common rates of rise are 10 to 30 cm/year (e.g. Ferdowsian et al. 2001).

In other countries, the causes and sources of dryland salinity are similar to Australia in some cases (e.g. north-east Thailand, parts of South Africa) but different in others (Ghassemi et al. 1995). For example, in the USA and Canada, the source of salt was primarily from marine sediments, rather than rainfall, and the cause of water table rise was replacement of grasslands with cropping systems, particularly systems that involve fallow. Fallow-based rotations have largely been displaced from Australian systems, but dryland salinity still occurs in regions where fallow is no longer practiced . In Argentina, current dryland salinity in the north-west of the Province of Buenos Aires is attributed to an extraordinary increase in annual rainfall in an area which is flat and naturally has relatively shallow saline water tables. In north-east Thailand, like Australia, most of the salt-affected land has resulted from forest clearing, but smaller areas are also attributed to construction of reservoirs and to various methods for making salt for commercial sale (which are not causes in Australia). In some coastal areas of Thailand (and various other parts of the world), the source of salt is seawater intrusion.

Latest publications by David Pannell include (and more plus links at his home page):

Pannell, D.J., Marshall, G.R., Barr, N., Curtis, A., Vanclay, F. and Wilkinson, R. (2006). Understanding and promoting adoption of conservation practices by rural landholders. Australian Journal of Experimental Agriculture (forthcoming). Full paper (161K) PDF version (182K)

Pannell, D.J. (2005). Salinity: new knowledge with big implications, A transcript submitted to ABC Radio National for the Ockham's Razor progam. Full paper (19K)

Marsh, S.P., Burton, M.P. and Pannell, D.J. (2006). Understanding farmers’ monitoring of water tables for salinity management, Australian Journal of Experimental Agriculture 46(7): (forthcoming).

Ridley AM and Pannell DJ (2005). SIF3: An investment framework for managing dryland salinity in Australia. SEA Working paper 1901. CRC for Plant-based Management of Dryland Salinity, University of Western Australia, Perth. Full paper (at SEA News site) Full paper (115K pdf) 2-page summary SIF3 project page

Ridley, A., and Pannell, D.J. (2005). The role of plants and plant-based R&D in managing dryland salinity in Australia, Australian Journal of Experimental Agriculture, 45: 1341-1355. Full journal paper (127K pdf)

Pannell, D.J. (2005). Farm, food and resource issues: politics and dryland salinity, Australian Journal of Experimental Agriculture 45: 1471-1480. Full journal paper (103K) Summary version (19K)

Books, Monographs, Major Reports

Pannell, D.J. and Schilizzi, S. (eds) (2006). Economics and the Future: Time and Discounting in Private and Public Decision Making, Edward Elgar, Cheltenham, UK and Northampton, MA, USA (forthcoming).

Graham, T., Pannell, D.J. and White, B. (eds) (2004). Dryland Salinity: Economic Issues at Farm, Catchment and Policy Levels, Cooperative Research Centre for Plant-Based Management of Dryland Salinity, Perth, 248 pp.

Frost, F.M., Hamilton, B., Lloyd, M. and Pannell, D.J. (2001). Salinity: A New Balance, The report of the Salinity Taskforce established to review salinity management in Western Australia, Perth. Full report (732K pdf file)

Water harvesting and supplemental irrigation for improved water productivity of dry farming systems in West Asia and North Africa %u20

Agricultural Research Service, USDA

......# Spud cover crops go deep
May 9, 2006
Deep-rooted cover crops can help potato farmers prevent erosion and protect groundwater by reducing nitrate leaching. That’s one conclusion of Agricultural Research Service (ARS) scientists who developed several important tools and techniques to help growers manage their land economically and responsibly.
Heavily fertilized crops with shallow roots, like potatoes, are more susceptible to nitrate leaching, according to Jorge Delgado, a soil scientist in the ARS Soil Plant Nutrient Research Unit at Fort Collins, Colo. However, nitrogen recovery can be significantly improved--and leaching minimized--by using a deep-rooted cover crop like winter rye, malting barley or winter wheat.
Deep-rooted cover crops reduce wind erosion, sequester carbon, cycle nutrients and draw nitrate further from the soil than crops with shallow roots. Crops like winter cover rye and wheat can even be used for grazing.
Complementary potato research is being conducted in ARS labs at Prosser, Wash., and Orono, Maine.
In Prosser, scientists measured how much nitrogen Brassica cover crops contributed to the soil and how much was taken up by subsequent potato crops. Those studies found that about 30 percent of the nitrogen on the surface of the crop field was cycled back to the soil. Planting Brassica cover crops could save growers $15 to $20 per acre at current fertilizer prices.
Orono researchers modeled the influence of temperature on crop residue decomposition and nitrogen availability in order to predict the best time to apply additional fertilizer to meet the crop’s needs and potentially reduce the amount of nitrate lost to groundwater.
These efforts promote "precision conservation," or management practices that incorporate elements of conservation and precision agriculture.
Read more about the research in the May 2006 issue of Agricultural Research magazine, available online at:
ARS is the U.S. Department of Agriculture’s principal scientific research agency.

Dow Jones eleven-story series on water began on Tuesday, August 15, 2006 and concluded on Friday, August 25, 2006.

All stories in the ongoing series on water can be found on Dow Jones page number 4233 (pay for service). Leads where openly available on wire services below:

15 Aug 2006 Ogallala Aquifer Decline Sparks Conservation, Innovation
The Ogallala aquifer, located deep beneath the central U.S., is being depleted at much higher rate than it is being recharged. The resulting water level declines in some areas are generating alarm in farming areas that depend on water from the aquifer to produce a crop. To combat the decline in water tables, some states have banned new well drilling outright, while others are offering incentives to farmers designed to reduce irrigated acreage or wean them from water-intensive crops like corn to more drought-resistant commodities like grain sorghum and cotton.

15 Aug 2006 Australian Grain Growers Turn Dry Weather An Advantage

16 Aug 2006 China May Face Food Shortages As Water Gets Scarce
China could face severe food shortages in the next 10-20 years if policy makers fail to address a worsening water shortage in the country. A lack of decisive action could lead the nation to a point of no return when it comes to China's growing dependence in imported grains and edible oils to feed its burgeoning population. Water shortages are considered a primary concern for Chinese agricultural planners trying to boost national grains output.

17 Aug 2006 Water Management Turns Crucial For Indian Farmers
India's rapid growth in recent years has thrown up a new challenge -- managing scarce water resources to meet the rising demand from an equally fast growing population. India's population -- which is expected to reach 1.6 billion people by 2050 -- holds the key to the nation's emergence as a global power, and the biggest challenge for policy makers is finding large volumes of food and water to meet basic needs. But the country appears to be falling behind in its struggle to keep pace with fast-paced growth and the demands that come with it.

21 Aug 2006 Drought Pinches Upper Mississippi River Shipping Traffic
Normally a twisting, churning river that inspires thoughts of adolescent adventure and riverboat gamblers, drought is turning the "Mighty Mississippi" into a harmless stream that is threatening to cripple shipping. A disruption in river shipping would send ripples through the U.S. economy, as the Mississippi is the largest inland waterway and the jugular through which the U.S. pumps vast amounts of grain and commodities to ports around the world.

22 Aug 2006 Drought-Tolerance One Research Goal For Rice Breeders

By Debbie Carlson

CHICAGO (Dow Jones)--Think of rice and the first picture that comes to mind is of flooded rice paddies with a farmer and his family wading through the water to tend the crop.

A staple for millions, a good harvest will keep many of those people from starvation. The best-producing regions grow paddy rice, where optimal yields in tropical regions can be as much as 8 or 9 tons a hectare. Many large corporate farming operations use the paddy production approach as well.

But to grow rice in a paddy requires abundant water supplies.

To measure strictly just what the crop uses to develop, paddy rice needs 6,000 cubic meters of water a hectare to make up the amount of water that transpires by the crop and evaporates from water and soil surface - but that doesn't include the water that is lost from the field by percolating through the soil. Sandy soils might lose as much as 10,000 cubic meters of water per hectare whereas clay-like soils that hold more water might need only 3,000
cubic meters.

That's an irrigation cost no farmer - whether a large-scale producer or a
subsistence planter - can easily afford...

22 Aug 2006 Drought-Tolerant Crops Could Raise New Policy Issues

22 Aug 2006 Public, Private Sectors Work On Drought-Tolerant Crops

23 Aug 2006 US, Canadian States Move To Guard Great Lakes Water

24 Aug 2006 Abundance of Water Makes Brazil The Last Ag Frontier

25 Aug 2006 Water Futures Contracts Seen In Long-Term Pipeline

GMO Pundit Posts

......# Salinity Solutions for Australia
......# Resurrection Plant
......# Imi Tolerant Maize
......# Genetics of mobile Genes in Plants
......# Origins of Farming and Effects on Human nutrition
......# Future Agricultural Challenges
......# Farm Productivity
......# Primer on Plant Hormones.
......# Nonhost resistance.
......# Rice breeding for better yields with DWARF4 gene
......# Explanation of hybrid vigour (heterosis)
......# More on how hybrid vigor (heterosis) works
......# Overview on benefits of plant breeding
......# Plant breeding and climate change.
......# Finding molecular markers to alter soy oil fatty acid profiles.
......# Signposts to the future in salinity and abiotic stress research.
......# Increase in GM crop market share in Canada.
......# Report on ten years of Canadian experience with GM crops.
......# Stress tolerance traits.
......# Detection of pathogen molecular patterns by Leucine-rich repeat LRR proteins in plants, insects (malaria parasite by Anopheles), and animals.
......# Cereal R genes
......# Canadians breed barley with less phytate.
......# How plants respond to carbon dioxide.
......# How hybrid vigour (heterosis) works.
......# Basic plant physiology review-textbook.
......# Co-evolution of pathogen and host- CSIRO Studies on flax and rusts.
......# Collected paper on genetics.
......# The Red Queen.

......# Primer on history of wheat breeding and inter-species crosses.

......# Dow Jones Details Water Policy Issues

......# How bad bacteria get into plants via stomata

......# Bruce Ames in the range and role of natural plant poisons: The 99.99% natural classic.

......# Second generation insect protected GM cottons.

......# Hybrid corn carries traits that protect against stress, Donald Duvick Review.

......# How pathogenic bacteria inject proteins into plant host cells.

Proceedings of the National Academy of Sciences, USA, PNAS

......#Nonhost Resistance to bacterial infection.

Papers relating to Leucine Rich Repearts and Plant disease Resistance;

1: Madsen LH, Collins NC, Rakwalska M, Backes G, Sandal N, Krusell L, Jensen J,
Waterman EH, Jahoor A, Ayliffe M, Pryor AJ, Langridge P, Schulze-Lefert P,
Stougaard J.
Barley disease resistance gene analogs of the NBS-LRR class: identification and
Mol Genet Genomics. 2003 Apr;269(1):150-61. Epub 2003 Mar 5.

2: Soriano JM, Vilanova S, Romero C, Llacer G, Badenes ML.
Characterization and mapping of NBS-LRR resistance gene analogs in apricot
(Prunus armeniaca L.).
Theor Appl Genet. 2005 Mar;110(5):980-9. Epub 2005 Feb 16.

3: Collins N, Park R, Spielmeyer W, Ellis J, Pryor AJ.
Resistance gene analogs in barley and their relationship to rust resistance
Genome. 2001 Jun;44(3):375-81.

4: Yaish MW, Saenz de Miera LE, Perez de la Vega M.
Isolation of a family of resistance gene analogue sequences of the nucleotide
binding site (NBS) type from Lens species.
Genome. 2004 Aug;47(4):650-9.

5: Xu Q, Wen X, Deng X.
Isolation of TIR and non-TIR NBS--LRR resistance gene analogues and
identification of molecular markers linked to a powdery mildew resistance locus
in chestnut rose (Rosa roxburghii Tratt).
Theor Appl Genet. 2005 Sep;111(5):819-30. Epub 2005 Oct 18.

6: Liu JJ, Ekramoddoullah AK.
Isolation, genetic variation and expression of TIR-NBS-LRR resistance gene
analogs from western white pine ( Pinus monticola Dougl. ex. D. Don.).
Mol Genet Genomics. 2003 Dec;270(5):432-41. Epub 2003 Oct 28.

7: Collins NC, Webb CA, Seah S, Ellis JG, Hulbert SH, Pryor A.
The isolation and mapping of disease resistance gene analogs in maize.
Mol Plant Microbe Interact. 1998 Oct;11(10):968-78.

8: Ramalingam J, Vera Cruz CM, Kukreja K, Chittoor JM, Wu JL, Lee SW, Baraoidan
M, George ML, Cohen MB, Hulbert SH, Leach JE, Leung H.
Candidate defense genes from rice, barley, and maize and their association with
qualitative and quantitative resistance in rice.
Mol Plant Microbe Interact. 2003 Jan;16(1):14-24.

Candidate genes involved in both recognition (resistance gene analogs [RGAs]) and general plant defense (putative defense response [DR]) were used as molecular markers to test for association with resistance in rice to blast, bacterial blight (BB), sheath blight, and brown plant-hopper (BPH). The 118 marker loci were either polymerase chain reaction-based RGA markers or restriction fragment length polymorphism (RFLP) markers that included RGAs or putative DR genes from rice, barley, and maize. The markers were placed on an existing RFLP map generated from a mapping population of 116 doubled haploid (DH) lines derived from a cross between an improved indica rice cultivar, IR64, and a traditional japonica cultivar, Azucena. Most of the RGAs and DR genes detected a single locus with variable copy number and mapped on different chromosomes. Clusters of RGAs were observed, most notably on chromosome 11 where many known blast and BB resistance genes and quantitative trait loci (QTL) for blast, BB, sheath blight, and BPH were located. Major resistance genes and QTL for blast and BB resistance located on different chromosomes were associated with several candidate genes. Six putative QTL for BB were located on chromosomes 2, 3, 5, 7, and 8 and nine QTL for BPH resistance were located to chromosomes 3, 4, 6, 11, and 12. The alleles of QTL for BPH resistance were mostly from IR64 and each explained between 11.3 and 20.6% of the phenotypic variance. The alleles for BB resistance were only from the Azucena parent and each explained at least 8.4% of the variation. Several candidate RGA and DR gene markers were associated with QTL from the pathogens and pest. Several RGAs were mapped to BB QTL. Dihydrofolate reductase thymidylate synthase co-localized with two BPH QTL associated with plant response to feeding and also to blast QTL. Blast QTL also were associated with aldose reductase, oxalate oxidase, JAMyb (a jasmonic acid-induced Myb transcription factor), and peroxidase markers. The frame map provides reference points to select candidate genes for cosegregation analysis using other mapping populations, isogenic lines, and mutants

9: Irigoyen ML, Loarce Y, Fominaya A, Ferrer E.
Isolation and mapping of resistance gene analogs from the Avena strigosa
Theor Appl Genet. 2004 Aug;109(4):713-24. Epub 2004 Jul 16.

10: Noir S, Combes MC, Anthony F, Lashermes P.
Origin, diversity and evolution of NBS-type disease-resistance gene homologues
in coffee trees (Coffea L.).
Mol Genet Genomics. 2001 Jun;265(4):654-62.

11: He L, Du C, Covaleda L, Xu Z, Robinson AF, Yu JZ, Kohel RJ, Zhang HB.
Cloning, characterization, and evolution of the NBS-LRR-encoding resistance
gene analogue family in polyploid cotton (Gossypium hirsutum L.).
Mol Plant Microbe Interact. 2004 Nov;17(11):1234-41.

12: van der Linden CG, Wouters DC, Mihalka V, Kochieva EZ, Smulders MJ, Vosman
Efficient targeting of plant disease resistance loci using NBS profiling.
Theor Appl Genet. 2004 Jul;109(2):384-93. Epub 2004 Apr 1.

Detection of an effector by an R protein triggers rapid activation of a very effective defense.

In this issue of PNAS, Dodds et al. (4) provide evidence for direct, allele-specific interaction between alleles of a particular R protein and the corresponding pathogen-encoded Avr proteins. In a remarkable arc of history, they do so by using cloned alleles from flax and flax rust loci that were defined genetically five decades ago by Flor (2, 3, 5, 6). Combined with other recent breakthroughs, this work suggests that plant R proteins can function either by directly detecting the corresponding Avr protein (the "receptor–ligand" model) or by perceiving alterations in plant machines that are targets of Avr protein action in the promotion of pathogen virulence [the "guard hypothesis" (7–9)].

4 Dodds, P. N., Lawrence, G. J., Catanzariti, A.-M., Teh, T., Wang, C.-I. A., Ayliffe, M. A., Kobe, B. & Ellis, J. G. (2006) Proc. Natl. Acad. Sci. USA 103, 8888–8893.
5 Ellis, J., Lawrence, G., Ayliffe, M., Anderson, P., Collins, N., Finnegan, J., Frost, D., Luck, J. & Pryor, T. (1997) Annu. Rev. Phytopathol 35, 271–291.

6 Dodds, P. N., Lawrence, G. J., Catanzariti, A. M., Ayliffe, M. A. & Ellis, J. G. (2004) Plant Cell 16, 755–768. The Melampsora lini AvrL567 avirulence genes are expressed in haustoria and their products are recognized inside plant cells.

Division of Plant Industry, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT 2601, Australia.

The Linum usitatissimum (flax) L gene alleles, which encode nucleotide binding site-Leu rich repeat class intracellular receptor proteins, confer resistance against the Melampsora lini (flax rust) fungus. At least 11 different L resistance specificities are known, and the corresponding avirulence genes in M. lini map to eight independent loci, some of which are complex and encode multiple specificities. We identified an M. lini cDNA marker that cosegregates in an F2 rust family with a complex locus determining avirulence on the L5, L6, and L7 resistance genes. Two related avirulence gene candidates, designated AvrL567-A and AvrL567-B, were identified in a genomic DNA contig from the avirulence allele, whereas the corresponding virulence allele contained a single copy of a related gene, AvrL567-C. Agrobacterium tumefaciens-mediated transient expression of the mature AvrL567-A or AvrL567-B (but not AvrL567-C) proteins as intracellular products in L. usitatissimum and Nicotiana tabacum (tobacco) induced a hypersensitive response-like necrosis that was dependent on coexpression of the L5, L6, or L7 resistance gene. An F1 seedling lethal or stunted growth phenotype also was observed when transgenic L. usitatissimum plants expressing AvrL567-A or AvrL567-B (but not AvrL567-C) were crossed to resistant lines containing L5, L6, or L7. The AvrL567 genes are expressed in rust haustoria and encode 127 amino acid secreted proteins. Intracellular recognition of these rust avirulence proteins implies that they are delivered into host cells across the plant membrane. Differences in the three AvrL567 protein sequences result from diversifying selection, which is consistent with a coevolutionary arms race.

7 van der Biezen, E. A. & Jones, J. D. G. (1998) Trends Biochem. Sci 23, 454–456.
8 Dangl, J. L. & Jones, J. D. G. (2001) Nature 411, 826–833.
9 Chisholm, S. T., Coaker, G., Day, B. & Staskawicz, B. J. (2006) Cell 124, 803–814.

Plant Cell. 2006 Jan;18(1):243-56. Epub 2005 Dec 2.
Haustorially expressed secreted proteins from flax rust are highly enriched for avirulence elicitors.

Catanzariti AM, Dodds PN, Lawrence GJ, Ayliffe MA, Ellis JG.

Division of Plant Industry, Commonwealth Scientific and Industrial Research Organization, Canberra ACT, Australia.

Rust fungi, obligate biotrophs that cause disease and yield losses in crops such as cereals and soybean (Glycine max), obtain nutrients from the host through
haustoria, which are specialized structures that develop within host cells.
Resistance of flax (Linum usitatissimum) to flax rust (Melampsora lini) involves the induction of a hypersensitive cell death response at haustoria formation sites, governed by gene-for-gene recognition between host resistance and pathogen avirulence genes. We identified genes encoding haustorially expressed secreted proteins (HESPs) by screening a flax rust haustorium-specific cDNA library. Among 429 unigenes, 21 HESPs were identified, one corresponding to the AvrL567 gene. Three other HESPs cosegregated with the independent AvrM, AvrP4, and AvrP123 loci. Expression of these genes in flax induced resistance gene-mediated cell death with the appropriate specificity, confirming their avirulence activity. AvrP4 and AvrP123 are Cys-rich proteins, and AvrP123 contains a Kazal Ser protease inhibitor signature, whereas AvrM contains no Cys residues. AvrP4 and AvrM induce cell death when expressed intracellularly, suggesting their translocation into plant cells during infection. However, secreted AvrM and AvrP4 also induce necrotic responses, with secreted AvrP4 more active than intracellular AvrP4, possibly as a result of enhanced formation of endoplasmic reticulum-dependent disulfide bonds. Addition of an endoplasmic reticulum retention signal inhibited AvrM-induced necrosis, suggesting that both AvrM and AvrP4 can reenter the plant cell after secretion in the absence of the pathogen.

Plant Biology

Interplay of the Arabidopsis nonhost resistance gene NHO1 with bacterial virulence
It is poorly understood why a particular plant species is resistant to the vast majority of potential pathogens that infect other plant species, a phenomenon referred to as "nonhost" resistance. Here, we show that Arabidopsis NHO1, encoding a glycerol kinase, is required for resistance to and induced by Pseudomonas syringae isolates from bean and tobacco. NHO1 is also required for resistance to the fungal pathogen Botrytis cinerea, indicating that NHO1 is not limited to bacterial resistance. Strikingly, P. s. pv. tomato DC3000, an isolate fully virulent on Arabidopsis, actively suppressed the NHO1 expression. This suppression is abolished in coi1 plants, indicating that DC3000 required an intact jasmonic acid signaling pathway in the plant to suppress NHO1 expression. Constitutive overexpression of NHO1 led to enhanced resistance to this otherwise virulent bacterium. The presence of avrB in DC3000, which activates a cultivar-specific "gene-for-gene" resistance in Arabidopsis, restored the induction of NHO1 expression. Thus, NHO1 is deployed for both general and specific resistance in Arabidopsis and targeted by the bacterium for parasitism.

Pharmaceuticals from crops.
.....# Phyto-Pharm online community

Sunday, December 18, 2005

Inclusion of risks and benefits in public policy decisions.

This in an exchange starting with an article by Daryll E. Ray in South West Farm Press.
Rick Roush argues in the follow up that Daryll is ignoring benefits.

Producers argue for sound science, some consumers prefer precautionary principle

Dec 14, 2005 9:40 AM
By Daryll. E. Ray

The precautionary principle is what our mothers were talking about when they told us that it is better to be safe than sorry.

U.S. agricultural and trade negotiators have been pressuring the Japanese to reopen their market, which has been closed to U.S. beef since BSE (Bovine Spongiform Encephalopathy or mad cow disease) was first detected in the U.S. herd at the end of 2003. The U.S. is also in a trade dispute with the EU (European Union) over the EU s restrictions on the importation of GMO (genetically modified organism) crops. In both cases the United States has argued that, on the basis of sound science, both of these trade restrictions ought to be lifted.?
Primedia Business - Southwest Farm Press, Click Here!

On the face of it, it would seem that the U.S. argument is very strong. After all, how could and why would one argue against sound science? For their part, the Europeans and the Japanese defend their actions on the basis of the precautionary principle. The precautionary principle is what our mothers were talking about when they told us that it is better to be safe than sorry. As long-term readers of this column know, we have written about these issues before. Our analysis of these two trade disagreements has been based on two ideas. The first is couched in economic terms arguing that the customer is always right.

If the Japanese are willing to pay for the BSE testing of every head of beef, the idea that the customer is always right would suggest that we would agree to the testing. Likewise, if the Europeans want non-GMO grain, then U.S. farmers ought to be working to provide them with non-GMO grain.?

Our second idea has been to identify why customers might assess the risk of GMO grains differently than the producers. After all, growing GMO crops makes it easier for producers to control weeds and insects. While producers receive the benefits, customers take the risks if at a later time it were to be shown that GMO crops posed some health risk. It makes no difference how low the probability of that event is? The probability is nonzero and therefore important in minds of some customers.?

This past summer we read a paper presented by Priya Om Verma and William R. Freudenberg at the 2005 Rural Sociological Society Annual Meeting that took a different look at the conflict between those advocating for the use of sound science and those advocating for the use of the precautionary principle in decision making. Verma and Freudenberg, of the University of California, Santa Barbara, argue that the precautionary principle may be the more scientific of the two approaches. ??The core of their analysis reduces the two arguments to their essentials. Those using the sound science as the justification for their policies - pressuring Europeans to buy GMOs or Japanese to purchase U.S. beef - are arguing that something is safe unless it is proven to be hazardous.

Thus, declaring something is safe runs the statistical risk that it is not.?Those supporting the precautionary principle are arguing that when there is a potential risk to life and safety, the prudent course of action is to err on the side of caution, risking the chance that one may reject an action or product as unsafe when in fact it may be safe.?Hurricane Katrina and the flooding of New Orleans provide us with a chance to apply these concepts to a situation most of us are familiar with. Those officials who supported cutting back on levee repairs were arguing that the likelihood of a Category 3 hurricane that would cause a breach in the levees was very small and that the money would be better spent elsewhere.

This is the sound science argument which takes the risk assuming the levees will hold when in fact they won t. Those who were arguing for the levee expenditures and protecting the wetlands surrounding New Orleans were basing their argument on the precautionary principle. As we have seen, the sound science argument favors short-term economic gain over against the potential of catastrophic long-term costs. In this case we can see that an ounce of prevention would have been worth more than a pound of cure.?Applying this back to the case of GMO sales to the Europeans, the United States is arguing in favor of immediate economic gains from increased trade over and against long-term health and/or safety problems that may arise if it were to turn out that GMOs pose a risk that does not show up for 10, 20, or 30 years.

Similarly, in the case of the sale of beef to the Japanese, the United States is arguing that the extra cost of testing each head of beef sold to the Japanese is unnecessary, given the low chance that any one animal would have BSE. The Japanese are arguing that given the long-term risks - if one imports enough untested beef, sooner or later a BSE positive animal will slip through - the cost of testing is a small price to pay for increased long-term safety.??As Verma and Freudenberg note, statistics teach us that these two risks are closely related. As one reduces the chance of making a short-term error - rejecting a product as unsafe when it is in fact safe - one increases the chance of making a long-term error.

There is a tradeoff between these two types of errors. We cannot have our cake and eat it too.?Their argument that the precautionary principle may be the more scientific of the two approaches is based on their contention that the precautionary principle recognizes the reality of scientific unknowns and acknowledges . . . scientific uncertainty.

They go on to say, Under conditions of scientific uncertainty, judging what is an acceptable level of risk for society is an inherently political responsibility . . . These are value-laden processes that reflect differing perspectives regarding what ought to be society s preferences for short-term economic risks versus longer-term risks to health and the environment.

Daryll E. Ray holds the Blasingame Chair of Excellence in Agricultural Policy, Institute of Agriculture, University of Tennessee, and is the Director of UT s Agricultural Policy Analysis Center (APAC). (865) 974-7407; Fax: (865) 974-7298; dray@utk.edu; http://www.agpolicy.org. Daryll Ray s column is written with the research and assistance of Harwood D. Schaffer, Research Associate with APAC

Not Just Sound Science or Precaution...But Risks and Benefits

- Rick Roush, rtroush.at.ucdavis.edu (On Agbioview)

Dear Prof. Ray:
Your analysis with the example of GM crops is interesting, but overlooks the documented advantages of GM crops to consumers, including reduced and safer pesticide residues in the environment, maybe even on food, reduced erosion due to reduced tillage, and reduced fuel use, never mind the health advantages to farm workers. Of particular interest ought to be reduced fumonisins in corn. There has even been some evidence of lower costs to consumers. I realize that consumers may not care about farm workers, but this has to be seen as a selfish attitude with regard to the people who produce food and fiber. On the other hand, consumers express considerable interest reducing the environmental foo[t] print of ag. That is why many of us who actually do pest management see advantages to the crops.

Perhaps it is up to decision makers to consider these issues even if busy and media-overloaded consumers fail to become aware of them. This is not just about "GMO crops mak(ing) it easier for producers to control weeds and insects". It's not just about a precautionary principle and sound science. It is about considering all of the risks and benefits, including the known risks of failure to adopt new technologies, as well as the hypothetical risks of doing so. If you are unaware of the refereed literature for these benefits, I am sure that my colleagues and I would be happy to offer some.

Response to Roush on Agbioview 'More on 'Sound Science or Precautionary Principle'
- Harwood D. Schaffer, hdschaffer.at.utk.edu

Rick, I am Daryl Ray's research associate and thought I would take the time to respond to your email. It appears to me that you have confused a discussion of research methodology with a discussion of the content of that research. In our article we were talking about methodology and in your response you were talking about the content of that research.

In our article we took out some of the technical language contained in Verma and Freudenburg's article. In the original they contended that arguments for "sound science" as the basis of making public policy decision in matters like BSE and GMOs indicated a preference for reducing the chance of committing a Type I error. Similarly then those using the "precautionary principle" indicate a preference for reducing the number of Type II errors. No matter where one comes down on the details of the arguments, that is the nature of the issue at hand. For any given technology one cannot reduce the risk of committing a Type I error without at the same time increase the risk of committing a Type II error. I infer from your comments that you have confidence in the technology and therefore are concerned about reducing the possibility of committing a Type I error. From a statistical point of view you then have to admit that there is a concomitant shift in the risk of committing a Type II error.

In either case you are correct: the issue is not one of science vs. non-science. Rather it is a matter of difference in risk preferences with some striving to reduce the risk of committing a Type I error while others are trying to reduce the risk of committing a Type II error. Those risk preferences are influenced by values and at that point values become a relevant part of the discussion and decision-making process in a democratic society.

Our purpose in writing the article was to present the issue of the trade-off between "sound science" and "precautionary principle" between Type I and Type II errors to a general audience that is not as well versed in statistical issues as you are.

Thanks for your response and your interest in public policy issues.
Sincerely yours, Harwood Schaffer, Research Associate, Agricultural Policy Analysis Center, PhD candidate, Department of Sociology, University of Tennessee

Response to Harwood, from Rick Roush, rtroush.at.ucdavis.edu
Dear Harwood :
No, I have not confused a discussion of research methodology with a discussion of the content of that research. Your approach and discussion is all about a one-sided view of the precautionary principle that considers only risks to the new technology, not known hazards of the current technologies. The only mention of the word "benefit" in your article was in the context of benefits to producers, with consumers taking all of the risks. This is an inadequate research methodology, where the benefits to consumers are never considered. Reality is not that simple.

I suggest that you have never had to make real world regulatory decisions, as I have, or this would be clearer to you. It is a key role of government to study issues and make some decisions for a general public that hasn t the time or expertise to study the questions in detail. I work on this for ag, but have to trust other experts to make technical decisions for the military, power generation and distribution, local transit, sewage, water supply, etc. I suggest that it even extends to social welfare. If one went solely with what the majority of the public wanted, Mississippi would not have been integrated in the 1980s when I lived there. In fact, there still was no public kindergarten when I arrived, because it was seen as welfare for black kids; Governor William Winter had to force it through against popular sentiment.

Here in California, it has been the role of government to make tough decisions on the mechanics of cars that people buy and other tactics to reduce air pollution, for example, even if individual consumers don t like them because of extra costs and inconvenience. There are limits on the number of fish you can catch, and protections for national and state parks, even if there is no direct, short term benefit to consumers. I see current GM crops as in the same vein; there is overwhelming evidence that they are reducing the environmental footprint of human habitation with essentially no risk to consumers.

What about the risks? We accept the risks of allowing planes to fly overhead because of the benefits to travelers and the airlines, even though we know that some planes occasionally will kill the innocent below who did not specifically accept the risks (as with the recent Southwest flight). This is not just a recent phenomenon; in old New York City, being kicked or otherwise injured by horses was a common source of mortality even for those who didn t own or work with them, but horses were tolerated for their overall benefits.

Your methodology for GM crops does not consider their benefits to consumers as the general public, but focuses on the fears that people have about the risks. You have enhanced this by comparing BSE, with known risks and relatively low cost risk avoidance, with GM crops, where there are no known risks and the costs of avoidance (stopping their use) are enormous.

Reducing the risk of a Type I error seems warranted whenever the Type II error is not distinguishable from zero. In this case, the overwhelming evidence is that current GM foods are at least as safe as anything produced conventionally. At least they get a safety review; most of what we eat has never been reviewed for safety, and even for some cases that have been assessed and score badly at least in some circumstances (like transfats, peanuts, and raw milk), we continue to allow them on the market! No GM crop would be allowed with those risks; we banned Starlink even though there was good evidence that it wasn t allergenic.

No, our disagreement is not about the content of research, but about the philosophical framework of research methodology for risk assessment.
Sincerely, Rick

Friday, December 16, 2005

Follow-up debate from Cell Biologist Professor David Schubert' s comments.

Cell Biologist Professor David Schubert has expressed a nicely put different perspective of GM food in the top Journal Nature Biotechnology:

A different perspective on GM food

As with good weblog postings, the comments and rejoinders to this contribution are at least as important as the initial posting. Nature Biotechnology carried these:
Divergent perspectives on GM food
Reply to 'Divergent perspectives on GM food'

Fortunately, the debate on Schuberts perspective continues unabated today. The following collection are some recent interesting remarks on Agbioview:

AgBioView from http://www.agbioworld.org December 14, 2005
Re: Schubert - Is Plant Breeding Different from GM?
Martin Mieschendah, martin.mieschendahl.at.uba.de

There is no doubt than genetic engineering breeding may lead to unintended effects (see e.g. Table. 6 in H. Kuiper et al.: Assessment of the food safety issues related to genetically modified foods, The Plant Journal 27(6), 503-528, 2001). But these risks are not different from those of conventional breeding.

To my knowledge so far only conventional bred plant varieties causing negative effects to the consumers have found its way to the market and had to be withdrawn. These were the potato variety Lenape that contained very high levels of toxic solanine, a pest-resistant celery variety that caused rashes in agricultural workers as it contained seven-fold more of the carcinogen psoralen than the control celery, and a traditionally bred squash that caused food poisoning (see e.g. AG Haselberger: Codex guidelines for GM food include the analysis of unintended effects, Nature Biotechnology 21-7, 739-741, 2003).

Favorite Papers for 2005: Safety in Conventional Status Quo? From Wayne Parrott

This past year I have been setting aside some papers that have crossed my desk. They caught my attention because they highlight the normal behavior of plants and agroecosystems. Everyone of these papers is about NON-transgenic crops and conventional agriculture. They caught my attention because if any single one of these had been associated with transgenes, an uproar would likely have ensued.

I wanted to call these to your attention because they highlight the lack of perspective and the double standard that continues to persist in the field. I've added my editorial remarks after each title. Enjoy.


Can almond nectar & pollen poison honey bees? (Kevan & Ebert. 2005. Am. Bee J. June 507-509)
- Yes, the pollen is toxic.

Mediation of pathogen resistance by exudation of antimicrobials from roots (Bais et al., 2005.Nature 434:217-221)
- Plants make and secrete toxins into the soil that kill potential pathogens

Reduced fitness of the Colorado potato beetle on potato plants grown in manure-amended soil (Alyokhin & Atlihan. 2005. Environ. Entomol. 34:963-968)
- Nice organic fertilizer can have negative impacts on potato beetles. Who knows what happens to those poor critters who depend on potato beetles for their livelihood.

Long-term effects of crop management on Rhizobium leguminosarum biovar viciae populations. (Depret et al., 2004. FEMS Microbiol. Ecol. 51:87-97)
- Normal crop rotations can alter soil microbial populations-- my guess is far more than Bt exudates ever could.

Copper amendment of agricultural soil selects for antibiotic resistance in the field. (Berg et al., 2005. Lett. Appl. Microbiol. 40:146-151)
- Perhaps Cornell's Environmental Impact Quotient should be amended to increase copper's hazards?

Andrew Apel comments on this further:
In regulatory matters, the doctrine of substantial equivalence has acted more or less effectively as a counterweight to the precautionary principle. Under the doctrine, if novel products are substantially equivalent to those currently on the market, they can be treated in a substantially equivalent way. However, application of the doctrine has been restricted to food and feed products.

Wayne's "Favorite papers for 2005" and other papers presented here in a similar vein suggest that the doctrine of substantial equivalence deserves to be extended to cover environmental impacts and genetic modifications. This would yield interesting avenues of inquiry and force valid comparisons.

The making of inappropriate comparisons plagues agricultural research. Consistently, trials of novel crops and crop protection products compare trial results to either "organic farming" results, or to "no farming at all" results. Quite credible scientists engage regularly in this sort of "comparison bias," which is inherently weighted against technology, and especially against novel technology. There will always be a side-effect not encountered in "organic farming" or "not farming at all," and if this side-effect is even notionally adverse, the technology being tested automatically becomes questionable.

Extending the doctrine of substantial equivalence to environmental impacts and genetic modifications would get around these improper and often ridiculous comparisons.

So for instance, one might ask, are Bt crops substantially as poisonous to honeybees as almonds? If so, should they be regulated in the same manner as almonds? (Which is to say, not at all)

One might also ask, is the impact of RR crops on soil microflora substantially equivalent to the impact of root-expressed antimicrobials in weed populations? If so, should RR crops be regulated in the same manneras weeds? (Which is to say, not at all)

From: "Roger and Carolyn Morton" Subject: re: Schubert - Is Plant Breeding Different from GM Date: Thu, 8 Dec 2005 00:09:45 +1100

I found the Schubert piece on Is Plant Breeding Different from GM? refreshing in that he actually talks science rather than ideology. However, I have three factual bones to pick.

1. The assertion that the recombination events of conventional breeding are non-mutageneic is wrong. Below are three references where the recombination junctions of mutants produced by convetional breeding have been analysised. This data shows how the recombination events of conventional breeding are mutagenic. And since the production of a conventional plant variety requires many cycles of crossing there will be a large number of mutatgeneic events happening in the production of a conventionally bred variety. Thus, conventional breeding and GM breeding are very similar in this regard.

Anderson PA, Lawrence GJ, Morrish BC, Ayliffe MA, Finnegan EJ, Ellis JG. Plant Cell 1997 Apr;9(4):641-51 Inactivation of the flax rust resistance gene M associated with loss of a repeated unit within the leucine-rich repeat coding region. M Parniske and JDG Jones Proc. Natl. Acad. Sci. USA. 1999 96: 5850-5855 Recombination between diverged clusters of the tomato Cf-9 plant disease resistance gene family D Leister, J Kurth, DA. Laurie, M Yano,T Sasaki, K Devos, A Graner, and P Schulze-Lefert Proc. Natl. Acad. Sci. USA. 1998 95 : 370-375 Rapid reorganization of resistance gene homologues in cereal genomes.

2. Another point I would take issue with is Schubert's assertion kanamycin resistance is uncommon in bacterial pathogens and that we should be wary of kanamycin resistance as a marker gene in plants. Isn't the point of the argument that kanamycin resistant bacteria are everywhere, we eat them all the time and they live in our guts? So how does adding a tiny fraction more kanamycin resistance DNA going to increase any risks? Does Schubert have evidence to refute these facts?

3. I would also call into question Schubert's claim that transpositional mutagensis does not happen in conventionally bred crops. What about corn? Isn't it common knowledge that transposons are mutagenic and active in the corn crop? - reference anyone? I think transposons are probably active in all crop plants - we just have not discovered them. For example a mass screening for rust resistance genes in Flax revealed a mutation that when examined further was discovered to be caused by a flax transposable element (JE. Luck et al Plant Journal 16 p365 1998) It had not been discovered because no-one had done a mass screening in the Flax plant.

Subject: Schubert - Is Plant Breeding Different from GM - post script
Date: Thu, 8 Dec 2005 16:55:57 +1100

Further on Schuberts talk about GM vs conventional breeding. Schubert makes the point that "for the last 10,000 years, humans have selected and bred plants that did not make them sick and promoted their health."

And I agree - we have done this. But what happens when a conventional plant breeder wants to find, say, a new insect or disease resistance gene for her pet crop? She goes out into the populations of wild relatives of her pet crop plant. Wild relatives that have not been subjected to 10,000 years of selection for low toxicity. She then crosses these with her pet crop plant, selects her resistant line and does a few backcrosses to dilute out the "other" genes. Now, what screening is done on this new conventionally bred crop to determine if it still contains toxins from the wild relatives? The answer is NONE. Why is this OK? If Schubert says the GM crops have this hypothetical risk of throwing up toxic metablolites and comounds novel to the diet and that this should require them to be subject to "metabolic profiling" then why shouldn't conventionally bred crops which also have the same hypothetical risk be also subject to the same "metabolic profiling"?

AgBioView from www.agbioworld.org: December 9, 2005
From: "Bruce Chassy" Subject: RE: Schubert - Is Plant Breeding Different from GM - post script Date: Thu, 8 Dec 2005 12:54:49 -0600

A response to Roger and Carolyn Morton. Both you and Schubert may have both over-looked the published literature a bit. But rejoice, there's already limited published evidence to support your claim.

See for example:

Gareth S. Catchpole, Manfred Beckmann, David P. Eno, Madhav Mondhe, Britta Zywicki, Janet Taylor, Nigel Hardy, Aileen Smith, Ross D. King, Douglas B. Kell, Oliver Fiehn, and John Draper. 2005. Hierarchical metabolomics demonstrates substantial compositional similarity between genetically modified and conventional potato crops. PNAS 102:14458-14462

This paper demonstrates that transgenic potatoes are virtually identical to their parental counterpart while assorted cultivars of potatoes display much greater metabolic variance. We should be clear, however, that this finding applies to potatoes. More research is needed is needed to determine if these findings can be generalized to all crops or if metabolomic screening could add anything to the safety assessment paradigm. It is quite another question to ask if we need any additional data to make a determination of safety. Food toxicologists, nutritionists and food safety experts who have evaluated the currently employed food safety paradigm are virtually unaminous in saying we do not. A point I will argue further on another day.

It should not be surprising that in spite of what Schubert claims, the people who are actually doing metabolic profiling feel that it is not yet suitable as a safety assessment technique. It is a technique that is both being researched and which they feel may be more useful in research than in regulation. Another way to say this is that Schubert is right in arguing metabolomics could be a powerful technique some day. What its exponents will admit is that we do not yet know for what it will be useful nor do we know how to interpret the results. One could not possibility expect them to make a stronger statement if they want continued funding for their research.

Bruce M. Chassy, Ph.D.
Professor of Nutritional Sciences
University of Illinois at Urbana-Champaign