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

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