Halophyte gene discovery
Halophyte 1KP Gene Discovery
Project Contact: Michael Deyholos, University of Alberta
Background
Although sodium (Na+) is naturally present in water and soil, most plants (unlike animals) have no use for sodium and in fact experience toxicity in the presence of even low concentrations of the ion. This is particularly alarming given the ongoing salinization and alkalization of much of the world’s arable land. A small minority (~1%) of plant species are classified as halophytes. These are plants that tolerate, and in many cases prefer, growth in high concentrations of sodium (>200mM). Halophytes are widely distributed in both phylogenetic and geographical terms. However, although some of the general physiological mechanisms of salinity tolerance are understood (e.g. use of compatible solutes, osmotic adjustment, transport, exclusion and sequestration), the diversity of these responses, and the underlying proteins are still largely unknown. A recent review of halophytes cites gene discovery through high-throughput genomics as one of the most pressing needs in the field (Flowers and Colmer, New Phytologist 2008.). We will address this need through the 1KP project.
Methods
We propose to sample one transcriptome from each of the well-defined halophytes listed below (two of the species* are already in the 1KP sequencing queue). Species will generally be sampled in situ, with the whole plant extracted. Plants will be vouchered with environmental conditions described in detail. The authors with compare the predicted proteins with those of closely related non-halophytes to identify novel biochemical pathways (e.g. for compatible solute synthesis or transport), as well as other novel proteins (e.g. Batis maritima has already been used as a source of enzymes for choloromethane production). Selected proteins will be tested in biochemical assays, e.g. yeast transporter assays to demonstrate functional relevance to salinity tolerance.
Target Species
Cochlearea officinalis [Scurvy grass] (Brassicaceae)
Plantago maritima [Sea plantain] (Plantaginaceae)
Beta vulgaris ssp. maritima [Sea beet] (Amaranthaceae)
*Triglochin maritima [Sea arrowgrass] (Juncaginaceae)
Armeria maritima [Sea thrift] (Plumbaginaceae)
Spergularia marina [Sea spurrey] (Caryophyllaceae)
Aster tripolium (Asteraceae)
Limonium vulgare [Sea lavender] (Plumbaginaceae)
Puccinellia maritime [Common saltmarsh-grass] (Poaceae)
Halimione portulacoides [Sea purslane] (Amaranthaceae)
Salicornia bigelovii [Dwarf salt-wort] or S. europaea (Amaranthaceae)
*Batis maritima [turtle weed] (Bataceae, Brassicales)
Atriplex nummularia or A. lentiformis (Chenopodiaceae)
Leptochloa fusca [kallar grass] (Cynodonteae, Eleusininae)
Salsola soda [saltwort] (Chenopodiaceae)
Kosteletzkya virginica [seashore mallow] (Malvaceae)
Research Team
The project participants have a strong record in plant stress genomics and a history of collaboration. Dr. Bohnert has published more than 230 articles, with a primary emphasis on the biochemistry and molecular genetics of osmotic stress http://www.life.illinois.edu/bohnert/. Dr. Bohnert led one of the first NSF-funded plant stress genomics projects (1999-2003), of which Dr. Deyholos was a post-doctoral fellow, and the two co-published four manuscripts from this work. Drs. Cheesman and Bohnert are both now located at the University of Illinois Urbana-Champagne, where they collaborate on studies of plant stress responses. Dr. Cheesman is presently leading a transcriptome analysis project for mangroves, an important group of halophytes http://mangrove.illinois.edu/.