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International Triticeae EST Cooperative (ITEC)

Rationale:

At the 9th International Wheat Genetics Symposium held at the University of Saskatchewan, Saskatoon August 2-7, 1998, a proposal was developed to establish a public database of Expressed Sequence Tags (ESTs) from species of the Triticeae. There were only 6 wheat ESTs and a handful of other Triticeae ESTs on record at this time!


Current Activities

2014:
There are now over 1,858,577 Triticeae ESTs available to the public! With the advent of next-generation sequencing (NGS) it seems that EST numbers have plateaued since 2009. A new avenue that is increasing is the presence of genome survey sequences (GSS) which may or may not include expressed genes; however in the NGS arena the RNA-Seq collections are growing. A re-assessment is in progress the delve into these resources. Perhaps a way to extract data out of the NCBI SRA resource or to rely on the NCBI UniProt resource may be called for. Resources for this information may be found at the National Center for Biotechnology Information (NCBI, Bethesda, MD) GenBank dbEST database.

Too much information! Everyone now has a sequencer.

As of January 1, 2013 the counts have ceased, dbEST lists:

	Hordeum vulgare + subsp. vulgare (barley)             501,838
	Triticum aestivum (wheat)                           1,286,998
	Hordeum vulgare subsp. spontaneum                      24,161
	Secale cereale                                          9,298
	Triticum monococcum                                    11,190
	Aegilops speltoides                                     4,316
	Triticum turgidum subsp. durum                         19,687
	Triticum turgidum                                       2,176
To keep up to date, check the latest EST listings at NCBI (number of sequences as of 1/1/2013):
	Aegilops sp.					(       4,523)
	Hordeum sp.					(     526,031)
	Secale sp.					(       9,298)
	Triticum sp.					(   1,329,396)

Other grass genera:
Avena sp. ( 79,586) Brachypodium sp. ( 206,255) Oryza sp. ( 1,342,414) Panicum sp. ( 720,785) Pennisetum sp. ( 24,802) Saccharum sp. ( 284,793) Sorghum sp. ( 232,681) Zea sp. ( 2,019,524)
Additional listings by genera may be found on the Triticeae sequence tally page.


Triticeae Sequence Timeline

1998:
At the 9th International Wheat Genetics Symposium held at the University of Saskatchewan, Saskatoon August 2-7, 1998, a proposal was developed to establish a public database of Expressed Sequence Tags (ESTs) from species of the Triticeae. There were only 6 wheat ESTs and a handful of other Triticeae ESTs on record at this time!

1999:
Sequencing was conducted by participating laboratories of ITEC:

Laboratory ID Number Source
Paul Bailey PSR 171 H. vulgare cv. Forester (inflorescence)
Catherine Feuillet SFR 1006 H. vulgare cv. Franka (seedling)
Andreas Graner MCG 1188 H. vulgare
R.G. Herrmann HWM 1013 H. vulgare cv. Barke (leaf)
Nicola Pecchioni ISC 957 H. vulgare cv. Nure (leaf)
Mark Sorrells BCD 431 H. vulgare anchor probe collection (leaf)
G. Wenzel HWM 890 H. vulgare cv. Barke (leaf)
P. Gustafson SCC 111 S. cereale
Olin Anderson WHE 1870 T. aestivum cv. Cheyenne (endosperm)
Rudi Appels CSB 1056 T. aestivum cv. Wyuna (endosperm)
Paul Bailey PSR 571 T. aestivum cv. Novosibirskaya 67 (pericarp/testa)
Paul Bailey PSR 230 T. aestivum cv. Soliel (endosperm)
Tom Blake TBL 303 T. aestivum cv. Cheyenne (endosperm)
Tim Close TJC 1164 T. aestivum cv. Chinese Spring
Sylvie Cloutier SCL 1002 T. aestivum cv. Thatcher Lr1 (leaf)
Tim Holton SCU 1152 T. aestivum cv. Wyuna (endosperm)
J.M. Jacquemin GBX 322 T. aestivum cv. Odeon (root)
J. Jia CNW 1052 T. aestivum PM Resistant line
Peter Langridge AWB 988 T. aestivum cv. Chinese Spring (meiotic)
Jhy-Jhu Lin JJL 449 T. aestivum cv. Catoctin (leaf)
Yasunari Ogihara MUG 2130 T. aestivum cv. Norin 26 (spikelet)
Gopolan Selvaraj TAS 762 T. aestivum
Wolfgang Schuch WWS 1076 T. aestivum cv. Novosibirskaya 67 (scutellum)
Wolfgang Schuch WWR 434 T. aestivum cv. Novosibirskaya 67 (root)
Mohammad Shariflou SUN 1029 T. aestivum
Marilyn Warburton MWL 1038 T. aestivum cv. Atlas (root)
Jorge Dubcovsky UCW 1000 T. monococcum cv. DV92
Philippe Joudrier MTD 1526 T. turgidum spp. durum cv. Siliana (root)
Mark Sorrells CDO 337 A. sativa anchor probe collection (leaf)

2000:
Phase One of this project was to have at least 40,000 ESTs available publicly from 1 July 2000. However, by the deadline date, slightly more than half of the intended goal was acheived. Over 24346 sequences were generated in Phase I of this project. Many thanks are extended to the participating laboratories shown above which contributed towards this effort. Since the initial planning for this project, many improvements have been realized for the capabilities of sequencing throughput.

2001:
Phase Two of this project plans to have 300,000 ESTs sequenced for wheat and 300,000 ESTs sequenced for barley. Other projects are in progress which may contribute toward this goal.

2002:
This was a bumper crop year bringing the collection of Triticeae ESTs climbing over 780,000. 154,485 Triticum aestivum ESTs were deposited by Scott Tingey from DuPont (E. I. DuPont de Nemours and Company). and 129,238 Triticum aestivum ESTs were deposited from the Yasunari Ogihara laboratory, Kihara Institute for Biological Research, Japan. A major resource of 67,852 Hordeum vulgare ESTs were added by the Andreas Graner laboratory at Institute for Plant Genetics & Crop Plant Research (IPK), Germany and 61,439 Hordeum vulgare ESTs were deposited by the Clemson University Genomics Institute (CUGI).

2003:
Over 7,000 wheat EST probes were mapped to the wheat genome by the Wheat EST Mapping Project (NSF DBI-9975989), and a project was well underway to build a Physical Map of the Wheat D Genome (NSF DBI-0077766) using BAC clones. Over 780,000 ESTs are still available for the Triticeae, with additional sequences still reported to be in the pipeline.

2004:
The Triticeae tally just reached 1,000,000 by the end of 2004. Significant strides were made in Triticeae research with the creation and implementation of the 22K Barley1 Affymetrix chip and the release of data through the BarleyBase project. Plans were initiated and preliminary testing was done for the creation of a Wheat Affymetrix chip.

July 18, 2004 : More than 7,000 additional Avena sativa EST sequences (a close relative to the Triticeae) were added to dbEST as reported at the VII International Oat Conference by H. Rines, USDA-ARS, University of Minnesota. Oat is a very close relative to the Triticeae family and has been a great resource for genome probes.

October, 2004 : Several papers appear in Genetics volume 168 describing the mapping of wheat ESTs to the wheat genome. Over 7,500 EST probes were able to detect over 16,000 loci using a series of aneuploid wheat lines derived from Triticum aestivum cv. Chinese Spring.

2005:
2005 was a good year, over 1,055,302 Triticeae ESTs were available to the public. These include sequences from the initial ITEC effort and other sequencing projects which have made their sequences publically available.

October 14, 2005: Triticum aestivum falls behind Zea mays in dbEST counts as the most represented single plant species in the dbEST collection.

October 21, 2005: Brachypodium distachyon, a close relative of wheat and possibly a model system for the study of wheat genes has over 20,000 sequences contributed to dbEST by J. Vogel, USDA-ARS, Albany, CA. For more information, visit the Brachypodium project web site.

2006:
April 28, 2006: Triticum aestivum receives a significant increase in dbEST counts from the Y. Ogihara laboratory, Japan (359,570) and Danyluk laboratory, Canada (82,048). Also a recent influx of ESTs from the rice plant place it as the top plant EST collection, followed by wheat, maize, and arabidopsis.

September 1, 2006: Both Rice and Maize (both Poaceae) are at the top of the EST collections for plant species, each having over 1,100,000 ESTs! Tr iticum aestivum trails at a mere 855,000 ESTs.

2007:
2008:
September 5, 2008: A majort contribution of Panicum virgatum EST sequences were deposited to Genbank from a JGI Sequencing project from libraries created from the C. Tobias laboratory at USDA ARS Western Regional Center, Albany, CA.

2009:
April 22, 2009: An additional 17,711 oat (Avena sativa L.) ESTs were submitted to dbEST. ESTs libraries were constructed for three seed development stages (watery, early milk and late milk/early dough) from the cultivar "CDC Dancer". This work was carried out by the Crop Development Centre at the University of Saskatchewan (Saskatoon, SK, Canada).

2012:
There are now over 1,858,577 Triticeae ESTs available to the public! With the advent of next-gen eration sequencing (NGS) it seems that EST numbers have plateaued since 2009. A new avenue that is increasing is the presence of genome survey sequences (GSS) which may or may not include expressed genes; however in the NGS arena the RNA-Seq collections are growing. A re-assessment is in progress the delve into these resources. Perhaps a way to extract data out of the NCBI SRA resource or to rely on the NCBI UniProt resource may be call ed for.


ITEC Steering Committee members:

E-mail: genome@pw.usda.gov

Peter Langridge, Univ. of Adelaide, AUSTRALIA
Olin Anderson, USDA-ARS, USA
Mike Gale (passed in 2009), John Innes Centre, UNITED KINGDOM
Perry Gustafson, USDA-ARS, USA
Pat McGuire, ITMI, UC Davis, USA
Cal Qualset, ITMI, UC Davis, USA

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