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United States Department of Agriculture

Agricultural Research Service

Research Project: WHEAT LEAF RUST GENOME SEQUENCING AND COMPARATIVE RESOURCES FOR RUST FUNGI

Location: Hard Winter Wheat Genetics Research Unit

2011 Annual Report


1a.Objectives (from AD-416)
The specific objectives of this proposal are to: (1) Sequence and assemble the complete genome of P. triticina isolate 1-1, Race 1 (BBBD), which is estimated to be between 100 - 120 Mb, using a hybrid of 454 and ABI (Sanger) Fosmid-end sequence; (2) Annotate gene structure using computational methods, 200,000 454 reads of ESTs from each of four new cDNA libraries, and other available ESTs; (3) Evaluate P. triticina polymorphism and diversity by comparing the sequenced strain with three additional isolates using Illumina/Solexa sequence; (4) Prompt public release of all reads, assemblies, annotation, and discovered polymorphisms; and (5) Develop education, training and outreach programs.


1b.Approach (from AD-416)
To achieve our objective we propose to:

1. Generate a whole genome shotgun assembly using an optimized combination of traditional and new sequencing technology data (Sanger and 454). 2. Annotate gene structure using computational methods, 200,000 454 reads of ESTs from each of four new cDNA libraries, and other available ESTs. 3. Evaluate the level of P. triticina DNA polymorphisms and diversity by sequencing three additional isolates of P. triticina using Illumina/Solexa sequence. 4. Prompt public release of all reads, assemblies, annotation, discovered polymorphisms, and EST alignments. 5. Develop education, training and outreach programs


3.Progress Report

A draft genome sequence of the wheat leaf rust fungus, scientific name Puccinia triticina, has been released to the public. Recently, collaborators in the project have been working on refining the quality of the sequence by attempting to sequence large insert DNA libraries. Also, three different races of leaf rust have been sequenced and compared with the draft sequence. The comparison has revealed that there is significant genetic variation within the leaf rust population. To further understand the variation, 56 different races have been identified and the DNA has been isolated. In the next year of this agreement, these 56 races will be sequenced and the DNA compared to try to understand how the races develop and where do they originate. Also, the genome sequence is being used to understand how the fungus infects wheat and causes disease. Three effector proteins, which may trigger resistance reactions to the rust, have been identified and are currently being characterized.

Progress on this agreement is monitored by regularly discussing program goals and approaches and by reviewing annual accomplishments reports.


Last Modified: 9/10/2014
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