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United States Department of Agriculture

Agricultural Research Service

Title: Alignment Between Genetic and Physical Maps of Gibberella zeae

Authors
item Lee, Jungkwan - KANSAS STATE UNIVERSITY
item Jurgenson, James - UNIVERSITY NORTHERN IOWA
item Leslie, John - KANSAS STATE UNIVERSITY
item Bowden, Robert

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 2, 2008
Publication Date: April 1, 2008
Citation: Lee, J., Jurgenson, J.E., Leslie, J.F., Bowden, R.L. 2008. Alignment Between Genetic and Physical Maps of Gibberella zeae. Applied and Environmental Microbiology.74:2349-2359.

Interpretive Summary: Gibberella zeae (Fusarium graminearum) is the primary cause of Fusarium Head Blight of wheat and barley. This disease has been one of the most important biological constraints on small grain production and marketing in the U.S. Previously, we described a genetic map of the genome of this fungus. Using sequenced DNA markers, we aligned the genetic map with the genomic DNA sequence of the fungus that was published by the Broad Institute.. The alignments grouped the linkage groups and supercontigs into four sets, confirming that there are four chromosomes in this fungus. Approximately 99% of the sequence was anchored to the genetic map, indicating the high quality of the sequence assembly and the relative completeness and validity of the genetic map.

Technical Abstract: We previously published a genetic map of Gibberella zeae (Fusarium graminearum) based on a cross between Kansas strain Z-3639 (lineage 7) and Japanese strain R-5470 (lineage 6). In this study, that genetic map was aligned with the third assembly of the genomic sequence of G. zeae strain PH-1 (lineage 7) released by The Broad Institute (Cambridge, MA). Seven sequenced structural genes and 108 sequenced markers from the nine linkage groups (LG) of the genetic map were aligned with nine supercontigs (SC) of the genomic sequence. LG 1, LG 7, LG 8 and LG 9 aligned with SC 2 and SC 5; LG 2 aligned with SC 3, SC 8 and SC 9; LG 3 aligned with SC 4 and SC 6; and LG 4, LG 5 and LG 6 aligned with SC 1 and SC 7. The nine linkage groups in the previous genetic map were reduced to six, and the total size of the genetic map was decreased from 1286 to 1140 cM. Eight genetic markers had no-hits on the genome assembly and were located in regions that correspond to the ends of supercontigs. Four of these markers were linked and mapped to the end of LG 2, which suggests that at least 150 kb of genomic sequence is missing from the end of SC 3 in the genome assembly. Approximately 99% of the sequence was anchored to the genetic map. The alignments grouped the linkage groups and supercontigs into four independent sets, which is consistent with four chromosomes in this fungus.

Last Modified: 11/26/2014
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