Alignment of Genetic and Physical Maps of Gibberella zeae

Department of Plant Pathology, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS 66506-5502, Department of Biology, University of Northern Iowa, Cedar Falls, IA 50614, USDA-ARS Plant Science and Entomology Research Unit, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS 66506-5502

^* To whom correspondence should be addressed. Email: rbowden{at}ksu.edu.

	Abstract

We previously published a genetic map of Gibberella zeae (Fusarium graminearum sensu lato) 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) using seven structural genes and 108 sequenced AFLP markers. Several linkage groups were combined based on the alignments, with the nine original linkage groups reduced to six, and the total size of the genetic map reduced from 1286 to 1140 cM. Nine supercontigs, comprising 99.2% of the genomic sequence assembly, were anchored to the genetic map. Eight markers (four from each parent) were not found in the genome assembly and four of these markers were closely linked, suggesting that > 150 kb of DNA sequence is missing from the PH-1 genome assembly. The alignments of the linkage groups and supercontigs yielded four independent sets, which is consistent with the four chromosomes reported in this fungus. Two proposed heterozygous inversions were confirmed by the alignments; otherwise colinearity of the genetic and physical maps was high. Two of four regions with segregation distortion were explained by the two selectable markers employed in making the cross. Average recombination rates for each chromosome were similar to those previously reported for G. zeae. Despite an inferred history of genetic isolation between lineage 6 and lineage 7, their chromosomes remain homologous and are capable of recombination along their entire lengths, even within the inversions. This genetic map can now be used in conjunction with the physical sequence to study phenotypes, e.g. fertility and fitness, and genetic features, e.g. centromeres and recombination frequency, that do not have a known molecular signature in the genome.