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A Genetic Map of Gibberella Zeae (Fusarium Graminearum)

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A Genetic Map of Gibberella Zeae (Fusarium Graminearum) Copyright 2002 by the Genetics Society of America A Genetic Map of Gibberella zeae (Fusarium graminearum) J. E. Jurgenson,* R. L. Bowden,† K. A. Zeller,† J. F. Leslie,†,1 N. J. Alexander‡ and R. D. Plattner‡ *Department of Biology, University of Northern Iowa, Cedar Falls, Iowa 50614, †Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506-5502 and ‡Mycotoxin Research Unit, USDA/ARS National Center for Agricultural Utilization Research, Peoria, Illinois 61604 Manuscript received November 1, 2001 Accepted for publication December 26, 2001 ABSTRACT We constructed a genetic linkage map of Gibberella zeae (Fusarium graminearum) by crossing complemen- tary nitrate-nonutilizing (nit) mutants of G. zeae strains R-5470 (from Japan) and Z-3639 (from Kansas). We selected 99 nitrate-utilizing (recombinant) progeny and analyzed them for amplified fragment length polymorphisms (AFLPs). We used 34 pairs of two-base selective AFLP primers and identified 1048 polymor- cM 1300ف phic markers that mapped to 468 unique loci on nine linkage groups. The total map length is with an average interval of 2.8 map units between loci. Three of the nine linkage groups contain regions in which there are high levels of segregation distortion. Selection for the nitrate-utilizing recombinant progeny can explain two of the three skewed regions. Two linkage groups have recombination patterns that are consistent with the presence of intercalary inversions. Loci governing trichothecene toxin amount and type (deoxynivalenol or nivalenol) map on linkage groups IV and I, respectively. The locus governing the type of trichothecene produced (nivalenol or deoxynivalenol) cosegregated with the TRI5 gene (which encodes trichodiene synthase) and probably maps in the trichothecene gene cluster. This linkage map will be useful in population genetic studies, in map-based cloning, for QTL (quantitative trait loci) analysis, for ordering genomic libraries, and for genomic comparisons of related species. IBBERELLA zeae (anamorph Fusarium graminear- toxin production (DON, 3-acetyldeoxynivalenol, 15-acetyl- G um) is the most important causal agent of Fu- deoxynivalenol, NIV, 4-acetylnivalenol, and zearalenone) sarium head blight (scab) of wheat and barley in the as well as in DNA sequence-based markers. The degree United States (McMullen et al. 1997) and China (Chen of genetic isolation and pathogenic specialization among et al. 2000). In the 1990s, scab caused an estimated $3 lineages remains unresolved (Carter et al. 2000). billion losses to wheat and barley farmers in the United Bowden and Leslie (1999) established that, under States alone (Windels 2000). Scab reduces wheat bak- laboratory conditions, members of at least three of the ing quality (Seitz et al. 1986) and harvested grain often phylogenetic lineages described by O’Donnell et al. is contaminated with mycotoxins such as nivalenol (2000) can interbreed and produce viable, recombinant (NIV), deoxynivalenol (DON), and zearalenone (Mara- progeny. The fertility of these interlineage crosses can sas et al. 1984; Tanaka et al. 1988). be relatively high and suggests that these strains are G. zeae is homothallic (Nelson et al. 1983; Yun et al. members of geographically separated and genetically 2000) and may produce abundant perithecia in the distinct populations rather than of distinct species. field, but can be outcrossed under laboratory conditions O’Donnell et al. (2000) described one putative natu- (Bowden and Leslie 1999). Despite being homothallic, rally occurring hybrid strain (collected in Nepal by A. E. the amount and distribution of genetic heterogeneity in Desjardins) between lineages 2 and 6. If isolates from field populations of this fungus suggest that outcrossing these genetically divergent populations interbreed, then occurs at a significant rate in the field (Bowden and there is the potential for the production of new geno- Leslie 1992; Walker et al. 2001). Recently, O’Donnell types that carry novel combinations of genes for patho- et al. (2000) used DNA sequences of elongation factor genicity, host range, or toxin production (Brasier 2000). ␣ ␤ (EF-1 ), phosphate permease genes (PHO), -tubu- A cross between isolates from two such distantly related lin (TUB), UTP-ammonia ligase (URA), trichothecene populations also should be rich in polymorphic markers 3-O-acetyltransferase (TRI101), and a putative reductase that could be used to generate a detailed genetic map. (RED) to resolve a set of G. zeae strains into at least seven Amplified fragment length polymorphism (AFLP) distinct phylogenetic lineages. Differences between strains analysis is a PCR-based DNA analysis technique that can in distinct lineages include qualitative differences in detect variations in restriction fragment length polymor- phisms (RFLP) on a genome-wide basis (Vos et al. 1995). Like restriction fragment length polymorphism analysis, 1Corresponding author: Department of Plant Pathology, 4002 Throck- morton Plant Sciences Center, Kansas State University, Manhattan, AFLPs can detect size differences in restriction frag- KS 66506-5502. E-mail: jfl@plantpath.ksu.edu ments caused by DNA insertions, deletions, or changes Genetics 160: 1451–1460 (April 2002) 1452 J. E. Jurgenson et al. in target restriction site sequences. As compared to 8633] of and the progeny (FGSC 8634–8732) from the map- RFLP analysis, however, the labor required to detect ping cross are available from the Fungal Genetics Stock Center (Department of Microbiology, University of Kansas Medical genetic polymorphisms with AFLPs is considerably re- Center, Kansas City, KS; http://www.fgsc.net). We analyzed 99 duced. AFLP analysis yields dominant band/no-band single ascospore-derived progeny from this cross. The fre- type markers that can be used to study genetic diversity quency of nitrate-utilizing ascospores was Ͻ1%, because most in fungal populations (e.g., Gonzalez et al. 1998; Pur- of the perithecia were homothallic selfs of Z-11572. wantara et al. 2000; Zeller et al. 2000) and to define We isolated ascospores from mature perithecia by inverting the carrot agar cross plates and collecting ascospores on the and distinguish species of Fusarium (Marasas et al. plate lid. These ascospores were suspended in 5 ml of sterile 2001). AFLPs have been used to develop recombination- water and then dilution plated onto a minimal agar medium based genetic maps in mapping populations of higher (Correll et al. 1987) amended with tergitol and sorbose plants such as barley, soybeans, and maize (Vuylsteke (Bowden and Leslie 1999). Plates were incubated for 5–7 Њ et al. 1999; Yin et al. 1999; Hua et al. 2000) and to days at 24 . Recombinant progeny, identified as nitrate uti- lizers, were collected and transferred to minimal medium supplement mapping efforts in fungi, e.g., in Phytophth- slants. Each of the recombinant progeny was subcultured from ora (van der Lee et al. 2001). When using 2-bp exten- a single macroconidium. Macroconidia were separated with sions in specific AFLP reactions, as is common in fungi, a Cailloux stage-mounted micromanipulator (Stoelting, Chi- there are 256 potential primer-pair combinations that cago). Cultures were maintained on minimal medium and can each be used to generate a unique DNA fingerprint stored as spore/hyphal fragment suspensions in 15% glycerol at Ϫ70Њ at Kansas State University. pattern for each pair of restriction enzymes used in the Analysis of DNA polymorphisms in the mapping population: initial digestion of the DNA. The genomic distribution We inoculated 50 ml of liquid complete medium (Correll -ϫ 105 macroco 5ف of markers generated by AFLPs is limited only by the et al. 1987) in 125-ml Erlenmeyer flasks with ml of a 2.5% aqueous (v/v) solution 1ف distribution of the restriction sites used to generate nidia suspended in them. of Tween 60 (Sigma, St. Louis). Cultures were incubated for 2–3 days at room temperature (22Њ–25Њ) on a rotary shaker Our objective in this study was to establish a recombi- (150 rpm). Tissue from each culture was collected by filtration nation-based genetic linkage map of G. zeae by crossing through a nongauze milk filter (Ken Ag Milk Filter, Ashland, phenotypically and genetically divergent strains from OH), washed with 100 ml sterile water, and blotted dry with different continents. Only one other detailed genetic paper towels. The tissue was frozen at Ϫ20Њ until DNA was map is presently available for any Gibberella species extracted. DNA extraction: DNA was isolated with a cetyltrimethyl am- (Xu and Leslie 1996). Generation of a genetic linkage monium bromide procedure (Kere´nyi et al. 1999) modified map for G. zeae will permit the correlation of physical from that of Murray and Thompson (1980). We estimated sequences with segregating phenotypes, the localization final DNA concentrations (in TE buffer) by comparison of of genes for toxin production, the identification of ge- DNA fluorescence of diluted aliquots of each DNA sample ␭ netically independent markers that can be used in char- against that of HindIII-digested bacteriophage DNA with an acterization of field populations, and the identification IS-1000 version 2.0 digital imaging system (Alpha Innotech, San Leandro, CA). Samples and sample dilutions were run in of genomic sequences that might be of particular impor- 1% agarose gels containing TAE (40 mm Tris-acetate, 1 mm tance in the evolution of this species. EDTA pH 8.0) and 0.5 ␮g/ml ethidium bromide. DNA yields ranged from 100 to 1000 ␮g of DNA per culture. The concen- tration of each DNA sample was adjusted to 20 ␮g/ml for use MATERIALS AND METHODS in AFLP analysis. AFLPs: AFLPs were generated with the protocol of Vos et Mapping cross: One of the parents of this cross was derived al. (1995) as modified by Zeller et al. (2000). AFLP primers from a DON-producing strain, Z-3639, originally isolated from were synthesized by Integrated DNA Technologies (Coralville, wheat in Kansas (Bowden and Leslie 1992) and belonging IA). The EcoRI primers in the final specific amplification reac- to lineage VII as described by O’Donnell et al.
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