BGN 29: Coordinator's report: Disease and Pest Resistance Genes

Coordinator's report: Disease and Pest Resistance Genes

Brian J. Steffenson

Department of Plant Pathology
North Dakota State University, Fargo, ND USA

Barr et al. (1998) mapped a new gene for cereal cyst nematode (Heterodora avenae) resistance in the Haruna Nijo/Galleon doubled haploid population. The resistance gene, present in the Australian barley cultivar Galleon, was mapped to chromosome 5H and was flanked by the RFLP markers XYL (6.2 cM proximal) and BCD298 (12.5 cM distal). Barr et al. (1998) designated this new resistance locus as Ha4. According to the gene nomenclature system of Moseman (1972), this new locus should be designated Rha4 (for dominant resistance) or rha4 (recessive resistance) once the gene action is determined in an F2 population.

Bauer et al. (1997) investigated the genetics of resistance to Barley Mild Mosaic Virus (BaMMV) in three barley accessions 10247, Bulgarian 347, and Russia 57. Ordon and Friedt (1993) had previously determined that the resistance genes in the three accessions were not allelic. A single recessive gene on chromosome 4HL was found to confer resistance to BaMMV in each of the three accessions. The resistance gene in Bulgarian 347, designated as ym9 (properly rym9), cosegregated with the RFLP markers MWG517 and MWG2037a. The resistance gene in Russia 57 (ym11 or rym11) confers resistance to all European strains of BaMMV and also Barley Yellow Mosaic Virus (BaYMV). This gene cosegregated with the RFLP markers MWG948 and MWG2134. Accession 10247 carries the resistance gene ym8 (rym8), which confers resistance to BaMMV and BaYMV-1. This gene was localized to the distal region of chromosome 4HL in the 14.8 cM interval between RFLP markers MWG051 and MWG616.

Borovkova et al. (1998) conducted an allelism test between Hor2596, carrying the leaf rust (Puccinia hordei) resistance gene Rph9, and Triumph, carrying Rph12. No recombinants were found in a population of 3,858 F2 progeny. From a classical genetic point of view and considering the large number of F2 progeny evaluated in the allelism test, it appears that the gene in Triumph is an allele at the Rph9 locus. The locus designation of Rph12 was assigned to the gene in Triumph (Jin et al. 1993) before the proper allelism tests were made. Thus, the Rph12 designation should be changed to the allele designation of Rph9.z according to the proposed nomenclature system of Franckowiak et al. (1997). The recommended allele designation for the Rph gene in Hor2596 is Rph9.i. Molecular and morphological markers were used to position these genes on chromosome 5HL. In two different crosses, Rph9 and Rph12 were found to be 26.5 and 24.4 cM proximal to ABC155, respectively.

El Attari et al. (1998) investigated partial resistance to the bacterial leaf streak pathogen (Xanthomonas campestris pv. hordei) in the Steptoe/Morex doubled haploid mapping population. Three quantitative trait loci (QTL) for partial resistance were detected on chromosomes 3H and 5H. One of the QTL on chromosome 3H explained 13% of the variation for disease severity and mapped in the interval of RFLP markers ABA307B and ABC171. The second QTL on this chromosome explained 20% of the variation and mapped in the interval of ABG377 and MWG555B. A third putative QTL was identified on chromosome 5H near ABC155 in one experiment. The multilocus allelic effects of the three QTL accounted for nearly 30% of the phenotypic variation for disease severity.

Garvin et al. (1997) studied the genetics of resistance to the leaf scald pathogen (Rhynchosporium secalis) in Iranian and Turkish accessions of Hordeum vulgare subsp. spontaneum. Leaf scald resistance was controlled by a single dominant gene in five accessions (lines 208, 219, 240, 242, and 245), by a single recessive gene in two accessions (lines 234 and 246), and by two unlinked dominant genes in one accession line 249). The chromosomal position of three genes was inferred by their linkage with isozyme genes selectively maintained in a heterozygous state during backcrossing. The resistance gene in line 208 was placed on chromosome 1H by its linkage (14.7±3.7 cM) with isozyme locus Gpi1, the resistance gene in line 242 was placed on chromosome 4H by its linkage (15.6±3.8 cM) with isozyme locus Acp2, and the resistance gene in line 246 was placed on chromosome 7H by its linkage (25.5±4.7 cM) with isozyme locus Est5. Since no other leaf scald resistance gene has been mapped to chromosome 1H, Garvin et al. (1997) designated the resistance locus in line 208 as Rrs14. Other Rrs loci or QTL have previously been described on chromosomes 4H and 7H (see Garvin et al. 1997). The allelic relationships of the Rrs loci in lines 242 and 246 with those previously described on chromosome 4H and 7H, respectively, have yet to be determined.

HS078 and HS084 are two Hordeum vulgare subsp. spontaneum accessions that possess resistance to a wide spectrum of leaf rust pathotypes. To determine the number and chromosomal location of resistance loci in these accessions, Ivandic et al. (1998) crossed them to the leaf rust susceptible line L94. Segregation data from both populations indicated that resistance was conferred by a single dominant gene. Using RFLP markers, the genes were mapped to the short arm of chromosome 2H. The order of common markers was the same in both populations with markers MWG2133 and MWG874 cosegregating with leaf rust resistance. Both accessions were presumed to carry the same gene and Rph16 and were proposed as the locus and allele symbols, respectively. A leaf rust resistance gene derived from Hordeum bulbosum was recently mapped to chromosome 2H by Pickering et al. (1998). The Hordeum bulbosum introgression carrying this gene appears to be distal to the chromosomal position of the resistance gene reported by Ivandic et al. (1998). In last year's report, the leaf rust resistance gene described by Pickering et al. (1998) was given the temporary designation of Rph.Hb. Allelism tests should be made between Rph1 and the two recently described leaf rust resistance genes on chromosome 2H. Rph1 was initially assigned to chromosome 2H by trisomic analysis (Tuleen and McDaniel 1971). Roane and Starling (1989) suggested that Rph1 may be on chromosome 2HS based on negative linkage data with morphological markers on chromosome 2HL. Rph16 and Rph.Hb appear to exhibit a markedly different resistance spectrum than Rph1 to pathotypes of Puccinia hordei. Allelism tests would clarify the relationships among these loci.

Qi et al. (1998) studied partial resistance to leaf rust in the well-characterized cultivar Vada. From a dense molecular marker map (561 AFLP markers) of a recombinant inbred line population derived from L94/Vada, six QTL contributing to partial resistance were identified. Three QTL (designated Rphq1, Rphq2, and Rphq3) were identified at the seedling stage as measured by latent period. Rphq1, Rphq2, and Rphq3 were mapped to chromosomes 7H, 2H, and 6H, respectively, and explained 56% of the phenotypic variation. Four QTL (Rphq2, Rphq3, Rphq4, and Rphq5) conferring adult plant partial resistance were identified in both greenhouse (latent period) and field (area under the disease progress curve) assessments. In the field, these four QTL accounted for 63% of the phenotypic variation. Another QTL for adult plant partial resistance (Rphq6) was identified in the greenhouse experiment. Together, the five QTL for adult plant partial resistance as measured in the greenhouse accounted for 59% of the phenotypic variation. Rphq4, Rphq5, and Rphq6 were mapped to chromosomes 5H, 4H, and 2H, respectively. Stage-specific QTL for resistance were identified in this study. Rphq4 and Rphq5 were highly effective at the adult plant stage, but not at the seedling stage. Rphq2 was highly effective at the seedling stage and relatively ineffective at the adult plant stage. Rphq3 was the only QTL conferring a substantial level of partial resistance at both growth stages. The map positions of the QTL conferring partial resistance did not coincide with those of known Rph loci conferring qualitative resistance.

Richter et al. (1998) mapped QTL conferring resistance to the net blotch pathogen (Pyrenophora teres f. teres) in a barley cross between the resistant Ethiopian landrace Hor9088 and the susceptible cultivar Arena. The percentage of leaf area affected by net blotch on the first and second seedling leaves was assessed seven and nine days post-inoculation (dpi). Linkage analysis and map construction were based on 284 AFLP markers and 22 anchoring RFLP markers. Three QTL were identified for net blotch resistance on the first leaf at both assessment dates. For the first assessment date (seven dpi), one QTL was identified on chromosome 4HL and two were identified on chromosome 6H. For the second assessment date (nine dpi), one QTL was identified on chromosome 3HL and two were identified on chromosome 6H. The QTL on chromosome 6H all mapped within a ~45 cM block. Three QTL also were identified for net blotch resistance on the second leaf at both assessment dates. For the first assessment date on the second leaf, one QTL was identified on chromosome 1HL and two were identified on chromosome 2H. For the second assessment date, one QTL was identified on chromosome 4HS and two were identified on chromosome 3HS. Different QTL were found for resistance on the first and second seedling leaves, which develop sequentially within a very short time. These data suggest the presence of stage-specific resistance loci within this brief time frame.

Spaner et al. (1998) used disease severity data assessed on doubled haploid progeny from the Harrington/TR306 mapping population to position loci affecting resistance to five diseases. Progeny were assessed in the field under natural disease epidemics at various locations in Canada and the United States. QTL conferring resistance to powdery mildew (Blumeria [=Erysiphe] graminis f. sp. hordei) were identified on chromosomes 4H and 5H; QTL conferring resistance to leaf rust were identified on chromosomes 2H, 5H, and 6H; QTL conferring resistance to stem rust (Puccinia graminis f. sp. tritici) were identified on chromosomes 4H and 7H; QTL conferring resistance to leaf scald were identified on chromosomes 3H, 4H, and 6H; and QTL conferring resistance to net blotch were identified on chromosomes 4H, 5H, 6H, and 7H. Some of the reported resistance QTL found by Spaner et al. (1998) coincided with previously described major resistance genes or QTL.

Steffenson et al. (1998) evaluated the Australian doubled haploid mapping populations of Harrington/Chebec and Clipper/Sahara to powdery mildew. A single gene was found to confer resistance in each of the populations with Harrington and Clipper contributing the resistance. The resistance gene from Harrington was mapped to chromosome 4H and was flanked by the RFLP markers CDO795 and PSR141 at 1.9 and 1.8 cM, respectively. This gene is presumed to be Mlg. The resistance gene from Clipper was mapped to chromosome 1H and was flanked by the RFLP markers PSR381 and ksuE18(A) at 6.2 and 4.8 cM, respectively. The resistance contributed by Clipper may be due to an allele at Mla.

Toojinda et al. (1998) used marker assisted selection to introgress stripe rust (Puccinia striiformis f. sp. hordei) resistance QTL, previously identified on chromosomes 4H and 5H from the Calicuchima-sib/Bowman mapping population, into another genetic background (BSR41/Steptoe). Several other stripe rust resistance QTL were identified in the new genetic background in addition to the previously identified chromosome 4H and 5H resistance QTL. One of these resistance QTL was from BSR41 and mapped to chromosome 3H. Several other QTL were contributed by the susceptible parent Steptoe, but could not be assigned to a chromosome. This study highlights the sometimes uncertain nature of predicting how QTL detected in one population will respond when transferred to another population.

Resistance gene analogs (RGAs)

The cloning of disease resistance genes from different plant species has revealed that most contain nucleotide binding sites (NBS) and a leucine rich repeat (LRR) domain. This information has led to the development of PCR-based strategies for the possible isolation of resistance gene families or resistance gene analogs (RGAs) based on the conserved NBS-LRR motifs (e.g. Kanazin et al. 1996; Seah et al. 1998). Some of the barley derived RGAs developed by Seah et al. (1998) mapped to regions of the barley genome containing known genes for resistance to the cereal cyst nematode (Ha2) and the corn leaf aphid. Rigorous genetic analyses should be made in the future to resolve the relationship between mapped RGAs and already characterized resistance loci.

Assigning new locus and allele symbols for disease and pest resistance genes.

To assign a new locus and allele symbol for disease and pest resistance genes in barley, it is incumbent upon the investigator(s) to provide evidence that 1) the resistance is conferred by a single gene, 2) the gene confers a unique infection response or reaction pattern compared to other "known" genes, and 3) allelism tests with potential alleles are negative and/or the gene maps to a unique location. These criteria are based on those recommended by Franckowiak et al. (1997) for leaf rust resistance genes, but are applicable for other resistance genes. In assigning locus symbols, it is recommended that the simple and sensible rules proposed by Moseman (1972) be used. To validate a new locus and allele, please send the appropriate information to me prior to publication, and I will post it on the Graingenes news group for all interested researchers to review. The proposed locus and allele will become validated if no objections are made by other researchers.

It is desirable to deposit both the original source of the resistance gene (i.e. a pure seed increase from a single plant selection) and the isolate of the pathogen used to identify the gene in an international germplasm and culture repository, respectively. This would ensure that these valuable materials are preserved indefinitely. The accession number and repository location could then be included in the publication validating the new locus and allele.


Barr, A.R., K.J. Chalmers, A. Karakousis, J.M. Kretschmer, S. Manning, R.C.M. Lance, J. Lewis, S.P. Jeffries, and P. Langridge. 1998. RFLP mapping of a new cereal cyst nematode resistance locus in barley. Plant Breed. 117:185-187.

Bauer, E., J. Weyen, A. Schiemann, A. Graner, and F. Ordon. 1997. Molecular mapping of novel resistance genes against Barley Mild Mosaic Virus (BaMMV). Theor. Appl. Genet. 95:1263-1269.

Borovkova, I.G., Y. Jin, and B.J. Steffenson. 1998. Chromosomal location and genetic relationship of leaf rust resistance genes Rph9 and Rph12. Phytopathology 88:76-80.

El Attari, H., A. Rebai, P.M. Hayes, G. Barrault, G. Dechamp-Guillaume, and A. Sarrafi. 1998. Potential of doubled-haploid lines and localization of quantitative trait loci (QTL) for partial resistance to bacterial leaf streak (Xanthomonas campestris pv. hordei) in barley. Theor. Appl. Genet. 96:95-100.

Franckowiak, J.D., Y. Jin, and B.J. Steffenson. 1997. Recommended allele symbols for leaf rust resistance genes in barley. Barley Genet. Newsletter 27:36-44.

Garvin, D.F., A.H.D. Brown, and J.J. Burdon. 1997. Inheritance and chromosome locations of scald-resistance genes derived from Iranian and Turkish wild barleys. Theor. Appl. Genet. 94:1086-1091.

Ivandic, V., U. Walther, and A. Graner. 1998. Molecular mapping of a new gene in wild barley conferring complete resistance to leaf rust (Puccinia hordei Otth). Theor. Appl. Genet. 97:1235-1239.

Jin, Y., G.D. Statler, J.D. Franckowiak, and B.J. Steffenson. 1993. Linkage between leaf rust resistance genes and morphological markers in barley. Phytopathology 83:230-233

Kanazin, V., L.F. Marek, and R.C. Shoemaker. 1996. Resistance gene analogs are conserved and clustered in soybean. Proc. Natl. Acad. Sci. USA 93:11746-11750.

Moseman, J.G. 1972. Report on genes for resistance to pests. Barley Genet. Newsletter 2:145-146.

Ordon, F., and W. Friedt. 1993. Mode of inheritance and genetic diversity of BaMMV resistance of exotic barley germplasms carrying genes different from 'ym4'. Theor. Appl. Genet. 86:229-233.

Pickering, R.A., B.J. Steffenson, A.M. Hill, and I. Borovkova. 1998. Association of leaf rust and powdery mildew resistance in a recombinant derived from a Hordeum vulgare x Hordeum bulbosum hybrid. Plant Breed. 117:83-84.

Qi, X., R.E. Niks, P. Stam, and P. Lindhout. 1998. Identification of QTLs for partial resistance to leaf rust (Puccinia hordei) in barley. Theor. Appl. Genet. 96:1205-1215.

Richter, K., J. Schondelmaier, and C. Jung. 1998. Mapping of quantitative trait loci affecting Drechslera teres resistance in barley with molecular markers. Theor. Appl. Genet. 97:1225-1234.

Roane, C.W. and T.M. Starling. 1989. Linkage studies with genes conditioning leaf rust reaction in barley. Barley Newsletter 33:190-192.

Seah, S., K. Sivasithamparam, A. Karakousis, and E.S. Lagudah. 1998. Cloning and characterization of a family of disease resistance gene analogs from wheat and barley. Theor. Appl. Genet. 97:937-945.

Spaner, D., L.P. Shugar, T.M. Choo, I. Falak, K.G. Briggs, W.G. Legge, D.E. Falk, S.E. Ullrich, N.A. Tinker, B.J.

Steffenson, and D.E. Mather. 1998. Mapping of disease resistance loci in barley on the basis of visual assessment of naturally occurring symptoms. Crop Sci. 38:843-850.

Steffenson, B., P. Langridge, and R. Effertz. 1998. Genetics and mapping of powdery mildew resistance in the Harrington/Chebec and Clipper/Sahara doubled haploid populations.

Toojinda, T., E. Baird, A. Booth, L. Broers, P. Hayes, W. Powell, W. Thomas, H. Vivar, and G. Young. 1998. Introgression of quantitative trait loci (QTLs) determining stripe rust resistance in barley: an example of marker-assisted line development. Theor. Appl. Genet. 96:123-131.

Tuleen, N.A., and M.E. McDaniel. 1971. Location of genes Pa and Pa5. Barley Newslettter 15:106-107.

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