QTL mapping of powdery mildew resistance in WI 2757 cucumber (Cucumis sativus L.)

Powdery mildew (PM) is a very important disease of cucumber (Cucumis sativus L.). Resistant cultivars have been deployed in production for a long time, but the genetic mechanisms of PM resistance in cucumber are not well understood. A 3-year QTL mapping study of PM resistance was conducted with 132 F_2:3 families derived from two cucumber inbred lines WI 2757 (resistant) and True Lemon (susceptible). A genetic map covering 610.4 cM in seven linkage groups was developed with 240 SSR marker loci. Multiple QTL mapping analysis of molecular marker data and disease index of the hypocotyl, cotyledon and true leaf for responses to PM inoculation identified six genomic regions in four chromosomes harboring QTL for PM resistance in WI 2757. Among the six QTL, pm1.1 and pm1.2 in chromosome 1 conferred leaf resistance. Minor QTL pm3.1 (chromosome 3) and pm4.1 (chromosome 4) contributed to disease susceptibility. The two major QTL, pm5.1 and pm5.2 were located in an interval of ~40 cM in chromosome 5 with each explaining 21.0–74.5 % phenotypic variations. Data presented herein support two recessively inherited, linked major QTL in chromosome 5 plus minor QTL in other chromosomes that control the PM resistance in WI 2757. The QTL pm5.2 for hypocotyl resistance plays the most important role in host resistance. Multiple observations in the same year revealed the importance of scoring time in the detection of PM resistance QTL. Results of this study provided new insights into phenotypic and genetic mechanisms of powdery mildew resistance in cucumber.     

QTL analysis of powdery mildew resistance in cucumber (Cucumis sativus L.)

A population of F₇ recombinant inbred lines (RILs) was made from a cross between susceptible (‘Santou’) and resistant (PI197088-1) lines of cucumber in order to study powdery mildew resistance loci. Susceptibility to powdery mildew in the F₇ RIL individuals showed a continuous distribution from susceptible to resistant, suggesting that powdery mildew resistance is controlled by quantitative trait loci (QTLs). A QTL analysis identified two and three loci for powdery mildew resistance under 26 and 20°C conditions, respectively. One QTL was found in the same position under both temperature conditions. Therefore, it is more likely that one major QTL acts under both temperature conditions and that other QTLs are specific to the two temperature conditions. The above results suggest that the four QTLs are controlled in a different temperature manner, and that their combination played an important role in expressing a high level of resistance to powdery mildew in this cucumber population. Sequence-tagged site (STS) markers associated with each QTL were developed and would be useful for breeding a cucumber line with a high level of powdery mildew resistance. Y. Sakata and N. Kubo contributed equally to this work and are considered as first authors.     

QTL mapping of downy and powdery mildew resistances in PI 197088 cucumber with genotyping-by-sequencing in RIL population

Key message

Host resistances in PI 197088 cucumber to downy and powdery mildew pathogens are conferred by 11 (3 with major effect) and 4 (1 major effect) QTL, respectively, and three of which are co-localized.

Abstract

The downy mildew (DM) and powdery mildew (PM) are the two most important foliar diseases of cucurbit crops worldwide. The cucumber accession PI 197088 exhibits high-level resistances to both pathogens. Here, we reported QTL mapping results for DM and PM resistances with 148 recombinant inbred lines from a cross between PI 197088 and the susceptible line ‘Coolgreen’. Phenotypic data on responses to natural DM and PM infection were collected in multi-year and multi-location replicated field trials. A high-density genetic map with 2780 single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing and 55 microsatellite markers was developed, which revealed genomic regions with segregation distortion and mis-assemblies in the ‘9930’ cucumber draft genome. QTL analysis identified 11 and 4 QTL for DM and PM resistances accounting for more than 73.5 and 63.0% total phenotypic variance, respectively. Among the 11 DM resistance QTL, dm5.1, dm5.2, and dm5.3 were major-effect contributing QTL, whereas dm1.1, dm2.1, and dm6.2 conferred susceptibility. Of the 4 QTL for PM resistance, pm5.1 was the major-effect QTL explaining 32.4% phenotypic variance and the minor-effect QTL pm6.1 contributed to disease susceptibility. Three PM QTL, pm2.1, pm5.1, and pm6.1, were co-localized with DM QTL dm2.1, dm5.2, and dm6.1, respectively, which was consistent with the observed linkage of PM and DM resistances in PI 197088. The genetic architecture of DM resistance in PI 197088 and another resistant line WI7120 (PI 330628) was compared, and the potential of using PI 197088 in cucumber breeding for downy and powdery mildew resistances is discussed.

     

Identification of QTLs for resistance to powdery mildew and SSR markers diagnostic for powdery mildew resistance genes in melon (Cucumis melo L.)

Powdery mildew caused by Podosphaera xanthii is an important foliar disease in melon. To find molecular markers for marker-assisted selection, we constructed a genetic linkage map of melon based on a population of 93 recombinant inbred lines derived from crosses between highly resistant AR 5 and susceptible ‘Earl’s Favourite (Harukei 3)’. The map spans 877 cM and consists of 167 markers, comprising 157 simple sequence repeats (SSRs), 7 sequence characterized amplified region/cleavage amplified polymorphic sequence markers and 3 phenotypic markers segregating into 20 linkage groups. Among them, 37 SSRs and 6 other markers were common to previous maps. Quantitative trait locus (QTL) analysis identified two loci for resistance to powdery mildew. The effects of these QTLs varied depending on strain and plant stage. The percentage of phenotypic variance explained for resistance to the pxA strain was similar between QTLs (R ² = 22–28%). For resistance to pxB strain, the QTL on linkage group (LG) XII was responsible for much more of the variance (41–46%) than that on LG IIA (12–13%). The QTL on LG IIA was located between two SSR markers. Using an independent population, we demonstrated the effectiveness of these markers. This is the first report of universal and effective markers linked to a gene for powdery mildew resistance in melon.     

Mapping and validation of powdery mildew resistance loci from spring wheat cv. Naxos with SNP markers

Powdery mildew, caused by Blumeria graminis f.sp. tritici, is a major wheat disease in maritime and temperate climates. Breeding for race-non-specific or partial resistance is a cost-effective and environmentally friendly disease control strategy. The German spring wheat cultivar Naxos has proven to be a good source for partial resistance to powdery mildew. The objectives of the present study were to map the resistance loci in Naxos with use of high-density SNP markers in the Shanghai3/Catbird x Naxos inbred line population and validate the results in a different genetic background; Soru#1 x Naxos. Both populations were genotyped with the Illumina iSelect 90K wheat chip, and integrated linkage maps developed by inclusion of previously genotyped SSR and DArT markers. With the new linkage maps, we detected a total of 12 QTL for powdery mildew resistance in Shanghai3/Catbird x Naxos, of which eight were derived from Naxos. Previously reported QTL on chromosome arms 1AS and 2BL were more precisely mapped and the SNP markers enabled discovery of new QTL on 1AL, 2AL, 5AS and 5AL. In the Soru#1 x Naxos population, four QTL for powdery mildew resistance were detected, of which three had resistance from Naxos. This mapping verified the 1AS and 2AL QTL detected in Shanghai3/Catbird x Naxos, and identified a new QTL from Naxos on 2BL. In conclusion, the improved linkage maps with SNP markers enabled discovery of new resistance QTL and more precise mapping of previously known QTL. Moreover, the results were validated in an independent genetic background.     

Identification of quantitative trait loci for resistance to powdery mildew in a Spanish barley landrace

The Spanish landrace-derived inbred line SBCC97, together with other lines from the Spanish Barley Core Collection, displays high resistance to powdery mildew, caused by the fungus Blumeria graminis f. sp. hordei. The objective of this study was to map quantitative trait loci (QTLs) for resistance to powdery mildew in a recombinant inbred line population derived from a cross between SBCC97 and the susceptible cultivar ‘Plaisant’. Phenotypic analysis was performed using four B. graminis isolates, and genetic maps were constructed with mainly simple sequence repeat (SSR) markers, following a sequential genotyping strategy. Two major QTLs with large effects were identified on chromosome 7H, and they accounted for up to 45% of the total phenotypic variance. The alleles for resistance at each QTL were contributed by the Spanish parent SBCC97. One locus was mapped to the short arm of chromosome 7HS, and was flanked by the resistance gene analogue (RGA) marker S9202 and the SSR GBM1060. This corresponded to the same chromosomal region in which a major race-specific resistance gene from Hordeum vulgare ssp. spontaneum, designated as mlt, had been identified previously. The second QTL was linked tightly to marker EBmac0755, and it shared its chromosomal location with the qualitative resistance gene Mlf, which has only been described previously in the wild ancestor H. spontaneum. This is the first report of these two QTLs occurring together in cultivated barley, and it paves the way for their use in barley breeding programs that are designed to transfer resistance alleles into elite cultivars.     

Linkage analysis of er-1, a recessive Pisum sativum gene for resistance to powdery mildew fungus (Erysiphe pisi D.C.)

Linkage analysis was used to determine the genetic map location of er-1, a recessive gene conditioning resistance to powdery mildew, on the Pisum sativum genome. Genetic linkage was demonstrated between er-1 and linkage group 6 markers after analyzing the progeny of two crosses, an F₂ population and a set of recombinant inbred lines. The classes of genetic markers surrounding er-1 include RFLP, RAPD and allozyme markers as well as the morphological marker Gty. A RAPD marker tightly linked to er-1 was identified by bulked segregant analysis. After DNA sequence characterization, specific PCR primers were designed to convert this RAPD marker into a sequence characterized amplified region (SCAR).     

QTL molecular marker location of powdery mildew resistance in cucumber (Cucumis sativus L.)

The cucumber lines, S94 (Northern China open-field type, powdery mildew (PM) susceptible) and S06 (European greenhouse type, PM resistant), and their F6:7 populations were used to investigate PM re-sistance under seedling spray inoculation in 2005/Autumn and 2006/Spring. QTL analysis was under-taken based on a constructed molecular linkage map of the corresponding F6 population using com-posite interval mapping. A total of four QTLs (pm1.1, pm2.1, pm4.1 and pm6.1) for PM resistance were identified and located on LG 1, 2, 4 and 6, respectively, explaining 5.2%-21.0% of the phenotypic variation. Three consistent QTLs (pm1.1, pm2.1 and pm4.1) were detected under the two test conditions. The QTL pm6.1 was only identified in 2005/Autumn. The total phenotypic variation explained by the QTLs was 52.0% and 42.0% in 2005/Autumn and 2006/Spring, respectively. Anchor markers tightly linked to those loci (<5 cM) could lay a basis for both molecular marker-assisted breeding and map-based gene cloning of the PM-resistance gene in cucumber.     

Genetic linkage map of melon (<Emphasis Type="Italic">Cucumis melo</Emphasis> L.) and localization of a major QTL for powdery mildew resistance

Powdery mildew caused by Podosphaera xanthii has become a major problem in melon since it occurs all year round irrespective of the growing system. The TGR-1551 melon genotype was found to be resistant to several melon diseases, among them powdery mildew. However, the corresponding resistance genes have been never mapped. We constructed an integrated genetic linkage map using an F2 population derived from a cross between the multi-resistant genotype TGR-1551 and the susceptible Spanish cultivar ‘Bola de Oro’. The map spans 1,284.9 cM, with an average distance of 3.6 cM among markers, and consists of 354 loci (188 AFLP, 39 RAPD, 111 SSR, 14 SCAR/CAPS/dCAPS, and two phenotypic traits) distributed in 14 linkage groups. QTL analysis identified one major QTL (Pm-R) on LG V for resistance to races 1, 2, and 5 of powdery mildew. The PM4-CAPS marker is closely linked to the Pm-R QTL at a genetic distance of 1.9 cM, and the PM3-CAPS marker is located within the support interval of this QTL. These codominant markers, together with the map information reported here, could be used for melon breeding, and particularly for genotyping selection of resistance to powdery mildew in this vegetable crop species.     

The adult plant rust resistance loci Lr34/Yr18 and Lr46/Yr29 are important determinants of partial resistance to powdery mildew in bread wheat line Saar

Powdery mildew, caused by Blumeria graminis f. sp. tritici is a major disease of wheat (Triticum aestivum L.) that can be controlled by resistance breeding. The CIMMYT bread wheat line Saar is known for its good level of partial and race non-specific resistance, and the aim of this study was to map QTLs for resistance to powdery mildew in a population of 113 recombinant inbred lines from a cross between Saar and the susceptible line Avocet. The population was tested over 2 years in field trials at two locations in southeastern Norway and once in Beijing, China. SSR markers were screened for association with powdery mildew resistance in a bulked segregant analysis, and linkage maps were created based on selected SSR markers and supplemented with DArT genotyping. The most important QTLs for powdery mildew resistance derived from Saar were located on chromosomes 7DS and 1BL and corresponded to the adult plant rust resistance loci Lr34/Yr18 and Lr46/Yr29. A major QTL was also located on 4BL with resistance contributed by Avocet. Additional QTLs were detected at 3AS and 5AL in the Norwegian testing environments and at 5BS in Beijing. The population was also tested for leaf rust (caused by Puccinia triticina) and stripe rust (caused by P. striiformis f. sp. tritici) resistance and leaf tip necrosis in Mexico. QTLs for these traits were detected on 7DS and 1BL at the same positions as the QTLs for powdery mildew resistance, and confirmed the presence of Lr34/Yr18 and Lr46/Yr29 in Saar. The powdery mildew resistance gene at the Lr34/Yr18 locus has recently been named Pm38. The powdery mildew resistance gene at the Lr46/Yr29 locus is designated as Pm39.     

Identification of a major locus conferring resistance to powdery mildew (Erysiphe polygoni DC) in mungbean (Vigna radiata L. Wilczek) by QTL analysis.

A major locus conferring resistance to the causal organism of powdery mildew, Erysiphe polygoni DC, in mungbean (Vigna radiata L. Wilczek) was identified using QTL analysis with a population of 147 recombinant inbred individuals. The population was derived from a cross between 'Berken', a highly susceptible variety, and ATF 3640, a highly resistant line. To test for response to powdery mildew, F7 and F8 lines were inoculated by dispersing decaying mungbean leaves with residual conidia of E. polygoni amongst the young plants to create an artificial epidemic and assayed in a glasshouse facility. To generate a linkage map, 322 RFLP clones were tested against the two parents and 51 of these were selected to screen the mapping population. The 51 probes generated 52 mapped loci, which were used to construct a linkage map spanning 350 cM of the mungbean genome over 10 linkage groups. Using these markers, a single locus was identified that explained up to a maximum of 86% of the total variation in the resistance response to the pathogen.     

Quantitative trait loci for resistance against powdery mildew in a segregating wheat×spelt population

 Powdery mildew is one of the major diseases of wheat in regions with a maritime or semi-continental climate and can strongly affect grain yield. The attempt to control powdery mildew with major resistance genes (Pm genes) has not provided a durable resistance. Breeding for quantitative resistance to powdery mildew is more promising, but is difficult to select on a phenotypic basis. In this study, we mapped and characterised quantitative trait loci (QTLs) for adult-plant powdery mildew resistance in a segregating population of 226 recombinant inbred lines derived from the cross of the Swiss wheat variety Forno with the Swiss spelt variety Oberkulmer. Forno possibly contains the Pm5 gene and showed good adult-plant resistance in the field. Oberkulmer does not have any known Pm gene and showed a moderate susceptible reaction. Powdery mildew resistance was assessed in field trials at two locations in 1995 and at three locations in 1996. The high heritability (h²=0.97) for powdery mildew resistance suggests that the environmental influence did not affect the resistance phenotype to a great extent. QTL analysis was based on a genetic map containing 182 loci with 23 linkage groups (2469 cM). With the method of composite interval mapping 18 QTLs for powdery mildew resistance were detected, explaining 77% of the phenotypic variance in a simultaneous fit. Two QTLs with major effects were consistent over all five environments. One of them corresponds to the Pm5 locus derived from Forno on chromosome 7B. The other QTL on 5A, was derived from the spelt variety Oberkulmer and did not correspond to any known Pm gene. In addition, five QTLs were consistent over three environments, and six QTLs over two environments. The QTL at the Pm5 locus showed a large effect, although virulent races for Pm5 were present in the mixture of isolates. Molecular markers linked with QTLs for adult-plant resistance offer the possibility of simultaneous marker-assisted selection for major and minor genes. Received: 22 September 1998 / Accepted: 26 October 1998     

Genetic mapping of <Emphasis Type="Italic">psl</Emphasis> locus and quantitative trait loci for angular leaf spot resistance in cucumber (<Emphasis Type="Italic">Cucumis sativus</Emphasis> L.)

One of the most important cucumber diseases is bacterial angular leaf spot (ALS), whose increased occurrence in open-field production has been observed over the last years. To map ALS resistance genes, a recombinant inbred line (RIL) mapping population was developed from a narrow cross of cucumber line Gy14 carrying psl resistance gene and susceptible B10 line. Parental lines and RILs were tested under growth chamber conditions as well as in the field for angular leaf spot symptoms. Based on simple sequence repeat and DArTseq, genotyping a genetic map was constructed, which contained 717 loci in seven linkage groups, spanning 599.7 cM with 0.84 cM on average between markers. Monogenic inheritance of the lack of chlorotic halo around the lesions, which is typical for ALS resistance and related with the presence of recessive psl resistance gene, was confirmed. The psl locus was mapped on cucumber chromosome 5. Two major quantitative trait loci (QTL) psl5.1 and psl5.2 related to disease severity were found and located next to each other on chromosome 5; moreover, psl5.1 was co-located with psl locus. Identified QTL were validated in the field experiment. Constructed genetic map and markers linked to ALS resistance loci are novel resources that can contribute to cucumber breeding programs.     

High-resolution mapping of zym, a recessive gene for Zucchini yellow mosaic virus resistance in cucumber

Key message

Using a high-resolution mapping approach, we identified a candidate gene for ZYMV resistance in cucumber. Our findings should assist the development of high-versatility molecular markers for MAS for ZYMV resistance.

Abstract

Zucchini yellow mosaic virus (ZYMV) causes significant disease, which leads to fruit yield loss in cucurbit crops. Since ZYMV resistance is often inherited recessively in cucumber, marker-assisted selection (MAS) is a useful tool for the development of resistant cucumber cultivars. Using 128 families of an F_2:3 population derived from a cross between susceptible ‘CS-PMR1’ and resistant ‘A192-18’ cucumber inbred lines, we confirmed that ZYMV resistance is conferred by a single recessive locus: zym ^A192-18 . We constructed a cucumber genetic linkage map that included 125 simple sequence repeat (SSR) markers segregating into 7 linkage groups (chromosomes). The zym ^A192-18 locus was mapped to chromosome 6, at genetic distances of 0.9 and 1.3 cM from two closely linked SSR markers. For high-resolution genetic mapping, we identified new molecular markers cosegregating with the zym ^A192-18 locus; using cucumber genomic and molecular marker resources and screening an F₂ population of 2,429 plants, we narrowed down the zym ^A192-18 locus to a <50-kb genomic region flanked by two SSR markers, which included six candidate genes. Sequence analysis of the candidate genes’ coding regions revealed that the vacuolar protein sorting-associated protein 4-like (VPS4-like) gene had two SNPs between the parental lines. Based on SNPs of the VPS-4-like gene, we developed zym ^A192-18 -linked DNA markers and found that genotypes associated with these markers were correlated with the ZYMV resistance phenotype in 48 cucumber inbred lines. According to our data, the gene encoding VPS4-like protein is a candidate for the zym ^A192-18 locus. These results may be valuable for MAS for ZYMV resistance in cucumber.     

Genetic mapping and localization of a major QTL for seedling resistance to downy mildew in Chinese cabbage (Brassica rapa ssp. pekinensis)

Downy mildew caused by the fungus Peronospora parisitica is a serious threat to members of the Brassicaceae family. Annually, a substantial loss of yield is caused by the widespread presence of this disease in warm and humid climates. The aim of this study was to localize the genetic factors affecting downy mildew resistance in Chinese cabbage (Brassica rapa ssp. pekinensis). To achieve this goal, we improved a preexisting genetic map of a doubled-haploid population derived from a cross between two diverse Chinese cabbage lines, 91-112 and T12-19, via microspore culture. Microsatellite simple sequence repeat (SSR) markers, isozyme markers, sequence-related amplified polymorphism markers, sequence-characterized amplified region markers and sequence-tagged-site markers were integrated into the previously published map to construct a composite Chinese cabbage map. In this way, the identities of linkage groups corresponding to the Brassica A genome reference map were established. The new map contains 519 markers and covers a total length of 1,070 cM, with an average distance between markers of 2.06 cM. All markers were designated as A1–A10 through alignment and orientation using 55 markers anchored to previously published B. rapa or B. napus reference maps. Of the 89 SSR markers mapped, 15 were newly developed from express sequence tags in Genbank. The phenotypic assay indicated that a single major gene controls seedling resistance to downy mildew, and that a major QTL was detected on linkage group A8 by both interval and MQM mapping methods. The RAPD marker K14-1030 and isozyme marker PGM flanked this major QTL in a region spanning 2.9 cM, and the SSR marker Ol12G04 was linked to this QTL by a distance of 4.36 cM. This study identified a potential chromosomal segment and tightly linked markers for use in marker-assisted selection to improve downy mildew resistance in Chinese cabbage.     

Genetic characterization of powdery mildew resistance in U.S. hard winter wheat

Powdery mildew significantly affects grain yield and end-use quality of winter wheat in the southern Great Plains. Employing resistance resources in locally adapted cultivars is the most effective means to control powdery mildew. Two types of powdery mildew resistance exist in wheat cultivars, i.e., qualitative and quantitative. Qualitative resistance is controlled by major genes, is race-specific, is not durable, and is effective in seedlings and in adult plants. Quantitative resistance is controlled by minor genes, is non-race-specific, is durable, and is predominantly effective in adult plants. In this study, we found that the segregation of powdery mildew resistance in a population of recombinant inbred lines developed from a cross between the susceptible cultivar Jagger and the resistant cultivar 2174 was controlled by a major QTL on the short arm of chromosome 1A and modified by four minor QTLs on chromosomes 1B, 3B, 4A, and 6D. The major QTL was mapped to the genomic region where the Pm3 gene resides. Using specific PCR markers for seven Pm3 alleles, 2174 was found to carry the Pm3a allele. Pm3a explained 61% of the total phenotypic variation in disease reaction observed among seedlings inoculated in the greenhouse and adult plants grown in the field and subjected to natural disease pressure. The resistant Pm3a allele was present among 4 of 31 cultivars currently being produced in the southern Great Plains. The genetic effects of several minor loci varied with different developmental stages and environments. Molecular markers associated with these genetic loci would facilitate incorporating genetic resistance to powdery mildew into improved winter wheat cultivars.     

A reference genetic map of Muscadinia rotundifolia and identification of Ren5, a new major locus for resistance to grapevine powdery mildew

Muscadinia rotundifolia, a species closely related to cultivated grapevine Vitis vinifera, is a major source of resistance to grapevine downy and powdery mildew, two major threats to cultivated traditional cultivars of V. vinifera respectively caused by the oomycete Plasmopara viticola and the ascomycete Erisyphe necator. The aim of the present work was to develop a reference genetic linkage map based on simple sequence repeat (SSR) markers for M. rotundifolia. This map was created using S1 M. rotundifolia cv. Regale progeny, and covers 948?cM on 20 linkage groups, which corresponds to the expected chromosome number for muscadine. The comparison of the genetic maps of V. vinifera and M. rotundifolia revealed a high macrosynteny between the genomes of both species. The S1 progeny was used to assess the general level of resistance of M. rotundifolia to P. viticola and E. necator, by scoring different parameters of pathogen development. A quantitative trait locus (QTL) analysis allowed us to highlight a major QTL on linkage group 14 controlling resistance to powdery mildew, which explained up to 58?% of the total phenotypic variance. This QTL was named ‘Resistance to Erysiphe Necator 5’ (Ren5). A microscopic evaluation E. necator mycelium development on resistant and susceptible genotypes of the S1 progeny showed that Ren5 exerts its action after the formation of the first appressorium, and acts by delaying, and then stopping, mycelium development.     

QTL analysis for resistance to bacterial wilt (Burkholderia caryophylli) in carnation (Dianthus caryophyllus) using an SSR-based genetic linkage map

Bacterial wilt (Burkholderia caryophylli (Burkholder) Yabuuchi et al.) is one of the most damaging diseases during carnation (Dianthus caryophyllus L.) cultivation in Japan. To find molecular markers for use in marker-assisted selection, we constructed a simple sequence repeat (SSR)-based genetic linkage map of carnation using an F₂ population of 90 plants derived from a cross between a highly resistant line (85-11) and a susceptible cultivar (Pretty Favvare). To develop a large number of SSR markers, we constructed four new SSR-enriched genomic libraries and conducted expressed sequence tag analysis. We mapped 178 SSR loci into 16 linkage groups. The map covered 843.6?cM, with an average distance of 6.5?cM between two loci. This is the first report of a genetic linkage map based mainly on SSR markers in the genus Dianthus. Quantitative trait locus (QTL) analysis identified one locus for resistance to bacterial wilt in linkage group (LG) B4. The locus explained 63.0% of the phenotypic variance for resistance to bacterial wilt. The SSR markers CES1161 and CES2643 that were closest to the QTL were efficient markers for selecting lines with resistance derived from line 85-11. A positional comparison using SSR markers as anchor loci revealed that LG B4 corresponded to LG A6 in a previously constructed map. We found that the position of the resistance locus derived from line 85-11 was similar to that of the major resistance locus observed for a highly resistant wild species, Dianthus capitatus ssp. andrzejowskianus.