Inheritance of resistance to leaf and glume blotch caused by Septoria nodorum Berk. in winter wheat

Sixteen crosses between eight winter wheat cultivars were screened for resistance to Septoria nodorum leaf and glume blotch in the F₁ and F₄ generations using artificial inoculation in the field. The F₁ of most crosses showed dominance for susceptibility on both ear and leaf. The effects of general combining ability were of similar magnitude as the effects for specific combining ability. On the basis of the phenotypic difference of the parents, no prediction was possible about the amount and the direction of genetic variance in the segregating populations. The variation observed in this study both within and among the segregating populations suggests a quantitative inheritance pattern influencing the expression of the two traits. The components of variance between F₂ families within a population were as high as (for S. nodorum blotch on the ear) or higher (for S. nodorum blotch on the leaf) than those between populations. Therefore, strong selection within a few populations may be as effective to obtain new resistant genotypes as selection in a large number of populations. In almost all crosses, progenies were found that were more resistant than the better parent. Thus transgression breeding may be a tool to breed for higher levels of resistance to S. nodorum blotch. Highly resistant genotypes were found even in combination with two susceptible parents. The genetic source for Septoria resistance is probably broader than is generally assumed and could be used to improve S. nodorum resistance by combination breeding followed by strong selection in large populations. Received: 18 January / Accepted: 30 April 1999     

Development of markers linked to Diuraphisnoxia resistance in wheat using a novel PCR-RFLP approach

Through random amplified polymorphic DNA (RAPD) analysis we identified a putative marker linked to the Dn5 resistance gene. This marker was converted to a more reliable sequence-characterised-amplified regions (SCAR) marker. The initial SCAR marker amplified the correct amplification product but failed to discern between the susceptible and resistant individuals. Hence, it was utilised to sequence the internal fragment. All nested primers designed from the internal sequences were also unable to produce any polymorphism between the susceptible and resistant cultivars. Restriction digests were then performed on these fragments, and the restriction enzyme EcoRI was able to discern between the susceptible and resistant F₂ individuals of the Dn5 population. This granted one marker amplified with the internal SCAR primer set OPF14₁₀₈₃ the ability to differentiate between parental individuals carrying the Dn5 genes. This marker was tested in a segregating F₂ population carrying the Dn5 resistance gene and proved able to differentiate between the segregating individuals. This marker may prove useful in marker assisted selection (MAS), although performing restriction digests may hamper the throughput of a high number of samples. Received: 4 August 1999 / Accepted: 27 August 1999     

Effects of alien cytoplasm substitution on the response of wheat cultivars to Septoria nodorum

The effects of alien cytoplasm substitution on the response of wheat to Septoria nodorum were studied, using alloplasmic series of two cultivars, Chris and Selkirk. In general, cytoplasmic substitution caused unidirectional effects on Septoria-response, alloplasmic lines of both cultivars expressing lower levels of partial resistance (in leaf and head tissue) but higher levels of yield tolerance than the corresponding euplasmic line. The reduced resistance in alloplasmics was closely associated with reduced incubation periods of Septoria infection in both leaf and head tissue. Cytoplasmic substitution resulted in increased yield tolerance to Septoria-infection in both the non-tolerant Selkirk and the relatively tolerant Chris. Unlike their effects on partial resistance, specific cytoplasms exerted similar effects on tolerance in the two parental cultivars, several cytoplasms of the D plasmatype being particularly effective in increasing Septoria-tolevance. The potential for the development of Septoria-toterant cultivars by the incorporation of alien cytoplasms is discussed, in view of the observed neutral effects of D plasmatype cytoplasms on other agronomic traits.     

Variation and classification of B low-molecular-weight glutenin subunit alleles in durum wheat

 The B low-molecular-weight (LMW) glutenin subunit composition of a collection of 88 durum wheat cultivars was analyzed. Extensive variation has been found and 18 different patterns were detected. Each cultivar exhibited 4–8 subunits, and altogether 20 subunits of different mobility were identified. The genetic control of all these subunits was determined through the analysis of nine F₂ populations and one backcross. Five subunits were controlled at the Glu-A3 locus, 14 at Glu-B3 and 1 at Glu-B2. At the Glu-A3 locus each cultivar possessed from zero to three bands and eight alleles were identified. At the Glu-B3 locus each cultivar showed four or five bands and nine alleles were detected. Only one band was encoded by the Glu-B2 locus. A nomenclature for these alleles is proposed and the relationship between them and the commonly used LMW-model nomenclature is discussed. Received: 10 February 1997 / Accepted: 25 April 1997     

Identification of RAPD markers for 11 Hessian fly resistance genes in wheat

 The pyramiding of genes that confer race- or biotype-specific resistance has become increasingly attractive as a breeding strategy now that DNA-based marker-assisted selection is feasible. Our objective here was to identify DNA markers closely linked to genes in wheat (Triticum aestivum L.) that condition resistance to Hessian fly [Mayetiola destructor (Say)]. We used a set of near-isogenic wheat lines, each carrying a resistance gene at 1 of 11 loci (H3, H5, H6, H9, H10, H11, H12, H13, H14, H16 or H17) and developed by backcrossing to the Hessian fly-susceptible wheat cultivar ‘Newton’. Using genomic DNA of these 11 lines and ‘Newton’, we have identified 18 randomly amplified polymorphic DNA (RAPD) markers linked to the 11 resistance genes. Seven of these markers were identified by denaturing gradient gel electrophoresis and the others by agarose gel electrophoresis. We confirmed linkage to the Hessian fly resistance loci by cosegregation analysis in F₂ populations of 50–120 plants for each different gene. Several of the DNA markers were used to determine the presence/absence of specific Hessian fly resistance genes in resistant wheat lines that have 1 or possibly multiple genes for resistance. The use of RAPD markers presents a valuable strategy for selection of single and combined Hessian fly resistance genes in wheat improvement. Received: 20 March 1996 / Accepted: 6 September 1996     

A genetic linkage map of durum wheat

 A genetic linkage map of tetraploid wheat [Triticum turgidum (L.) Thell.] was constructed using segregation data from a population of 65 recombinant inbred lines (RILs) derived from a cross between the durum wheat cultivar Messapia and accession MG4343 of T. turgidum (L.) Thell. ssp dicoccoides (Korn.) Thell. A total of 259 loci were analysed, including 244 restriction fragment length polymorphisms (RFLPs), one PCR (polymerase chain reaction) marker (a sequence coding for a LMW (low-molecular-weight) glutenin subunit gene located at the Glu-B3 locus), seven biochemical (six seed-storage protein loci and one isozyme locus) and seven morphological markers. A total of 213 loci were mapped at a LOD≥3 on all 14 chromosomes of the A and B genomes. The total length of the map is 1352 cM and the average distance between adjacent markers is 6.3 cM. Forty six loci could not be mapped at a LOD≥3. A fraction (18.6%) of the markers deviated significantly from the expected Mendelian ratios; clusters of loci showing distorted segregation were found on chromosomes 1B, 3AL, 4AL, 6AL and 7AL. The durum wheat map was compared with the published maps of bread wheat using several common RFLP markers and general features are discussed. The markers detected the known structural rearrangements involving chromosomes 4A, 5A and 7B as well as the translocation between 2B-6B, but not the deletion on 2BS. This map provides a useful tool for analysing and breeding economically important quantitative traits and for marker-assisted selection, as well as for studies of genome organisation in small grain cereal species. Received: 5 January 1998 / Accepted: 31 March 1998     

Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat

Genetic variation present in 64 durum wheat accessions was investigated by using three sources of microsatellite (SSR) markers: EST-derived SSRs (EST-SSRs) and two sources of SSRs isolated from total genomic DNA. Out of 245 SSR primer pairs screened, 22 EST-SSRs and 20 genomic-derived SSRs were polymorphic and used for genotyping. The EST-SSR primers produced high quality markers, but had the lowest level of polymorphism (25%) compared to the other two sources of genomic SSR markers (53%). The 42 SSR markers detected 189 polymorphic alleles with an average number of 4.5 alleles per locus. The coefficient of similarity ranged from 0.28 to 0.70 and the estimates of similarity varied when different sources of SSR markers were used to genotype the accessions. This study showed that EST-derived SSR markers developed in bread wheat are polymorphic in durum wheat when assaying loci of the A and B genomes. A minumum of ten EST-SSRs generated a very low probability of identity (0.36×10⁻¹²) indicating that these SSRs have a very high discriminatory power. EST-SSR markers directly sample variation in transcribed regions of the genome, which may enhance their value in marker-assisted selection, comparative genetic analysis and for exploiting wheat genetic resources by providing a more-direct estimate of functional diversity. Received: 19 December 2000 / Accepted: 17 April 2001     

Relationship between leaf stages and epistasis for resistance to Stagonospora nodorum in durum wheat

Ten varieties and eight generations (2F1, 2F2, 2B1 and 2B2) of durum wheat derived from two crosses were evaluated for resistance to natural infection by Stagonospora nodorum blotch (SNB) at the 2-3 and 6-7 leaf stages at two sites over two years. There were significant differences in the incidence of SNB between leaf stages in most of the wheat varieties, with resistance being most evident at the 6-7 leaf stage. Separate analyses of the mean values for each generation showed that the genetic mechanism of defense against the pathogen depended upon the leaf stage. At the 2-3 leaf stage, only additive and dominance effects were implicated in the control of SNB for the two crosses at the two sites and for the two replications. For the 6-7 leaf stage, inheritance was more complicated and an epistatic effect was involved. Narrow-sense heritability values (range: 0.63-0.67) were consistent between crosses and leaf stages. These findings indicate a lack of resistance to SNB at the 2-3 leaf stage whereas resistance was observed at the 6-7 leaf stage and involved the genetic mechanisms of plant defense such as epistasis.     

Bacteria associated with Stagonospora (Septoria) nodorum increase pathogenicity of the fungus

In studies with a laboratory isolate of the fungal pathogen Stagonospora ( Septoria ) nodorum three different isolates of bacteria were closely associated with the fungus. Bacteria were also closely associated with fresh isolates of S. nodorum obtained from artificially and naturally infected field material. Although a range of bacteria was isolated, only one type of bacterium was found to be associated with each isolate of S. nodorum . In co-inoculation studies with pycnidiospores of the fungus on detached leaves, some of the bacterial isolates significantly increased the pathogenicity of the fungus, particularly Xanthomonas maltophilia , Sphingobacterium multivorum , Enterobacter agglomerans and Erwinia amylovora . Evidence is presented indicating that one of the ways that the 'helper bacteria' may assist in the establishment of infections is by the production of lipases that were not detected in germinating fungal spores.     

Identification of molecular markers linked to the Yr15 stripe rust resistance gene of wheat originated in wild emmer wheat, Triticum dicoccoides

 The Yr15 gene of wheat confers resistance to the stripe rust pathogen Puccinia striiformis West., which is one of the most devastating diseases of wheat throughout the world. In the present study, molecular markers flanking the Yr15 gene of wheat have been identified using the near-isogenic-lines approach. RFLP screening of 76 probe-enzyme combinations revealed one polymorphic marker (Nor/TaqI) between the susceptible and the resistant lines. In addition, out of 340 RAPD primers tested, six produced polymorphic RAPD bands between the susceptible and the resistant lines. The genetic linkage of the polymorphic markers was tested on segregating F₂ population (123 plants) derived from crosses between stripe rust-susceptible Triticum durum wheat, cv D447, and a BC₃F₉ resistant line carrying Yr15 in a D447 background. A 2.8-kb fragment produced by the Nor RFLP probe and a 1420-bp PCR product generated by the RAPD primer OPB13 showed linkage, in coupling, with the Yr15 gene. Employing the standard maximum-likelihood technique it was found that the order OPB13 ₁₄₂₀ –Yr15–Nor1 on chromosome 1B appeared to be no less than 1000-times more probable than the closest alternative. The map distances between OPB13 ₁₄₂₀ –Yr15–Nor1 are 27.1 cM and 11.0 cM for the first and second intervals, respectively. The application of marker-assisted selection for the breeding of new wheat cultivars with the stripe rust resistance gene is discussed. Received: 27 February 1997/Accepted: 7 March 1997     

Global migration patterns in the fungal wheat pathogen Phaeosphaeria nodorum

The global migration patterns of the fungal wheat pathogen Phaeosphaeria nodorum were analysed using 12 microsatellite loci. Analysis of 693 isolates from nine populations indicated that the population structure of P. nodorum is characterized by high levels of genetic diversity and a low degree of subdivision between continents. To determine whether genetic similarity of populations was a result of recent divergence or extensive gene flow, the microsatellite data were analysed using an isolation-with-migration model. We found that the continental P. nodorum populations diverged recently, but that enough migration occurred to reduce population differentiation. The migration patterns of the pathogen indicate that immigrants originated mainly from populations in Europe, China and North America.     

A 1B-coded low-molecular-weight glutenin subunit associated with quality in durum wheats shows strong similarity to a subunit present in some bread wheat cultivars

Received: 25 May 1999 / Accepted: 22 June 1999     

Microsatellite markers linked to six Russian wheat aphid resistance genes in wheat

The Russian wheat aphid (RWA), Diuraphis noxia Mordvilko, is a serious economic pest of wheat and barley in North America, South America, and South Africa. Using aphid-resistant cultivars has proven to be a viable tactic for RWA management. Several dominant resistance genes have been identified in wheat, Triticum aestivum, including Dn1 in PI 137739, Dn2 in PI 262660, and at least three resistance genes (Dn5+) in PI 294994. The identification of RWA-resistant genes and the development of resistant cultivars may be accelerated through the use of molecular markers. DNA of wheat from near-isogenic lines and segregating F₂ populations was amplified with microsatellite primers via PCR. Results revealed that the locus for wheat microsatellite GWM111 (Xgwm111), located on wheat chromosome 7DS (short arm), is tightly linked to Dn1, Dn2 and Dn5, as well as Dnx in PI 220127. Segregation data indicate RWA resistance in wheat PI 220127 is also conferred by a single dominant resistance gene (Dnx). These results confirm that Dn1, Dn2 and Dn5 are tightly linked to each other, and provide new information about their location, being 7DS, near the centromere, instead of as previously reported on 7DL. Xgwm635 (near the distal end of 7DS) clearly marked the location of the previously suggested resistance gene in PI 294994, here designated as Dn8. Xgwm642 (located on 1DL) marked and identified another new gene Dn9, which is located in a defense gene-rich region of wheat chromosome 1DL. The locations of markers and the linked genes were confirmed by di-telosomic and nulli-tetrasomic analyses. Genetic linkage maps of the above RWA resistance genes and markers have been constructed for wheat chromosomes 1D and 7D. These markers will be useful in marker-assisted breeding for RWA-resistant wheat. Received: 17 May 2000 / Accepted: 13 June 2000     

Genetic architecture of resistance to Septoria tritici blotch in European wheat

Background

Septoria tritici blotch is an important leaf disease of European winter wheat. In our survey, we analyzed Septoria tritici blotch resistance in field trials with a large population of 1,055 elite hybrids and their 87 parental lines. Entries were fingerprinted with the 9 k SNP array. The accuracy of prediction of Septoria tritici blotch resistance achieved with different genome-wide mapping approaches was evaluated based on robust cross validation scenarios.

Results

Septoria tritici blotch disease severities were normally distributed, with genotypic variation being significantly (P < 0.01) larger than zero. The cross validation study revealed an absence of large effect QTL for additive and dominance effects. Application of genomic selection approaches particularly designed to tackle complex agronomic traits allowed to double the accuracy of prediction of Septoria tritici blotch resistance compared to calculation methods suited to detect QTL with large effects.

Conclusions

Our study revealed that Septoria tritici blotch resistance in European winter wheat is controlled by multiple loci with small effect size. This suggests that the currently achieved level of resistance in this collection is likely to be durable, as involvement of a high number of genes in a resistance trait reduces the risk of the resistance to be overcome by specific pathogen isolates or races.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-14-858) contains supplementary material, which is available to authorized users.     

Sources of resistance and susceptibility to Septoria tritici blotch of wheat

An association genetics analysis was conducted to investigate the genetics of resistance to Septoria tritici blotch, caused by the fungus Zymoseptoria tritici (alternatively Mycosphaerella graminicola), in cultivars and breeding lines of wheat (Triticum aestivum) used in the UK between 1860 and 2000. The population was tested with Diversity Array Technology (DArT) and simple‐sequence repeat (SSR or microsatellite) markers. The lines formed a single population with no evidence for subdivision, because there were several common ancestors of large parts of the pedigree. Quantitative trait loci (QTLs) controlling Septoria resistance were postulated on 11 chromosomes, but 38% of variation was not explained by the identified QTLs. Calculation of best linear unbiased predictions (BLUPs) identified lineages of spring and winter wheat carrying different alleles for resistance and susceptibility. Abundant variation in Septoria resistance may be exploited by crossing well‐adapted cultivars in different lineages to achieve transgressive segregation and thus breed for potentially durable quantitative resistance, whereas phenotypic selection for polygenic quantitative resistance should be effective in breeding cultivars with increased resistance. The most potent allele reducing susceptibility to Septoria, on chromosome arm 6AL, was associated with reduced leaf size. Genes which increase susceptibility to Septoria may have been introduced inadvertently into UK wheat breeding programmes from cultivars used to increase yield, rust resistance and eyespot resistance between the 1950s and 1980s. This indicates the need to consider trade‐offs in plant breeding when numerous traits are important and to be cautious about the use of non‐adapted germplasm.     

Identification of molecular markers associated with linoleic acid desaturation in Brassica napus

 Linolenic acid is a component of canola oil that is readily oxidized, which results in a reduced frying stability and shelf life of the oil. The reduction of linolenic acid in canola seed has therefore been an important breeding objective for many years. The inheritance of linolenic acid concentrations in seed oil is polygenic and is also strongly influenced by the environment. For these reasons, molecular markers are sought to assist in early and reliable selection of desired low linolenic acid genotypes in breeding programmes. Molecular markers associated with low linolenic acid loci were identified in a doubled-haploid population derived from a cross between the Brassica napus lines, ‘Apollo’ (low linolenic)×YN90-1016 (high linolenic) using RAPDs and bulked segregant analysis. A total of 16 markers were distributed over three linkage groups, which individually accounted for 32%, 14% and 5% of the phenotypic variation in linolenic acid content. The rapeseed fad3 gene was mapped near the locus controlling 14% of the variation. The mode of inheritance appeared to be additive, and a QTL analysis showed that collectively the three loci explained 51% of the phenotypic variation within this population. PCR fragments for low linolenic acid ‘Apollo’ alleles (3% linolenic acid) were identified at all three loci. Simultaneous selection for low linolenic acid ‘Apollo’ alleles at each locus resulted in a group of DH lines with 4.0% linolenic acid. The use of these makers in the breeding programme will enhance the breeding of low linolenic acid B. napus cultivars for production in Canada. Received: 23 September 1997 / Accepted: 21 October 1997     

Citrus phylogeny and genetic origin of important species as investigated by molecular markers

Citrus phylogeny was investigated using RAPD, SCAR and cpDNA markers. The genotypes analyzed included 36 accessions belonging to Citrus together with 1 accession from each of the related genera Poncirus, Fortunella, Microcitrus and Eremocitrus. Phylogenetic analysis with 262 RAPDs and 14 SCARs indicated that Fortunella is phylogenetically close to Citrus while the other three related genera are distant from Citrus and from each other. Within Citrus, the separation into two subgenera, Citrus and Papeda, designated by Swingle, was clearly observed except for C. celebica and C. indica. Almost all the accessions belonging to subgenus Citrus fell into three clusters, each including 1 genotype that was considered to be a true species. Different phylogenetic relationships were revealed with cpDNA data. Citrus genotypes were separated into subgenera Archicitrus and Metacitrus, as proposed by Tanaka, while the division of subgenera Citrus and Papeda disappeared. C. medica and C. indica were quite distant from other citrus as well from related genera. C. ichangensis appeared to be the ancestor of the mandarin cluster, including C. tachibana. Lemon and Palestine sweet lime were clustered into the Pummelo cluster led by C. latipes. C. aurantifolia was located in the Micrantha cluster. Furthermore, genetic origin was studied on 17 cultivated citrus genotypes by the same molecular markers, and a hybrid origin was hypothesized for all the tested genotypes. The assumptions are discussed with respect to previous studies; similar results were obtained for the origin of orange and grapefruit. Hybrids of citron and sour orange were assumed for lemon, Palestine sweet lime, bergamot and Volkamer lemon, while a citron × mandarin hybrid was assumed for Rangpur lime and Rough lemon. For Mexican lime our molecular data indicated C. micrantha to be the female parent and C. medica as the male one. Received: 5 October 1999 / Accepted: 3 November 1999     

Genetic analysis of durable resistance against leaf rust in durum wheat

The Italian durum wheat cultivar Creso possesses a high level of durable resistance to leaf rust based on both hypersensitive and non-hypersensitive components. In order to investigate the genetic basis of this resistance, a segregating population composed of 123 recombinant inbred lines (RILs) derived from the cross Creso × Pedroso, was evaluated for disease severity in adult plants under field conditions. Furthermore, the resistance of parents and RILs was evaluated by assessing macroscopically the latency period and microscopically the number and type of pathogen colonies formed following artificial inoculation with a specific isolate. This experiment was performed at controlled conditions at two developmental stages. Besides some minor QTLs, one major QTL explaining both reduction of disease severity in the field and increased latency period was found on the long arm of chromosome 7B, and closely associated PCR-based and DArT markers were identified. Daniela Marone and Ana I. Del Olmo contributed equally to the work.     

Identification of molecular markers linked to quantitative trait loci for soybean resistance to corn earworm

 One hundred and thirty nine restriction fragment length polymorphisms (RFLPs) were used to construct a soybean (Glycine max L. Merr.) genetic linkage map and to identify quantitative trait loci (QTLs) associated with resistance to corn earworm (Helicoverpa zea Boddie) in a population of 103 F₂-derived lines from a cross of ‘Cobb’ (susceptible) and PI229358 (resistant). The genetic linkage map consisted of 128 markers which converged onto 30 linkage groups covering approximately 1325 cM. There were 11 unlinked markers. The F₂-derived lines and the two parents were grown in the field under a plastic mesh cage near Athens, Ga., in 1995. The plants were artificially infested with corn earworm and evaluated for the amount of defoliation. Using interval-mapping analysis for linked markers and single-factor analysis of variance (ANOVA), markers were tested for an association with resistance. One major and two minor QTLs for resistance were identified in this population. The PI229358 allele contributed insect resistance at all three QTLs. The major QTL is linked to the RFLP marker A584 on linkage group (LG) ‘M’ of the USDA/Iowa State University public soybean genetic map. It accounts for 37% of the total variation for resistance in this cross. The minor QTLs are linked to the RFLP markers R249 (LG ‘H’) and Bng047 (LG ‘D1’). These markers explain 16% and 10% of variation, respectively. The heritability (h²) for resistance was estimated as 64% in this population. Received: 15 October 1997 / Accepted: 4 November 1997     

AFLP and pedigree-based genetic diversity estimates in modern cultivars of durum wheat [ Triticum turgidum L. subsp. durum (Desf.) Husn.

A substantial amount of between and within cultivar genetic variation was detected in all the 13 registered modern Canadian durum wheat (Triticum turgidum L. ssp. durum (Desf.) Husn.) cultivars based upon amplified restriction fragment polymorphism (AFLP). Of the approximately 950 detected AFLP markers, only 89 were polymorphic, with 41 between cultivars whereas the remaining 48 showed polymorphism within at least one cultivar. The ancestry of Canadian durum wheat cultivars was traced back to 125 cultivars, selections, and breeding lines including 17 landraces. Mean pair-wise genetic distance based on the kinship coefficient was 0.76. On the other hand, AFLP-based mean pair-wise genetic distance was 0.40. Even though there was a large difference between the means of the two diversity measures, a moderate positive correlation (r=0.457, p<0.002) was detected between the two distance matrices. Cluster analysis with the entire AFLP data divided all cultivars into three major groups reflecting their breeding origins. One group contained ’Pelissier’ alone, which was a selection from a landrace introduced into the US from Algeria. On the other hand such groupings among cultivars were not evident when KIN was used for genetic diversity measures instead. The level of genetic variation among individuals within a cultivar at the breeders’ seed level was estimated based on an inter-haplotypic distance matrix derived from the AFLP data. We found that the level of genetic variation within the most-developed cultivars is fairly substantial despite rigorous selection pressure aimed at cultivar purity in breeding programs. Comparison of AFLP and pedigree-based genetic diversity estimates in crop species such as durum wheat can provide important information for plant improvement. Received: 26 January 2001 / Accepted: 31 May 2001