Monika Messmer

Identification of molecular markers linked to the Agropyron elongatum-derived leaf rust resistance gene Lr24 in wheat

The objective of this study was to identify molecular markers linked to the wheat leaf rust resistance gene Lr24 derived from Agropyron elongatum (3DL/3Ag translocation). Two near isogenic lines (NILs), ‘Arina’ and Lr24/7* “Arina”, were screened for polymorphism at the DNA level with 115 RFLP probes. Twenty-one of these probes map to the homoeologous group 3. In addition, 360 RAPD primers were tested on the NILs. Six RFLP probes showed polymorphism between the NILs, and 11 RAPD primers detected one additional band in the resistant NIL. The genetic linkage of the polymorphic markers with Lr24 was tested on a segregating F2 population (150 plants) derived from a cross between the leaf rust resistant Lr24/7* “Arina” and the susceptible spelt (Triticum spelta) variety ‘Oberkulmer’. All 6 RFLP markers were completely linked to Lr24: one was inherited as a codominant marker (PSR1205), one was in coupling phase (PSR1203) and 4 were in repulsion phase (PSR388, PSR904, PSR931, PSR1067) with Lr24. The localization of these probes on chromosome 3D was confirmed by nulli-tetrasomic analysis. Distorted genotypic segregation was found for the Codominant RFLP marker PSR1205. This distortion can be explained by the occurrence of hemizygous plants. One of the 11 RAPD markers (OPJ-09) also showed complete linkage to theLr24 resistance gene. The polymorphic RAPD fragment was cloned and sequenced. Specific primers were synthesized, and they produced an amplification product only in the resistant plants. This specific marker allows a reliable and rapid screening of a large number of genotypes in practical breeding. Analysis of 6 additional lines containing Lr24 revealed that 3 lines have a smaller chromosomal segment of A. elongatum than lines derived from ‘Agent’, a commonly used gene donor for the Lr24 resistance gene.

Genetic analysis of durable leaf rust resistance in winter wheat

Abstract Quantitative resistance that delays the epidemic development of leaf rust in wheat is an important source for durable resistance breeding. The Swiss winter wheat variety ’Forno’ shows a high level of quantitative resistance against leaf rust. This resistance has been effective for more than 10 years and can therefore be considered to be durable. In order to map quantitative trait loci (QTL) for durable leaf rust resistance we analysed 204 F5 recombinant inbred lines (RILs) of the cross between the winter wheat ’Forno’ and the winter spelt ’Oberkulmer’ for their level of leaf rust resistance (LR) and leaf tip necrosis (LTN) in four different environments. Both traits showed a continuous distribution and were significantly correlated (r=−0.5). Across environments we detected 8 QTL for leaf rust resistance (6 inherited from ’Forno’) and 10 QTL for the quantitative expression of LTN (6 inherited from ’Forno’). Of the 6 QTL responsible for the durable leaf rust resistance of ’Forno’, 1 major QTL coincided with a thaumatin locus on 7BL explaining 35% of the phenotypic variance. Four QTL for LR coincided with QTL for LTN. At these loci the alleles of ’Forno’ increased the level of resistance as well as the extent of LTN, indicating pleiotropy.

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

Abstract 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.

Genetic diversity in European wheat and spelt breeding material based on RFLP data

Fifty-two winter wheat (Triticum aestivum L.), nine spring wheat, and 20 spelt (Triticum spelta L.) lines representing part of the European breeding germplasm, were assayed for RFLPs (restriction fragment length polymorphisms) with 56 wheat DNA clones and two barley cDNA clones. Objectives of this study were to (1) determine the level of variation for RFLPs in the wheat and spelt breeding lines, (2) characterize the genetic diversity within the European winter wheat germplasm, and (3) evaluate the usefulness of RFLP markers for pedigree analysis and the grouping of wheat and spelt lines of various origins. Seventy-three of the 166 RFLP loci detected with 58 probes and one restriction enzyme were polymorphic for the 81 lines. The percentage of polymorphic loci was greatest for the B genome (58%) and smallest for the D genome (21%). Among the 81 lines, 271 different RFLP bands were detected. RFLP band frequencies of the winter wheat lines differed considerably (≥0.5) from those of the spring wheat lines at five loci, and from those of the spelt lines at 17 loci. Eight cultivars that had a major impact as progenitors on the development of improved winter wheat cultivars accounted for 93% of the observed RFLP bands in winter wheat. Genetic distance (GD) estimates between two lines ranged between 0.01 and 0.21. Mean GD estimates within winter wheat (0.083), within spring wheat (0.108) and within spelt (0.096) were smaller than between spring and winter wheat (0.114), and greatest between winter wheat and spelt (0.132) and spring wheat and spelt (0.148). Principal coordinate analysis performed on GD estimates revealed a clear separation of wheat and spelt germplasm. Novel spelt lines with various proportions of wheat germplasm were positioned between wheat and traditional spelt lines. The spring wheat lines formed a distinct group at the periphery of the distribution of the winter wheat lines. Subgroupings of the winter wheat lines according to the cluster analysis were in good agreement with their origin, and lines with common ancestors were grouped together.

Genetic and physical characterization of theLR1 leaf rust resistance locus in wheat (Triticum aestivum L.)

The objective of this study was to characterize the leaf rust resistance locusLr1 in wheat. Restriction fragment length polymorphism (RELP) analysis was performed on the resistant lineLr1/6*Thatcher and the susceptible varieties Thatcher and Frisal, as well as on the segregating F2 populations. Seventeen out of 37 RFLP probes mapping to group 5 chromosomes showed polymorphism betweenLr1/6*Thatcher and Frisal, whereas 11 probes were polymorphic between the near-isogenic lines (NILs)Lr1/6*Thatcher and Thatcher. Three of these probes were linked to the resistance gene in the segregating F2 populations. One probe (pTAG621) showed very tight linkage toLr1 and mapped to a single-copy region on chromosome 5D. The map location of pTAG621 at the end of the long arm of chromosome 5D was confirmed by the absence of the band in the nulli-tetrasomic line N5DT5B of Chinese Spring and a set of deletion lines of Chinese Spring lacking the distal part of 5DL. Twenty-seven breeding lines containing theLr1 resistance gene in different genetic backgrounds showed the same band asLr1/6*Thatcher when hybridized with pTAG621. The RFLP marker was converted to a sequence-tagged-site marker using polymerase chain reaction (PCR) amplification. Sequencing of the specific fragment amplified from both NILs revealed point mutations as well as small insertion/deletion events. These were used to design primers that allowed amplification of a specific product only from the resistant lineLr1/6*Thatcher. This STS, specific for theLr1 resistance gene, will allow efficient selection for the disease resistance gene in wheat breeding programmes. In addition, the identification of a D-genome-specific probe tightly linked toLr1 should ultimately provide the basis for positional cloning of the gene.

Genetic linkage map of a wheat × spelt cross

Abstract We constructed a genetic map of a cross between the Swiss winter wheat (Triticum aestivum L.) variety Forno and the Swiss winter spelt (Triticum spelta L.) variety Oberkulmer. For the linkage analysis,176 polymorphic RFLP probes and nine microsatellites were tested on 204 F5 recombinant inbred lines (RILs) of Forno×Oberkulmer revealing 242 segregating marker loci. Thirty five percent of these loci showed significant (P>0.05) deviation from a 1 : 1 segregation, and the percentage of Forno alleles ranged from 21% to 83% for individual marker loci. Linkage analysis was performed with the program MAPMAKER using the Haldane mapping function. Using a LOD threshold of 10, we obtained 37 linkage groups. After finding the best order of marker loci within linkage groups by multi-point analysis we assembled the linkage groups into 23 larger units by lowering the LOD threshold. All except one of the 23 new linkage groups could be assigned to physical chromosomes or chromosome arms according to hybridisation patterns of nulli-tetrasomic lines of Chinese Spring and published wheat maps. This resulted in a genetic map comprising 230 marker loci and spanning 2469 cM. Since the analysed population is segregating for a wide range of agronomically important traits, this genetic map is an ideal basis for the identification of quantitative trait loci (QTLs) for these traits.

Genetics of Disease Resistance

Disease resistant plants are one of the prerequisites for sustainable agriculture. To understand and rationally use the naturally occurring disease resistance, its genetic basis has been investigated in great detail. These studies showed that there are two different genetic mechanisms for disease resistance: monogenic resistance is based on single genes whereas quantitative resistance depends on two or more genes. In most cases, single resistance genes confer complete resistance but are only active against certain races of the pathogen, i.e. they show a genetic interaction with genes from the pathogen. This resistance is based on an active recognition event between the product of the plant resistance gene and the product of the avirulence gene of the pathogen. Resistance genes are clustered at some loci in the genome or exist as different alleles conferring resistance towards specific pathogen races. Quantitative resistance shows no obvious genetic interaction with the pathogen and slows down the disease development by increasing latency period and other parameters related to the epidemic. Resistance breeding in crop plants depends on both types of resistance. Monogenic resistances are easy to work with but are frequently not durable. Consequently, quantitative resistance is preferred. The application of molecular markers has allowed the genetics of quantitative resistance to be determined and quantitative trait loci involved in resistance to be identified. Molecular markers have also contributed to improved breeding strategies for monogenic resistance genes in order to combine them in the “gene pyramiding” strategy for a more durable resistance. Finally, molecular markers have allowed the isolation of the first disease resistance genes. The cloning of such genes from crop plants and their wild relatives will open new possibilities for their sustainable use in breeding.

Tagging and Validation of a Major Quantitative Trait Locus for Leaf Rust Resistance and Leaf Tip Necrosis in Winter Wheat Cultivar Forno

ABSTRACT A major leaf rust (Puccinia triticina) resistance quantitative trait locus (QTL) (QLrP.sfr-7DS) previously has been described on chromosome 7DS in the winter wheat (Triticum aestivum) cv. Forno. It was detected in a population of single-seed descent (SSD) lines derived from the cross Arina x Forno. QLrP.sfr-7DS conferred a durable and slow-rusting resistance phenotype, co-segregated with a QTL for leaf tip necrosis (LTN) and was mapped close to Xgwm295 at a very similar location as the adult plant leaf rust resistance gene Lr34 found in some spring wheat lines. Here, we describe the validation of this QTL by mapping it to the same chromosomal region close to Xgwm295 on chromosome 7DS in a population of SSD lines from the winter wheat x spelt (T. spelta) cross Forno x Oberkulmer. In both populations, the log of the likelihood ratio curves for leaf rust resistance and LTN peaked at identical or very similar locations, indicating that both traits are due to the same gene. We have improved the genetic map in the target region of QLrP.sfr-7DS using microsatellite and expressed sequence tag (EST) markers. Two EST loci (Xsfr.BF473324 and Xsfr.BE493812) define a genetic interval of 7.6 centimorgans containing QLrP.sfr-7DS, a considerably more precise genetic location for this QTL than previously described both in spring and winter wheat. The identified genetic interval is physically located in the distal 39% of chromosome 7DS. Single-marker analysis identified Xsfr.BF473324 and Xgwm1220 as the most informative loci for QLrP.sfr-7DS and QLtn.sfr-7DS. In the rice genome, the two ESTs flanking the QLrP.sfr-7DS/QLtn.sfr-7DS chromosomal segment in wheat are conserved on chromosome 6S in a region colinear with wheat chromosome 7DS. There, they define a physical region of three rice bacterial artificial chromosomes spanning approximately 300 kb.

Nutrient use efficiency and arbuscular mycorrhizal root colonisation of winter wheat cultivars in different farming systems of the DOK long-term trial.

BACKGROUND For organic farming, cultivars are required with high nutrient use efficiency under nutrient limited conditions. Arbuscular mycorrhizal fungi (AMF) are known to contribute to nutrient uptake under low input conditions. We compared nutrient use efficiency (NUE) of old and modern organically and conventionally bred cultivars in organic and conventional systems and assessed AMF-root colonisation (AMF-RC) in relation to nutrient concentrations. RESULTS Cultivars and systems had a statistically significant effect on nitrogen (N) and phosphorus (P) concentrations and NUE parameters, whereas no genotype x environment interactions appeared. In contrast to N and P uptake, the NUE parameters were higher under organic than under conventional conditions. NUE for N increased with the year of release of cultivars. In the organic systems, the organically bred cultivars could not outperform the conventionally bred cultivars in grain yield and NUE parameters. AMF-RC was higher in the organic than in the conventional system, but did not differ among cultivars. CONCLUSION Cultivars achieving high NUE in the organic systems were found among modern cultivars, irrespective of the breeding programme. Nutrient conditions during the breeding programme did not affect AMF-RC. No clear evidence was found that AMF symbiosis contributed more to nutrient concentrations under low input than under high input conditions.

Yield and Economic Performance of Organic and Conventional Cotton-Based Farming Systems – Results from a Field Trial in India

The debate on the relative benefits of conventional and organic farming systems has in recent time gained significant interest. So far, global agricultural development has focused on increased productivity rather than on a holistic natural resource management for food security. Thus, developing more sustainable farming practices on a large scale is of utmost importance. However, information concerning the performance of farming systems under organic and conventional management in tropical and subtropical regions is scarce. This study presents agronomic and economic data from the conversion phase (2007–2010) of a farming systems comparison trial on a Vertisol soil in Madhya Pradesh, central India. A cotton-soybean-wheat crop rotation under biodynamic, organic and conventional (with and without Bt cotton) management was investigated. We observed a significant yield gap between organic and conventional farming systems in the 1st crop cycle (cycle 1: 2007–2008) for cotton (−29%) and wheat (−27%), whereas in the 2nd crop cycle (cycle 2: 2009–2010) cotton and wheat yields were similar in all farming systems due to lower yields in the conventional systems. In contrast, organic soybean (a nitrogen fixing leguminous plant) yields were marginally lower than conventional yields (−1% in cycle 1, −11% in cycle 2). Averaged across all crops, conventional farming systems achieved significantly higher gross margins in cycle 1 (+29%), whereas in cycle 2 gross margins in organic farming systems were significantly higher (+25%) due to lower variable production costs but similar yields. Soybean gross margin was significantly higher in the organic system (+11%) across the four harvest years compared to the conventional systems. Our results suggest that organic soybean production is a viable option for smallholder farmers under the prevailing semi-arid conditions in India. Future research needs to elucidate the long-term productivity and profitability, particularly of cotton and wheat, and the ecological impact of the different farming systems.