Identification and mapping of genes for partial resistance to Puccinia hordei Otth in barley

In plant-pathogen systems, qualitative resistance with hypersensitivity has been extensively studied. This resistance can be explained with the gene-for-gene model which has been confirmed at the molecular level. This hypersensitive resistance is widely used in plant breeding programmes. However, this resistance is often not durable because the resistance genes can easily be overcome by new variants of the pathogen. Alternatively, quantitative resistance is widely considered to be more durable. However, the polygenic nature of the resistance in the host and the large experimental error in disease tests hamper its application in plant breeding programmes. These same drawbacks also hampered the study of the genetics and of the mechanism of quantitative resistance.Recently, various types of DNA markers have been developed that open a new gateway towards further study of quantitative traits, including quantitative resistance. In this thesis, barley ( Hordeum vulgare L.)-barley leaf rust ( Pucciniahordei Otth) is chosen as a model system to study the quantitative resistance. This plant-pathosystem has been extensively studied by Parlevliet and his colleagues at the Department of Plant Breeding of the Wageningen Agricultural University. Several recombinant inbred populations had been developed from crosses between partially resistant cultivars or lines, e.g., 'Vada' and 116-5, and an extremely susceptible line, viz., L94. Two populations, L94 x 'Vada' and L94 x 116-5, were used to generate molecular linkage maps and, consecutively, genes for partial resistance in these populations were identified and mapped to the barley genome.In chapter 2, a compilation of publicly available RFLP marker linkage maps of barley is presented. The data from four maps were used to produce an integrated map. The overall order of markers on the individual maps was similar, enabling the construction of this integrated map. The integrated map contained 880 markers, covering 1060 cM. Marker clustering was observed in the centromeric regions of the seven chromosomes.The AFLP fingerprint technique was used to generate molecular markers in barley as described in chapter 3. With 24 primer combinations a total of 2188 different amplification products were generated from 16 selected barley lines. The size of these amplification products ranged from 80 to 510 bp. Of these barley lines, L94 versus 'Vada' showed the highest polymorphism rate (29%), and 'Proctor' versus 'Nudinka' showed the lowest (12%). The efficiency of primer combinations for identifying genetic markers was similar for any set of barley lines. By using 24 AFLP primer combinations, more than 100 markers could be generated that segregated in at least two of six crossing combinations, and therefore could be used as common markers to compare linkage maps.A high-density AFLP marker linkage map which was constructed using a recombinant inbred population (103 RILs, F 9 ) derived from a cross between L94 and 'Vada' is presented in chapter 4. The constructed map contained 561 AFLP markers, three morphological markers, one disease resistance gene and one STS marker, covering a genetic distance of 1062 cM. Uneven distributions of AFLP markers over the chromosomes and strong clustering of markers around the centromeres were found. A skeletal map with a uniform distribution of markers was extracted from the high-density map, and was applied to detect and map loci underlying partial resistance.The same set of 103 RILs was evaluated in the seedling and in the adult plant stages in the greenhouse and in the field for resistance to leaf rust isolates 1.2.1 and 24, and quantitative trait loci (QTLs) for partial resistance to these two isolates were identified and mapped on the L94 x 'Vada' map (chapters 5 and 6, respectively). Six QTLs were identified for partial resistance to isolate 1.2.1. Three QTLs were effective in the seedling stage and contributed approximately 55% to the phenotypic variance. Five QTLs were effective in the adult plant stage and contributed approximately 60% to the phenotypic variance. In addition to the three QTLs that were also effective against isolate 1.2.1. in the seedling stage, an additional QTL for resistance of seedlings to isolate 24 was identified. These four QTLs for resistance to isolate 24 jointly explained more than 45% of total phenotypic variance. Also, six QTLs collectively explained approximately 59% of the phenotypic variance of resistance to isolate 24 in the adult plant stage. Of the eight QTLs detected to be effective in the adult plant stage, three were effective to both isolates and five were effective to only one of the two isolates. The isolate specificity of the QTLs supports the hypothesis of Parlevliet and Zadoks that a minor gene-for-minor gene interaction can occur in partial resistance. Of the ten identified QTLs for resistance to the two isolates in this population, QTLs Rphq2 and Rhpq3 were the only two effective in both the seedling and the adult plant stages. The remaining QTLs were effective in either of the two developmental stages.Chapter 7 present results of mapping QTLs for partial resistance to leaf rust isolate 1.2.1 on another AFLP linkage map which was constructed by using 117 RILs (F 8 ) derived from a cross between L94 and 116-5. Three QTLs were effective in the seedling stage, jointly contributing 42% to the total phenotypic variance. Also, three QTLs were effective in the adult plant stage, collectively explaining 35% of the phenotypic variance. Rphq3 , with a major-effect, was the only QTL being effective in both developmental stages. This QTL was also found to be effective in the L94 x 'Vada' population. The remaining QTLs in the L94 x 116-5 population were mapped to different positions on the linkage map than those found in the L94 x 'Vada' population. This suggests that loci for partial resistance to leaf rust are scattered all over the barley genome. Consequently, a strategy to accumulate many resistance genes in a single cultivar is feasible, which would result in a very high level of partial resistance.Studies in chapters 5, 6 and 7 showed that map positions of QTLs for partial resistance do not coincide with those of the race-specific resistance genes ( Rph genes), supporting the theory that genes for partial resistance and genes for hypersensitive resistance are entirely different gene families.