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  • 1
    ISSN: 1432-2242
    Keywords: Key words Hordeum vulgare ; AFLP markers ; Genetic linkage map ; Recombinant inbred lines ; Locus specificity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  By using 25 primer combinations, 563 AFLP markers segregating in a recombinant inbred population (103 lines, F9) derived from L94/Vada were generated. The 38 AFLP markers in common to the existing AFLP/RFLP combined Proctor/Nudinka map, one STS marker, and four phenotypic markers with known map positions, were used to assign present AFLP linkage groups to barley chromosomes. The constructed high-density molecular map contains 561 AFLP markers, three morphological markers, one disease resistance gene and one STS marker, and covers a 1062-cM genetic distance, corresponding to an average of one marker per 1.9 cM. However, extremely uneven distributions of AFLP markers and strong clustering of markers around the centromere were identified in the present AFLP map. Around the centromeric region, 289 markers cover a genetic distance of 155 cM, corresponding to one marker per 0.5 cM; on the distal parts, 906 cM were covered by 277 markers, corresponding to one marker per 3.3 cM. Three gaps larger than 20 cM still exist on chromosomes 1, 3 and 5. A skeletal map with a uniform distribution of markers can be extracted from the high-density map, and can be applied to detect and map loci underlying quantitative traits. However, the application of this map is restricted to barley species since hardly any marker in common to a closely related Triticum species could be identified.
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  • 2
    ISSN: 1432-2242
    Keywords: Key words Tetrasomic inheritance ; Solanum tuberosum ; AFLP ; Bulked segregant analysis ; R2 resistance gene
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Due to the complexity of tetrasomic inheritance, mapping studies in potato (Solanum tuberosum L.) are generally conducted at the diploid level. In the present study we tested the feasibility of Bulked Segregant Analysis (BSA) using a tetraploid offspring for the identification of AFLP markers linked to the R2 allele, which confers race-specific resistance to Phytophthora infestans. Eleven bulk-specific AFLP markers, detected in fingerprints of 205 AFLP primer combinations, could be mapped in a linkage group encompassing the R2 locus. The efficiency of BSA at the tetraploid level, determined by the frequency of single-dose restriction fragments (SDRF), was much higher than expected on the basis of overall genetic dissimilarity between the parental clones. The fortuitous detection of AFLPs with linkage to the R2 allele is explained on the basis of specific genetic dissimilarity between cultivated potato and the chromosomal segment introgressed from S. demissum carrying the resistant R2 allele. AFLP markers common to those with linkage to R2 were visually recognized by their electrophoretic mobility in the AFLP fingerprint in a parental clone of a reference mapping population. Using these common AFLP markers we anchored the linkage group comprising the R2 allele to potato chromosome 4.
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  • 3
    ISSN: 1432-2242
    Keywords: Key words Partial resistance ; Leaf rust ; Barley ; QTL mapping ; Puccinia hordei ; Hordeum vulgare ; Latent period
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The partial resistance to leaf rust in barley is a quantitative resistance that is not based on hypersensitivity. To map the quantitative trait loci (QTLs) for partial resistance to leaf rust, we obtained 103 recombinant inbred lines (RILs) by single-seed descent from a cross between the susceptible parent L94 and the partially resistant parent Vada. These RILs were evaluated at the seedling and adult plant stages in the greenhouse for the latent period (LP) of the rust fungus, and in the field for the level of infection, measured as area under the disease progress curve (AUDPC). A dense genetic map based on 561 AFLP markers had been generated previously for this set of RILs. QTLs for partial resistance to leaf rust were mapped using the “Multiple Interval Mapping” method with the putative QTL markers as cofactors. Six QTLs for partial resistance were identified in this population. Three QTLs, Rphq1, Rphq2 and Rphq3, were effective at the seedling stage and contributed approximately 55% to the phenotypic variance. Five QTLs, Rph2, Rphq3, Rphq4, Rphq5, and/or Rphq6 contributed approximtely. 60% of the phenotypic variance and were effective at the adult plant stage. Therefore, only the QTLs Rphq2 and Rhpq3 were not plant-stage dependent. The identified QTLs showed mainly additive effects and only one significant interaction was detected, i.e. between Rphq1 and Rphq2. The map positions of these QTLs did not coincide with those of the race-specific resistance genes, suggesting that genes for partial resistance and genes for hypersensitive resistance represent entirely different gene families. Also, three QTLs for days to heading, of which two were also involved in plant height, were identified in the present recombinant inbred population. These QTLs had been mapped previously on the same positions in different populations. The perspectives of these results for breeding for durable resistance to leaf rust are discussed.
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  • 4
    ISSN: 1432-2242
    Keywords: Key words Marker-assisted selection ; Quantitative trait loci ; Arabidopsis ; Selection methods
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Parents were selected from a well-characterised Arabidopsis recombinant inbred line (RIL) population based on (1) their phenotype for flowering time or (2) marker and QTL information that had been assessed previously. The F2 offspring obtained from pairs of selected RILs was analysed for these traits, and the results obtained with these two methods of selection were compared. Selection based on marker and QTL information gave approximately the same result as selection based on phenotype. The relative high heritability of flowering time in Arabidopsis facilitated successful phenotypical selection. The difference in selection result that was anticipated to be in favour of the marker-assisted approach was therefore not observed.
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  • 5
    ISSN: 1432-2242
    Keywords: Key words Barley ; Puccinia hordei ; Partial resistance ; QTL mapping ; Isolate specificity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  By using a high-density AFLP marker linkage map, six QTLs for partial resistance to barley leaf rust (Puccinia hordei) isolate 1.2.1. have been identified in the RIL offspring of a cross between the partially resistant cultivar ’Vada’ and the susceptible line L94. Three QTLs were effective at the seedling stage, and five QTLs were effective at the adult plant stage. To study possible isolate specificity of the resistance, seedlings and adult plants of the 103 RILs from the cross L94×’Vada’ were also inoculated with another leaf rust isolate, isolate 24. In addition to the two QTLs that were effective against isolate 1.2.1. at the seedling stage, an additional QTL for seedling resistance to isolate 24 was identified on the long arm of chromosome 7. Of the eight detected QTLs effective at the adult plant stage, three were effective in both isolates and five were effective in only one of the two isolates. Only one QTL had a substantial effect at both the seedling and the adult plant stages. The expression of the other QTLs was developmental-stage specific. The isolate specificity of the QTLs supports the hypothesis of Parlevliet and Zadoks (1977) that partial resistance may be based on a minor-gene-for-minor-gene interaction.
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  • 6
    ISSN: 1432-2242
    Keywords: Key words Hordeum vulgare ; Amplified fragment length polymorphism (AFLP) ; Quantitative trait loci (QTLs) ; Yield ; Physiological traits ; Crop-growth model
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  An amplified fragment length polymorphism (AFLP) map covering 965 cM was constructed using 94 recombinant inbred lines of a cross between the spring barley varieties Prisma and Apex. This map was employed to identify quantitative trait loci (QTLs) controlling plant height, yield and yield-determining physiological characters using an approximate multiple-QTL model, the MQM method. The seven physiological traits were parameters used in a process-based crop-growth model that predicts barley biomass production as affected by daily temperature and radiation. The traits were measured in experiments conducted over 2 years. Except for the relative growth rate of leaf area, all traits examined had at least one QTL in each year. QTLs and their effects were found to vary with developmental stages for one trait, the fraction of shoot biomass partitioned to leaves, that was measured at several stages. Most of the traits were associated, though to different extents, with the denso dwarfing gene (the height-reducing allele in Prisma) located on the long arm of chromosome 3. Some of the QTLs were mapped to similar positions in both years. The results in relation to effects of the dwarfing gene, the physiological basis for QTL×environment interaction, and the relative importance of the parameter traits with respect to yield, are discussed.
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  • 7
    ISSN: 1432-2242
    Keywords: Arabidopsis thaliana ; Flowering time ; Genotype-by-environment interaction ; Mapping ; Quantitative trait loci
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The interval mapping method is widely used for the genetic mapping of quantitative trait loci (QTLs), though true resolution of quantitative variation into QTLs is hampered with this method. Separation of QTLs is troublesome, because single-QTL is models are fitted. Further, genotype-by-environment interaction, which is of great importance in many quantitative traits, can only be approached by separately analyzing the data collected in multiple environments. Here, we demonstrate for the first time a novel analytic approach (MQM mapping) that accommodates both the mapping of multiple QTLs and genotype-by-environment interaction. MQM mapping is compared to interval mapping in the mapping of QTLs for flowering time in Arabidopsis thaliana under various photoperiod and vernalization conditions.
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  • 8
    ISSN: 1432-2242
    Keywords: Key words Bootstrap analysis ; Coefficient of co-ancestry ; Cultivar identification ; Genetic similarity ; Hordeum vulgare
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Thirty one barley lines were used to investigate the agreement between three relationship measures: genetic similarities based on 681 AFLP-markers, coefficients of co-ancestry based on pedigree data, and generalised distance based on 25 morpological characters (morphological distance). Bootstrap analysis was used to estimate the accuracy of the correlation estimates. AFLP-based genetic similarities showed a poor-to-moderate correlation with the coefficients of co-ancestry within the core set of 25 European two-row spring barleys. Morphological distance was not significantly correlated with either genetic similarity or the coefficient of co-ancestry. The precision of all correlation-coefficient estimates, however, was low. The inclusion of two European winter barleys, two North American two-row spring barleys, and two North American six-row spring barleys in the AFLP-analysis resulted in a much stronger correlation between genetic similarity and the coefficient of co-ancestry. This suggests good opportunities for the use of AFLP-markers to assess genetic diversity by distinguishing between the major ecotypes of barley. Additionally, each of the eight primer combinations used in the AFLP-analysis was able to identify all 31 lines uniquely, showing the usefulness of AFLPs for cultivar identification. Because of the inaccuracy of the investigated relationship measures, resulting in low values of the correlation-coefficient estimates, prediction of the breeding behaviour of parent combinations may be improved by the use of a combination of relationship measures, thus decreasing the effect of their individual independent errors.
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  • 9
    ISSN: 1432-2242
    Keywords: Key words Zea mays L. ; AFLP® ; Methylation AFLP® ; Genetic map ; DNA methylation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  This study demonstrates the relative ease of generating high-density linkage maps using the AFLP® technology. Two high-density AFLP linkage maps of Zea mays L. were generated based on: (1) a B73 × Mo17 recombinant inbred population and (2) a D32 × D145 immortalized F2 population. Although AFLP technology is in essence a mono-allelic marker system, markers can be scored quantitatively and used to deduce zygosity. AFLP markers were generated using the enzyme combinations EcoRI/MseI and PstI/MseI. A total of 1539 and 1355 AFLP markers have been mapped in the two populations, respectively. Among the mapped PstI/MseIAFLP markers we have included fragments bounded by a methylated PstI site (mAFLP markers). Mapping these mAFLP markers shows that the presence of C-methylation segregates in perfect accordance with the primary target sequence, leading to Mendelian inheritance. Simultaneous mapping of PstI/MseIAFLP and PstI/MseI mAFLP markers allowed us to identify a number of epi-alleles, showing allelic variation in the CpNpG methylation only. However, their frequency in maize is low. Map comparison shows that, despite some rearrangements, most of the AFLP markers that are common in both populations, map at similar positions. This would indicate that AFLP markers are predominantly single-locus markers. Changes in map order occur mainly in marker-dense regions. These marker-dense regions, representing clusters of mainly EcoRI/MseI AFLP and PstI/MseI mAFLP markers, co- localize well with the putative centromeric regions of the maize chromosomes. In contrast, PstI/MseImarkers are more uniformly distributed over the genome.
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  • 10
    ISSN: 1439-0523
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Genes contributing to the quantitative variation of a complex crop trait can be numerous. However, using existing approaches, the number of quantitative trait loci (QTL) detected for a trait is limited. Therefore, rather than looking for QTL for a complex trait itself, determining QTL for underlying component traits might give more information. In this study the potential of component analysis in QTL mapping of complex traits was examined using grain yield in spring barley as an example. Grain yield was divided into three components: number of spikes/m2, number of kernels/spike, and 1000-kernel weight. These traits were measured for individuals of a recombinant inbred-line population in field trials conducted over 2 years. By the use of an approximate multiple QTL model, one to eight QTL were detected for each trait in a year. Some QTL were mapped to similar positions in both years. Almost all QTL for yield were found at the position of or in close proximity to QTL for its component traits. A number of QTL for component traits were not detected when yield itself was subjected to QTL analysis. However, relative to the QTL for yield itself, all component-trait QTL did not explain the variation in yield better. The results in relation to the potential of using component analysis in studying complex crop traits are discussed.
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