Browsing by Subject "Mapping"

Now showing 1 - 3 of 3

Development and fine mapping of markers closely linked to the SCMV resistance loci Scmv1 and Scmv2 in European maize (Zea mays L.)
(2002) Dußle, Christina M.; Melchinger, Albrecht E.
Sugarcane mosaic virus (SCMV) is an important disease in European maize cultivars (Zea mays L.). Because of its non-persistent transmission by aphid vectors, it is not possible to control SCMV directly. Therefore, cultivation of resistant maize varieties is an efficient way to control SCMV infections. The overall objectives of this study were the genetic analysis of SCMV resistance in cross F7 x FAP1360A and the identification of closely linked markers to the SCMV resistance genes Scmv1 on chromosome 6 and Scmv2 on chromosome 3 for map-based cloning and marker-assisted selection (MAS). The technical objectives were to (1) identify in particular the location of Scmv1 and Scmv2 on chromosomes 3 and 6 in cross F7 x FAP1360A, (2) estimate the gene action of the alleles present at these loci, (3) enrich the SCMV resistance regions surrounding Scmv1 and Scmv2 with amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers by applying a modified targeted bulked segregant analysis, tBSA, (4) convert AFLP markers into codominant, simple PCR-based markers as a tool for MAS and map-based cloning of Scmv1 and Scmv2 and, (5) assess resistance gene analogues (RGAs) as potential candidate genes for Scmv1 and Scmv2. Quantitative trait loci (QTL) mapping SSR markers revealed the presence of two QTL on chromosome 6 (Scmv1a and Scmv1b) and one QTL on chromosome 3 (Scmv2). tBSA identified 24 AFLP and 25 SSR markers adjacent to either Scmv1 or Scmv2. AFLP marker E35M62-1, closely linked to Scmv1 on chromosome 6, was successfully converted into an indel marker. For chromosome 3, AFLP marker E33M61-2 was converted into a CAPS marker. Both converted AFLP markers mapped to the same chromosome region as their original AFLP markers. Development of CAPS of the RGAs and mapping in relation to SCMV resistance genes Scmv1 and Scmv2 identified pic19 and pic13 as potential candidates for these resistance genes. In this study, useful markers were developed for applications in MAS. Because inheritance of SCMV resistance is strongly affected by the environment, MAS enables the selection of resistant individuals independently of field experiments. Furthermore, MAS can assist breeders to identify resistant individuals before flowering and to pyramid resistance genes in elite inbred lines. Another benefit of these closely linked markers is their application for map-based cloning. Final evidence, whether there are one or more genes clustered on chromosomes 3 and 6, conferring resistance against SCMV, can only be solved after cloning these genes.
Entwicklung, Charakterisierung und Kartierung von Mikrosatellitenmarkern bei der Zuckerrübe (Beta vulgaris L.)
(2001) Dörnte, Jost; Geiger, Hartwig H.
Simple sequence repeats (SSRs) or microsatellites were isolated from a sugarbeet (Beta vulgaris L.) genomic phage library. The size-fractionated library was screened for the occurrence of the motifes (GA)n, (GT)n, (TGA)n, (AGA)n and (CCG)n. The motifes (GA)n and (GT)n were found to occur most frequently in the sugarbeet genome (every 225 kb). In contrast, the trimer motifes were half as frequent (every 527 kb). A total of 217 microsatellite sequences were found in the sequenced clones. Most of the repeats were imperfect and/or compound. Sequence comparison revealed that 23% of the clones wich containing the (GT)n motif are variants of a previously described satellite DNA (SCHMIDT et al. 1991). Of 102 primer pairs tested on sugarbeet DNA, 71 gave a single product in the expected size. On 23 sugarbeet samples 64 of the 71 SSR-markers reveald length polymorphisms. The number of detected alleles per marker ranged from 2 to 13 (average 4,9) and the PIC-values ranged from 0,17 to 0,86 (average 0,58). A cluster analysis of the 23 samples confirms the pedigree data. The developed SSR markers were compared with RFLP and AFLP markers. Therefore nine sugarbeet lines, each with five single plants per line, were analysed. The SSR analyse shows the lowest similarity between the nine lines. The similarity inside the lines revealed no differences between the marker assays. Thirtythree SSR markers were genetically mapped into the RFLP framework maps of 2 F2-populations. The markers are randomly distributed over eight linkage groups of sugar beet.
Gene mining in doubled haploid lines from European maize landraces with association mapping
(2014) Strigens, Alexander Carl Georg; Melchinger, Albrecht E.
Since the introduction of maize into Europe, open-pollinated varieties of flint maize were cultivated across the continent. Natural selection promoted adaptation to the climatic conditions prevailing in the different regions. With the advent of hybrid breeding in Europe during the 1950’s, some of the genes responsible for the specific adaptations of the landraces to abiotic and biotic stress were captured in the first developed inbred lines, but most of their genetic diversity is still untapped. Development of inbred lines out of this material by recurrent selfing is very tedious due to strong inbreeding depression. In contrast, the doubled-haploid (DH) technology allows producing fully homozygous lines out of landraces in only one step. This allows their precise characterization in replicated trials and identification of new genes by genome wide association (GWA) mapping. In this study we genotyped a set of 132 DH lines derived from European Flint landraces and 364 elite European flint (EU-F), European dent (EU-D) and North-American dent (NA-D) inbred lines with 56,110 single nucleotide polymorphism (SNP) markers. The lines were evaluated in field trials for morphologic and agronomic traits and GWA mapping was performed to identify underlying quantitative trait loci (QTL). In particular, our objectives were to (1) develop a robust method for quantifying early growth with a non-destructive remote-sensing platform, (2) evaluate the importance of early growth performance of inbred lines with regard to their testcross performance, (3) determine the potential of GWA mapping to identify genes underlying early growth and cold tolerance related traits, (4) evaluate the phenotypic and genotypic diversity recovered in the DH lines derived from the landraces, (5) estimate the effect of the DH method on the recovered genetic diversity, (6) identify new genes by GWA mapping in the DH lines derived from landraces, and (8) discuss the potential of DH lines derived from landraces to improve the genetic diversity and performance of elite maize germplasm. A phenotyping platform using spectral reflectance and light curtains was used to perform repeated measurements of biomass and estimate relative growth rates (RGR) of the DH and inbred lines, as well as of two testcrosses of 300 dent inbred lines. The DH lines derived from the landraces Schindelmeiser and Gelber Badischer had the highest RGR followed by EU-F lines, DH lines derived from Bugard, EU-D lines and, finally, NA-D lines. For inbred lines, whole plant dry matter yield (DMY) was positively correlated with RGR (r = 0.49), whereas this relation was weaker in the testcrosses (r = 0.29). RGR of the inbred lines correlated with RGR of their testcrosses (r = 0.42), but it had no influence on testcross DMY. A set of 375 EU-F, EU-D and NA-D lines were further evaluated in growth chambers under chilling (16/13°C) and optimal (27/25°C) temperatures. Photosynthetic and early growth performance were estimated for each treatment and an adaptation index (AI) built as the chilling to optimal performance ratio. Nineteen QTL were identified by GWA mapping for trait performance and AI. Candidate genes involved in ethylene signaling, brassinolide, and lignin biosynthesis were found in their vicinity. Several QTL for photosynthetic performance co-located with previously reported QTL and the QTL identified for shoot dry wieght under optimal conditions co-located with a QTL for RGR. Comparison of the DH lines derived from landraces with the EU-F lines showed that genotypic variances in single DH populations were greater than in the EU-F breeding population. A high average genetic distance among the DH lines derived from the same landrace as well as a rapid decay of linkage disequilibrium suggests a high effective population size of the landraces. Because no systematic phenotypic differences were observed between the landraces and synthetic landraces obtained by intermating the corresponding DH lines, the expected purge of lethal recessive alleles during the DH production did neither improve grain yield performance nor affect the recovered genetic diversity. Performing GWA in the DH lines derived from landraces as well as the EU-F, and EU-D lines allowed the identification of 49 QTL for 27 traits. A larger set of DH lines derived from more landraces might solve problems arising from population structure and allow a much higher power for the detection of new alleles. In conclusion, the introgression of DH lines derived from landraces into the elite breeding material would strongly broaden its genetic base. However, grain yield performance was 22% higher in EU-F lines than in the DH lines derived from landraces. Selection of the best DH lines would allow partially bridging this yield gap and marker-assisted selection may allow introgression of positive QTL without introducing negative features by linkage drag.