Institut für Pflanzenzüchtung, Saatgutforschung und Populationsgenetik

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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.
Identification of essentially derived varieties in maize (Zea mays L.) using molecular markers, morphological traits, and heterosis
(2004) Heckenberger, Martin; Melchinger, Albrecht E.
The ‘breeder’s exemption’ as fixed in the UPOV convention on plant variety protec-tion allows the use of protected germplasm for the development of new plant varieties. The aim of this concept is the creation of new genetic variation to guarantee a continuous breeding progress. However, the use of molecular markers in backcrossing programs and genetic engineering has created the technical basis to develop new plant varieties without original breeding efforts. Therefore, the concept of ‘essential derivation’ was implemented into the 1991 Act of the UPOV convention to distinguish between varieties that resulted from intensive and creative selection programs and cultivars that were developed without major genetic changes from these former varieties. Accordingly, a variety is deemed to be essentially derived from an initial variety (IV), if it (i) was predominantly derived from the IV, (ii) is clearly distinguishable from the IV, and (iii) genetically conforms to the IV in the expression of it’s essential characteristics. The goal of this thesis was to evaluate and compare different approaches to assess conformity in the expression of the essential characteristics between IV and essentially derived varieties (EDVs) and to derive a theoretical and experimental basis for the devel-opment of thresholds to distinguish between independently derived varieties and EDVs in maize (Zea mays L.). The main focus was set on the evaluation of genetic distances based on ‘simple sequence repeats’ (SSRs) and ‘amplified fragment length poly¬morphisms’ (AFLPs) as well as the factors contributing to the GD between parental inbreds and their progeny lines. Furthermore, the ability of heterosis and morphological distances for identification of EDVs was examined. In detail, the objectives were to (1) analyze the factors influencing genetic distances (GD) based on SSRs and AFLPs between related maize inbred lines, (2) investigate the power of SSR- and AFLP-based GD estimates, morphological distances and heterosis for discriminating between progenies derived from F2, BC1, and BC2 populations, (3) exemplify theoretical and simulated results with experimental data, and (4) draw conclusions with regard to EDV thresholds suggested in the literature. A total of 220 flint, dent, and US maize inbred lines was genotyped with 100 SSRs equally distributed across the maize genome. The 220 lines comprised 163 triplets. A triplet consisted of one progeny and both parental lines, where the former was developed from an F2-, BC1-, or BC2 population. A subset of 58 lines (38 triplets) was genotyped addition-ally with 20 AFLP primer combinations. Furthermore, morphological traits and heterosis were observed for these 38 triplets in a field experiment over two years and three locations. The distributions of GD values for parental lines and their F2- and BC1-derived progeny overlapped for simulated as well as for experimen-tal data. Assuming that the derivation of a line from an F2 population was an accepted breed-ing procedure and the derivation from a BC1 population would not be accepted, we ob-served Type II errors (β) ranging from 0.23 to 0.37 depending on the germplasm pool for a given Type I error (α) of 0.05. For a threshold between BC1 and BC2, β ranged from 0.40 to 0.60 with an increasing tendency for higher BC levels. For fixed GD thresholds of T=0.25, 0.20, 0.15, and 0.10 suggested in the literature, substantial differences for α and β were found between different germplasm pools. Therefore, thresholds need to be gene pool specific and different thresholds for potential EDVs from intra-pool crosses than for progenies from inter-pool crosses must be applied. Discrimination of F2-, BC1-, and BC2-derived progeny lines on the basis of heterosis and morphological distances revealed β values ranging from 0.50 to 0.95 depending on the trait or combination of traits. Therefore, heterosis and morphological distances were fairly inappropriate tools for identification of EDVs due to the larger overlaps of F2-, BC1-, and BC2-distributions compared to GDs based on molecular markers. In general, SSRs and AFLPs were the most adequate tools to uncover close pedigree relationships between maize inbred lines and to discriminate among lines derived with ac-cepted or non-accepted breeding procedures. Therefore, the results presented in this study provide an example for identification of EDVs and can be transferred to other diploid crops by adjusting the corresponding thresholds.
Prediction of hybrid performance in maize using molecular markers
(2008) Schrag, Tobias; Melchinger, Albrecht E.
Maize breeders develop a large number of inbred lines in each breeding cycle, but, owing to resource constraints, evaluate only a small proportion of all possible crosses among these lines in field trials. Therefore, predicting the performance of hybrids by utilising the data available from related crosses to identify untested but promising hybrids is extremely important. The objectives of this thesis research were to develop and evaluate methods for marker-based prediction of hybrid performance (HP) in unbalanced data as typically generated in commercial maize hybrid breeding programs. For HP prediction, a promising approach uses the sum of effects across quantitative trait loci (QTL) as predictor. However, comparison of this approach with established prediction methods based on general combining ability (GCA) was lacking. In addition, prediction of specific combining ability (SCA) is also possible with this approach, but was so far not used for HP prediction. The objectives of the first study in this thesis were to identify QTL for grain yield and grain dry matter content, combine GCA with marker-based SCA estimates for HP prediction, and compare marker-based prediction with established methods. Hybrids from four Dent × Flint factorial mating experiments were evaluated in field trials and their parental inbreds were genotyped with amplified fragment length polymorphism (AFLP) markers. Efficiency for prediction of hybrids, of which both parents were testcross evaluated (Type 2), was assessed by leave-one-out cross-validation. The established GCA-based method predicted HP better than the approach exclusively based on markers. However, with greater relevance of SCA, combining GCA with marker-based SCA estimates was superior compared with HP prediction based on GCA only. Linkage disequilibrium between markers was expected to reduce the prediction efficiency due to inflated QTL effects and reduced power. Thus, in the second study, multiple linear regression (MLR) with forward selection was employed for HP prediction. In addition, adjacent markers in strong linkage disequilibrium were combined into haplotype blocks. An approach based on total effects of associated markers (TEAM) was developed for multi-allelic haplotype blocks. Genome scans to search for significant QTL involve multiple testing of many markers, which increases the rate of false-positive associations. Thus, the TEAM approach was enhanced by controlling the false discovery rate. Considerable loss of marker information can be caused by few missing observations, if the prediction method depends on complete marker data. Therefore, the TEAM approach was improved to cope with missing marker observations. Modification of the cross-validation procedure reflected, that often only a subset of parental lines is crossed with all lines from the opposite heterotic group in a factorial mating design. The prediction approaches were evaluated with the same field data as in the previous study. The results suggested that with haplotype blocks instead of original marker data, similar or higher efficiencies for HP prediction can be achieved. Marker-based HP prediction of inter-group crosses between lines, which were marker genotyped but not testcross evaluated, was not investigated hitherto. Heterosis, which considerably contributes to maize grain yield, was so far not incorporated into marker-based HP prediction. Combined analyses of field trials from multiple experiments of a breeding program provide valuable data for HP prediction. With a mixed linear model analysis of such unbalanced data from nine factorial mating experiments, best linear unbiased prediction (BLUP) values for HP, GCA, SCA, line per se performance, and heterosis of 400 hybrids were obtained in the third study. The prediction efficiency was assessed in cross-validation for prediction of hybrids, of which none (Type 0) or one (Type 1) parental inbred was testcross evaluated. An extension of the established HP prediction method based on BLUP of GCA and SCA, but not using marker data, resulted in prediction efficiency intermediate for Type 1 and very low for Type 0 hybrids. Combining line per se with marker-based heterosis estimates (TEAM-LM) mostly resulted in the highest prediction efficiencies of grain yield and grain dry matter content for both Type 0 and Type 1 hybrids. For the heterotic trait grain yield, the highest prediction efficiencies were generally obtained with marker-based TEAM approaches. In conclusion, this thesis research provided methods for the marker-based prediction of HP. The experimental results suggested that marker-based HP prediction is an efficient tool which supports the selection of superior hybrids and has great potential to accelerate commercial hybrid breeding programs in a very cost-effective manner. The significance of marker-based HP prediction is further enhanced by recent advances in production of doubled haploid lines and high-throughput technologies for rapid and inexpensive marker assays.

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