Biomedical subjects

Albrecht E Melchinger

Publications and source records attributed to Albrecht E Melchinger.

12 recordsLinked to original sources

PubMed2006

Power to detect higher-order epistatic interactions in a metabolic pathway using a new mapping strategy.

Epistatic interactions among quantitative trait loci (QTL) contribute substantially to the variation in complex traits. The main objectives of this study were to (i) compare three- vs. four-step genome scans to identify three-way epistatic interactions among QTL belonging to a metabolic pathway, (ii) investigate by computer simulations the power and proportion of false positives (PFP) for detecting three-way interactions among QTL in recombinant inbred line (RIL) populations derived from a nested mating design, and (iii) compare these estimates to those obtained for detecting three-way interactions among QTL in RIL populations derived from diallel and different partial diallel mating designs. The single-nucleotide polymorphism haplotype data of B73 and 25 diverse maize inbreds were used to simulate the production of various RIL populations. Compared to the three-step genome scan, the power to detect three-way interactions was higher with the four-step genome scan. Higher power to detect three-way interactions was observed for RILs derived from optimally allocated distance-based designs than from nested designs or diallel designs. The power and PFP to detect three-way interactions using a nested design with 5000 RILs were for both the 4-QTL and the 12-QTL scenario of a magnitude that seems promising for their identification.

Chromosome Mapping↗

PubMed2006

Hybrid maize breeding with doubled haploids: II. Optimum type and number of testers in two-stage selection for general combining ability.

Optimum allocation of test resources is of crucial importance for the efficiency of breeding programs. Our objectives were to (1) determine the optimum allocation of the number of lines, test locations, as well as number and type of testers in hybrid maize breeding using doubled haploids with two breeding strategies for improvement of general combining ability (GCA), (2) compare the maximum selection gain (DeltaG) achievable under both strategies, and (3) give recommendations for the optimum implementation of doubled haploids in commercial hybrid maize breeding. We calculated DeltaG by numerical integration for two two-stage selection strategies with evaluation of (1) testcross performance in both stages (BS1) or (2) line per se performance in the first stage followed by testcross performance in the second stage (BS2). Different assumptions were made regarding the budget, variance components (VCs), and the correlation between line per se performance and GCA. Selection gain for GCA increased with a broader genetic base of the tester. Hence, testers combining a large number of divergent lines are advantageous. However, in applied breeding programs, the use of single- or double-cross testers in the first and inbred testers in the second selection stage may be a good compromise between theoretical and practical requirements. With a correlation between line per se performance and GCA of 0.50, DeltaG for BS1 is about 5% higher than for BS2, if an economic weight of line per se performance is neglected. With increasing economic weight of line per se performance, relative efficiency of BS2 increased rapidly resulting in a superiority of BS2 over BS1 already for an economic weight for line per se performance larger than 0.1. Considering the importance of an economic seed production, an economic weight larger than 0.1 seems realistic indicating the necessity of separate breeding strategies for seed and pollen parent heterotic groups.

Breeding↗

PubMed2006

A new test for family-based association mapping with inbred lines from plant breeding programs.

Association mapping holds great promise for the detection of quantitative trait loci (QTL) in plant breeding populations. The main objectives of this study were to (1) adapt the quantitative pedigree disequilibrium test to typical pedigrees of inbred lines produced in plant breeding programs, (2) compare the newly developed quantitative inbred pedigree disequilibrium test (QIPDT) with the commonly employed logistic regression ratio test (LRRT), with respect to the power and type I error rate of QTL detection, and (3) demonstrate the use of the QIPDT by applying it to flowering data of European elite maize inbreds. QIPDT and LRRT were compared based on computer simulations modeling 55 years of hybrid maize breeding in Central Europe. Furthermore, we applied QIPDT to a cross-section of 49 European elite maize inbred lines genotyped with 722 amplified fragment length polymorphism markers and phenotyped in four environments for days to anthesis. Compared to LRRT, the power to detect QTL was higher with QIPDT when using data collected routinely in plant breeding programs. Application of QIPDT to the 49 European maize inbreds resulted in a significant (P < 0.05) association located at a position for which a consensus QTL was detected in a previous study. The results of our study suggested that QIPDT is a promising QTL detection method for data collected routinely in plant breeding programs.

Breeding↗

PubMed2006

Marker-based prediction of the parental genome contribution to inbred lines derived from biparental crosses.

Molecular markers can be employed to predict the parental genome contribution to inbred lines. The proportion alpha of alleles originating from parent P1 at markers polymorphic between the parental lines P1 and P2 is commonly used as a predictor for the genome contribution of parent P1 to an offspring line. Our objectives were to develop a new marker-based predictor xi for the parental genome contribution, which takes into account not only the alleles at marker loci but also their map distance, and to compare the prediction precision of xi with that of alternative methods. We derived formulas for xi for inbreds derived from biparental crosses (F1 and backcrosses) with the single-seed descent or double-haploid method and presented an extension xi* possessing statistical optimum properties. In a simulation study, alpha showed a systematic overestimation of large parental genome contribution that was not observed for xi. The mean squared prediction error of xi was at least 50% smaller than that of alpha for linkage maps with unequal distances between adjacent markers. A data set from a study on plant variety protection in maize was used to illustrate the application of xi. We conclude that xi provides substantially greater prediction precision than the commonly used predictor alpha in a broad range of applications in genetics and breeding.

Computer Simulation↗

PubMed2006

Hybrid maize breeding with doubled haploids: I. One-stage versus two-stage selection for testcross performance.

Optimum allocation of resources is of fundamental importance for the efficiency of breeding programs. The objectives of our study were to (1) determine the optimum allocation for the number of lines and test locations in hybrid maize breeding with doubled haploids (DHs) regarding two optimization criteria, the selection gain deltaG(k) and the probability P(k) of identifying superior genotypes, (2) compare both optimization criteria including their standard deviations (SDs), and (3) investigate the influence of production costs of DHs on the optimum allocation. For different budgets, number of finally selected lines, ratios of variance components, and production costs of DHs, the optimum allocation of test resources under one- and two-stage selection for testcross performance with a given tester was determined by using Monte Carlo simulations. In one-stage selection, lines are tested in field trials in a single year. In two-stage selection, optimum allocation of resources involves evaluation of (1) a large number of lines in a small number of test locations in the first year and (2) a small number of the selected superior lines in a large number of test locations in the second year, thereby maximizing both optimization criteria. Furthermore, to have a realistic chance of identifying a superior genotype, the probability P(k) of identifying superior genotypes should be greater than 75%. For budgets between 200 and 5,000 field plot equivalents, P(k) > 75% was reached only for genotypes belonging to the best 5% of the population. As the optimum allocation for P(k)(5%) was similar to that for deltaG(k), the choice of the optimization criterion was not crucial. The production costs of DHs had only a minor effect on the optimum number of locations and on values of the optimization criteria.

Breeding↗

PubMed2005

Trends in genetic diversity among European maize cultivars and their parental components during the past 50 years.

It has been claimed that the system that delivers the products of plant breeding reduces the diversity of cultivated varieties leading to an increased genetic vulnerability. The main goal of our study was to monitor the temporal trends in genetic diversity over the past five decades among maize cultivars with the largest acreage in Central Europe. Our objectives were to (1) investigate how much of the genetic diversity present in important adapted open-pollinated varieties (OPVs) has been captured in the elite flint germ plasm pool, (2) examine changes in the genetic diversity among the most important commercial hybrids as well as in their dent and flint parents, (3) analyze temporal changes in allele frequencies between the dent and flint parental inbreds, and (4) investigate linkage disequilibrium (LD) trends between pairs of loci within the set of parental dent and flint lines. We examined 30 individuals of five prominent OPVs from Central Europe, 85 maize hybrids of economic importance, and their dent and flint parental components with 55 SSRs. LD was significant at probability level P=0.01 for 20.2% of the SSR marker pairs in the 82 dent lines and for 17.2% in the 66 flint lines. The dent and flint heterotic groups were clearly separated already at the beginning of hybrid breeding in Central Europe. Furthermore, the genetic variation within and among varieties decreased significantly during the five decades. The five OPVs contain numerous unique alleles that were absent in the elite flint pool. Consequently, OPVs could present useful sources for broadening the genetic base of elite maize breeding germ plasm.

Europe↗

PubMed2005

Genetic structure and diversity of European flint maize populations determined with SSR analyses of individuals and bulks.

Landraces of maize represent a valuable genetic resource for breeding and genetic studies. Using simple sequence repeat (SSR) markers, we analysed five flint maize populations from Central Europe that had played an important role in the pre-hybrid era in Germany. Our objectives were to (1) investigate the molecular genetic diversity within and among the populations based on the SSR analysis of individuals, (2) compare these results of the SSR analysis based on individuals with those based on bulks, (3) examine genotype frequencies for deviations from Hardy-Weinberg equilibrium (HWE) at individual loci, and (4) test for linkage disequilibrium (LD) between pairs of loci within populations. Thirty individuals and their bulked DNA per population were fingerprinted with 55 SSR markers. Across all populations, 46.7% of the SSR markers deviated significantly from HWE, with an excess of homozygosity in 97% of the cases. This excess of homozygosity can largely be explained by experimental errors during the amplification of SSRs apart from genuine genetic causes. Allele frequencies of the SSR analyses of individuals and bulks were significantly correlated (r=0.85, P< 0.01), suggesting that SSR analysis of bulks is very cost-effective for large-scale molecular characterisation of germ plasm collections. No evidence for genome-wide LD among pairs of loci was observed, indicating that the populations are well suited for high resolution association mapping studies.

Europe↗

PubMed2005

Linkage disequilibrium in European elite maize germplasm investigated with SSRs.

Information about the extent and genomic distribution of linkage disequilibrium (LD) is of fundamental importance for association mapping. The main objectives of this study were to (1) investigate genetic diversity within germplasm groups of elite European maize (Zea mays L.) inbred lines, (2) examine the population structure of elite European maize germplasm, and (3) determine the extent and genomic distribution of LD between pairs of simple sequence repeat (SSR) markers. We examined genetic diversity and LD in a cross section of European and US elite breeding material comprising 147 inbred lines genotyped with 100 SSR markers. For gene diversity within each group, significant (P<0.05) differences existed among the groups. The LD was significant (P<0.05) for 49% of the SSR marker pairs in the 80 flint lines and for 56% of the SSR marker pairs in the 57 dent lines. The ratio of linked to unlinked loci in LD was 1.1 for both germplasm groups. The high incidence of LD suggests that the extent of LD between SSR markers should allow the detection of marker-phenotype associations in a genome scan. However, our results also indicate that a high proportion of the observed LD is generated by forces, such as relatedness, population stratification, and genetic drift, which cause a high risk of detecting false positives in association mapping.

Chromosome Mapping↗

PubMed2005

Validation of Dwarf8 polymorphisms associated with flowering time in elite European inbred lines of maize (Zea mays L.).

The timing of transition from vegetative growth to flowering is important in nature as well as in agriculture. One of several pathways influencing this transition in plants is the gibberellin (GA) pathway. In maize (Zea mays L.), the Dwarf8 (D8) gene has been identified as an orthologue of the gibberellic acid-insensitive (GAI) gene, a negative regulator of GA response in Arabidopsis. Nine intragenic polymorphisms in D8 have been linked with variation in flowering time of maize. We tested the general applicability of these polymorphisms as functional markers in an independent set of inbred lines. Single nucleotide primer extension (SNuPe) and gel-based indel markers were developed, and a set of 71 elite European inbred lines were phenotyped for flowering time and plant height across four environments. To control for population structure, we genotyped the plant material with 55 simple sequence repeat markers evenly distributed across the genome. When population structure was ignored, six of the nine D8 polymorphisms were significantly associated with flowering time and none with plant height. However, when population structure was taken into consideration, an association with flowering time was only detected in a single environment, whereas an association across environments was identified between a 2-bp indel in the promoter region and plant height. As the number of lines with different haplotypes within subpopulations was a limiting factor in the analysis, D8 alleles would need to be compared in isogenic backgrounds for a reliable estimation of allelic effects.

Analysis of Variance↗

PubMed2005

Identification by suppression subtractive hybridization of genes that are differentially expressed between near-isogenic maize lines in association with sugarcane mosaic virus resistance.

The molecular mechanisms underlying the development and progression of sugarcane mosaic virus (SCMV) infection in maize are poorly understood. A study of differential expression was conducted to identify genes involved in resistance to SCMV. In this study, we combined suppression subtractive hybridization and macroarray hybridization to identify genes that are differently expressed in the near isogenic lines F7+ (SCMV resistant) and F7 (susceptible). Altogether, 302 differentially expressed genes were identified in four comparisons based on constitutively expressed and inducible genes, and on compatible and incompatible plant-virus interactions. Apart from genes related to metabolism, most of the functionally classified genes identified belonged to three pathogenesis-related categories: cell rescue, defense, cell death and ageing, signal transduction, and transcription. The latter three groups accounted for 56-66% of the genes classified. Some 19% (60 of 302) of the identified genes had previously been assigned to 29 bins distributed over all ten maize chromosomes. Among the mapped genes, 31% (18 of 58) were located within the Scmv2 and Scmv1 regions on chromosomes 3 and 6, respectively, which have been associated with resistance to SCMV. Promising candidate genes for Scmv1 have been identified, such as AA661457 (receptor-like kinase Xa21-binding protein 3). The implications of the genomic distribution of differentially expressed genes identified by this isogenic comparison are discussed in the context of breeding for resistance.

Chromosome Mapping↗

PubMed2005

Selection theory for marker-assisted backcrossing.

Marker-assisted backcrossing is routinely applied in breeding programs for gene introgression. While selection theory is the most important tool for the design of breeding programs for improvement of quantitative characters, no general selection theory is available for marker-assisted backcrossing. In this treatise, we develop a theory for marker-assisted selection for the proportion of the genome originating from the recurrent parent in a backcross program, carried out after preselection for the target gene(s). Our objectives were to (i) predict response to selection and (ii) give criteria for selecting the most promising backcross individuals for further backcrossing or selfing. Prediction of response to selection is based on the marker linkage map and the marker genotype of the parent(s) of the backcross population. In comparison to standard normal distribution selection theory, the main advantage of our approach is that it considers the reduction of the variance in the donor genome proportion due to selection. The developed selection criteria take into account the marker genotype of the candidates and consider whether these will be used for selfing or backcrossing. Prediction of response to selection is illustrated for model genomes of maize and sugar beet. Selection of promising individuals is illustrated with experimental data from sugar beet. The presented approach can assist geneticists and breeders in the efficient design of gene introgression programs.

Alleles↗

PubMed2004

Quantitative trait locus mapping based on resampling in a vast maize testcross experiment and its relevance to quantitative genetics for complex traits.

From simulation studies it is known that the allocation of experimental resources has a crucial effect on power of QTL detection as well as on accuracy and precision of QTL estimates. In this study, we used a very large experimental data set composed of 976 F(5) maize testcross progenies evaluated in 19 environments and cross-validation to assess the effect of sample size (N), number of test environments (E), and significance threshold on the number of detected QTL, the proportion of the genotypic variance explained by them, and the corresponding bias of estimates for grain yield, grain moisture, and plant height. In addition, we used computer simulations to compare the usefulness of two cross-validation schemes for obtaining unbiased estimates of QTL effects. The maximum, validated genotypic variance explained by QTL in this study was 52.3% for grain moisture despite the large number of detected QTL, thus confirming the infinitesimal model of quantitative genetics. In both simulated and experimental data, the effect of sample size on power of QTL detection as well as on accuracy and precision of QTL estimates was large. The number of detected QTL and the proportion of genotypic variance explained by QTL generally increased more with increasing N than with increasing E. The average bias of QTL estimates and its range were reduced by increasing N and E. Cross-validation performed well with respect to yielding asymptotically unbiased estimates of the genotypic variance explained by QTL. On the basis of our findings, recommendations for planning of QTL mapping experiments and allocation of experimental resources are given.

Chromosome Mapping↗