Browsing by Subject "Marker-assisted selection"

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Genome-wide prediction of testcross performance and phenotypic stability for important agronomic and quality traits in elite hybrid rye (Secale cereale L.)
(2016) Wang, Yu; Miedaner, Thomas
Genomic selection offers a greater potential for improving complex, quantitative traits in winter rye than marker-assisted selection. Prediction accuracies for grain yield for unrelated test populations have, however, to be improved. Nevertheless, they are already favorable for selecting phenotypic stability of quality traits.
Model selection by cross-validation in multi-environment trials
(2017) Hadasch, Steffen; Piepho, Hans-Peter
In plant breeding, estimation of the performance of genotypes across a set of tested environments (genotype means), and the estimation of the environment-specific performances of the genotypes (genotype-environment means) are important tasks. For this purpose, breeders conduct multi-environment trials (MET) in which a set of genotypes is tested in a set of environments. The data from such experiments are typically analysed by mixed models as such models for example allow modelling the genotypes using random effects which may be correlated according to their genetic information. The data from MET are often high-dimensional and the covariance matrix of the data may contain many parameters that need to be estimated. To circumvent computational burdens, the data can be analysed in a stage-wise fashion. In the stage-wise analysis, the covariance matrix of the data needs to be taken into account in the estimation of the individual stages. In the analysis of MET data, there is usually a set of candidate models from which the one that fits bets to the objective of the breeder needs to be determined. Such a model selection can be done by cross validation (CV). In the application of CV schemes, different objectives of the breeder can be evaluated using an appropriate sampling strategy. In the application of a CV, both the sampling strategy and the evaluation of the model need to take the correlation of the data into account to evaluate the model performance adequately. In this work, two different types of models that are used for the analysis of MET were focused. In Chapter 2, models that use genetic marker information to estimate the genotype means were considered. In Chapters 3 and 4, the estimation of genotype-environment means using models that include multiplicative terms to describe the genotype-environment interaction, namely the additive main effects and multiplicative interaction (AMMI), and the genotype and genotype-environment interaction (GGE) model, were focused. In all the Chapters, the models were estimated in a stage-wise fashion. Furthermore, CV was used in Chapters 2 and 3 to determine the most appropriate model from a set of candidate models. In Chapter 2, two traits of a biparental lettuce (Lactuca sativa L.) population were analysed by models for (i) phenotypic selection, (ii) marker-assisted selection using QTL-linked markers, (iii) genomic prediction using all available molecular markers, and (iv) a combination of genomic prediction and QTL-linked markers. Using different sampling strategies in a CV, the predictive performances of these models were compared in terms of different objectives of a breeder, namely predicting unobserved genotypes, predicting genotypes in an unobserved environment, and predicting unobserved genotypes in an unobserved environment. Generally, the genomic prediction model outperformed marker assisted and phenotypic selection when there are only a few markers with large effects, while the marker assisted selection outperformed genomic prediction when the number of markers with large effects increases. Furthermore, the results obtained for the different objectives indicate that the predictive performance of the models in terms of predicting (unobserved) genotypes in an unobserved environment is reduced due to the presence of genotype-environment interaction. In AMMI/GGE models, the number of multiplicative terms can be determined by CV. In Chapter 3, different CV schemes were compared in a simulation study in terms of recovering the true (simulated) number of multiplicative terms, and in terms of the mean squared error of the estimated genotype-environment means. The data were simulated using the estimated variance components of a randomized complete block design and a resolvable incomplete block design. The effects of the experimental design (replicates and blocks) need to be taken into account in the application of a CV in order to evaluate the predictive performance of the model adequately. In Chapter 3, the experimental design was accounted for by an adjustment of the data for the design effects estimated from all data before applying a CV scheme. The results of the simulation study show that an adjustment of the data is required to determine the number of multiplicative terms in AMMI/GGE models. Furthermore, the results indicate that different CV schemes can be used with similar efficiencies provided that the data were adjusted adequately. AMMI/GGE models are typically estimated in a two-stage analysis in which the first stage consists of estimating the genotype-environment means while the second stage consists of estimating main effects of genotypes and environments and the multiplicative interaction. The genotype-environment means estimated in the first stage are not independent when effects of the experimental design are modelled as random effects. In such a case, estimation of the second stage should be done by a weighted (generalized least squares) estimation where a weighting matrix is used to take the covariance matrix of the estimated genotype-environment means into account. In Chapter 4, three different algorithms which can take the full covariance matrix of the genotype-environment means into account are introduced to estimate the AMMI/GGE model in a weighted fashion. To investigate the effectiveness of the weighted estimation, the algorithms were implemented using different weighting matrices, including (i) an identity matrix (unweighted estimation), (ii) a diagonal approximation of the inverse covariance matrix of the genotype-environment means, and (iii) the full inverse covariance matrix. The different weighting strategies were compared in a simulation study in terms of the mean squared error of the estimated genotype-environment means, multiplicative interaction effects, and Biplot coordinates. The results of the simulation study show that weighted estimation of the AMMI/GGE model generally outperformed unweighted estimation. Furthermore, the effectiveness of a weighted estimation increased when the heterogeneity in the covariance matrix of the estimated genotype-environment means increased. The analysis of MET in a stage-wise fashion is an efficient procedure to estimate a model for MET data, whereas the covariance structure of the data needs to be taken into account in each stage in order to estimate the model appropriately. When correlated data are used in a CV, the correlation can be taken into account by an appropriate choice of training and validation data, by an adjustment of the data before applying a CV scheme and by the success criterion used in a CV scheme.
QTL mapping of resistance to Sclerotinia sclerotiorum (Lib.) De Bary in sunflower (Helianthus annuus L.)
(2005) Micic, Zeljko; Melchinger, Albrecht E.
Sclerotinia sclerotiorum (Lib.) de Bary is one of the most important pathogens of sunflower. Three different disease symptoms can be caused by S. sclerotiorum: Sclerotinia wilt, midstalk- and head rot. An improvement of the resistance against S. sclerotiorum would contribute to yield security and thus increase the profitability of sunflower cultivation. We investigated resistance to midstalk rot with respect to the prospects of marker-assisted selection (MAS). The bjectives were to (1) identify quantitative trait loci (QTL) involved in resistance against Sclerotinia sclerotiorum, (2) map their position in the genome, (3) characterize their gene effects, and (4) estimate their consistency across generations of the cross NDBLOSsel x CM625. Two sunflower lines with high resistance level to S. sclerotiorum and different genetic origins (NDBLOSsel and TUB-5-3234) were used as parents. They were crossed with a highly susceptible line CM625 to develop two mapping populations. A modified leaf test was used for the evaluation of midstalk-rot resistance. Three resistance traits and two morphological traits were measured. Disease resistance of 354 F3 families of the population NDBLOSsel x CM625 was screened in field trials with two different sowing times in 1999. A total 317 recombinant inbred lines (RIL) derived from F3 families were tested in 2002/2003. The 434 F3 families of cross CM625 x TUB-5-3234 were screened in 2000/2001. The field trials were conducted by using generalized lattice designs with three replications and five infected plants per replication. Highly significant genetic variation between F3 families and RIL was observed for the resistance traits in all field trials. Heritabilities ( ) were highest for stem lesion and lowest for leaf lesion for all three experiments. The resistance traits were moderately correlated with each other. For the construction of the genetic map of population NDBLOSsel x CM625, 352 F2 individuals were analyzed with 117 SSR marker loci. On the basis of results from the QTL mapping in F3 families, 41 markers were selected and genotyped in 248 RIL. A "selective genotyping" (SG) approach was used for population CM625 x TUB-5-3234. Based on the results measured in F3 families for stem lesion, the SSR genotype at 72 marker loci was determined for the 60 most resistant and 60 most susceptible F2 individuals. For QTL mapping and estimation, the method of the "composite interval of mapping" was used. For stem lesion in the population NDBLOSsel x CM625, eight QTL were detected explaining 33.7% of the genetic variance ( ). The QTL on LG8 explained 36.7% of the phenotypic variance (R2adj). All other QTL for this trait explained between 3.3 and 6.0% of R2adj. Nine QTL were detected for leaf lesion. The proportion of the phenotypic variance explained by individual QTL ranged from 3.4 to 11.3%. All detected QTL for leaf lesion explained 25.3% of the genetic variance in cross validation. For speed of fungal growth, 6 QTL were detected, which explained from 4.6 to 10.2% R2adj. Cross validation explained 24.4% of. Most QTL showed additive gene action. QTL occurring consistently across generations can be recommended for MAS and therefore, the QTL results between RIL and F3 families of population NDBLOSsel x CM625 were compared. One common QTL was identified for leaf lesion, two for stem lesion and three for speed of fungal growth. In population CM625 x TUB-5-3234, four QTL for stem lesion, three QTL for leaf lesion and three QTL for speed of fungal growth were identified. Owing to the SG approach we conjecture that not all QTL were found. The comparison of QTL results between two F3 populations showed two common QTL for stem lesion on LG4 and LG8. The QTL on LG4 originated from the susceptible parent CM625. The QTL on LG8 probably corresponds to the QTL with the largest effect determined in the population NDBLOSsel x CM625. Regarding MAS, our results indicate that two QTL detected for stem lesion and speed of fungal growth in population NDBLOSsel x CM625 are promising. They were consistent across environments, and showed no adverse correlation to leaf morphology in trials with the RIL. In mapping population CM625  TUB-5-3234, it remained unclear whether TUB-5-3234 can contribute new alleles with sufficiently large effects for resistance that were not identified in line NDBLOSsel and would be useful in MAS. The genomic region on LG10 should be analyzed in more detail with respect to its importance for resistance in multiple plant parts (head and stalk) and to verify its association with leaf morphology. Resistance breeding of sunflower against S. sclerotiorum is difficult due to the complex inheritance of the trait. This study showed that both the resistance source NDBLOSsel and the identified markers are promising in improving resistance by MAS. For a broader resistance against S. sclerotiorum, it is necessary to detect new resistance genes from different sources to pyramide them in elite lines.
Resistance breeding in maize (Zea mays L.) against the European corn borer (Ostrinia nubilalis Hübner) and the use of DNA-markers for marker-assisted selection
(2005) Papst, Christine; Melchinger, Albrecht E.
The European corn borer (Ostrinia nubilalis Hb., ECB) is an important pest in maize production. Feeding of ECB larvae causes grain yield losses of up to 30% and promotes ear and stalk rots caused by Fusarium spp.. Maize cultivars carrying the Bt gene are highly resistant to ECB larvae feeding. However, the use of transgenic cultivars is controversially discussed. In contrast, the natural host plant resistance (HPR) is regarded as more durable. The main objective of this study was to identify quantitative trait loci (QTL) for HPR against ECB and to draw conclusions about their usefulness in marker-assisted selection (MAS). The specific research questions were: (1) Where are QTL for ECB resistance and related agronomic traits located in the maize genome and what are their genetic effects? (2) How consistent are QTL detected across unrelated populations? (3) How consistent are QTL detected for line per se and testcross performance? (4) Which physiological mechanisms underlie the resistance against ECB larvae feeding? (5) What is the association between ECB resistance and mycotoxin concentrations in grain maize? Two unrelated dent populations (A and B) were developed. For Experiment 1 the F2:3 families were evaluated for line per se performance for ECB resistance. All F2:3 families of Population B were testcrossed with a susceptible tester line and also evaluated for ECB resistance (Experiment 2). Two sets of F2:3 families from Population B, each comprising the most resistant and the most susceptible lines, were selected (Experiment 3). In Experiment 4, 10 maize cultivars consisting of four pairs of transgenic hybrids and their isogenic counterparts were used to determine the association between mycotoxin concentration and ECB resistance. All entries in Experiment 4 were analyzed for mycotoxin concentration of deoxynivalenol (DON), fumonisin (FUM), fusarenon-X (FUS), moniliformin (MON) and nivalenol (NIV) in grain samples. In all four experiments, resistance to ECB larvae feeding was evaluated using manual infestation with ECB larvae. Furthermore agronomic and quality traits were recorded. In Experiment 1, two QTL for resistance were detected in Population A, both explaining about 25% of the genotypic variance. No common QTL for resistance traits was found across Populations A and B. Possible explanations for the low consistency of QTL across populations are a low power of QTL detection caused by small population sizes, sampling, and environmental effects. Furthermore, population-specific QTL regions cannot be ruled out. In Experiment 2, six QTL for resistance explaining 27% of the genotypic variance were found for testcross performance. Three common QTL for resistance were detected for line per se and testcross performance. Phenotypic as well as genotypic correlations between line per se and testcross performance were low for resistance, indicating a moderate consistency across the different types of progeny. The low consistency across both types of progeny is presumably attributable to the low power of QTL detection in TC progenies caused by a decreased genotypic variance and masking effects of the tester allele. Despite the low consistency of QTL across populations and progenies in the present study, a comparison with other reports from the literature revealed that most of the QTL occurred in clusters. Given the low percentage of genotypic variance explained by QTL-marker associations, we conclude that MAS will not be efficient for resistance breeding against ECB with the current molecular marker techniques. In Experiment 3, significant correlations were observed between resistance and quality traits, such as digestibility and stalk strength. These findings confirm the importance of increased cell-wall fortification for resistance against ECB larvae feeding, and support the hypothesis that candidate genes for resistance are involved in lignin biosynthesis. The analyses of mycotoxin concentrations in Experiment 4 showed that DON, FUM, and MON were the most prevalent mycotoxins in maize kernels. Differences between protected and infested plots were only significant for DON and FUM. Transgenic Bt hybrids showed lower mycotoxin concentrations in kernels than the other hybrids. However, only low correlations were found between ECB resistance and mycotoxin concentrations across all 10 hybrids. Therefore, selection for ECB resistance does not necessarily reduce mycotoxin concentration, suggesting that each complex of characters must be improved simultaneously by breeding. Even if MAS for resistance against the ECB does not seem promising at the moment, the information about QTL regions may be a first step for further research on possible candidate genes, e.g., brown midrib genes located in the common QTL regions with effects on the lignin biosynthesis. Genotypes with an improved digestibility, without impairing ECB resistance by reduced cell-wall strength, would be most promising.