Association mapping in tetraploid potato

The results of a four year project within the Centre for BioSystems Genomics (www.cbsg.nl), entitled “Association mapping and family genotyping in potato” are described in this thesis. This project was intended to investigate whether a recently emerged methodology, association mapping, could provide the means to improve potato breeding efficiency. In an attempt to answer this research question a set of potato cultivars representative for the commercial potato germplasm was selected. In total 240 cultivars and progenitor clones were chosen. In a later stage this set was expanded with 190 recent breeds contributed by five participating breeding companies which resulted in a total of 430 genotypes. In a pilot experiment, the results of which are reported in Chapter 2, a subset of 220 of the abovementioned 240 cultivars and progenitor clones was used. Phenotypic data was retrieved through contributions of the participating breeding companies and represented summary statistics of recent observations for a number of traits across years and locations, calculated following company specific procedures. With AFLP marker data, in the form of normalised log-transformed band intensities, obtained from five well-known primer combinations, the extent of linkage disequilibrium (LD), using the r2 statistic, was estimated. Population structure within the set of 220 cultivars was analysed by deploying a clustering approach. No apparent, nor statistically supported population structure was revealed and the LD seemed to decay below the threshold of 0.1 at a genetic distance of about 3cM with this set of marker data. Furthermore, marker-trait associations were investigated by fitting single marker regression models for phenotypic traits on marker band intensities with and without correction for population structure. Population structure correction was performed in a straightforward way by incorporating a design matrix into the model assuming that each breeding company represented a different breeding germplasm pool. The potential of association mapping in tetraploid potato has been demonstrated in this pilot experiment, because existing phenotypic data, a modest number of AFLP markers, and a relatively straightforward statistical analysis allowed identification of interesting associations for a number of agro-morphological and quality traits. These promising results encouraged us to engage into an encompassing genome-wide association mapping study in potato. Two association mapping panels were compiled. One panel comprising 205 genotypes, all of which were also present in the set used for the pilot experiment, and another panel containing in total 299 genotypes including the entire set of 190 recent breeds together with a series of standard cultivars, about 100 of which are in common with the first panel. Phenotypic data for the association panel with 205 genotypes were obtained in a field trial performed in 2006 in Wageningen at two locations with two replicates. We will refer to this set as the “2006 field trial”. Phenotypic data for the other panel with 299 genotypes was contributed by the five participating breeding companies and consisted of multi-year-multi-location data obtained during generations of clonal selection. The 2006 data were nicely balanced, because the trial was designed in that way. The historical breeding dataset was highly unbalanced. Analysis of these two differing phenotypic datasets was performed to deliver insight in variance components for the genotypic main effects and the genotype by environment interaction (GEI), besides estimated genotype main effects across environments. Both phenotypic datasets were analysed separately within a mixed model framework including terms for GEI. In Chapter 3 we describe both phenotypic datasets by comparing variance components, heritabilities (=repeatabilities), intra-dataset relationships and inter-dataset relationships. Broader aspects related to phenotypic datasets and their analysis are discussed as well. To retrieve information about hidden population structure and genetic relatedness, and to estimate the extent of LD in potato germplasm, we used marker information generated with 41 AFLP primer combinations and 53 microsatellite loci on a collection of 430 genotypes. These 430 genotypes contain all genotypes present in the two association mapping panels introduced before plus a few extra genotypes to increase potato germplasm coverage. Two methods were used: a Bayesian approach and a distance-based clustering approach. Chapter 4 describes the results of this exercise. Both strategies revealed a weak level of structure in our material. Groups were detected which complied with criteria such as their intended market segment, as well as groups differing in their year of first registration on a national list. Linkage disequilibrium, using the r2 statistic, appeared to decay below the threshold of 0.1 across linkage groups at a genetic distance of about 5cM on average. The results described in Chapter 4 are promising for association mapping research in potato. The odds are reasonable that useful marker-trait associations can be detected and that the potential mapping resolution will suffice for detection of QTL in an association mapping context. In Chapter 5 a comprehensive genome-wide association mapping study is presented. The adjusted genotypic means obtained from two association mapping panels as a result of phenotypic analysis performed in Chapter 3 were combined with marker information in two association mapping models. Marker information consisted of normalised log-transformed band intensities of 41 AFLP primer combinations and allele dosage information from 53 microsatellites. A baseline model without correction for population structure and a more advanced model with correction for population structure and genetic relatedness were applied. Population structure and genetic relatedness were estimated using available marker information. Interesting QTL could be identified for 19 agro-morphological and quality traits. The observed QTL partly confirm previous studies e.g. for tuber shape and frying colour, but also new QTL have been detected e.g. for after baking darkening and enzymatic browning. In the final chapter, the general discussion, results of preceding chapters are evaluated and their implications for research as well as breeding are discussed. <br/

Phenotypic analyses of multi-environment data for two diverse tetraploid potato collections: comparing an academic panel with an industrial panel

Phenotypic analyses of two different association panels of tetraploid potato cultivars are presented. Association panels are sets of variously related genotypes assembled for association analysis purposes. The aims of this research were to inspect, analyse and compare two phenotypic data sets, a first step in association mapping analysis. A first panel of 205 contemporary and historical cultivars, selected to represent the commercial potato germplasm pool, was evaluated in two trials in 2006, one on sandy soil and the other on clay soil, both with two replications. It was called the academic panel. Data for the second panel with 299 genotypes were compiled from contributions from five breeding companies and included 66 locations and 18 years. Each of the participating breeding companies contributed data from their clonal selection programmes for 38 advanced breeding clones and a series of standard cultivars. It was called the industrial panel. Variance components for genotypic main effects and genotype-by-environment interactions were calculated, and estimates for the random genotypic main effects were produced. The genotypic main effects for 19 agro-morphological and quality traits were used to study trait by trait correlations within each panel. In addition, for the genotypes shared by both panels, the correlation of genetic main effects between the panels was investigated. The heritability of all traits was high and no large differences were observed between panels. Coefficients of trait variation were highly correlated (r¿=¿0.9) for both panels and trait by trait correlations in both panels showed highly similar patterns. These results demonstrate that a single-year balanced field trial as well as using breeders’ records yields robust phenotypic information that can be used in a genome-wide association study. Issues related to data management and definition of traits are discussed

Wave-Equation Reflection Tomography: Annihilators and Sensitivity Kernals

In seismic tomography, the finite frequency content of broad-band data leads to interference effects in the process of medium reconstruction, which are ignored in traditional ray theoretical implementations. Various ways of looking at these effects in the framework of transmission tomography can be found in the literature. Here,we consider inverse scattering of bodywaves to develop a method of wave-equation reflection tomography with broad-band waveform data— which in exploration seismics is identified as a method of wave-equation migration velocity analysis. In the transition from transmission to reflection tomography the usual cross correlation between modelled and observed waveforms of a particular phase arrival is replaced by the action of operators (annihilators) to the observed broad-bandwave fields. Using the generalized screen expansion for one-way wave propagation, we develop the Fréchet (or sensitivity) kernel, and show how it can be evaluated with an adjoint state method. We cast the reflection tomography into an optimization procedure; the kernel appears in the gradient of this procedure.We include a numerical example of evaluating the kernel in a modified Marmousi model, which illustrates the complex dependency of the kernel on frequency band and, hence, scale. In heterogeneous media the kernels reflect proper wave dynamics and do not reveal a self-similar dependence on frequency: low-frequency wave components sample preferentially the smoother parts of the model, whereas the high-frequency data are—as expected—more sensitive to the stronger heterogeneity.We develop the concept for acoustic waves but there are no inherent limitations for the extension to the fully elastic case.TOTAL (Firm)National Science Foundation (U.S.) (grant EAR-0409816

One-Way Wave Propagators For Velocity Analysis On Curvilinear Coordinates

Due to present computational limitations, migration by the one-way wave equation remains an integral tool in seismic exploration. For the realistic interpretation of common image point gathers, it is necessary that migration be free from artifacts from caustics and turning waves. In order to permit situations where turning waves occur, we perform our migration on specially chosen curvilinear coordinates where waves do not travel horizontally. We present an implementation of the curvilinear one-way wave equation using a rational approximation and discuss its application in migration velocity analysis, as well as transmission and reflection tomography

Local Analysis of Inverse Problems: H\"{o}lder Stability and Iterative Reconstruction

We consider a class of inverse problems defined by a nonlinear map from parameter or model functions to the data. We assume that solutions exist. The space of model functions is a Banach space which is smooth and uniformly convex; however, the data space can be an arbitrary Banach space. We study sequences of parameter functions generated by a nonlinear Landweber iteration and conditions under which these strongly converge, locally, to the solutions within an appropriate distance. We express the conditions for convergence in terms of H\"{o}lder stability of the inverse maps, which ties naturally to the analysis of inverse problems

Reverse-time migration-based reflection tomography using teleseismic free surface multiples

Converted and multiply reflected phases from teleseismic events are routinely used to create structural images of the crust–mantle boundary (Moho) and the elasticity contrasts within the crust and upper mantle. The accuracy of these images is to a large extent determined by the background velocity model used to propagate these phases to depth. In order to improve estimates of 3-D velocity variations and, hence, improve imaging, we develop a method of reverse-time migration-based reflection tomography for use with wavefields from teleseismic earthquakes recorded at broad-band seismograph arrays. Reflection tomography makes use of data redundancy—that is, the ability to generate numerous structural images of the subsurface with different parts of the wavefield. In exploration seismology (where it is known as migration velocity analysis) reflection tomography typically involves the generation of an extended image (e.g. offset- or angle-gathers), and the fitness of the background model is evaluated through the application of image-domain annihilators. In regional-scale passive source seismology, however, annihilation-based methods are inadequate because the sparse and irregular distribution of teleseismic sources is not likely to produce illumination over a sufficient range of angles. To overcome this problem we turn towards a source-indexed moveout scheme. Instead of extended image annihilation, we determine the success of the tomographic velocity model by cross correlating images produced with multiply scattered waves from different teleseismic sources. The optimal velocity model is the one that minimizes correlation power between windowed images away from zero depth shift. We base our inversion scheme on the seismic adjoint method and a conjugate gradient solver. For each image pair, the update direction is determined by correlations between downgoing wavefields with upgoing adjoint wavefields for both images. The sensitivity kernels used in this method is similar to those found in other forms of adjoint tomography, but their shapes are controlled by the spatial distribution of the error function. We present the method and a proof-of-concept with 2-D synthetic data

Source-Indexed Migration Velocity Analysis with Global Passive Data

The reverse-time migration of global seismic data generated by free-surface multiples is regularly used to constrain the crustal structure, but its accuracy is to a large extent determined by the accuracy of the 3-D background velocity model used for wave propagation. To this improve the velocity model and hence the accuracy of the migrated image, we wish to apply the technique of migration velocity analysis (MVA) to global passive data. Applications of MVA in the active setting typically focus on o ffset- or angle-gather annihilation, a process that takes advantage of data redundancy to form an extended image, and then applies an annihilation operator to determine the success of image formation. Due to the nature of regional-scale passive seismic arrays, it is unlikely that the data in most of these studies will be su cient to form an extended image volume for use in annihilation-based MVA. In order to make use of the sparse and irregular array design of these arrays, we turn towards a shot-pro le moveout scheme for migration velocity analysis introduced by Xie and Yang (2008). In the place of extended image annihilation, we determine the success of the migration velocity model by using a weighted image correlation power norm. We compare pairs of images formed by migrating each teleseismic source by image cross-correlation in the depth direction. We look for a suitable background model by penalizing the amount of correlation power away from zero depth shift. The total weighted correlation power between source-pro le images is then used as the error function and optimized via conjugate gradient. We present the method and a proof-of-concept with 2-D synthetic data

Characteristics of Injuries in the Logging Industry of Louisiana, USA: 1986 to 1998

Characterizing injuries and their trends will allow safety managers to concentrate their resources on the areas of safety that will be most effective in the workplace. Injuries reported to the Louisiana Office of Workers' Compensation Administration for 1986 to 1998 were characterized according to the part of the body affected, the nature of the injury, the source of the injury, and the type of accident for the timber harvesting industry. Many of the injuries in the logging sector were sprains / strains to the knees. Injuries resulting from falling onto structures and surfaces were common and rising. Although the number of accidents in each category is generally decreasing, some trends should be of concern. There was no significant linear trend in overall accident rates since 1991. While the proportion of cuts and lacerations declined, the proportion of fractures increased. This coincided with a time period when logging operations in Louisiana experienced rapid mechanization and insurance companies started enforcing the use of personal protective equipment. The proportion of transportation accidents rose more than any other category. Some suggestions on focusing and improving current safety programs are given. The need for continued and improved training of managers and employees seems to be most critical