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/

Average-based versus high-and low-impact indicators for the evaluation of scientific distributions

Albarran et al. (2011a) introduced a novel methodology for the evaluation of citation distributions consisting of a pair of high- and a low-impact measures defined over the set of articles with citations below or above a critical citation level CCL. Albarran et al. (2011b) presented the first empirical applications to a situation in which the world citation distribution in 22 scientific fields is partitioned into three geographical areas: the U.S., the European Union, and the rest of the world. In this paper, we compare our results with those obtained with average-based indicators. For reasonable CCLs, such as the 80th percentile of the world citation distribution in each field, the cardinal differences between the results obtained with our high-impact index and the mean citation rate are of a large order of magnitude. When, in addition, the percentage in the top 5% of most cited articles or the percentage of uncited articles are used, there are still important quantitative differences with respect to the high- and low-impact indicators advocated in our approach when the CCL is fixed at the 80th or the 95th percentile.

Multi-locus phylogeny of Pleosporales: a taxonomic, ecological and evolutionary re-evaluation

Five loci, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, are used for analysing 129 pleosporalean taxa representing 59 genera and 15 families in the current classification of Pleosporales. The suborder Pleosporineae is emended to include four families, viz. Didymellaceae, Leptosphaeriaceae, Phaeosphaeriaceae and Pleosporaceae. In addition, two new families are introduced, i.e. Amniculicolaceae and Lentitheciaceae. Pleomassariaceae is treated as a synonym of Melanommataceae, and new circumscriptions of Lophiostomataceae s. str, Massarinaceae and Lophiotrema are proposed. Familial positions of Entodesmium and Setomelanomma in Phaeosphaeriaceae, Neophaeosphaeria in Leptosphaeriaceae, Leptosphaerulina, Macroventuria and Platychora in Didymellaceae, Pleomassaria in Melanommataceae and Bimuria, Didymocrea, Karstenula and Paraphaeosphaeria in Montagnulaceae are clarified. Both ecological and morphological characters show varying degrees of phylogenetic significance. Pleosporales is most likely derived from a saprobic ancestor with fissitunicate asci containing conspicuous ocular chambers and apical rings. Nutritional shifts in Pleosporales likely occured from saprotrophic to hemibiotrophic or biotrophic

Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals

Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions

Orders out of chaos – molecular phylogenetics reveals the complexity of shark and stingray tapeworm relationships

Novel molecular data are presented to resolve the long-standing issue of the non-monophyly of the elasmobranch-hosted tapeworm order Tetraphyllidea relative to the other acetabulate eucestode orders. Bayesian Inference analyses of various combinations of full ssrDNA, and full or partial lsrDNA (D1-D3), sequence data, which included 134 species representing 97 genera across the 15 eucestode orders, were conducted. New ssrDNA data were generated for 82 species, partial lsrDNA data for 53 species, and full lsrDNA data for 29 species. The monophyly of each of the elasmobranch-hosted orders Cathetocephalidea, Litobothriidea, Lecanicephalidea, and Rhinebothriidea was confirmed, as was the non-monophyly of the Tetraphyllidea. Two relatively stable groups of tetraphyllidean taxa emerged and are hereby designated as new orders. The Onchoproteocephalidea n. ord. is established to recognize the integrated nature of one undescribed and ten described genera of hook-bearing tetraphyllideans, previously of the family Onchobothriidae, with the members of the order Proteocephalidea. The Phyllobothriidea n. ord. is established for a subset of 12 non-hooked genera characterized by scoleces bearing four bothridia each with an anterior accessory sucker; most parasitise sharks and have been assigned to the Phyllobothriidae at one time or another. Tentative ordinal placements are suggested for 8 additional genera; placements for the remaining tetraphyllidean genera have not yet emerged. We propose these 17 genera remain in the “Tetraphyllidea”. Among these, particularly labile across analyses were Anthobothrium, Megalonchos, Carpobothrium, Calliobothrium, and Caulobothrium. The unique association of Chimaerocestus with holocephalans, rather than with elasmobranchs, appears to represent a host-switching event. Both of the non-elasmobranch hosted clades of acetabulate cestodes (i.e., Proteocephalidea and Cyclophyllidea and their kin) appear to have had their origins with elasmobranch cestodes. Across analyses, the sister group to the clade of “terrestrial” cestode orders was found to be an elasmobranch-hosted genus; as was the sister to the freshwater fish and tetrapod-hosted Proteocephalidea. Whilst further data are required to resolve outstanding nomenclatural and phylogenetic issues, the present analyses contribute significantly to an understanding of the evolutionary radiation of the entire Cestoda. Clearly, elasmobranch tapeworms comprise the backbone of cestode phylogeny

Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography

Soil bacteria that also form mutualistic symbioses in plants encounter two major levels of selection. One occurs during adaptation to and survival in soil, and the other occurs in concert with host plant speciation and adaptation. Actinobacteria from the genus Frankia are facultative symbionts that form N2-fixing root nodules on diverse and globally distributed angiosperms in the “actinorhizal” symbioses. Three closely related clades of Frankia sp. strains are recognized; members of each clade infect a subset of plants from among eight angiosperm families. We sequenced the genomes from three strains; their sizes varied from 5.43 Mbp for a narrow host range strain (Frankia sp. strain HFPCcI3) to 7.50 Mbp for a medium host range strain (Frankia alni strain ACN14a) to 9.04 Mbp for a broad host range strain (Frankia sp. strain EAN1pec.) This size divergence is the largest yet reported for such closely related soil bacteria (97.8%–98.9% identity of 16S rRNA genes). The extent of gene deletion, duplication, and acquisition is in concert with the biogeographic history of the symbioses and host plant speciation. Host plant isolation favored genome contraction, whereas host plant diversification favored genome expansion. The results support the idea that major genome expansions as well as reductions can occur in facultative symbiotic soil bacteria as they respond to new environments in the context of their symbioses